Publications

2024
2023
2022
2021
2020
2019
2018
2017
2016
2015
2014
2013
2012
2011

2024↑

F. Tosti Guerra, E. Poppleton, P. Šulc, and L. Rovigatti. Annamo: coarse-grained modeling for folding and assembly of rna and dna systems. Journal of Chemical Physics, 2024. doi:10.1063/5.0202829.
[abstract▼] [BibTeX▼]

The folding of RNA and DNA strands plays crucial roles in biological systems and bionanotechnology. However, studying these processes with high-resolution numerical models is beyond current computational capabilities due to the timescales and system sizes involved. In this article, we present a new coarse-grained model for investigating the folding dynamics of nucleic acids. Our model represents three nucleotides with a patchy particle and is parameterized using well-established nearest-neighbor models. Thanks to the reduction of degrees of freedom and to a bond-swapping mechanism, our model allows for simulations at timescales and length scales that are currently inaccessible to more detailed models. To validate the performance of our model, we conducted extensive simulations of various systems: We examined the thermodynamics of DNA hairpins, capturing their stability and structural transitions, the folding of an MMTV pseudoknot, which is a complex RNA structure involved in viral replication, and also explored the folding of an RNA tile containing a k-type pseudoknot. Finally, we evaluated the performance of the new model in reproducing the melting temperatures of oligomers and the dependence on the toehold length of the displacement rate in toehold-mediated displacement processes, a key reaction used in molecular computing. All in all, the successful reproduction of experimental data and favorable comparisons with existing coarse-grained models validate the effectiveness of the new model. © 2024 Author(s).
```
@article{Rovigatti-YmZi1oqN,
    author = "Tosti Guerra, F. and Poppleton, E. and Šulc, P. and Rovigatti, L.",
    title = "ANNaMo: Coarse-grained modeling for folding and assembly of RNA and DNA systems",
    year = "2024",
    journal = "Journal of Chemical Physics",
    volume = "160",
    number = "20",
    doi = "10.1063/5.0202829",
    type = "Article",
    publication_stage = "Final",
    source = "Scopus"
}
```
S. S. Gomez and L. Rovigatti. Diffusion, viscosity, and linear rheology of valence-limited disordered fluids. Journal of Chemical Physics, 2024. doi:10.1063/5.0209151.
[abstract▼] [BibTeX▼]

We numerically investigate the dynamics and linear rheology of disordered systems made of patchy particles, focusing on the role of valence, temperature, and bonding mechanism. We demonstrate that the dynamics is enslaved to bonding, giving rise to an activated behavior at low temperatures. By independently computing the diffusion constant and the viscosity from the simulations, we also confirm the validity of the Stokes-Einstein relation in valence-limited systems, with two caveats: (i) the diffusion constant requires a finite-size correction, at least at the intermediate density we investigate, and (ii) there is the onset of a breakdown that appears at the lowest temperatures considered. Finally, our results show that the storage and loss moduli of mixtures of divalent and M-valent particles exhibit an apparent power-law dependence on frequency, hinting at the possibility of using the composition to finely tune the rheological response of these materials. Our results compare well with literature experimental data on valence-limited DNA nanostars. In addition, the wealth of data we present and analyze here will help develop and test theoretical frameworks aimed at describing the dynamics of flexible limited-valence particles that self-assemble into disordered networks. © 2024 Author(s).
```
@article{Rovigatti-cRxsK9Gu,
    author = "Gomez, Samuel S. and Rovigatti, Lorenzo",
    title = "Diffusion, viscosity, and linear rheology of valence-limited disordered fluids",
    year = "2024",
    journal = "Journal of Chemical Physics",
    volume = "160",
    number = "18",
    doi = "10.1063/5.0209151",
    type = "Article",
    publication_stage = "Final",
    source = "Scopus"
}
```
H. Liu, M. Matthies, J. Russo, L. Rovigatti, R. P. Narayanan, T. Diep, D. McKeen, O. Gang, N. Stephanopoulos, F. Sciortino, H. Yan, F. Romano, and P. Šulc. Inverse design of a pyrochlore lattice of dna origami through model-driven experiments. Science, 384(6697):776 – 781, 2024. doi:10.1126/science.adl5549.
[abstract▼] [BibTeX▼]

Sophisticated statistical mechanics approaches and human intuition have demonstrated the possibility of self-assembling complex lattices or finite-size constructs. However, attempts so far have mostly only been successful in silico and often fail in experiment because of unpredicted traps associated with kinetic slowing down (gelation, glass transition) and competing ordered structures. Theoretical predictions also face the difficulty of encoding the desired interparticle interaction potential with the experimentally available nano- and micrometer-sized particles. To overcome these issues, we combine SAT assembly (a patchy-particle interaction design algorithm based on constrained optimization) with coarse-grained simulations of DNA nanotechnology to experimentally realize trap-free self-assembly pathways. We use this approach to assemble a pyrochlore three-dimensional lattice, coveted for its promise in the construction of optical metamaterials, and characterize it with small-angle x-ray scattering and scanning electron microscopy visualization. © 2024 American Association for the Advancement of Science. All rights reserved.
```
@article{Rovigatti-lsRRro7t,
    author = "Liu, Hao and Matthies, Michael and Russo, John and Rovigatti, Lorenzo and Narayanan, Raghu Pradeep and Diep, Thong and McKeen, Daniel and Gang, Oleg and Stephanopoulos, Nicholas and Sciortino, Francesco and Yan, Hao and Romano, Flavio and Šulc, Petr",
    title = "Inverse design of a pyrochlore lattice of DNA origami through model-driven experiments",
    year = "2024",
    journal = "Science",
    volume = "384",
    number = "6697",
    pages = "776 – 781",
    doi = "10.1126/science.adl5549",
    type = "Article",
    publication_stage = "Final",
    source = "Scopus"
}
```
G. Mattiotti, M. Micheloni, L. Petrolli, L. Rovigatti, L. Tubiana, S. Pasquali, and R. Potestio. Molecular dynamics characterization of the free and encapsidated rna2 of ccmv with the oxrna model. Macromolecular Rapid Communications, 2024. doi:10.1002/marc.202400639.
[abstract▼] [BibTeX▼]

The cowpea chlorotic mottle virus (CCMV) has emerged as a model system to assess the balance between electrostatic and topological features of single-stranded RNA viruses, specifically in the context of the viral self-assembly. Yet, despite its biophysical significance, little structural data on the RNA content of the CCMV virion is available. Here, the conformational dynamics of the RNA2 fragment of CCMV was assessed via coarse-grained molecular dynamics simulations, employing the oxRNA2 force field. The behavior of RNA2 was characterized both as a freely-folding molecule and within a mean-field depiction of the capsid. For the former, the role of the salt concentration, the temperature and of ad hoc constraints on the RNA termini was verified on the equilibrium properties of RNA2. For the latter, a multi-scale approach was employed to derive a potential profile of the viral cavity from atomistic structures of the CCMV capsid in solution. The conformational ensembles of the encapsidated RNA2 were significantly altered with respect to the freely-folding counterparts, as shown by the emergence of long-range motifs and pseudoknots. Finally, the role of the N-terminal tails of the CCMV subunits is highlighted as a critical feature in the construction of a proper electrostatic model of the CCMV capsid. © 2024 The Author(s). Macromolecular Rapid Communications published by Wiley-VCH GmbH.
```
@article{Rovigatti--GxtubES,
    author = "Mattiotti, Giovanni and Micheloni, Manuel and Petrolli, Lorenzo and Rovigatti, Lorenzo and Tubiana, Luca and Pasquali, Samuela and Potestio, Raffaello",
    title = "Molecular Dynamics Characterization of the Free and Encapsidated RNA2 of CCMV with the oxRNA Model",
    year = "2024",
    journal = "Macromolecular Rapid Communications",
    volume = "45",
    number = "24",
    doi = "10.1002/marc.202400639",
    type = "Article",
    publication_stage = "Final",
    source = "Scopus"
}
```

N. D. Pasquale, R. Davidchack, and L. Rovigatti. Cleaving: a lammps package to compute surface free energies. Journal of Open Source Software, 9(94):5886, 2024. doi:10.21105/joss.05886.
[BibTeX▼]

@article{Rovigatti-RfCh0mUC,
    author = "Pasquale, Nicodemo Di and Davidchack, Ruslan and Rovigatti, Lorenzo",
    doi = "10.21105/joss.05886",
    year = "2024",
    publisher = "The Open Journal",
    volume = "9",
    number = "94",
    pages = "5886",
    title = "CLEAVING: a LAMMPS package to compute surface free energies",
    journal = "Journal of Open Source Software"
}

2023↑

J. P. K. Doye, H. Fowler, D. Prešern, J. Bohlin, L. Rovigatti, F. Romano, P. Šulc, C. K. Wong, A. A. Louis, J. S. Schreck, M. C. Engel, M. Matthies, E. Benson, E. Poppleton, and B. E. K. Snodin. The oxdna coarse-grained model as a tool to simulate dna origami. Methods in Molecular Biology, 2639:93 – 112, 2023. doi:10.1007/978-1-0716-3028-0_6.
[abstract▼] [BibTeX▼]

@article{Rovigatti-OnoI2hcK,
    author = "Doye, Jonathan P. K. and Fowler, Hannah and Prešern, Domen and Bohlin, Joakim and Rovigatti, Lorenzo and Romano, Flavio and Šulc, Petr and Wong, Chak Kui and Louis, Ard A. and Schreck, John S. and Engel, Megan C. and Matthies, Michael and Benson, Erik and Poppleton, Erik and Snodin, Benedict E. K.",
    title = "The oxDNA Coarse-Grained Model as a Tool to Simulate DNA Origami",
    year = "2023",
    journal = "Methods in Molecular Biology",
    volume = "2639",
    pages = "93 – 112",
    doi = "10.1007/978-1-0716-3028-0\_6",
    type = "Book chapter",
    publication_stage = "Final",
    source = "Scopus"
}

N. Di Pasquale, T. Hudson, M. Icardi, L. Rovigatti, and M. Spinaci. A systematic analysis of the memory term in coarse-grained models: the case of the markovian approximation. European Journal of Applied Mathematics, 34(2):326 – 345, 2023. doi:10.1017/S0956792522000158.
[abstract▼] [BibTeX▼]

The systematic development of coarse-grained (CG) models via the Mori-Zwanzig projector operator formalism requires the explicit description of a deterministic drift term, a dissipative memory term and a random fluctuation term. The memory and fluctuating terms are related by the fluctuation-dissipation relation and are more challenging to sample and describe than the drift term due to complex dependence on space and time. This work proposes a rational basis for a Markovian data-driven approach to approximating the memory and fluctuating terms. We assumed a functional form for the memory kernel and under broad regularity hypothesis, we derived bounds for the error committed in replacing the original term with an approximation obtained by its asymptotic expansions. These error bounds depend on the characteristic time scale of the atomistic model, representing the decay of the autocorrelation function of the fluctuating force; and the characteristic time scale of the CG model, representing the decay of the autocorrelation function of the momenta of the beads. Using appropriate parameters to describe these time scales, we provide a quantitative meaning to the observation that the Markovian approximation improves as they separate. We then proceed to show how the leading-order term of such expansion can be identified with the Markovian approximation usually considered in the CG theory. We also show that, while the error of the approximation involving time can be controlled, the Markovian term usually considered in CG simulations may exhibit significant spatial variation. It follows that assuming a spatially constant memory term is an uncontrolled approximation which should be carefully checked. We complement our analysis with an application to the estimation of the memory in the CG model of a one-dimensional Lennard-Jones chain with different masses and interactions, showing that even for such a simple case, a non-negligible spatial dependence for the memory term exists. © The Author(s), 2022. Published by Cambridge University Press.
```
@article{Rovigatti-JBD3nQJ4,
    author = "Di Pasquale, Nicodemo and Hudson, Thomas and Icardi, Matteo and Rovigatti, Lorenzo and Spinaci, Marco",
    title = "A systematic analysis of the memory term in coarse-grained models: The case of the Markovian approximation",
    year = "2023",
    journal = "European Journal of Applied Mathematics",
    volume = "34",
    number = "2",
    pages = "326 – 345",
    doi = "10.1017/S0956792522000158",
    type = "Article",
    publication_stage = "Final",
    source = "Scopus"
}
```
V. Sorichetti, A. Ninarello, J. Ruiz-Franco, V. Hugouvieux, E. Zaccarelli, C. Micheletti, W. Kob, and L. Rovigatti. Structure and elasticity of model disordered, polydisperse, and defect-free polymer networks. Journal of Chemical Physics, 2023. doi:10.1063/5.0134271.
[abstract▼] [BibTeX▼]

The elasticity of disordered and polydisperse polymer networks is a fundamental problem of soft matter physics that is still open. Here, we self-assemble polymer networks via simulations of a mixture of bivalent and tri- or tetravalent patchy particles, which result in an exponential strand length distribution analogous to that of experimental randomly cross-linked systems. After assembly, the network connectivity and topology are frozen and the resulting system is characterized. We find that the fractal structure of the network depends on the number density at which the assembly has been carried out, but that systems with the same mean valence and same assembly density have the same structural properties. Moreover, we compute the long-time limit of the mean-squared displacement, also known as the (squared) localization length, of the cross-links and of the middle monomers of the strands, showing that the dynamics of long strands is well described by the tube model. Finally, we find a relation connecting these two localization lengths at high density and connect the cross-link localization length to the shear modulus of the system. © 2023 Author(s).
```
@article{Rovigatti-gdQgU4FG,
    author = "Sorichetti, Valerio and Ninarello, Andrea and Ruiz-Franco, José and Hugouvieux, Virginie and Zaccarelli, Emanuela and Micheletti, Cristian and Kob, Walter and Rovigatti, Lorenzo",
    title = "Structure and elasticity of model disordered, polydisperse, and defect-free polymer networks",
    year = "2023",
    journal = "Journal of Chemical Physics",
    volume = "158",
    number = "7",
    doi = "10.1063/5.0134271",
    type = "Article",
    publication_stage = "Final",
    source = "Scopus"
}
```
L. Rovigatti and F. Sciortino. Entropy-driven phase behavior of associative polymer networks. SciPost Physics, 2023. doi:10.21468/SciPostPhys.15.4.163.
[abstract▼] [BibTeX▼]

Polymer chains decorated with a fraction of monomers capable of forming reversible bonds form transient polymer networks that are important in soft and biological systems. If chains are flexible and the attractive monomers are all of the same species, the network formation occurs continuously as density increases. By contrast, it has been recently shown [L. Rovigatti and F. Sciortino, Phys. Rev. Lett. 129, 047801 (2022)] that, if the attractive monomers are of two different and alternating types, the entropic gain of swapping intra-molecular bonds for inter-molecular connections induces a first order phase transition in the fully-bonded (i.e. low-temperature or, equivalently, large monomer-monomer attraction strength) limit and the network forms abruptly on increasing density. Here we use simulations to show that this phenomenon is robust with respect to thermal fluctuations, disorder and change in the polymer architecture, demonstrating its generality and likely relevance for the wide class of materials that can be modelled as associative (transient) polymer networks. Copyright L. Rovigatti and F. Sciortino.
```
@article{Rovigatti-1bKAGZEW,
    author = "Rovigatti, Lorenzo and Sciortino, Francesco",
    title = "Entropy-driven phase behavior of associative polymer networks",
    year = "2023",
    journal = "SciPost Physics",
    volume = "15",
    number = "4",
    doi = "10.21468/SciPostPhys.15.4.163",
    type = "Article",
    publication_stage = "Final",
    source = "Scopus"
}
```

