arXiv subjects

Lorenzo Rovigatti

Publications and source records attributed to Lorenzo Rovigatti.

At least 19 recordsLinked to original sources

arXiv2026

A single-chain nanoparticle-based mean-field theory for associative polymers

Associative polymers are a class of polymers containing attractive stickers that can reversibly bind to each other. Their fully-bonded state gives rise, in dilute conditions, to a fluid phase of so-called single-chain nanoparticles (SCNPs). These constructs have been used in a wide range of applications, from the design of new materials (e.g. biomolecular condensates) to drug-delivery vectors. The thermodynamic properties of SCNPs sensitively depend on the number of different sticker types, since numerical simulations show that a continuous transition to a network of chains upon increase of polymer concentration in the single sticker-type case can be replaced by an abrupt network formation (via a first-order phase transition) in the multiple sticker-type case. We present here a theory that, using the SCNP fluid as the reference system, quantifies the free energy change associated with transferring an intra-molecular bond to an inter-molecular bond, elucidating the impact on the phase separation process of the sticker topology. Despite its simplicity, the theory highlights which microscopic assumptions (loop statistics, chain-level excluded volume) are most relevant for accurately capturing the thermodynamics of these systems. Our results match available numerical predictions obtained via coarse grained simulations of these systems, highlighting in particular the sensitivity of the phase behaviour on the sequence of the stickers along the chain.

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arXiv2025

Entropy-driven phase behaviour of all-DNA associative polymers

Associative polymers (APs) with reversible, specific interactions between ``sticker'' sites exhibit a phase behavior that depends on a delicate balance between distinct contributions controlling the binding. For highly-bonded systems, it is entropy that mostly determines if, on increasing concentration, the network forms progressively or \textit{via} a first-order transition. With the aim of introducing an experimentally-viable system tailored to test the subtle dependence of the phase behavior on the binding site topology, here we numerically investigate AP polymers made of DNA, where ``sticker'' sites made by short DNA sequences are interspersed in a flexible backbone of poly-T spacers. Due to their self-complementarity, each binding sequence can associate with another identical sticky sequence. We compare two architectures: one with a single sticker type, $(AA)_6$, and one with two distinct alternating types, $(AB)_6$. At low temperature, when most of the stickers are involved in a bond, the $(AA)_6$ system remains homogeneous, while the $(AB)_6$ system exhibits phase separation, driven primarily by entropic factors, mirroring predictions from simpler bead-spring models. Analysis of bond distributions and polymer conformations confirms that the predominantly entropic driving force behind this separation arises from the different topological constraints associated with intra- versus inter-molecular bonding. Our results establish DNA APs as a controllable, realistic platform for studying in the laboratory how the thermodynamics of associative polymer networks depends on the bonding site architecture in a clean and controlled way.

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arXiv2025

A phase-field model for solutions of DNA-made particles

We present a phase-field model based on the Cahn-Hilliard equation to investigate the properties of phase separation in DNA nanostar systems. Leveraging a realistic free-energy functional derived from Wertheim theory, our model captures the thermodynamic properties of self-assembling DNA nanostars under various conditions. This approach allows for the study of both one-component and multi-component systems, including mixtures of different nanostar species and cross-linkers. Through numerical simulations, we demonstrate the model ability to replicate experimental observations, including liquid-liquid phase separation, surface tension variation, and the structural organisation of multi-component systems. Our results highlight the versatility and predictive power of the Cahn-Hilliard framework, particularly for complex systems where detailed simulations are computationally prohibitive. This work provides a robust foundation for studying DNA-based materials and their potential applications in nanotechnology and biophysics, including liquid-liquid phase separation in cellular environments.

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arXiv2025

A Falsifiability Test for Classical Nucleation Theory

Classical nucleation theory (CNT) is built upon the capillarity approximation, i.e., the assumption that the nucleation properties can be inferred from the bulk properties of the melt and the crystal. Although CNT's simplicity and usefulness cannot be overstated, experiments and simulations regularly uncover significant deviations from its predictions, which are often reconciled through phenomenological extensions of the CNT, fueling the debate over the general validity of the theory. In this study, we present a falsifiability test for any nucleation theory grounded in the capillarity approximation. We focus on cases where the theory predicts no differences in nucleation rates between different crystal polymorphs. We then introduce a system in which all polymorphs have the same free energy (both bulk and interfacial) across all state points. Through extensive molecular simulations, we show that the polymorphs exhibit remarkably different nucleation properties, directly contradicting CNT's predictions. We argue that CNT's primary limitation lies in its neglect of structural fluctuations within the liquid phase.

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arXiv2024

Solid-liquid interfacial free energy from computer simulations: Challenges and recent advances

The theory of interfacial properties in liquid-liquid or liquid-vapour systems is nearly 200 years old. The advent of computational tools has greatly advanced the field, mainly through the use of Molecular Dynamics simulations. Despite the successes and advances in the theory of interfacial phenomena for liquid-liquid systems, the study of solid-liquid interfaces remains a challenge both theoretically and experimentally. The main reason why the treatment of solid-liquid systems has fallen behind that of liquid-liquid systems is that there are complications that arise whenever an interface involving solid systems is considered involving both theory of the solid-liquid interface and the calculations using MD simulations. An example of the former is that, contrary to the liquid-liquid case, the interfacial properties of solids depend on the lattice orientation. The main complications in these calculations arise from the fact that for solids the ``mechanical route'' cannot be used. To overcome this problem, several numerical approaches were proposed. The main purpose of this review is to provide an overview of these different methodologies and to discuss their strengths and weaknesses. We classify these methodologies into two main groups: direct and indirect methods. Direct methods are those that can calculate directly the properties of interfaces, while in indirect approaches the properties of the interface are not the primary result of the simulations. We also included a discussion on the origin of the difficulties in considering solid interfaces from a thermodynamic point of view. In the second part of the review, we discuss two key related topics: nucleation theory and curved interfaces. They both represent an important problem in the study of interfaces and in the context of solid-liquid ones for which the research is still extremely active.

