arXiv subjects

Valerio Sorichetti

Publications and source records attributed to Valerio Sorichetti.

9 recordsLinked to original sources

arXiv2026

Beads, springs and fields: particle-based vs continuum models in cell biophysics

Quantitative modeling has become an essential tool in modern biophysics, driven by advances in both experimental techniques and theoretical frameworks. Powerful high-resolution techniques now provide detailed datasets spanning molecular to tissue scales, allowing to visualize cellular structures with unprecedented detail. In parallel, developments in soft and active matter physics have established a robust theoretical basis for describing biological systems. In this context, two main modeling paradigms have emerged: particle-based models, which explicitly represent discrete components and their interactions, and continuum models, which describe systems through spatially varying fields. We compare these approaches across biological scales, highlighting their respective strengths, limitations, and domains of applicability. To keep our discussion biologically relevant, we focus on five systems of fundamental importance: the cytoskeleton, membranes, chromatin, biomolecular condensates and tissues. With this Review, we thus aim to provide a framework for both theorists and experimentalists to select appropriate modeling strategies, and highlight future directions in biophysical modeling.

cond-mat.soft↗

arXiv2023

Transverse fluctuations control the assembly of semiflexible filaments

The kinetics of the assembly of semiflexible filaments through end-to-end annealing is key to the structure of the cytoskeleton, but is not understood. We analyze this problem through scaling theory and simulations, and uncover a regime where filaments ends find each other through bending fluctuations without the need for the whole filament to diffuse. This results in a very substantial speed-up of assembly in physiological regimes, and could help understand the dynamics of actin and intermediate filaments in biological processes such as wound healing and cell division.

cond-mat.soft↗

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.

cond-mat.soft↗

arXiv2022

Runaway Transition in Irreversible Polymer Condensation with Cyclisation

The process of polymer condensation, i.e. the formation of bonds between reactive end-groups, is ubiquitous in both industry and biology. Here we study generic systems undergoing polymer condensation in competition with cyclisation. Using a generalised Smoluchowski theory, molecular dynamics simulations and experiments using DNA and T4 ligase, we find that this system displays a transition, from a regime with finite-length chains at infinite time and dominated by rings to one dominated by linear polymers that grow in time. Finally, we show that fluids prepared close to the transition may have profoundly different compositions and rheology at large condensation times.

cond-mat.soft↗

arXiv2021

Dynamics of nanoparticles in polydisperse polymer networks: From free diffusion to hopping

Using molecular dynamics simulations we study the static and dynamic properties of spherical nanoparticles (NPs) embedded in a disordered and polydisperse polymer network. Purely repulsive (RNP) as well as weakly attractive (ANP) polymer-NP interactions are considered. It is found that for both types of particles the NP dynamics at intermediate and at long times is controlled by the confinement parameter $C=σ_N/λ$, where $σ_N$ is the NP diameter and $λ$ is the dynamic localization length of the crosslinks. Three dynamical regimes are identified: i) For weak confinement ($C \lesssim 1$) the NPs can freely diffuse through the mesh; ii) For strong confinement ($C \gtrsim 1$) NPs proceed by means of activated hopping; iii) For extreme confinement ($C \gtrsim 3$) the mean squared displacement shows on intermediate time scales a quasi-plateau since the NPs are trapped by the mesh for very long times. Escaping from this local cage is a process that depends strongly on the local environment, thus giving rise to an extremely heterogeneous relaxation dynamics. The simulation data are compared with the two main theories for the diffusion process of NPs in gels. Both theories give a very good description of the $C-$dependence of the NP diffusion constant, but fail to reproduce the heterogeneous dynamics at intermediate time scales.

cond-mat.soft↗

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.

cond-mat.soft↗

arXiv2019

Characterizing the mesh size of polymer solutions via the pore size distribution

In order to characterize the geometrical mesh size $ξ$, we simulate a solution of coarse-grained polymers with densities ranging from the dilute to the concentrated regime and for different chain lengths. Conventional ways to estimate $ξ$ rely either on scaling assumptions which give $ξ$ only up to an unknown multiplicative factor, or on measurements of the monomer density fluctuation correlation length $ξ_c$. We determine $ξ_c$ from the monomer structure factor and from the radial distribution function, and find that the identification $ξ=ξ_c$ is not justified outside of the semidilute regime. In order to better characterize $ξ$, we compute the pore size distribution (PSD) following two different definitions, one by Torquato et al. (Ref.1) and one by Gubbins et al. (Ref.2). We show that the mean values of the two distributions, $\langle r \rangle_T$ and $\langle r \rangle_G$, both display the behavior predicted for $ξ$ by scaling theory, and argue that $ξ$ can be identified with either one of these quantities. This identification allows to interpret the PSD as the distribution of mesh sizes, a quantity which conventional methods cannot access. Finally, we show that it is possible to map a polymer solution on a system of hard or overlapping spheres, for which Torquato's PSD can be computed analytically and reproduces accurately the PSD of the solution. We give an expression that allows $\langle r \rangle_T$ to be estimated with great accuracy in the semidilute regime by knowing only the radius of gyration and the density of the polymers.

cond-mat.soft↗

arXiv2019

Addition to Structure and dynamics of a polymer-nanoparticle composite: Effect of nanoparticle size and volume fraction

In our previous publication (Ref. 1) we have shown that the data for the normalized diffusion coefficient of the polymers, $D_p/D_{p0}$, falls on a master curve when plotted as a function of $h/λ_d$, where $h$ is the mean interparticle distance and $λ_d$ is a dynamic length scale. In the present note we show that also the normalized diffusion coefficient of the nanoparticles, $D_N/D_{N0}$, collapses on a master curve when plotted as a function of $h/R_h$, where $R_h$ is the hydrodynamic radius of the nanoparticles.

cond-mat.soft↗

arXiv2018

Structure and dynamics of a polymer-nanoparticle composite: Effect of nanoparticle size and volume fraction

We use molecular dynamics simulations to study a semidilute, unentangled polymer solution containing well dispersed, weakly attractive nanoparticles (NP) of size ($σ_N$) smaller than the polymer radius of gyration $R_g$. We find that if $σ_N$ is larger than the monomer size the polymers swell, while smaller NPs cause chain contraction. The diffusion coefficient of polymer chains ($D_p$) and NPs ($D_N$) decreases if the volume fraction $ϕ_N$ is increased. The decrease of $D_p$ can be well described in terms of a confinement parameter, while $D_N$ shows a more complex dependence on $σ_N$, which results from an interplay between energetic and entropic effects. When $ϕ_N$ exceeds a $σ_N$-dependent value, the NPs are no longer well dispersed and $D_N$ and $D_p$ increase if $ϕ_N$ is increased.

cond-mat.soft↗