E. Poppleton, M. Matthies, D. Mandal, F. Romano, P. Šulc, and L. Rovigatti. Oxdna: coarse-grained simulations of nucleic acids made simple. Journal of Open Source Software, 8(81):4693, 2023.
[BibTeX▼]

@article{Rovigatti-45vemKMu,
    author = "Poppleton, Erik and Matthies, Michael and Mandal, Debesh and Romano, Flavio and {\v{S}}ulc, Petr and Rovigatti, Lorenzo",
    title = "oxDNA: coarse-grained simulations of nucleic acids made simple",
    journal = "Journal of Open Source Software",
    volume = "8",
    number = "81",
    pages = "4693",
    year = "2023"
}

2022↑

J. Russo, F. Romano, L. Kroc, F. Sciortino, L. Rovigatti, and P. Sulc. Sat-assembly: a new approach for designing self-assembling systems. Journal of Physics Condensed Matter, 2022. doi:10.1088/1361-648X/ac5479.
[abstract▼] [BibTeX▼]

We propose a general framework for solving inverse self-assembly problems, i.e. designing interactions between elementary units such that they assemble spontaneously into a predetermined structure. Our approach uses patchy particles as building blocks, where the different units bind at specific interaction sites (the patches), and we exploit the possibility of having mixtures with several components. The interaction rules between the patches is determined by transforming the combinatorial problem into a Boolean satisfiability problem (SAT) which searches for solutions where all bonds are formed in the target structure. Additional conditions, such as the non-satisfiability of competing structures (e.g. metastable states) can be imposed, allowing to effectively design the assembly path in order to avoid kinetic traps. We demonstrate this approach by designing and numerically simulating a cubic diamond structure from four particle species that assembles without competition from other polymorphs, including the hexagonal structure. © 2022 IOP Publishing Ltd.
```
@article{Rovigatti-KjpfUS6k,
    author = "Russo, John and Romano, Flavio and Kroc, Lukas and Sciortino, Francesco and Rovigatti, Lorenzo and Sulc, Petr",
    title = "SAT-assembly: a new approach for designing self-assembling systems",
    year = "2022",
    journal = "Journal of Physics Condensed Matter",
    volume = "34",
    number = "35",
    doi = "10.1088/1361-648X/ac5479",
    type = "Article",
    publication_stage = "Final",
    source = "Scopus"
}
```
L. Rovigatti and F. Sciortino. Designing enhanced entropy binding in single-chain nanoparticles. Physical Review Letters, 2022. doi:10.1103/PhysRevLett.129.047801.
[abstract▼] [BibTeX▼]

Single-chain nanoparticles (SCNPs) are a new class of bio- and soft-matter polymeric objects in which a fraction of the monomers are able to form equivalently intra- or interpolymer bonds. Here we numerically show that a fully entropic gas-liquid phase separation can take place in SCNP systems. Control over the discontinuous (first-order) change - from a phase of independent diluted (fully-bonded) polymers to a phase in which polymers entropically bind to each other to form a (fully-bonded) polymer network - can be achieved by a judicious design of the patterns of reactive monomers along the polymer chain. Such a sensitivity arises from a delicate balance between the distinct entropic contributions controlling the binding. © 2022 American Physical Society.
```
@article{Rovigatti-woiJiJP1,
    author = "Rovigatti, Lorenzo and Sciortino, Francesco",
    title = "Designing Enhanced Entropy Binding in Single-Chain Nanoparticles",
    year = "2022",
    journal = "Physical Review Letters",
    volume = "129",
    number = "4",
    doi = "10.1103/PhysRevLett.129.047801",
    type = "Article",
    publication_stage = "Final",
    source = "Scopus"
}
```
L. Rovigatti, J. Russo, F. Romano, M. Matthies, L. Kroc, and P. Šulc. A simple solution to the problem of self-assembling cubic diamond crystals. Nanoscale, 14(38):14268 – 14275, 2022. doi:10.1039/d2nr03533b.
[abstract▼] [BibTeX▼]

The self-assembly of colloidal diamond (CD) crystals is considered as one of the most coveted goals of nanotechnology, both from the technological and fundamental points of view. For applications, colloidal diamond is a photonic crystal which can open new possibilities of manipulating light for information processing. From a fundamental point of view, its unique symmetry exacerbates a series of problems that are commonly faced during the self-assembly of target structures, such as the presence of kinetic traps and the formation of crystalline defects and alternative structures (polymorphs). Here we demonstrate that all these problems can be systematically addressed via SAT-assembly, a design framework that converts self-assembly into a Boolean satisfiability problem (SAT). Contrary to previous solutions (requiring four or more components), we prove that the assembly of the CD crystal only requires a binary mixture. Moreover, we use molecular dynamics simulations of a system composed by nearly a million nucleotides to test a DNA nanotechnology design that constitutes a promising candidate for experimental realization. © 2022 The Royal Society of Chemistry.
```
@article{Rovigatti-MkYY79J3,
    author = "Rovigatti, Lorenzo and Russo, John and Romano, Flavio and Matthies, Michael and Kroc, Lukáš and Šulc, Petr",
    title = "A simple solution to the problem of self-assembling cubic diamond crystals",
    year = "2022",
    journal = "Nanoscale",
    volume = "14",
    number = "38",
    pages = "14268 – 14275",
    doi = "10.1039/d2nr03533b",
    type = "Article",
    publication_stage = "Final",
    source = "Scopus"
}
```

2021↑

J. Tauber, L. Rovigatti, S. Dussi, and J. van der Gucht. Sharing the load: stress redistribution governs fracture of polymer double networks. Macromolecules, 54(18):8563 – 8574, 2021. doi:10.1021/acs.macromol.1c01275.
[abstract▼] [BibTeX▼]

The stress response of polymer double networks depends not only on the properties of the constituent networks but also on the interactions arising between them. Here, we demonstrate, via coarse-grained simulations, that both their global stress response and their microscopic fracture mechanics are governed by load sharing through these internetwork interactions. By comparing our results with affine predictions, where stress redistribution is by definition homogeneous, we show that stress redistribution is highly inhomogeneous. In particular, the affine prediction overestimates the fraction of broken chains by almost an order of magnitude. Furthermore, homogeneous stress distribution predicts a single fracture process, while in our simulations, fracture of sacrificial chains takes place in two steps governed by load sharing within a network and between networks, respectively. Our results thus provide a detailed microscopic picture of how inhomogeneous stress redistribution after rupture of chains governs the fracture of polymer double networks. © 2021 The Authors. Published by American Chemical Society
```
@article{Rovigatti-51Ikdhls,
    author = "Tauber, Justin and Rovigatti, Lorenzo and Dussi, Simone and van der Gucht, Jasper",
    title = "Sharing the Load: Stress Redistribution Governs Fracture of Polymer Double Networks",
    year = "2021",
    journal = "Macromolecules",
    volume = "54",
    number = "18",
    pages = "8563 – 8574",
    doi = "10.1021/acs.macromol.1c01275",
    type = "Article",
    publication_stage = "Final",
    source = "Scopus"
}
```
M. Formanek, L. Rovigatti, E. Zaccarelli, F. Sciortino, and A. J. Moreno. Gel formation in reversibly cross-linking polymers. Macromolecules, 54(14):6613 – 6627, 2021. doi:10.1021/acs.macromol.0c02670.
[abstract▼] [BibTeX▼]

By means of Langevin dynamics simulations, we investigate the gel formation of randomly functionalized polymers in solution, with the ability to form both intra- and intermolecular reversible bonds. Under highly dilute conditions, these polymers form soft nano-objects (so-called single-chain nanoparticles, SCNPs), resulting from the purely intramolecular cross-linking of the reactive functional groups. Here, we show that the competition between intra- and intermolecular bonds at finite concentration is governed by a delicate balance of various entropic contributions and leads to a density-dependent effective valence. System-spanning networks are formed at relatively low monomer densities and their stability is mediated by just a small number of intermolecular connections per chain. The formation of intermolecular bonds furthermore can induce a nonmonotonic dependence of the polymer size on the density for long bond lifetimes. Concomitantly, the polymers in the percolating cluster adopt an intramolecular structure characteristic for self-avoiding chains, which constitutes a strong contrast to the fractal globular behavior of intramolecularly cross-linked SCNPs in crowded solutions with purely topological interactions (no intermolecular bonds). Finally, we study the dynamics of the system, which displays signatures expected for reversible gel-forming systems. An interesting behavior emerges in the reorganization dynamics of the percolating cluster: the relaxation is mostly mediated by the diffusion over long distances, through breaking and formation of bonds, of chains that do not leave the percolating cluster. Regarding the few chains that are transiently free, the time they spend until they reattach to the cluster is solely governed by the bond strength. © 2021 American Chemical Society. All rights reserved.
```
@article{Rovigatti-cQXnU_Vb,
    author = "Formanek, Maud and Rovigatti, Lorenzo and Zaccarelli, Emanuela and Sciortino, Francesco and Moreno, Angel J.",
    title = "Gel Formation in Reversibly Cross-Linking Polymers",
    year = "2021",
    journal = "Macromolecules",
    volume = "54",
    number = "14",
    pages = "6613 – 6627",
    doi = "10.1021/acs.macromol.0c02670",
    type = "Article",
    publication_stage = "Final",
    source = "Scopus"
}
```
S. Biagi, L. Rovigatti, M. Abbasi, L. Bureau, F. Sciortino, and C. Misbah. Hydrodynamic instability and flow reduction in polymer brush coated channels. Soft Matter, 17(40):9235 – 9245, 2021. doi:10.1039/d1sm00638j.
[abstract▼] [BibTeX▼]

A polymer brush is a passive medium. At equilibrium the knowledge of its chemical composition and thickness is enough for a full system characterization. However, when the brush is exposed to fluid flow it reveals a much more intriguing nature, in which filamentous protrusions and the way they interact among themselves and with the surrounding fluid are of outmost importance. Here we investigate such a rich behaviorvianumerical simulations. We focus on the brush hydrodynamic response at low Reynolds numbers, observing a significant fluid flow reduction inside a polymer-brush coated channel. We find that the reduction of the flow inside the channel is significantly larger than what would happen if the brush effect consisted only in reducing the effective channel width. This amplified reduction is understood as being due to the morphological instability of the brush-liquid interface which is shown to have an elastic origin: the mechanical stress acting on the brush due to the imposed flow is partially released by the interface modulation. In turn, this modulation dissipates more energy than a flat interface in the surrounding fluid, causing a reduction of flow velocity. Our results and interpretations provide an explanation for recent experimental measurements. © The Royal Society of Chemistry 2021.
```
@article{Rovigatti-rjMcT1WE,
    author = "Biagi, Sofia and Rovigatti, Lorenzo and Abbasi, Mehdi and Bureau, Lionel and Sciortino, Francesco and Misbah, Chaouqi",
    title = "Hydrodynamic instability and flow reduction in polymer brush coated channels",
    year = "2021",
    journal = "Soft Matter",
    volume = "17",
    number = "40",
    pages = "9235 – 9245",
    doi = "10.1039/d1sm00638j",
    type = "Article",
    publication_stage = "Final",
    source = "Scopus"
}
```
A. Sengar, T.E. Ouldridge, O. Henrich, L. Rovigatti, and P. Šulc. A primer on the oxdna model of dna: when to use it, how to simulate it and how to interpret the results. Frontiers in Molecular Biosciences, 2021. doi:10.3389/fmolb.2021.693710.
[abstract▼] [BibTeX▼]

The oxDNA model of Deoxyribonucleic acid has been applied widely to systems in biology, biophysics and nanotechnology. It is currently available via two independent open source packages. Here we present a set of clearly documented exemplar simulations that simultaneously provide both an introduction to simulating the model, and a review of the model’s fundamental properties. We outline how simulation results can be interpreted in terms of—and feed into our understanding of—less detailed models that operate at larger length scales, and provide guidance on whether simulating a system with oxDNA is worthwhile. © Copyright © 2021 Sengar, Ouldridge, Henrich, Rovigatti and Šulc.
```
@article{Rovigatti-0wtfP4zp,
    author = "Sengar, A. and Ouldridge, T.E. and Henrich, O. and Rovigatti, L. and Šulc, P.",
    title = "A Primer on the oxDNA Model of DNA: When to Use it, How to Simulate it and How to Interpret the Results",
    year = "2021",
    journal = "Frontiers in Molecular Biosciences",
    volume = "8",
    doi = "10.3389/fmolb.2021.693710",
    type = "Review",
    publication_stage = "Final",
    source = "Scopus"
}
```
E. Poppleton, R. Romero, A. Mallya, L. Rovigatti, and P. Šulc. Oxdna.org: a public webserver for coarse-grained simulations of dna and rna nanostructures. Nucleic Acids Research, 49(W1):W491 – W498, 2021. doi:10.1093/nar/gkab324.
[abstract▼] [BibTeX▼]

OxDNA and oxRNA are popular coarse-grained models used by the DNA/RNA nanotechnology community to prototype, analyze and rationalize designed DNA and RNA nanostructures. Here, we present oxDNA.org, a graphical web interface for running, visualizing and analyzing oxDNA and oxRNA molecular dynamics simulations on a GPU-enabled high performance computing server. OxDNA.org automatically generates simulation files, including a multi-step relaxation protocol for structures exported in non-physical states from DNA/RNA design tools. Once the simulation is complete, oxDNA.org provides an interactive visualization and analysis interface using the browser-based visualizer oxView to facilitate the understanding of simulation results for a user's specific structure. This online tool significantly lowers the entry barrier of integrating simulations in the nanostructure design pipeline for users who are not experts in the technical aspects of molecular simulation. The webserver is freely available at oxdna.org. © 2021 The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.
```
@article{Rovigatti-YoIcPOpT,
    author = "Poppleton, Erik and Romero, Roger and Mallya, Aatmik and Rovigatti, Lorenzo and Šulc, Petr",
    title = "OxDNA.org: A public webserver for coarse-grained simulations of DNA and RNA nanostructures",
    year = "2021",
    journal = "Nucleic Acids Research",
    volume = "49",
    number = "W1",
    pages = "W491 – W498",
    doi = "10.1093/nar/gkab324",
    type = "Article",
    publication_stage = "Final",
    source = "Scopus"
}
```
V. Sorichetti, A. Ninarello, J. M. Ruiz-Franco, V. Hugouvieux, W. Kob, E. Zaccarelli, and L. Rovigatti. Effect of chain polydispersity on the elasticity of disordered polymer networks. Macromolecules, 54(8):3769 – 3779, 2021. doi:10.1021/acs.macromol.1c00176.
[abstract▼] [BibTeX▼]