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arXiv2024

Diffusion, viscosity and linear rheology of valence-limited disordered fluids

We numerically investigate the dynamics and linear rheology of disordered systems made of patchy particles, focussing on the role of valence, temperature and bonding mechanism. We demonstrate that the dynamics is enslaved to bonding, giving rise to an activated behaviour at low temperature. 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 analyse here will help to develop and test theoretical frameworks aimed at describing the dynamics of flexible limited-valence particles that self-assemble into disordered networks.

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arXiv2023

Inverse design of a pyrochlore lattice of DNA origami through model-driven experiments

Sophisticated statistical mechanics approaches and human intuition have demonstrated the possibility to self-assemble complex lattices or finite size constructs, but have mostly only been successful in silico. The proposed strategies quite often fail in experiment due to unpredicted traps associated to kinetic slowing down (gelation, glass transition), as well as to competing ordered structures. An additional challenge that theoretical predictions face is the difficulty to encode the desired inter-particle interaction potential with the currently available library of nano- and micron-sized particles. To overcome these issues, we conjugate here SAT-assembly -- a patchy-particle interaction design algorithm based on constrained optimization solvers -- with coarse-grained simulations of DNA nanotechnology to experimentally realize trap-free self-assembly pathways. As a proof of concept we investigate the assembly of the pyrochlore (also known as tetrastack) lattice, a highly coveted 3D crystal lattice due to its promise in construction of optical metamaterials. We confirm the successful assembly with two different patchy DNA origami designs via SAXS as well as SEM visualization of the silica-coated lattice. Our approach offers a versatile modeling pipeline that starts from patchy particles designed in silico and ends with wireframe DNA origami that self-assemble into the desired structure.

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arXiv2023

Entropy-driven phase behavior of associative polymer networks

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 (\textit{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.

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arXiv2023

Structure and elasticity of model disordered, polydisperse and defect-free polymer networks

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 crosslinked 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 crosslinks 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 crosslink localization length to the shear modulus of the system.

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arXiv2022

Designing enhanced entropy binding in single-chain nano particles

Single-chain nanoparticles (SCNP) 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 inter-polymer 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.

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arXiv2022

A simple solution to the problem of self-assembling cubic diamond crystals

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 satisfiability problem. 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.

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arXiv2022

Two-step deswelling in the Volume Phase Transition of thermoresponsive microgels

Thermoresponsive microgels are one of the most investigated class 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. Here we fill this gap by combining experiments and 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 several microgels with different cross-linker concentrations, charge contents and charge distributions, we build a unifying master-curve able to predict the two-step deswelling. Our results have direct relevance on fundamental soft condensed matter science and on microgel applications ranging from materials to biomedical technologies.

cond-mat.soft↗

arXiv2022

SAT-assembly: A new approach for designing self-assembling systems

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.

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arXiv2021

Sharing the load: stress redistribution governs fracture of polymer double networks

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 inter-network 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.

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arXiv2021

A primer on the oxDNA model of DNA: When to use it, how to simulate it and how to interpret the results

The oxDNA model of DNA 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.

q-bio.BM↗

arXiv2021

The effect of internal architecture on the assembly of soft particles at fluid interfaces

Monolayers of soft colloidal particles confined at fluid interfaces have been attracting increasing interest for fundamental studies and applications alike. However, establishing the relation between their internal architecture, which is controlled during synthesis, and their structural and mechanical properties upon interfacial confinement, which define the monolayer's properties, remains an elusive task. Here, we propose a comprehensive study elucidating this relation for a system of microgels with tunable architecture. We synthesize core-shell microgels, whose soft core can be chemically degraded in a controlled fashion, yielding particles ranging from analogues of standard batch-synthesized to completely hollow microgels after total core removal. We characterize the internal structure of these particles, their swelling properties in bulk and their morphologies upon adsorption at an oil-water interface via a combination of numerical simulations and complementary experiments. In particular, we confirm that hollow microgels are mechanically stable in bulk aqueous conditions and that the progressive removal of the core leads to a significant flattening of the microgels, which become disk-like particles, at the interface. At low compression, the mechanical response of the monolayer is dominated by the presence of loosely crosslinked polymers forming a corona surrounding the particle 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. These findings shed new light on which structural features of soft particles determine their interfacial behaviour, enabling new design strategies for tailored materials.

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arXiv2021

The effect of chain polydispersity on the elasticity of disordered polymer networks

Due to their unique structural and mechanical properties, randomly-crosslinked 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 (\textit{e.g.} chain-length and end-to-end distributions), we generate disordered phantom networks with different crosslinker concentrations $C$ and initial density $ρ_{\rm init}$ 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 $ρ_{\rm init}$. We rationalise 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 non-monotonic function of the density of elastically-active strands, and that this behaviour has a purely entropic origin. Our results show that if short chains are abundant, as it is always the case for randomly-crosslinked polymer networks, the knowledge of the exact chain conformation distribution is essential for predicting correctly the elastic properties. Finally, we apply our theoretical approach to published experimental data, qualitatively confirming our interpretations.

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arXiv2020

Gel Formation in Reversibly Cross-Linking Polymers

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 non-monotonic 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 irreversible 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.

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