Due to their unique structural and mechanical properties, randomly cross-linked polymer networks play an important role in many different fields, ranging from cellular biology to industrial processes. In order to elucidate how these properties are controlled by the physical details of the network (e.g., chain-length and end-to-end distributions), we generate disordered phantom networks with different cross-linker concentrations C and initial densities ρinit and evaluate their elastic properties. We find that the shear modulus computed at the same strand concentration for networks with the same C, which determines the number of chains and the chain-length distribution, depends strongly on the preparation protocol of the network, here controlled by ρinit. We rationalize this dependence by employing a generic stress-strain relation for polymer networks that does not rely on the specific form of the polymer end-to-end distance distribution. We find that the shear modulus of the networks is a nonmonotonic function of the density of elastically active strands, and that this behavior has a purely entropic origin. Our results show that if short chains are abundant, as it is always the case for randomly cross-linked polymer networks, the knowledge of the exact chain conformation distribution is essential for correctly predicting the elastic properties. Finally, we apply our theoretical approach to literature experimental data, qualitatively confirming our interpretations. © 2021 The Authors. Published by American Chemical Society.
```
@article{Rovigatti-Y60_BIIr,
    author = "Sorichetti, Valerio and Ninarello, Andrea and Ruiz-Franco, José M. and Hugouvieux, Virginie and Kob, Walter and Zaccarelli, Emanuela and Rovigatti, Lorenzo",
    title = "Effect of Chain Polydispersity on the Elasticity of Disordered Polymer Networks",
    year = "2021",
    journal = "Macromolecules",
    volume = "54",
    number = "8",
    pages = "3769 – 3779",
    doi = "10.1021/acs.macromol.1c00176",
    type = "Article",
    publication_stage = "Final",
    source = "Scopus"
}
```
J. Vialetto, F. Camerin, F. Grillo, S. N. Ramakrishna, L. Rovigatti, E. Zaccarelli, and L. Isa. Effect of internal architecture on the assembly of soft particles at fluid interfaces. ACS Nano, 15(8):13105 – 13117, 2021. doi:10.1021/acsnano.1c02486.
[abstract▼] [BibTeX▼]

Monolayers of soft colloidal particles confined at fluid interfaces are at the core of a broad range of technological processes, from the stabilization of responsive foams and emulsions to advanced lithographic techniques. However, establishing a fundamental relation between their internal architecture, which is controlled during synthesis, and their structural and mechanical properties upon interfacial confinement remains an elusive task. To address this open issue, which defines the monolayer's properties, we synthesize core-shell microgels, whose soft core can be chemically degraded in a controlled fashion. This strategy allows us to obtain a series of particles ranging from analogues of standard batch-synthesized microgels to completely hollow ones after total core removal. Combined experimental and numerical results show that our hollow particles have a thin and deformable shell, leading to a temperature-responsive collapse of the internal cavity and a complete flattening after adsorption at a fluid interface. Mechanical characterization shows that a critical degree of core removal is required to obtain soft disk-like particles at an oil-water interface, which present a distinct response to compression. At low packing fractions, the mechanical response of the monolayer is dominated by the outer polymer chains forming a corona surrounding the particles within the interfacial plane, regardless of the presence of a core. By contrast, at high compression, the absence of a core enables the particles to deform in the direction orthogonal to the interface and to be continuously compressed without altering the monolayer structure. These findings show how fine, single-particle architectural control during synthesis can be engineered to determine the interfacial behavior of microgels, enabling one to link particle conformation with the resulting material properties. © 2021 The Authors. Published by American Chemical Society.
```
@article{Rovigatti-Yyd1eCYk,
    author = "Vialetto, Jacopo and Camerin, Fabrizio and Grillo, Fabio and Ramakrishna, Shivaprakash N. and Rovigatti, Lorenzo and Zaccarelli, Emanuela and Isa, Lucio",
    title = "Effect of Internal Architecture on the Assembly of Soft Particles at Fluid Interfaces",
    year = "2021",
    journal = "ACS Nano",
    volume = "15",
    number = "8",
    pages = "13105 – 13117",
    doi = "10.1021/acsnano.1c02486",
    type = "Article",
    publication_stage = "Final",
    source = "Scopus"
}
```
G. Del Monte, D. Truzzolillo, F. Camerin, A. Ninarello, E. Chauveau, L. Tavagnacco, N. Gnan, L. Rovigatti, S. Sennato, and E. Zaccarelli. Two-step deswelling in the volume phase transition of thermoresponsive microgels. Proceedings of the National Academy of Sciences of the United States of America, 2021. doi:10.1073/pnas.2109560118.
[abstract▼] [BibTeX▼]

Thermoresponsive microgels are one of the most investigated types of soft colloids, thanks to their ability to undergo a Volume Phase Transition (VPT) close to ambient temperature. However, this fundamental phenomenon still lacks a detailed microscopic understanding, particularly regarding the presence and the role of charges in the deswelling process. This is particularly important for the widely used poly(N-isopropylacrylamide)-based microgels, where the constituent monomers are neutral but charged groups arise due to the initiator molecules used in the synthesis. Here, we address this point combining experiments with state-of-the-art simulations to show that the microgel collapse does not happen in a homogeneous fashion, but through a two-step mechanism, entirely attributable to electrostatic effects. The signature of this phenomenon is the emergence of a minimum in the ratio between gyration and hydrodynamic radii at the VPT. Thanks to simulations of microgels with different cross-linker concentrations, charge contents, and charge distributions, we provide evidence that peripheral charges arising from the synthesis are responsible for this behavior and we further build a universal master curve able to predict the twostep deswelling. Our results have direct relevance on fundamental soft condensed matter science and on applications where microgels are involved, ranging from materials to biomedical technologies. © 2021 National Academy of Sciences. All rights reserved.
```
@article{Rovigatti-ZvItic7B,
    author = "Del Monte, Giovanni and Truzzolillo, Domenico and Camerin, Fabrizio and Ninarello, Andrea and Chauveau, Edouard and Tavagnacco, Letizia and Gnan, Nicoletta and Rovigatti, Lorenzo and Sennato, Simona and Zaccarelli, Emanuela",
    title = "Two-step deswelling in the Volume Phase Transition of thermoresponsive microgels",
    year = "2021",
    journal = "Proceedings of the National Academy of Sciences of the United States of America",
    volume = "118",
    number = "37",
    doi = "10.1073/pnas.2109560118",
    type = "Article",
    publication_stage = "Final",
    source = "Scopus"
}
```

2020↑

I. E. Ventura Rosales, L. Rovigatti, E. Bianchi, C. N. Likos, and E. Locatelli. Shape control of soft patchy nanoparticles under confinement. Nanoscale, 12(41):21188 – 21197, 2020. doi:10.1039/d0nr05058j.
[abstract▼] [BibTeX▼]

Molecular building blocks undergoing a hierarchical assembly process form nano-scale objects which can further assemble into supramolecular structures. When the intermediate units have a limited valence in bonding, complex structures with tailored properties can be created. Here, we consider a composite, star-shaped particle made of f diblock copolymer chains uniformly grafted on a spherical colloid and investigate its first self-assembly stage both in the bulk and under lateral confinement. By means of numerical simulations, we show that, in the bulk, this system develops aggregates whose number and size depend on the temperature as well as on the relative ratio of solvophobic monomers. The emerging aggregates are referred to as patches and impart directionality in bonding to the complex particle. We further characterize how we can control, by changing the lateral confinement, the shape of the brush and the patch properties as a function of the distance between the confining walls. We find that the number of the patches can be determined by tuning the degree of confinement imposed on the particle. Finally, we employ a continuum mechanics model, known as the Liquid Drop Model, to gain insight into the elastic properties of the system. This theoretical approach allows to connect the patch properties to the elastic response of the composite particle. © 2020 The Royal Society of Chemistry.
```
@article{Rovigatti-6nVWAbgC,
    author = "Ventura Rosales, Ivonne Elizabeth and Rovigatti, Lorenzo and Bianchi, Emanuela and Likos, Christos N. and Locatelli, Emanuele",
    title = "Shape control of soft patchy nanoparticles under confinement",
    year = "2020",
    journal = "Nanoscale",
    volume = "12",
    number = "41",
    pages = "21188 – 21197",
    doi = "10.1039/d0nr05058j",
    type = "Article",
    publication_stage = "Final",
    source = "Scopus"
}
```
F. Camerin, N. Gnan, J. Ruiz-Franco, A. Ninarello, L. Rovigatti, and E. Zaccarelli. Microgels at interfaces behave as 2d elastic particles featuring reentrant dynamics. Physical Review X, 2020. doi:10.1103/PhysRevX.10.031012.
[abstract▼] [BibTeX▼]

Soft colloids are increasingly used as model systems to address fundamental issues such as crystallization and the glass and jamming transitions. Among the available classes of soft colloids, microgels are emerging as the gold standard. Since their great internal complexity makes their theoretical characterization very hard, microgels are commonly modeled, at least in the small-deformation regime, within the simple framework of linear elasticity theory. Here we show that there exist conditions where its range of validity can be greatly extended, providing strong numerical evidence that microgels adsorbed at an interface follow the two-dimensional Hertzian theory, and hence behave like 2D elastic particles, up to very large deformations, in stark contrast to what found in bulk conditions. We are also able to estimate Young's modulus of the individual particles and, by comparing it with its counterpart in bulk conditions, we demonstrate a significant stiffening of the polymer network at the interface. Finally, by analyzing dynamical properties, we predict multiple reentrant phenomena: By a continuous increase of particle density, microgels first arrest and then refluidify due to the high penetrability of their extended coronas. We observe this anomalous behavior in a range of experimentally accessible conditions for small and loosely cross-linked microgels. The present work thus establishes microgels at interfaces as a new model system for fundamental investigations, paving the way for the experimental synthesis and research on unique high-density liquidlike states. In addition, these results can guide the development of novel assembly and patterning strategies on surfaces and the design of novel materials with desired interfacial behavior. © 2020 authors.
```
@article{Rovigatti-4bja7TDQ,
    author = "Camerin, Fabrizio and Gnan, Nicoletta and Ruiz-Franco, José and Ninarello, Andrea and Rovigatti, Lorenzo and Zaccarelli, Emanuela",
    title = "Microgels at Interfaces Behave as 2D Elastic Particles Featuring Reentrant Dynamics",
    year = "2020",
    journal = "Physical Review X",
    volume = "10",
    number = "3",
    doi = "10.1103/PhysRevX.10.031012",
    type = "Article",
    publication_stage = "Final",
    source = "Scopus"
}
```
M. Heidenreich, J. M. Georgeson, E. Locatelli, L. Rovigatti, S. K. Nandi, A. Steinberg, Y. Nadav, E. Shimoni, S. A. Safran, J. P. K. Doye, and E. D. Levy. Designer protein assemblies with tunable phase diagrams in living cells. Nature Chemical Biology, 16(9):939 – 945, 2020. doi:10.1038/s41589-020-0576-z.
[abstract▼] [BibTeX▼]

Protein self-organization is a hallmark of biological systems. Although the physicochemical principles governing protein–protein interactions have long been known, the principles by which such nanoscale interactions generate diverse phenotypes of mesoscale assemblies, including phase-separated compartments, remain challenging to characterize. To illuminate such principles, we create a system of two proteins designed to interact and form mesh-like assemblies. We devise a new strategy to map high-resolution phase diagrams in living cells, which provide self-assembly signatures of this system. The structural modularity of the two protein components allows straightforward modification of their molecular properties, enabling us to characterize how interaction affinity impacts the phase diagram and material state of the assemblies in vivo. The phase diagrams and their dependence on interaction affinity were captured by theory and simulations, including out-of-equilibrium effects seen in growing cells. Finally, we find that cotranslational protein binding suffices to recruit a messenger RNA to the designed micron-scale structures. [Figure not available: see fulltext.]. © 2020, The Author(s), under exclusive licence to Springer Nature America, Inc.
```
@article{Rovigatti-dfkCf2Wb,
    author = "Heidenreich, Meta and Georgeson, Joseph M. and Locatelli, Emanuele and Rovigatti, Lorenzo and Nandi, Saroj Kumar and Steinberg, Avital and Nadav, Yotam and Shimoni, Eyal and Safran, Samuel A. and Doye, Jonathan P. K. and Levy, Emmanuel D.",
    title = "Designer protein assemblies with tunable phase diagrams in living cells",
    year = "2020",
    journal = "Nature Chemical Biology",
    volume = "16",
    number = "9",
    pages = "939 – 945",
    doi = "10.1038/s41589-020-0576-z",
    type = "Article",
    publication_stage = "Final",
    source = "Scopus"
}
```
G. Del Monte, F. Camerin, A. Ninarello, N. Gnan, L. Rovigatti, and E. Zaccarelli. Charge affinity and solvent effects in numerical simulations of ionic microgels. Journal of Physics Condensed Matter, 2020. doi:10.1088/1361-648X/abc4cb.
[abstract▼] [BibTeX▼]

Ionic microgel particles are intriguing systems in which the properties of thermo-responsive polymeric colloids are enriched by the presence of charged groups. In order to rationalize their properties and predict the behaviour of microgel suspensions, it is necessary to develop a coarse-graining strategy that starts from the accurate modelling of single particles. Here, we provide a numerical advancement of a recently-introduced model for charged co-polymerized microgels by improving the treatment of ionic groups in the polymer network. We investigate the thermoresponsive properties of the particles, in particular their swelling behaviour and structure, finding that, when charged groups are considered to be hydrophilic at all temperatures, highly charged microgels do not achieve a fully collapsed state, in favorable comparison to experiments. In addition, we explicitly include the solvent in the description and put forward a mapping between the solvophobic potential in the absence of the solvent and the monomer-solvent interactions in its presence, which is found to work very accurately for any charge fraction of the microgel. Our work paves the way for comparing single-particle properties and swelling behaviour of ionic microgels to experiments and to tackle the study of these charged soft particles at a liquid-liquid interface. © 2020 The Author(s). Published by IOP Publishing Ltd.
```
@article{Rovigatti-m6mqWtBI,
    author = "Del Monte, Giovanni and Camerin, Fabrizio and Ninarello, Andrea and Gnan, Nicoletta and Rovigatti, Lorenzo and Zaccarelli, Emanuela",
    title = "Charge affinity and solvent effects in numerical simulations of ionic microgels",
    year = "2020",
    journal = "Journal of Physics Condensed Matter",
    volume = "33",
    number = "8",
    doi = "10.1088/1361-648X/abc4cb",
    type = "Article",
    publication_stage = "Final",
    source = "Scopus"
}
```

2019↑

A. Ninarello, J. J. Crassous, D. Paloli, F. Camerin, N. Gnan, L. Rovigatti, P. Schurtenberger, and E. Zaccarelli. Modeling microgels with a controlled structure across the volume phase transition. Macromolecules, 52(20):7584 – 7592, 2019. doi:10.1021/acs.macromol.9b01122.
[abstract▼] [BibTeX▼]

Thermoresponsive microgels are soft colloids that find widespread use as model systems for soft matter physics. Their complex internal architecture, made of a disordered and heterogeneous polymer network, has been so far a major challenge for computer simulations. In this work, we put forward a coarse-grained model of microgels whose structural properties are in quantitative agreement with results obtained with small-angle X-ray scattering experiments across a wide range of temperatures, encompassing the volume phase transition. These results bridge the gap between experiments and simulations of individual microgel particles, paving the way to theoretically address open questions about their bulk properties with unprecedented nano- and microscale resolution. Copyright © 2019 American Chemical Society.
```
@article{Rovigatti-fe7r8rz8,
    author = "Ninarello, Andrea and Crassous, Jérôme J. and Paloli, Divya and Camerin, Fabrizio and Gnan, Nicoletta and Rovigatti, Lorenzo and Schurtenberger, Peter and Zaccarelli, Emanuela",
    title = "Modeling Microgels with a Controlled Structure across the Volume Phase Transition",
    year = "2019",
    journal = "Macromolecules",
    volume = "52",
    number = "20",
    pages = "7584 – 7592",
    doi = "10.1021/acs.macromol.9b01122",
    type = "Article",
    publication_stage = "Final",
    source = "Scopus"
}
```
L. Rovigatti, N. Gnan, A. Ninarello, and E. Zaccarelli. Connecting elasticity and effective interactions of neutral microgels: the validity of the hertzian model. Macromolecules, 52(13):4895 – 4906, 2019. doi:10.1021/acs.macromol.9b00099.
[abstract▼] [BibTeX▼]

An important open problem in materials science is whether a direct connection exists between single-particle elastic properties and macroscopic bulk behavior. Here, we address this question by focusing on the archetype of soft colloids: thermoresponsive microgels. These colloidal-sized polymer networks are often assumed to interact through a simple Hertzian potential, a classic model in linear elasticity theory. By developing an appropriate methodology that can be generalized to any kind of soft particle, we are able to calculate all the elastic moduli of nonionic microgels across their volume phase transition (VPT). Remarkably, we reproduce many features seen in experiments, including the appearance of a minimum in the Poisson's ratio close to the VPT. By calculating the particle-particle effective interactions and the resulting collective behavior, we find that the Hertzian model works well up to moderate values of the packing fraction. Copyright © 2019 American Chemical Society.
```
@article{Rovigatti-t7i4T2An,
    author = "Rovigatti, Lorenzo and Gnan, Nicoletta and Ninarello, Andrea and Zaccarelli, Emanuela",
    title = "Connecting elasticity and effective interactions of neutral microgels: The validity of the hertzian model",
    year = "2019",
    journal = "Macromolecules",
    volume = "52",
    number = "13",
    pages = "4895 – 4906",
    doi = "10.1021/acs.macromol.9b00099",
    type = "Article",
    publication_stage = "Final",
    source = "Scopus"
}
```
P. H. Handle, L. Rovigatti, and F. Sciortino. Q-independent slow dynamics in atomic and molecular systems. Physical Review Letters, 2019. doi:10.1103/PhysRevLett.122.175501.
[abstract▼] [BibTeX▼]

Investigating million-atom systems for very long simulation times, we demonstrate that the collective density-density correlation time (τα) in simulated supercooled water and silica becomes wave-vector independent (q0) when the probing wavelength is several times larger than the interparticle distance. The q independence of the collective density-density correlation functions, a feature clearly observed in light-scattering studies of some soft-matter systems, is thus a genuine feature of many (but not all) slow-dynamics systems, either atomic, molecular, or colloidal. Indeed, we show that when the dynamics of the density fluctuations includes particle-type diffusion, as in the case of the Lennard-Jones binary-mixture model, the q0 regime does not set in and the relaxation time continues to scale as τα∼q-2 even at small q. © 2019 American Physical Society.
```
@article{Rovigatti-Nm_ClX25,
    author = "Handle, Philip H. and Rovigatti, Lorenzo and Sciortino, Francesco",
    title = "Q-Independent Slow Dynamics in Atomic and Molecular Systems",
    year = "2019",
    journal = "Physical Review Letters",
    volume = "122",
    number = "17",
    doi = "10.1103/PhysRevLett.122.175501",
    type = "Article",
    publication_stage = "Final",
    source = "Scopus"
}
```
F. Camerin, M. Á. Fernández-Rodríguez, L. Rovigatti, M.-N. Antonopoulou, N. Gnan, A. Ninarello, L. Isa, and E. Zaccarelli. Microgels adsorbed at liquid-liquid interfaces: a joint numerical and experimental study. ACS Nano, 13(4):4548 – 4559, 2019. doi:10.1021/acsnano.9b00390.
[abstract▼] [BibTeX▼]

Soft particles display highly versatile properties with respect to hard colloids and even more so at fluid-fluid interfaces. In particular, microgels, consisting of a cross-linked polymer network, are able to deform and flatten upon adsorption at the interface due to the balance between surface tension and internal elasticity. Despite the existence of experimental results, a detailed theoretical understanding of this phenomenon is still lacking due to the absence of appropriate microscopic models. In this work, we propose an advanced modeling of microgels at a flat water/oil interface. The model builds on a realistic description of the internal polymeric architecture and single-particle properties of the microgel and is able to reproduce its experimentally observed shape at the interface. Complementing molecular dynamics simulations with in situ cryo-electron microscopy experiments and atomic force microscopy imaging after Langmuir-Blodgett deposition, we compare the morphology of the microgels for different values of the cross-linking ratios. Our model allows for a systematic microscopic investigation of soft particles at fluid interfaces, which is essential to develop predictive power for the use of microgels in a broad range of applications, including the stabilization of smart emulsions and the versatile patterning of surfaces. © 2019 American Chemical Society.
```
@article{Rovigatti-jT7kaokV,
    author = "Camerin, Fabrizio and Fernández-Rodríguez, Miguel Ángel and Rovigatti, Lorenzo and Antonopoulou, Maria-Nefeli and Gnan, Nicoletta and Ninarello, Andrea and Isa, Lucio and Zaccarelli, Emanuela",
    title = "Microgels Adsorbed at Liquid-Liquid Interfaces: A Joint Numerical and Experimental Study",
    year = "2019",
    journal = "ACS Nano",
    volume = "13",
    number = "4",
    pages = "4548 – 4559",
    doi = "10.1021/acsnano.9b00390",
    type = "Article",
    publication_stage = "Final",
    source = "Scopus"
}
```
G. Del Monte, A. Ninarello, F. Camerin, L. Rovigatti, N. Gnan, and E. Zaccarelli. Numerical insights on ionic microgels: structure and swelling behaviour. Soft Matter, 15(40):8113 – 8128, 2019. doi:10.1039/c9sm01253b.
[abstract▼] [BibTeX▼]

Recent progress has been made in the numerical modelling of neutral microgel particles with a realistic, disordered structure. In this work we extend this approach to the case of co-polymerised microgels where a thermoresponsive polymer is mixed with acidic groups. We compare the cases where counterions directly interact with microgel charges or are modelled implicitly through a Debye-Hückel description. We do so by performing extensive numerical simulations of single microgels across the volume phase transition (VPT) varying the temperature and the fraction of charged monomers. We find that the presence of charges considerably alters the microgel structure, quantified by the monomer density profiles and by the form factors of the microgels, particularly close to the VPT. We observe significant deviations between the implicit and explicit models, with the latter comparing more favourably to available experiments. In particular, we observe a shift of the VPT temperature to larger values as the amount of charged monomers increases. We also find that below the VPT the microgel-counterion complex is almost neutral, while it develops a net charge above the VPT. Interestingly, under these conditions the collapsed microgel still retains a large amount of counterions inside its structure. Since these interesting features cannot be captured by the implicit model, our results show that it is crucial to explicitly include the counterions in order to realistically model ionic thermoresponsive microgels. This journal is © The Royal Society of Chemistry.
```
@article{Rovigatti-f9aseXq5,
    author = "Del Monte, Giovanni and Ninarello, Andrea and Camerin, Fabrizio and Rovigatti, Lorenzo and Gnan, Nicoletta and Zaccarelli, Emanuela",
    title = "Numerical insights on ionic microgels: Structure and swelling behaviour",
    year = "2019",
    journal = "Soft Matter",
    volume = "15",
    number = "40",
    pages = "8113 – 8128",
    doi = "10.1039/c9sm01253b",
    type = "Article",
    publication_stage = "Final",
    source = "Scopus"
}
```
A. Suma, E. Poppleton, M. Matthies, P. Šulc, F. Romano, A. A. Louis, J. P. K. Doye, C. Micheletti, and L. Rovigatti. Tacoxdna: a user-friendly web server for simulations of complex dna structures, from single strands to origami. Journal of Computational Chemistry, 40(29):2586 – 2595, 2019. doi:10.1002/jcc.26029.
[abstract▼] [BibTeX▼]

Simulations of nucleic acids at different levels of structural details are increasingly used to complement and interpret experiments in different fields, from biophysics to medicine and materials science. However, the various structural models currently available for DNA and RNA and their accompanying suites of computational tools can be very rarely used in a synergistic fashion. The tacoxDNA webserver and standalone software package presented here are a step toward a long-sought interoperability of nucleic acids models. The webserver offers a simple interface for converting various common input formats of DNA structures and setting up molecular dynamics (MD) simulations. Users can, for instance, design DNA rings with different topologies, such as knots, with and without supercoiling, by simply providing an XYZ coordinate file of the DNA centre-line. More complex DNA geometries, as designable in the cadnano, CanDo and Tiamat tools, can also be converted to all-atom or oxDNA representations, which can then be used to run MD simulations. Though the latter are currently geared toward the native and LAMMPS oxDNA representations, the open-source package is designed to be further expandable. TacoxDNA is available at http://tacoxdna.sissa.it. © 2019 Wiley Periodicals, Inc. © 2019 Wiley Periodicals, Inc.
```
@article{Rovigatti-dSFueC4Q,
    author = "Suma, Antonio and Poppleton, Erik and Matthies, Michael and Šulc, Petr and Romano, Flavio and Louis, Ard A. and Doye, Jonathan P. K. and Micheletti, Cristian and Rovigatti, Lorenzo",
    title = "TacoxDNA: A user-friendly web server for simulations of complex DNA structures, from single strands to origami",
    year = "2019",
    journal = "Journal of Computational Chemistry",
    volume = "40",
    number = "29",
    pages = "2586 – 2595",
    doi = "10.1002/jcc.26029",
    type = "Article",
    publication_stage = "Final",
    source = "Scopus"
}
```
L. Rovigatti, N. Gnan, L. Tavagnacco, A. J. Moreno, and E. Zaccarelli. Numerical modelling of non-ionic microgels: an overview. Soft Matter, 15(6):1108 – 1119, 2019. doi:10.1039/c8sm02089b.
[abstract▼] [BibTeX▼]

Microgels are complex macromolecules. These colloid-sized polymer networks possess internal degrees of freedom and, depending on the polymer(s) they are made of, can acquire a responsiveness to variations of the environment (temperature, pH, salt concentration, etc.). Besides being valuable for many practical applications, microgels are also extremely important to tackle fundamental physics problems. As a result, these last years have seen a rapid development of protocols for the synthesis of microgels, and more and more research has been devoted to the investigation of their bulk properties. However, from a numerical standpoint the picture is more fragmented, as the inherently multi-scale nature of microgels, whose bulk behaviour crucially depends on the microscopic details, cannot be handled at a single level of coarse-graining. Here we present an overview of the methods and models that have been proposed to describe non-ionic microgels at different length-scales, from the atomistic to the single-particle level. We especially focus on monomer-resolved models, as these have the right level of details to capture the most important properties of microgels, responsiveness and softness. We suggest that these microscopic descriptions, if realistic enough, can be employed as starting points to develop the more coarse-grained representations required to investigate the behaviour of bulk suspensions. © 2019 The Royal Society of Chemistry.
```
@article{Rovigatti-jtW8P7rr,
    author = "Rovigatti, Lorenzo and Gnan, Nicoletta and Tavagnacco, Letizia and Moreno, Angel J. and Zaccarelli, Emanuela",
    title = "Numerical modelling of non-ionic microgels: An overview",
    year = "2019",
    journal = "Soft Matter",
    volume = "15",
    number = "6",
    pages = "1108 – 1119",
    doi = "10.1039/c8sm02089b",
    type = "Review",
    publication_stage = "Final",
    source = "Scopus"
}
```

2018↑

L. Rovigatti, G. Nava, T. Bellini, and F. Sciortino. Self-dynamics and collective swap-driven dynamics in a particle model for vitrimers. Macromolecules, 51(3):1232 – 1241, 2018. doi:10.1021/acs.macromol.7b02186.
[abstract▼] [BibTeX▼]

We numerically investigate the self-dynamics and collective dynamics of a simple model for vitrimers - polymeric covalent networks that have the ability to dynamically rearrange the bond structure via exchange reactions, preserving the total connectivity. Specifically, we study a binary mixture of tetrafunctional and bifunctional particles by means of molecular dynamics simulations that naturally incorporate the bond-swapping mechanism. We specifically focus on the dynamics at small wavevector q by simulating 800 »000 particles. We observe two distinct collective relaxation processes: (i) a fast vibrational damped mode and (ii) a slow network restructuring dynamics. Unexpectedly, the slow process is characterized by a wavevector-independent (q0) mode originating from the swap motion of the bonds. © 2018 American Chemical Society.
```
@article{Rovigatti-DZ8l13AX,
    author = "Rovigatti, Lorenzo and Nava, Giovanni and Bellini, Tommaso and Sciortino, Francesco",
    title = "Self-Dynamics and Collective Swap-Driven Dynamics in a Particle Model for Vitrimers",
    year = "2018",
    journal = "Macromolecules",
    volume = "51",
    number = "3",
    pages = "1232 – 1241",
    doi = "10.1021/acs.macromol.7b02186",
    type = "Article",
    publication_stage = "Final",
    source = "Scopus"
}
```
M. J. Bergman, N. Gnan, M. Obiols-Rabasa, J.-M. Meijer, L. Rovigatti, E. Zaccarelli, and P. Schurtenberger. A new look at effective interactions between microgel particles. Nature Communications, 2018. doi:10.1038/s41467-018-07332-5.
[abstract▼] [BibTeX▼]

Thermoresponsive microgels find widespread use as colloidal model systems, because their temperature-dependent size allows facile tuning of their volume fraction in situ. However, an interaction potential unifying their behavior across the entire phase diagram is sorely lacking. Here we investigate microgel suspensions in the fluid regime at different volume fractions and temperatures, and in the presence of another population of small microgels, combining confocal microscopy experiments and numerical simulations. We find that effective interactions between microgels are clearly temperature dependent. In addition, microgel mixtures possess an enhanced stability compared to hard colloid mixtures - a property not predicted by a simple Hertzian model. Based on numerical calculations we propose a multi-Hertzian model, which reproduces the experimental behavior for all studied conditions. Our findings highlight that effective interactions between microgels are much more complex than usually assumed, displaying a crucial dependence on temperature and on the internal core-corona architecture of the particles. © 2018, The Author(s).
```
@article{Rovigatti-rATpch9d,
    author = "Bergman, Maxime J. and Gnan, Nicoletta and Obiols-Rabasa, Marc and Meijer, Janne-Mieke and Rovigatti, Lorenzo and Zaccarelli, Emanuela and Schurtenberger, Peter",
    title = "A new look at effective interactions between microgel particles",
    year = "2018",
    journal = "Nature Communications",
    volume = "9",
    number = "1",
    doi = "10.1038/s41467-018-07332-5",
    type = "Article",
    publication_stage = "Final",
    source = "Scopus"
}
```
L. Rovigatti, J. Russo, and F. Romano. How to simulate patchy particles⋆. European Physical Journal E, 2018. doi:10.1140/epje/i2018-11667-x.
[abstract▼] [BibTeX▼]

Abstract.: Patchy particles is the name given to a large class of systems of mesoscopic particles characterized by a repulsive core and a discrete number of short-range and highly directional interaction sites. Numerical simulations have contributed significantly to our understanding of the behaviour of patchy particles, but, although simple in principle, advanced simulation techniques are often required to sample the low temperatures and long time-scales associated with their self-assembly behaviour. In this work we review the most popular simulation techniques that have been used to study patchy particles, with a special focus on Monte Carlo methods. We cover many of the tools required to simulate patchy systems, from interaction potentials to biased moves, cluster moves, and free-energy methods. The review is complemented by an educationally oriented Monte Carlo computer code that implements all the techniques described in the text to simulate a well-known tetrahedral patchy particle model. Graphical abstract: [Figure not available: see fulltext.]. © 2018, EDP Sciences, SIF, Springer-Verlag GmbH Germany, part of Springer Nature.
```
@article{Rovigatti-oFQKvBHv,
    author = "Rovigatti, Lorenzo and Russo, John and Romano, Flavio",
    title = "How to simulate patchy particles⋆",
    year = "2018",
    journal = "European Physical Journal E",
    volume = "41",
    number = "5",
    doi = "10.1140/epje/i2018-11667-x",
    type = "Article",
    publication_stage = "Final",
    source = "Scopus"
}
```

L. Rovigatti, F. Romano, and J. Russo. Topical issue on advances in computational methods for soft matter systems. European Physical Journal E, 2018. doi:10.1140/epje/i2018-11695-6.
[BibTeX▼]

@article{Rovigatti-soZxEMEY,
    author = "Rovigatti, Lorenzo and Romano, Flavio and Russo, John",
    title = "Topical Issue on Advances in Computational Methods for Soft Matter Systems",
    year = "2018",
    journal = "European Physical Journal E",
    volume = "41",
    number = "8",
    doi = "10.1140/epje/i2018-11695-6",
    type = "Editorial",
    publication_stage = "Final",
    source = "Scopus"
}

J. Ruiz-Franco, L. Rovigatti, and E. Zaccarelli. On the effect of the thermostat in non-equilibrium molecular dynamics simulations. European Physical Journal E, 2018. doi:10.1140/epje/i2018-11689-4.
[abstract▼] [BibTeX▼]

Abstract.: The numerical investigation of the statics and dynamics of systems in non-equilibrium in general, and under shear flow in particular, has become more and more common. However, not all the numerical methods developed to simulate equilibrium systems can be successfully adapted to out-of-equilibrium cases. This is especially true for thermostats. Indeed, even though thermostats developed to work under equilibrium conditions sometimes display good agreement with rheology experiments, their performance rapidly degrades beyond weak dissipation and small shear rates. Here we focus on gauging the relative performances of three thermostats, Langevin, dissipative particle dynamics, and Bussi-Donadio-Parrinello under varying parameters and external conditions. We compare their effectiveness by looking at different observables and clearly demonstrate that choosing the right thermostat (and its parameters) requires a careful evaluation of, at least, temperature, density and velocity profiles. We also show that small modifications of the Langevin and DPD thermostats greatly enhance their performance in a wide range of parameters. Graphical abstract: [Figure not available: see fulltext.]. © 2018, EDP Sciences, SIF, Springer-Verlag GmbH Germany, part of Springer Nature.
```
@article{Rovigatti-6EJhV7pQ,
    author = "Ruiz-Franco, José and Rovigatti, Lorenzo and Zaccarelli, Emanuela",
    title = "On the effect of the thermostat in non-equilibrium molecular dynamics simulations",
    year = "2018",
    journal = "European Physical Journal E",
    volume = "41",
    number = "7",
    doi = "10.1140/epje/i2018-11689-4",
    type = "Article",
    publication_stage = "Final",
    source = "Scopus"
}
```

C. Cardelli, V. Bianco, L. Rovigatti, F. Nerattini, L. Tubiana, C. Dellago, and I. Coluzza. Erratum: author correction: the role of directional interactions in the designability of generalized heteropolymers (scientific reports (2017) 7 1 (4986)). Scientific reports, 8(1):4592, 2018. doi:10.1038/s41598-018-22649-3.
[abstract▼] [BibTeX▼]

@article{Rovigatti-MB8yJfzJ,
    author = "Cardelli, Chiara and Bianco, Valentino and Rovigatti, Lorenzo and Nerattini, Francesca and Tubiana, Luca and Dellago, Christoph and Coluzza, Ivan",
    title = "Erratum: Author Correction: The role of directional interactions in the designability of generalized heteropolymers (Scientific reports (2017) 7 1 (4986))",
    year = "2018",
    journal = "Scientific reports",
    volume = "8",
    number = "1",
    pages = "4592",
    doi = "10.1038/s41598-018-22649-3",
    type = "Erratum",
    publication_stage = "Final",
    source = "Scopus"
}

E. Locatelli and L. Rovigatti. An accurate estimate of the free energy and phase diagram of all-dna bulk fluids. Polymers, 2018. doi:10.3390/polym10040447.
[abstract▼] [BibTeX▼]

We present a numerical study in which large-scale bulk simulations of self-assembled DNA constructs have been carried out with a realistic coarse-grained model. The investigation aims at obtaining a precise, albeit numerically demanding, estimate of the free energy for such systems. We then, in turn, use these accurate results to validate a recently proposed theoretical approach that builds on a liquid-state theory, theWertheim theory, to compute the phase diagram of all-DNA fluids. This hybrid theoretical/numerical approach, based on the lowest-order virial expansion and on a nearest-neighbor DNA model, can provide, in an undemanding way, a parameter-free thermodynamic description of DNA associating fluids that is in semi-quantitative agreement with experiments. We show that the predictions of the scheme are as accurate as those obtained with more sophisticated methods. We also demonstrate the flexibility of the approach by incorporating non-trivial additional contributions that go beyond the nearest-neighbor model to compute the DNA hybridization free energy. © 2018 by the authors.
```
@article{Rovigatti-sJWPGlKz,
    author = "Locatelli, Emanuele and Rovigatti, Lorenzo",
    title = "An accurate estimate of the free energy and phase diagram of all-DNA Bulk Fluids",
    year = "2018",
    journal = "Polymers",
    volume = "10",
    number = "4",
    doi = "10.3390/polym10040447",
    type = "Article",
    publication_stage = "Final",
    source = "Scopus"
}
```

F. Romano and L. Rovigatti. A nucleotide-level computational approach to DNA-based materials. 2018. doi:10.1007/978-3-319-71578-0_3.
[BibTeX▼]

@book{Rovigatti-IiOr6VDG,
    author = "Romano, Flavio and Rovigatti, Lorenzo",
    title = "A nucleotide-level computational approach to DNA-based materials",
    year = "2018",
    journal = "Design of Self-Assembling Materials",
    pages = "71 – 90",
    doi = "10.1007/978-3-319-71578-0\_3",
    type = "Book chapter",
    publication_stage = "Final",
    source = "Scopus",
    publisher = ""
}

F. Camerin, N. Gnan, L. Rovigatti, and E. Zaccarelli. Modelling realistic microgels in an explicit solvent. Scientific Reports, 2018. doi:10.1038/s41598-018-32642-5.
[abstract▼] [BibTeX▼]

Thermoresponsive microgels are polymeric colloidal networks that can change their size in response to a temperature variation. This peculiar feature is driven by the nature of the solvent-polymer interactions, which triggers the so-called volume phase transition from a swollen to a collapsed state above a characteristic temperature. Recently, an advanced modelling protocol to assemble realistic, disordered microgels has been shown to reproduce experimental swelling behavior and form factors. In the original framework, the solvent was taken into account in an implicit way, condensing solvent-polymer interactions in an effective attraction between monomers. To go one step further, in this work we perform simulations of realistic microgels in an explicit solvent. We identify a suitable model which fully captures the main features of the implicit model and further provides information on the solvent uptake by the interior of the microgel network and on its role in the collapse kinetics. These results pave the way for addressing problems where solvent effects are dominant, such as the case of microgels at liquid-liquid interfaces. © 2018, The Author(s).
```
@article{Rovigatti-Bxen-RAF,
    author = "Camerin, F. and Gnan, N. and Rovigatti, L. and Zaccarelli, E.",
    title = "Modelling realistic microgels in an explicit solvent",
    year = "2018",
    journal = "Scientific Reports",
    volume = "8",
    number = "1",
    doi = "10.1038/s41598-018-32642-5",
    type = "Article",
    publication_stage = "Final",
    source = "Scopus"
}
```
M. C. Engel, D. M. Smith, M. A. Jobst, M. Sajfutdinow, T. Liedl, F. Romano, L. Rovigatti, A. A. Louis, and J. P. K. Doye. Force-induced unravelling of dna origami. ACS Nano, 12(7):6734 – 6747, 2018. doi:10.1021/acsnano.8b01844.
[abstract▼] [BibTeX▼]

The mechanical properties of DNA nanostructures are of widespread interest as applications that exploit their stability under constant or intermittent external forces become increasingly common. We explore the force response of DNA origami in comprehensive detail by combining AFM single molecule force spectroscopy experiments with simulations using oxDNA, a coarse-grained model of DNA at the nucleotide level, to study the unravelling of an iconic origami system: the Rothemund tile. We contrast the force-induced melting of the tile with simulations of an origami 10-helix bundle. Finally, we simulate a recently proposed origami biosensor, whose function takes advantage of origami behavior under tension. We observe characteristic stick-slip unfolding dynamics in our force-extension curves for both the Rothemund tile and the helix bundle and reasonable agreement with experimentally observed rupture forces for these systems. Our results highlight the effect of design on force response: we observe regular, modular unfolding for the Rothemund tile that contrasts with strain-softening of the 10-helix bundle which leads to catastropic failure under monotonically increasing force. Further, unravelling occurs straightforwardly from the scaffold ends inward for the Rothemund tile, while the helix bundle unfolds more nonlinearly. The detailed visualization of the yielding events provided by simulation allows preferred pathways through the complex unfolding free-energy landscape to be mapped, as a key factor in determining relative barrier heights is the extensional release per base pair broken. We shed light on two important questions: how stable DNA nanostructures are under external forces and what design principles can be applied to enhance stability. © 2018 American Chemical Society.
```
@article{Rovigatti-ucfRiPAy,
    author = "Engel, Megan C. and Smith, David M. and Jobst, Markus A. and Sajfutdinow, Martin and Liedl, Tim and Romano, Flavio and Rovigatti, Lorenzo and Louis, Ard A. and Doye, Jonathan P. K.",
    title = "Force-Induced Unravelling of DNA Origami",
    year = "2018",
    journal = "ACS Nano",
    volume = "12",
    number = "7",
    pages = "6734 – 6747",
    doi = "10.1021/acsnano.8b01844",
    type = "Article",
    publication_stage = "Final",
    source = "Scopus"
}
```
L. Rovigatti, N. Gnan, and E. Zaccarelli. Internal structure and swelling behaviour of in silico microgel particles. Journal of Physics Condensed Matter, 2018. doi:10.1088/1361-648X/aaa0f4.
[abstract▼] [BibTeX▼]

Microgels are soft colloids that, by virtue of their polymeric nature, can react to external stimuli such as temperature or pH by changing their size. The resulting swelling/deswelling transition can be exploited in fundamental research as well as for many diverse practical applications, ranging from art restoration to medicine. Such an extraordinary versatility stems from the complex internal structure of the individual microgels, each of which is a crosslinked polymer network. Here we employ a recently-introduced computational method to generate realistic microgel configurations and look at their structural properties, both in real and Fourier space, for several temperatures across the volume phase transition as a function of the crosslinker concentration and of the confining radius employed during the 'in-silico' synthesis. We find that the chain-length distribution of the resulting networks can be analytically predicted by a simple theoretical argument. In addition, we find that our results are well-fitted to the fuzzy-sphere model, which correctly reproduces the density profile of the microgels under study. © 2017 IOP Publishing Ltd.
```
@article{Rovigatti-nBC8s1ky,
    author = "Rovigatti, Lorenzo and Gnan, Nicoletta and Zaccarelli, Emanuela",
    title = "Internal structure and swelling behaviour of in silico microgel particles",
    year = "2018",
    journal = "Journal of Physics Condensed Matter",
    volume = "30",
    number = "4",
    doi = "10.1088/1361-648X/aaa0f4",
    type = "Article",
    publication_stage = "Final",
    source = "Scopus"
}
```

2017↑

M. Ronti, L. Rovigatti, J. M. Tavares, A. O. Ivanov, S. S. Kantorovich, and F. Sciortino. Free energy calculations for rings and chains formed by dipolar hard spheres. Soft Matter, 13(43):7870 – 7878, 2017. doi:10.1039/c7sm01692a.
[abstract▼] [BibTeX▼]

We employ a method based on Monte Carlo grand-canonical simulations to precisely calculate partition functions of non-interacting chains and rings formed by dipolar hard spheres (DHS) at low temperature. The extended low temperature region offered by such cluster calculations, compared to what had been previously achieved with standard simulations, opens up the possibility of exploring a part of the DHS phase diagram which was inaccessible before. The reported results offer the unique opportunity of verifying well-established theoretical models based on the ideal gas of cluster approximation in order to clarify their range of validity. They also provide the basis for future studies in which cluster-cluster interactions will be included. © 2017 The Royal Society of Chemistry.
```
@article{Rovigatti-8YAkkT9Q,
    author = "Ronti, Michela and Rovigatti, Lorenzo and Tavares, José M. and Ivanov, Alexey O. and Kantorovich, Sofia S. and Sciortino, Francesco",
    title = "Free energy calculations for rings and chains formed by dipolar hard spheres",
    year = "2017",
    journal = "Soft Matter",
    volume = "13",
    number = "43",
    pages = "7870 – 7878",
    doi = "10.1039/c7sm01692a",
    type = "Article",
    publication_stage = "Final",
    source = "Scopus"
}
```
L. Rovigatti, V. Bianco, J. M. Tavares, and F. Sciortino. Communication: re-entrant limits of stability of the liquid phase and the speedy scenario in colloidal model systems. Journal of Chemical Physics, 2017. doi:10.1063/1.4974830.
[abstract▼] [BibTeX▼]

A re-entrant gas-liquid spinodal was proposed as a possible explanation of the apparent divergence of the compressibility and specific heat off supercooling water. Such a counter-intuitive possibility, e.g., a liquid that becomes unstable to gas-like fluctuations on cooling at positive pressure, has never been observed, neither in real substances nor in off-lattice simulations. More recently, such a re-entrant scenario has been dismissed on the premise that the re-entrant spinodal would collide with the gas-liquid coexisting curve (binodal) in the pressure-temperature plane. Here we study, numerically and analytically, two previously introduced one-component patchy particle models that both show (i) a re-entrant limit of stability of the liquid phase and (ii) a re-entrant binodal, providing a neat in silico (and in charta) realization of such unconventional thermodynamic scenario. © 2017 Author(s).
```
@article{Rovigatti-0FphayT7,
    author = "Rovigatti, Lorenzo and Bianco, Valentino and Tavares, José Maria and Sciortino, Francesco",
    title = "Communication: Re-entrant limits of stability of the liquid phase and the Speedy scenario in colloidal model systems",
    year = "2017",
    journal = "Journal of Chemical Physics",
    volume = "146",
    number = "4",
    doi = "10.1063/1.4974830",
    type = "Article",
    publication_stage = "Final",
    source = "Scopus"
}
```
S. Roldán-Vargas, L. Rovigatti, and F. Sciortino. Connectivity, dynamics, and structure in a tetrahedral network liquid. Soft Matter, 13(2):514 – 530, 2017. doi:10.1039/c6sm02282k.
[abstract▼] [BibTeX▼]

We report a detailed computational study by Brownian dynamics simulations of the structure and dynamics of a liquid of patchy particles which forms an amorphous tetrahedral network upon decreasing the temperature. The highly directional particle interactions allow us to investigate the system connectivity by discriminating the total set of particles into different populations according to a penta-modal distribution of bonds per particle. With this methodology we show how the particle bonding process is not randomly independent but it manifests clear bond correlations at low temperatures. We further explore the dynamics of the system in real space and establish a clear relation between particle mobility and particle connectivity. In particular, we provide evidence of anomalous diffusion at low temperatures and reveal how the dynamics is affected by the short-time hopping motion of the weakly bounded particles. Finally we widely investigate the dynamics and structure of the system in Fourier space and identify two quantitatively similar length scales, one dynamic and the other static, which increase upon cooling the system and reach distances of the order of few particle diameters. We summarize our findings in a qualitative picture where the low temperature regime of the viscoelastic liquid is understood in terms of an evolving network of long time metastable cooperative domains of particles. © The Royal Society of Chemistry.
```
@article{Rovigatti-heIs-0WW,
    author = "Roldán-Vargas, Sándalo and Rovigatti, Lorenzo and Sciortino, Francesco",
    title = "Connectivity, dynamics, and structure in a tetrahedral network liquid",
    year = "2017",
    journal = "Soft Matter",
    volume = "13",
    number = "2",
    pages = "514 – 530",
    doi = "10.1039/c6sm02282k",
    type = "Article",
    publication_stage = "Final",
    source = "Scopus"
}
```
E. Locatelli, P. H. Handle, C. N. Likos, F. Sciortino, and L. Rovigatti. Condensation and demixing in solutions of dna nanostars and their mixtures. ACS Nano, 11(2):2094 – 2102, 2017. doi:10.1021/acsnano.6b08287.
[abstract▼] [BibTeX▼]

We present a numerical/theoretical approach to efficiently evaluate the phase diagram of self-assembling DNA nanostars. Combining input information based on a realistic coarse-grained DNA potential with the Wertheim association theory, we derive a parameter-free thermodynamic description of these systems. We apply this method to investigate the phase behavior of single components and mixtures of DNA nanostars with different numbers of sticky arms, elucidating the role of the system functionality and of salt concentration. Specifically, we evaluate the propensity to demix, the gas-liquid phase boundaries and the location of the critical points. The predicted critical parameters compare very well with existing experimental results for the available compositions. The approach developed here is very general, easily extensible to other all-DNA systems, and provides guidance for future experiments. © 2017 American Chemical Society.
```
@article{Rovigatti-TtWORRWG,
    author = "Locatelli, Emanuele and Handle, Philip H. and Likos, Christos N. and Sciortino, Francesco and Rovigatti, Lorenzo",
    title = "Condensation and Demixing in Solutions of DNA Nanostars and Their Mixtures",
    year = "2017",
    journal = "ACS Nano",
    volume = "11",
    number = "2",
    pages = "2094 – 2102",
    doi = "10.1021/acsnano.6b08287",
    type = "Article",
    publication_stage = "Final",
    source = "Scopus"
}
```
E. Bianchi, B. Capone, I. Coluzza, L. Rovigatti, and P. D. J. Van Oostrum. Limiting the valence: advancements and new perspectives on patchy colloids, soft functionalized nanoparticles and biomolecules. Physical Chemistry Chemical Physics, 19(30):19847 – 19868, 2017. doi:10.1039/c7cp03149a.
[abstract▼] [BibTeX▼]

Limited bonding valence, usually accompanied by well-defined directional interactions and selective bonding mechanisms, is nowadays considered among the key ingredients to create complex structures with tailored properties: even though isotropically interacting units already guarantee access to a vast range of functional materials, anisotropic interactions can provide extra instructions to steer the assembly of specific architectures. The anisotropy of effective interactions gives rise to a wealth of self-assembled structures both in the realm of suitably synthesized nano- and micro-sized building blocks and in nature, where the isotropy of interactions is often a zero-th order description of the complicated reality. In this review, we span a vast range of systems characterized by limited bonding valence, from patchy colloids of new generation to polymer-based functionalized nanoparticles, DNA-based systems and proteins, and describe how the interaction patterns of the single building blocks can be designed to tailor the properties of the target final structures. © 2017 the Owner Societies.
```
@article{Rovigatti-M13lFjty,
    author = "Bianchi, Emanuela and Capone, Barbara and Coluzza, Ivan and Rovigatti, Lorenzo and Van Oostrum, Peter D. J.",
    title = "Limiting the valence: Advancements and new perspectives on patchy colloids, soft functionalized nanoparticles and biomolecules",
    year = "2017",
    journal = "Physical Chemistry Chemical Physics",
    volume = "19",
    number = "30",
    pages = "19847 – 19868",
    doi = "10.1039/c7cp03149a",
    type = "Review",
    publication_stage = "Final",
    source = "Scopus"
}
```
N. Gnan, L. Rovigatti, M. Bergman, and E. Zaccarelli. In silico synthesis of microgel particles. Macromolecules, 50(21):8777 – 8786, 2017. doi:10.1021/acs.macromol.7b01600.
[abstract▼] [BibTeX▼]

Microgels are colloidal-scale particles individually made of cross-linked polymer networks that can swell and deswell in response to external stimuli, such as changes to temperature or pH. Despite a large amount of experimental activities on microgels, a proper theoretical description based on individual particle properties is still missing due to the complexity of the particles. To go one step further, here we propose a novel methodology to assemble realistic microgel particles in silico. We exploit the self-assembly of a binary mixture composed of tetravalent (cross-linkers) and bivalent (monomer beads) patchy particles under spherical confinement in order to produce fully bonded networks. The resulting structure is then used to generate the initial microgel configuration, which is subsequently simulated with a bead-spring model complemented by a temperature-induced hydrophobic attraction. To validate our assembly protocol, we focus on a small microgel test case and show that we can reproduce the experimental swelling curve by appropriately tuning the confining sphere radius, something that would not be possible with less sophisticated assembly methodologies, e.g., in the case of networks generated from an underlying crystal structure. We further investigate the structure (in reciprocal and real space) and the swelling curves of microgels as a function of temperature, finding that our results are well described by the widely used fuzzy sphere model. This is a first step toward a realistic modeling of microgel particles, which will pave the way for a careful assessment of their elastic properties and effective interactions. © 2017 American Chemical Society.
```
@article{Rovigatti-o2sVGdTL,
    author = "Gnan, Nicoletta and Rovigatti, Lorenzo and Bergman, Maxime and Zaccarelli, Emanuela",
    title = "In Silico Synthesis of Microgel Particles",
    year = "2017",
    journal = "Macromolecules",
    volume = "50",
    number = "21",
    pages = "8777 – 8786",
    doi = "10.1021/acs.macromol.7b01600",
    type = "Article",
    publication_stage = "Final",
    source = "Scopus"
}
```
I. C. Gârlea, E. Bianchi, B. Capone, L. Rovigatti, and C. N. Likos. Hierarchical self-organization of soft patchy nanoparticles into morphologically diverse aggregates. Current Opinion in Colloid and Interface Science, 30:1 – 7, 2017. doi:10.1016/j.cocis.2017.03.008.
[abstract▼] [BibTeX▼]

We present a concise review of the large variety of self-assembly scenarios observed in solutions of diblock copolymer stars with a solvophilic inner block and a solvophobic outer block. A variety of modeling approaches and simulation techniques at different levels of detail reveals that individual molecules assume configurations akin to patchy colloids, but with a patchiness that depends on physical parameters and can adjust to external stimuli such as temperature and pH. These soft, patchy building blocks inter-associate at finite concentrations into micellar or gel-like solutions, including spherical and wormlike micelles, or they display macroscopic phase separation. The connections between single-molecule conformation and the structure of the concentrated solution are discussed, and coarse-grained strategies for these novel molecular entities are critically compared to one another. © 2017 Elsevier Ltd
```
@article{Rovigatti-IGd9ri6l,
    author = "C. Gârlea, Ioana and Bianchi, Emanuela and Capone, Barbara and Rovigatti, Lorenzo and N. Likos, Christos",
    title = "Hierarchical self-organization of soft patchy nanoparticles into morphologically diverse aggregates",
    year = "2017",
    journal = "Current Opinion in Colloid and Interface Science",
    volume = "30",
    pages = "1 – 7",
    doi = "10.1016/j.cocis.2017.03.008",
    type = "Review",
    publication_stage = "Final",
    source = "Scopus"
}
```
C. Cardelli, V. Bianco, L. Rovigatti, F. Nerattini, L. Tubiana, C. Dellago, and I. Coluzza. The role of directional interactions in the designability of generalized heteropolymers. Scientific Reports, 2017. doi:10.1038/s41598-017-04720-7.
[abstract▼] [BibTeX▼]

Heteropolymers are important examples of self-assembling systems. However, in the design of artificial heteropolymers the control over the single chain self-assembling properties does not reach that of the natural bio-polymers, and in particular proteins. Here, we introduce a sufficiency criterion to identify polymers that can be designed to adopt a predetermined structure and show that it is fulfilled by polymers made of monomers interacting through directional (anisotropic) interactions. The criterion is based on the appearance of a particular peak in the radial distribution function, that we show being a universal feature of all designable heteropolymers, as it is present also in natural proteins. Our criterion can be used to engineer new self-assembling modular polymers that will open new avenues for applications in materials science. © 2017 The Author(s).
```
@article{Rovigatti-mOVeiPU4,
    author = "Cardelli, Chiara and Bianco, Valentino and Rovigatti, Lorenzo and Nerattini, Francesca and Tubiana, Luca and Dellago, Christoph and Coluzza, Ivan",
    title = "The role of directional interactions in the designability of generalized heteropolymers",
    year = "2017",
    journal = "Scientific Reports",
    volume = "7",
    number = "1",
    doi = "10.1038/s41598-017-04720-7",
    type = "Article",
    publication_stage = "Final",
    source = "Scopus"
}
```

2016↑

L. Rovigatti, B. Capone, and C. N. Likos. Soft self-assembled nanoparticles with temperature-dependent properties. Nanoscale, 8(6):3288 – 3295, 2016. doi:10.1039/c5nr04661k.
[abstract▼] [BibTeX▼]

The fabrication of versatile building blocks that reliably self-assemble into desired ordered and disordered phases is amongst the hottest topics in contemporary materials science. To this end, microscopic units of varying complexity, aimed at assembling the target phases, have been thought, designed, investigated and built. Such a path usually requires laborious fabrication techniques, especially when specific functionalisation of the building blocks is required. Telechelic star polymers, i.e., star polymers made of a number of f di-block copolymers consisting of solvophobic and solvophilic monomers grafted on a central anchoring point, spontaneously self-assemble into soft patchy particles featuring attractive spots (patches) on the surface. Here we show that the tunability of such a system can be widely extended by controlling the physical and chemical parameters of the solution. Indeed, under fixed external conditions the self-assembly behaviour depends only on the number of arms and on the ratio of solvophobic to solvophilic monomers. However, changes in temperature and/or solvent quality make it possible to reliably change the number and size of the attractive patches. This allows the steering of the mesoscopic self-assembly behaviour without modifying the microscopic constituents. Interestingly, we also demonstrate that diverse combinations of the parameters can generate stars with the same number of patches but different radial and angular stiffness. This mechanism could provide a neat way of further fine-tuning the elastic properties of the supramolecular network without changing its topology. © 2016 The Royal Society of Chemistry.
```
@article{Rovigatti-OsHvCz9s,
    author = "Rovigatti, Lorenzo and Capone, Barbara and Likos, Christos N.",
    title = "Soft self-assembled nanoparticles with temperature-dependent properties",
    year = "2016",
    journal = "Nanoscale",
    volume = "8",
    number = "6",
    pages = "3288 – 3295",
    doi = "10.1039/c5nr04661k",
    type = "Article",
    publication_stage = "Final",
    source = "Scopus"
}
```
S. Biagi, L. Rovigatti, F. Sciortino, and C. Misbah. Surface wave excitations and backflow effect over dense polymer brushes. Scientific Reports, 2016. doi:10.1038/srep22257.
[abstract▼] [BibTeX▼]

Polymer brushes are being increasingly used to tailor surface physicochemistry for diverse applications such as wetting, adhesion of biological objects, implantable devices and much more. Here we perform Dissipative Particle Dynamics simulations to study the behaviour of dense polymer brushes under flow in a slit-pore channel. We discover that the system displays flow inversion at the brush interface for several disconnected ranges of the imposed flow. We associate such phenomenon to collective polymer dynamics: a wave propagating on the brush surface. The relation between the wavelength, the amplitude and the propagation speed of the flow-generated wave is consistent with the solution of the Stokes equations when an imposed traveling wave is assumed as the boundary condition (the famous Taylor's swimmer).
```
@article{Rovigatti-ZcXBBrHM,
    author = "Biagi, Sofia and Rovigatti, Lorenzo and Sciortino, Francesco and Misbah, Chaouqi",
    title = "Surface wave excitations and backflow effect over dense polymer brushes",
    year = "2016",
    journal = "Scientific Reports",
    volume = "6",
    doi = "10.1038/srep22257",
    type = "Article",
    publication_stage = "Final",
    source = "Scopus"
}
```
N. A. Mahynski, L. Rovigatti, C. N. Likos, and A. Z. Panagiotopoulos. Bottom-up colloidal crystal assembly with a twist. ACS Nano, 10(5):5459 – 5467, 2016. doi:10.1021/acsnano.6b01854.
[abstract▼] [BibTeX▼]

Globally ordered colloidal crystal lattices have broad utility in a wide range of optical and catalytic devices, for example, as photonic band gap materials. However, the self-assembly of stereospecific structures is often confounded by polymorphism. Small free-energy differences often characterize ensembles of different structures, making it difficult to produce a single morphology at will. Current techniques to handle this problem adopt one of two approaches: that of the "top-down" or "bottom-up" methodology, whereby structures are engineered starting from the largest or smallest relevant length scales, respectively. However, recently, a third approach for directing high fidelity assembly of colloidal crystals has been suggested which relies on the introduction of polymer cosolutes into the crystal phase [Mahynski, N.; Panagiotopoulos, A. Z.; Meng, D.; Kumar, S. K. Nat. Commun. 2014, 5, 4472]. By tuning the polymers morphology to interact uniquely with the void symmetry of a single desired crystal, the entropy loss associated with polymer confinement has been shown to strongly bias the formation of that phase. However, previously, this approach has only been demonstrated in the limiting case of close-packed crystals. Here, we show how this approach may be generalized and extended to complex open crystals, illustrating the utility of this "structure-directing agent" paradigm in engineering the nanoscale structure of ordered colloidal materials. The high degree of transferability of this paradigms basic principles between relatively simple crystals and more complex ones suggests that this represents a valuable addition to presently known self-assembly techniques. © 2016 American Chemical Society.
```
@article{Rovigatti-lvdTx_RK,
    author = "Mahynski, Nathan A. and Rovigatti, Lorenzo and Likos, Christos N. and Panagiotopoulos, Athanassios Z.",
    title = "Bottom-Up Colloidal Crystal Assembly with a Twist",
    year = "2016",
    journal = "ACS Nano",
    volume = "10",
    number = "5",
    pages = "5459 – 5467",
    doi = "10.1021/acsnano.6b01854",
    type = "Article",
    publication_stage = "Final",
    source = "Scopus"
}
```
B. E. K. Snodin, F. Romano, L. Rovigatti, T. E. Ouldridge, A. A. Louis, and J. P. K. Doye. Direct simulation of the self-assembly of a small dna origami. ACS Nano, 10(2):1724 – 1737, 2016. doi:10.1021/acsnano.5b05865.
[abstract▼] [BibTeX▼]

By using oxDNA, a coarse-grained nucleotide-level model of DNA, we are able to directly simulate the self-assembly of a small 384-base-pair origami from single-stranded scaffold and staple strands in solution. In general, we see attachment of new staple strands occurring in parallel, but with cooperativity evident for the binding of the second domain of a staple if the adjacent junction is already partially formed. For a system with exactly one copy of each staple strand, we observe a complete assembly pathway in an intermediate temperature window; at low temperatures successful assembly is prevented by misbonding while at higher temperature the free-energy barriers to assembly become too large for assembly on our simulation time scales. For high-concentration systems involving a large staple strand excess, we never see complete assembly because there are invariably instances where two copies of the same staple both bind to the scaffold, creating a kinetic trap that prevents the complete binding of either staple. This mutual staple blocking could also lead to aggregates of partially formed origamis in real systems, and helps to rationalize certain successful origami design strategies. © 2016 American Chemical Society.
```
@article{Rovigatti-jNtwtZGb,
    author = "Snodin, Benedict E. K. and Romano, Flavio and Rovigatti, Lorenzo and Ouldridge, Thomas E. and Louis, Ard A. and Doye, Jonathan P. K.",
    title = "Direct Simulation of the Self-Assembly of a Small DNA Origami",
    year = "2016",
    journal = "ACS Nano",
    volume = "10",
    number = "2",
    pages = "1724 – 1737",
    doi = "10.1021/acsnano.5b05865",
    type = "Article",
    publication_stage = "Final",
    source = "Scopus"
}
```
J. Fernandez-Castanon, F. Bomboi, L. Rovigatti, M. Zanatta, A. Paciaroni, L. Comez, L. Porcar, C.J. Jafta, G.C. Fadda, T. Bellini, and F. Sciortino. Small-angle neutron scattering and molecular dynamics structural study of gelling dna nanostars. Journal of Chemical Physics, 2016. doi:10.1063/1.4961398.
[abstract▼] [BibTeX▼]

DNA oligomers with properly designed sequences self-assemble into well defined constructs. Here, we exploit this methodology to produce bulk quantities of tetravalent DNA nanostars (each one composed of 196 nucleotides) and to explore the structural signatures of their aggregation process. We report small-angle neutron scattering experiments focused on the evaluation of both the form factor and the temperature evolution of the scattered intensity at a nanostar concentration where the system forms a tetravalent equilibrium gel. We also perform molecular dynamics simulations of one isolated tetramer to evaluate the form factor numerically, without resorting to any approximate shape. The numerical form factor is found to be in very good agreement with the experimental one. Simulations predict an essentially temperature-independent form factor, offering the possibility to extract the effective structure factor and its evolution during the equilibrium gelation. © 2016 Author(s).
```
@article{Rovigatti-Kp6pE49V,
    author = "Fernandez-Castanon, J. and Bomboi, F. and Rovigatti, L. and Zanatta, M. and Paciaroni, A. and Comez, L. and Porcar, L. and Jafta, C.J. and Fadda, G.C. and Bellini, T. and Sciortino, F.",
    title = "Small-angle neutron scattering and molecular dynamics structural study of gelling DNA nanostars",
    year = "2016",
    journal = "Journal of Chemical Physics",
    volume = "145",
    number = "8",
    doi = "10.1063/1.4961398",
    type = "Article",
    publication_stage = "Final",
    source = "Scopus"
}
```

2015↑

L. Rovigatti, P. Šulc, I. Z. Reguly, and F. Romano. A comparison between parallelization approaches in molecular dynamics simulations on gpus. Journal of Computational Chemistry, 36(1):1 – 8, 2015. doi:10.1002/jcc.23763.
[abstract▼] [BibTeX▼]

We test the relative performances of two different approaches to the computation of forces for molecular dynamics simulations on graphics processing units. A "vertex-based" approach, where a computing thread is started per particle, is compared to an "edge-based" approach, where a thread is started per each potentially non-zero interaction. We find that the former is more efficient for systems with many simple interactions per particle while the latter is more efficient if the system has more complicated interactions or fewer of them. By comparing computation times on more and less recent graphics processing unit technology, we predict that, if the current trend of increasing the number of processing cores - as opposed to their computing power - remains, the "edge-based" approach will gradually become the most efficient choice in an increasing number of cases. © 2014 Wiley Periodicals, Inc.
```
@article{Rovigatti-0CG4iZ1h,
    author = "Rovigatti, Lorenzo and Šulc, Petr and Reguly, István Z. and Romano, Flavio",
    title = "A comparison between parallelization approaches in molecular dynamics simulations on GPUs",
    year = "2015",
    journal = "Journal of Computational Chemistry",
    volume = "36",
    number = "1",
    pages = "1 – 8",
    doi = "10.1002/jcc.23763",
    type = "Article",
    publication_stage = "Final",
    source = "Scopus"
}
```
A.O. Ivanov, S.S. Kantorovich, L. Rovigatti, J.M. Tavares, and F. Sciortino. Low temperature structural transitions in dipolar hard spheres: the influence on magnetic properties. Journal of Magnetism and Magnetic Materials, 383:272 – 276, 2015. doi:10.1016/j.jmmm.2014.10.013.
[abstract▼] [BibTeX▼]

We investigate the structural chain-to-ring transition at low temperature in a gas of dipolar hard spheres (DHS). Due to the weakening of entropic contribution, ring formation becomes noticeable when the effective dipole-dipole magnetic interaction increases. It results in the redistribution of particles from usually observed flexible chains into flexible rings. The concentration (ρ) of DHS plays a crucial part in this transition: at a very low ρ only chains and rings are observed, whereas even a slight increase of the volume fraction leads to the formation of branched or defect structures. As a result, the fraction of DHS aggregated in defect-free rings turns out to be a non-monotonic function of ρ. The average ring size is found to be a slower increasing function of ρ when compared to that of chains. Both theory and computer simulations confirm the dramatic influence of the ring formation on the ρ-dependence of the initial magnetic susceptibility (χ) when the temperature decreases. The rings due to their zero total dipole moment are irresponsive to a weak magnetic field and drive to the strong decrease of the initial magnetic susceptibility. © 2014 Elsevier B.V.
```
@article{Rovigatti-KKILTsCV,
    author = "Ivanov, A.O. and Kantorovich, S.S. and Rovigatti, L. and Tavares, J.M. and Sciortino, F.",
    title = "Low temperature structural transitions in dipolar hard spheres: The influence on magnetic properties",
    year = "2015",
    journal = "Journal of Magnetism and Magnetic Materials",
    volume = "383",
    pages = "272 – 276",
    doi = "10.1016/j.jmmm.2014.10.013",
    type = "Article",
    publication_stage = "Final",
    source = "Scopus"
}
```
L. Rovigatti, N. Gnan, A. Parola, and E. Zaccarelli. How soft repulsion enhances the depletion mechanism. Soft Matter, 11(4):692 – 700, 2015. doi:10.1039/c4sm02218a.
[abstract▼] [BibTeX▼]

We investigate binary mixtures of large colloids interacting through soft potentials with small, ideal depletants. We show that softness has a dramatic effect on the resulting colloid-colloid effective potential when the depletant-to-colloid size ratio q is small, with significant consequences on the colloidal phase behaviour. We provide an exact relationship that allows us to obtain the effective pair potential for any type of colloid-depletant interaction in the case of ideal depletants, without having to rely on complicated and expensive full-mixture simulations. We also show that soft repulsion among depletants further enhances the tendency of colloids to aggregate. Our theoretical and numerical results demonstrate that-in the limit of small q-soft mixtures cannot be mapped onto hard systems and hence soft depletion is not a mere extension of the widely used Asakura-Oosawa potential. This journal is © The Royal Society of Chemistry 2014.
```
@article{Rovigatti--AguraqB,
    author = "Rovigatti, Lorenzo and Gnan, Nicoletta and Parola, Alberto and Zaccarelli, Emanuela",
    title = "How soft repulsion enhances the depletion mechanism",
    year = "2015",
    journal = "Soft Matter",
    volume = "11",
    number = "4",
    pages = "692 – 700",
    doi = "10.1039/c4sm02218a",
    type = "Article",
    publication_stage = "Final",
    source = "Scopus"
}
```
S. S. Kantorovich, A. O. Ivanov, L. Rovigatti, J. M. Tavares, and F. Sciortino. Temperature-induced structural transitions in self-assembling magnetic nanocolloids. Physical Chemistry Chemical Physics, 17(25):16601 – 16608, 2015. doi:10.1039/c5cp01558h.
[abstract▼] [BibTeX▼]

With the help of a unique combination of density functional theory and computer simulations, we discover two possible scenarios, depending on concentration, for the hierarchical self-assembly of magnetic nanoparticles on cooling. We show that typically considered low temperature clusters, i.e. defect-free chains and rings, merge into more complex branched structures through only three types of defects: four-way X junctions, three-way Y junctions and two-way Z junctions. Our accurate calculations reveal the predominance of weakly magnetically responsive rings cross-linked by X defects at the lowest temperatures. We thus provide a strategy to fine-tune magnetic and thermodynamic responses of magnetic nanocolloids to be used in medical and microfluidics applications. This journal is © the Owner Societies 2015.
```
@article{Rovigatti-ePzjq8y8,
    author = "Kantorovich, Sofia S. and Ivanov, Alexey O. and Rovigatti, Lorenzo and Tavares, Jose M. and Sciortino, Francesco",
    title = "Temperature-induced structural transitions in self-assembling magnetic nanocolloids",
    year = "2015",
    journal = "Physical Chemistry Chemical Physics",
    volume = "17",
    number = "25",
    pages = "16601 – 16608",
    doi = "10.1039/c5cp01558h",
    type = "Article",
    publication_stage = "Final",
    source = "Scopus"
}
```

2014↑

L. Rovigatti, F. Smallenburg, F. Romano, and F. Sciortino. Gels of dna nanostars never crystallize. ACS Nano, 8(4):3567 – 3574, 2014. doi:10.1021/nn501138w.
[abstract▼] [BibTeX▼]

Using state-of-the-art numerical techniques, we show that, upon lowering the temperature, tetravalent DNA nanostars form a thermodynamically stable, fully bonded equilibrium gel. In contrast to atomic and molecular network formers, in which the disordered liquid is always metastable with respect to some crystalline phase, we find that the DNA nanostar gel has a lower free energy than the diamond crystal structure in a wide range of concentrations. This unconventional behavior, here verified for the first time in a realistic model, arises from the large arm flexibility of the DNA nanostars, a property that can be tuned by design. Our results confirm the thermodynamic stability of the recently experimentally realized DNA hydrogels. © 2014 American Chemical Society.
```
@article{Rovigatti-XN8_A_-w,
    author = "Rovigatti, Lorenzo and Smallenburg, Frank and Romano, Flavio and Sciortino, Francesco",
    title = "Gels of DNA nanostars never crystallize",
    year = "2014",
    journal = "ACS Nano",
    volume = "8",
    number = "4",
    pages = "3567 – 3574",
    doi = "10.1021/nn501138w",
    type = "Article",
    publication_stage = "Final",
    source = "Scopus"
}
```
L. Rovigatti, F. Bomboi, and F. Sciortino. Accurate phase diagram of tetravalent dna nanostars. Journal of Chemical Physics, 2014. doi:10.1063/1.4870467.
[abstract▼] [BibTeX▼]

We evaluate, by means of molecular dynamics simulations employing a realistic DNA coarse-grained model, the phase behaviour and the structural and dynamic properties of tetravalent DNA nanostars, i.e., nanoconstructs completely made of DNA. We find that, as the system is cooled down, tetramers undergo a gas-liquid phase separation in a region of concentrations which, if the difference in salt concentration is taken into account, is comparable with the recently measured experimental phase diagram [S. Biffi, R. Cerbino, F. Bomboi, E. M. Paraboschi, R. Asselta, F. Sciortino, and T. Bellini, Proc. Natl. Acad. Sci. U.S.A. 110, 15633 (2013)]. We also present a mean-field free energy for modelling the phase diagram based on the bonding contribution derived by Wertheim in his studies of associating liquids. Combined with mass-action law expressions appropriate for DNA binding and a numerically evaluated reference free energy, the resulting free energy qualitatively reproduces the numerical data. Finally, we report information on the nanostar structure, e.g., geometry and flexibility of the single tetramer and of the collective behaviour, providing a useful reference for future small angle scattering experiments, for all investigated temperatures and concentrations. © 2014 AIP Publishing LLC.
```
@article{Rovigatti-WXVi3M6y,
    author = "Rovigatti, Lorenzo and Bomboi, Francesca and Sciortino, Francesco",
    title = "Accurate phase diagram of tetravalent DNA nanostars",
    year = "2014",
    journal = "Journal of Chemical Physics",
    volume = "140",
    number = "15",
    doi = "10.1063/1.4870467",
    type = "Article",
    publication_stage = "Final",
    source = "Scopus"
}
```

2013↑

J. P.K. Doye, T. E. Ouldridge, A. A. Louis, F. Romano, P. Šulc, C. Matek, B. E.K. Snodin, L. Rovigatti, J. S. Schreck, R. M. Harrison, and W. P.J. Smith. Coarse-graining dna for simulations of dna nanotechnology. Physical Chemistry Chemical Physics, 15(47):20395 – 20414, 2013. doi:10.1039/c3cp53545b.
[abstract▼] [BibTeX▼]

To simulate long time and length scale processes involving DNA it is necessary to use a coarse-grained description. Here we provide an overview of different approaches to such coarse-graining, focussing on those at the nucleotide level that allow the self-assembly processes associated with DNA nanotechnology to be studied. OxDNA, our recently-developed coarse-grained DNA model, is particularly suited to this task, and has opened up this field to systematic study by simulations. We illustrate some of the range of DNA nanotechnology systems to which the model is being applied, as well as the insights it can provide into fundamental biophysical properties of DNA. © 2013 the Owner Societies.
```
@article{Rovigatti-an72g88Y,
    author = "Doye, Jonathan P.K. and Ouldridge, Thomas E. and Louis, Ard A. and Romano, Flavio and Šulc, Petr and Matek, Christian and Snodin, Benedict E.K. and Rovigatti, Lorenzo and Schreck, John S. and Harrison, Ryan M. and Smith, William P.J.",
    title = "Coarse-graining DNA for simulations of DNA nanotechnology",
    year = "2013",
    journal = "Physical Chemistry Chemical Physics",
    volume = "15",
    number = "47",
    pages = "20395 – 20414",
    doi = "10.1039/c3cp53545b",
    type = "Review",
    publication_stage = "Final",
    source = "Scopus"
}
```
S. Kantorovich, A. O. Ivanov, L. Rovigatti, J. M. Tavares, and F. Sciortino. Nonmonotonic magnetic susceptibility of dipolar hard-spheres at low temperature and density. Physical Review Letters, 2013. doi:10.1103/PhysRevLett.110.148306.
[abstract▼] [BibTeX▼]

We investigate, via numerical simulations, mean field, and density functional theories, the magnetic response of a dipolar hard sphere fluid at low temperatures and densities, in the region of strong association. The proposed parameter-free theory is able to capture both the density and temperature dependence of the ring-chain equilibrium and the contribution to the susceptibility of a chain of generic length. The theory predicts a nonmonotonic temperature dependence of the initial (zero field) magnetic susceptibility, arising from the competition between magnetically inert particle rings and magnetically active chains. Monte Carlo simulation results closely agree with the theoretical findings. © 2013 American Physical Society.
```
@article{Rovigatti-QKLTC209,
    author = "Kantorovich, Sofia and Ivanov, Alexey O. and Rovigatti, Lorenzo and Tavares, José Maria and Sciortino, Francesco",
    title = "Nonmonotonic magnetic susceptibility of dipolar hard-spheres at low temperature and density",
    year = "2013",
    journal = "Physical Review Letters",
    volume = "110",
    number = "14",
    doi = "10.1103/PhysRevLett.110.148306",
    type = "Article",
    publication_stage = "Final",
    source = "Scopus"
}
```
S. Dussi, L. Rovigatti, and F. Sciortino. On the gas-liquid phase separation and the self-assembly of charged soft dumbbells. Molecular Physics, 111(22-23):3608 – 3617, 2013. doi:10.1080/00268976.2013.838315.
[abstract▼] [BibTeX▼]

We investigate the phase behaviour of charged soft dumbbells, particles composed of two soft but oppositely charged sites, as a function of the separation between the sites. Through successive umbrella sampling Monte Carlo simulations, we evaluate the equilibrium particle density of states. For elongated dumbbells, we recover the expected critical behaviour. However, reducing the elongation we are unable to locate the gas-liquid critical point in the accessible region of temperature and density. Correspondingly, the self-assembly of the particles in ring structures becomes dominant with respect to the formation of chain-like structures. Our results enrich the debate on the competition between self-assembly and phase separation and contribute to the long-standing dilemma about the putative gas-liquid criticality in dipolar fluids. © 2013 Taylor & Francis.
```
@article{Rovigatti-giyYqwyn,
    author = "Dussi, Simone and Rovigatti, Lorenzo and Sciortino, Francesco",
    title = "On the gas-liquid phase separation and the self-assembly of charged soft dumbbells",
    year = "2013",
    journal = "Molecular Physics",
    volume = "111",
    number = "22-23",
    pages = "3608 – 3617",
    doi = "10.1080/00268976.2013.838315",
    type = "Article",
    publication_stage = "Final",
    source = "Scopus"
}
```
L. Rovigatti, D. De Las Heras, J. M. Tavares, M. M. Telo Da Gama, and F. Sciortino. Computing the phase diagram of binary mixtures: a patchy particle case study. Journal of Chemical Physics, 2013. doi:10.1063/1.4802026.
[abstract▼] [BibTeX▼]

We investigate the phase behaviour of 2D mixtures of bi-functional and three-functional patchy particles and 3D mixtures of bi-functional and tetra-functional patchy particles by means of Monte Carlo simulations and Wertheim theory. We start by computing the critical points of the pure systems and then we investigate how the critical parameters change upon lowering the temperature. We extend the successive umbrella sampling method to mixtures to make it possible to extract information about the phase behaviour of the system at a fixed temperature for the whole range of densities and compositions of interest. © 2013 AIP Publishing LLC.
```
@article{Rovigatti-WH5l8fYz,
    author = "Rovigatti, Lorenzo and De Las Heras, Daniel and Tavares, José Maria and Telo Da Gama, Margarida M. and Sciortino, Francesco",
    title = "Computing the phase diagram of binary mixtures: A patchy particle case study",
    year = "2013",
    journal = "Journal of Chemical Physics",
    volume = "138",
    number = "16",
    doi = "10.1063/1.4802026",
    type = "Article",
    publication_stage = "Final",
    source = "Scopus"
}
```
L. Rovigatti, J. M. Tavares, and F. Sciortino. Self-assembly in chains, rings, and branches: a single component system with two critical points. Physical Review Letters, 2013. doi:10.1103/PhysRevLett.111.168302.
[abstract▼] [BibTeX▼]

We study the interplay between phase separation and self-assembly in chains, rings, and branched structures in a model of particles with dissimilar patches. We extend Wertheim's first order perturbation theory to include the effects of ring formation and to theoretically investigate the thermodynamics of the model. We find a peculiar shape for the vapor-liquid coexistence, featuring reentrant behavior in both phases and two critical points, despite the single-component nature of the system. The emergence of the lower critical point is caused by the self-assembly of rings taking place in the vapor, generating a phase with lower energy and lower entropy than the liquid. Monte Carlo simulations of the same model fully support these unconventional theoretical predictions. © 2013 American Physical Society.
```
@article{Rovigatti-QWmlWY_8,
    author = "Rovigatti, Lorenzo and Tavares, José Maria and Sciortino, Francesco",
    title = "Self-assembly in chains, rings, and branches: A single component system with two critical points",
    year = "2013",
    journal = "Physical Review Letters",
    volume = "111",
    number = "16",
    doi = "10.1103/PhysRevLett.111.168302",
    type = "Article",
    publication_stage = "Final",
    source = "Scopus"
}
```
L. Rovigatti, S. Kantorovich, A. O. Ivanov, J. M. Tavares, and F. Sciortino. Branching points in the low-temperature dipolar hard sphere fluid. Journal of Chemical Physics, 2013. doi:10.1063/1.4821935.
[abstract▼] [BibTeX▼]

In this contribution, we investigate the low-temperature, low-density behaviour of dipolar hard-sphere (DHS) particles, i.e., hard spheres with dipoles embedded in their centre. We aim at describing the DHS fluid in terms of a network of chains and rings (the fundamental clusters) held together by branching points (defects) of different nature. We first introduce a systematic way of classifying inter-cluster connections according to their topology, and then employ this classification to analyse the geometric and thermodynamic properties of each class of defects, as extracted from state-of-the-art equilibrium Monte Carlo simulations. By computing the average density and energetic cost of each defect class, we find that the relevant contribution to inter-cluster interactions is indeed provided by (rare) three-way junctions and by four-way junctions arising from parallel or anti-parallel locally linear aggregates. All other (numerous) defects are either intra-cluster or associated to low cluster-cluster interaction energies, suggesting that these defects do not play a significant part in the thermodynamic description of the self-assembly processes of dipolar hard spheres. © 2013 AIP Publishing LLC.
```
@article{Rovigatti-aEsRzqWi,
    author = "Rovigatti, Lorenzo and Kantorovich, Sofia and Ivanov, Alexey O. and Tavares, José Maria and Sciortino, Francesco",
    title = "Branching points in the low-temperature dipolar hard sphere fluid",
    year = "2013",
    journal = "Journal of Chemical Physics",
    volume = "139",
    number = "13",
    doi = "10.1063/1.4821935",
    type = "Article",
    publication_stage = "Final",
    source = "Scopus"
}
```

2012↑

L. Rovigatti, J. Russo, and F. Sciortino. Structural properties of the dipolar hard-sphere fluid at low temperatures and densities. Soft Matter, 8(23):6310 – 6319, 2012. doi:10.1039/c2sm25192b.
[abstract▼] [BibTeX▼]

Through extensive state-of-the-art numerical simulations, we study the behavior of the dipolar hard sphere model at low temperatures and low densities, shedding light on a region of the phase diagram where a topological phase transition has long been thought to occur. We show that the system exhibits remarkable and unusual behaviors, like a very low density percolation locus and a stabilization of rings over chain structures. This unexpected abundance of rings comes from a delicate balance between the lower ring energy and the end-to-end chain entropy, and hints at a possible mechanism for the suppression of the gas-liquid phase separation. Our results open the possibility for refined theoretical approaches which, in addition to the previously encompassed chain and branched geometries, must also include the significant contribution arising from ring formation. © 2012 The Royal Society of Chemistry.
```
@article{Rovigatti-EQ-HdGuC,
    author = "Rovigatti, Lorenzo and Russo, John and Sciortino, Francesco",
    title = "Structural properties of the dipolar hard-sphere fluid at low temperatures and densities",
    year = "2012",
    journal = "Soft Matter",
    volume = "8",
    number = "23",
    pages = "6310 – 6319",
    doi = "10.1039/c2sm25192b",
    type = "Article",
    publication_stage = "Final",
    source = "Scopus"
}
```
C. De Michele, L. Rovigatti, T. Bellini, and F. Sciortino. Self-assembly of short dna duplexes: from a coarse-grained model to experiments through a theoretical link. Soft Matter, 8(32):8388 – 8398, 2012. doi:10.1039/c2sm25845e.
[abstract▼] [BibTeX▼]

Short blunt-ended DNA duplexes comprising 6 to 20 base pairs self-assemble into polydisperse semi-flexible chains due to hydrophobic stacking interactions between terminal base pairs. Above a critical concentration, which depends on temperature and duplex length, such chains order into liquid crystal phases. Here, we investigate the self-assembly of such double-helical duplexes with a combined numerical and theoretical approach. We simulate the bulk system employing the coarse-grained DNA model recently proposed by Ouldridge et al. [J. Chem. Phys., 2011, 134, 08501]. Then we evaluate the input quantities for the theoretical framework directly from the DNA model. The resulting parameter-free theoretical predictions provide an accurate description of the simulation results in the isotropic phase and theoretical values for the isotropic-nematic phase boundaries which are in line with experimental findings. In addition, the developed theoretical framework makes it possible to provide a route to estimate the stacking free energy. © 2012 The Royal Society of Chemistry.
```
@article{Rovigatti-ma1X5DCI,
    author = "De Michele, Cristiano and Rovigatti, Lorenzo and Bellini, Tommaso and Sciortino, Francesco",
    title = "Self-assembly of short DNA duplexes: From a coarse-grained model to experiments through a theoretical link",
    year = "2012",
    journal = "Soft Matter",
    volume = "8",
    number = "32",
    pages = "8388 – 8398",
    doi = "10.1039/c2sm25845e",
    type = "Article",
    publication_stage = "Final",
    source = "Scopus"
}
```
J. M. Tavares, L. Rovigatti, and F. Sciortino. Quantitative description of the self-assembly of patchy particles into chains and rings. Journal of Chemical Physics, 2012. doi:10.1063/1.4737930.
[abstract▼] [BibTeX▼]

We numerically study a simple fluid composed of particles having a hard-core repulsion complemented by two patchy attractive sites on the particle poles. An appropriate choice of the patch angular width allows for the formation of ring structures which, at low temperatures and low densities, compete with the growth of linear aggregates. The simplicity of the model makes it possible to compare simulation results and theoretical predictions based on the Wertheim perturbation theory, specialized to the case in which ring formation is allowed. Such a comparison offers a unique framework for establishing the quality of the analytic predictions. We find that the Wertheim theory describes remarkably well the simulation results. © 2012 American Institute of Physics.
```
@article{Rovigatti-f1A2QMx_,
    author = "Tavares, José Maria and Rovigatti, Lorenzo and Sciortino, Francesco",
    title = "Quantitative description of the self-assembly of patchy particles into chains and rings",
    year = "2012",
    journal = "Journal of Chemical Physics",
    volume = "137",
    number = "4",
    doi = "10.1063/1.4737930",
    type = "Article",
    publication_stage = "Final",
    source = "Scopus"
}
```
P. Šulc, F. Romano, T. E. Ouldridge, L. Rovigatti, J. P. K. Doye, and A. A. Louis. Sequence-dependent thermodynamics of a coarse-grained dna model. Journal of Chemical Physics, 2012. doi:10.1063/1.4754132.
[abstract▼] [BibTeX▼]

We introduce a sequence-dependent parametrization for a coarse-grained DNA model [T. E. Ouldridge, A. A. Louis, and J. P. K. Doye, J. Chem. Phys. 134, 085101 (2011)]10.1063/1.3552946 originally designed to reproduce the properties of DNA molecules with average sequences. The new parametrization introduces sequence-dependent stacking and base-pairing interaction strengths chosen to reproduce the melting temperatures of short duplexes. By developing a histogram reweighting technique, we are able to fit our parameters to the melting temperatures of thousands of sequences. To demonstrate the flexibility of the model, we study the effects of sequence on: (a) the heterogeneous stacking transition of single strands, (b) the tendency of a duplex to fray at its melting point, (c) the effects of stacking strength in the loop on the melting temperature of hairpins, (d) the force-extension properties of single strands, and (e) the structure of a kissing-loop complex. Where possible, we compare our results with experimental data and find a good agreement. A simulation code called oxDNA, implementing our model, is available as a free software. © 2012 American Institute of Physics.
```
@article{Rovigatti-fgQrECR2,
    author = "Šulc, Petr and Romano, Flavio and Ouldridge, Thomas E. and Rovigatti, Lorenzo and Doye, Jonathan P. K. and Louis, Ard A.",
    title = "Sequence-dependent thermodynamics of a coarse-grained DNA model",
    year = "2012",
    journal = "Journal of Chemical Physics",
    volume = "137",
    number = "13",
    doi = "10.1063/1.4754132",
    type = "Article",
    publication_stage = "Final",
    source = "Scopus"
}
```

2011↑

L. Rovigatti, W. Kob, and F. Sciortino. The vibrational density of states of a disordered gel model. Journal of Chemical Physics, 2011. doi:10.1063/1.3626869.
[abstract▼] [BibTeX▼]

We investigate the vibrational density of states (vDOS) in harmonic approximation of a binary mixture of colloidal patchy particles with two and three patches for different relative compositions x2. At low temperature, this system forms a thermo-reversible gel, i.e., a fully bonded network of chains of two-patches particles, in which the branching points are provided by three-patches particles. For all the compositions, we find in the vDOS a pronounced peak at low frequency whose height grows on increasing the fraction of two-functional particles or equivalently with the average length of the chains. To identify the various spectral features, we compare the vDOS of the whole system with the one of small representative structures of the network and with the vDOS of a long linear chain of two-patches particles and we find that these structures are indeed able to rationalize the various peaks in the vDOS of the full system. At large x2 the vDOSs of the gel and of the long chain show remarkable similarities. Analyzing the dispersion relations and the spectrum of the linear chain we show that the excess of low frequency modes, the analog of the boson peak in glassy disordered systems, arises from the strong coupling between rotations and translations. © 2011 American Institute of Physics.
```
@article{Rovigatti-yXgQ7VxD,
    author = "Rovigatti, Lorenzo and Kob, Walter and Sciortino, Francesco",
    title = "The vibrational density of states of a disordered gel model",
    year = "2011",
    journal = "Journal of Chemical Physics",
    volume = "135",
    number = "10",
    doi = "10.1063/1.3626869",
    type = "Article",
    publication_stage = "Final",
    source = "Scopus"
}
```
L. Rovigatti and F. Sciortino. Self and collective correlation functions in a gel of tetrahedral patchy particles. Molecular Physics, 109(23-24):2889 – 2896, 2011. doi:10.1080/00268976.2011.609148.
[abstract▼] [BibTeX▼]

We discuss the results of intensive Brownian dynamics simulations of a simple model of tetrahedral patchy particles in the optimal network density region. This choice allows us to investigate the evolution of the structure and of the dynamics in a wide range of temperatures without encountering any phase separation. The slowing down of the dynamics in this model system is driven by the progressive bond formation and the increasing bond lifetime. Although dynamical arrest is different from the glass case, where excluded volume interactions are dominant, the decay of the self- and collective correlation functions of the resulting fluid bears similarities with that observed in glassy systems. Copyright © 2011 Taylor and Francis Group, LLC.
```
@article{Rovigatti-2jR6Ckx3,
    author = "Rovigatti, Lorenzo and Sciortino, Francesco",
    title = "Self and collective correlation functions in a gel of tetrahedral patchy particles",
    year = "2011",
    journal = "Molecular Physics",
    volume = "109",
    number = "23-24",
    pages = "2889 – 2896",
    doi = "10.1080/00268976.2011.609148",
    type = "Article",
    publication_stage = "Final",
    source = "Scopus"
}
```
L. Rovigatti, J. Russo, and F. Sciortino. No evidence of gas-liquid coexistence in dipolar hard spheres. Physical Review Letters, 2011. doi:10.1103/PhysRevLett.107.237801.
[abstract▼] [BibTeX▼]

We report accurate calculations of the particle density of states in the dipolar hard-sphere fluid. Implementing efficient and tailored Monte Carlo algorithms, we are able to explore, in equilibrium, the low temperature region where a phase separation between a dilute gas of chain ends and a high-density liquid of chain junctions has been predicted to occur. Our data clearly show that the density of states remains always single peaked, definitively excluding the possibility of critical phenomena in the investigated temperature and density region. The analysis of the low temperature configurations shows that at low densities particles preferentially self-assemble into closed rings, strongly suppressing the chain ends concentration. © 2011 American Physical Society.
```
@article{Rovigatti-JtuHZ2I5,
    author = "Rovigatti, Lorenzo and Russo, John and Sciortino, Francesco",
    title = "No evidence of gas-liquid coexistence in dipolar hard spheres",
    year = "2011",
    journal = "Physical Review Letters",
    volume = "107",
    number = "23",
    doi = "10.1103/PhysRevLett.107.237801",
    type = "Article",
    publication_stage = "Final",
    source = "Scopus"
}
```