arXiv subjects

Vania Calandrini

Publications and source records attributed to Vania Calandrini.

7 recordsLinked to original sources

arXiv2026

Quasi-two-dimensional dispersions of Brownian particles with competitive interactions: Dynamical clustering, non-Gaussianity and hydrodynamic correlations

We conduct a comprehensive dynamical analysis of quasi-two-dimensional (Q2D) dispersions of Brownian particles with competing short-range attractive (SA) and long-range repulsive (LR) interactions using Langevin dynamics (LD) and multiparticle collision dynamics (MPC). As the attractive interaction is strengthened, self-diffusion is significantly suppressed, and clustering gives rise to pronounced subdiffusive behavior. We find that cluster lifetimes are influenced more strongly by attraction strength than by particle concentration. Two dynamical criteria for the transition from non-clustered to clustered phases are identified in terms of the mean cluster lifetime and the relaxation time of local hexagonal order, respectively. Moreover, clustered Q2D-SALR systems exhibit pronounced non-Gaussian dynamics. In particular, the self-van Hove function in the equilibrium-cluster phase displays an approximately exponential form, consistent with an underlying diffusing-diffusivity mechanism. Importantly, MPC simulations reveal the critical role of hydrodynamic interactions (HIs) in collective dynamics. We observe that the anomalously enhanced large-scale collective diffusion characteristic of hydrodynamically interacting Q2D systems is qualitatively preserved in Q2D-SALR dispersions. However, this enhancement suppresses the intermediate-range-order peak in the hydrodynamic function compared to its three-dimensional counterpart. Furthermore, by analyzing the time-dependent evolution of hydrodynamic function and the sound mode in hydrodynamic correlations, we find that clustering in Q2D-SALR systems leads to an earlier onset of HIs than in Q2D hard-sphere reference systems, implying HIs become relevant already on inertial timescales.

cond-mat.soft↗

arXiv2025

Hamiltonian model for energy condensation in classical systems: Relevance to proteins

Recent experimental evidence for collective protein vibrations in the terahertz (THz) domain indicates that energy in biomolecular systems can self-organize in an orderly manner, as anticipated by Fr\"ohlich's theory of condensates within a quantum framework. As a first step to bridge THz experiments with theory, we study the Hamiltonian dynamics of a classical network of coupled normal modes representing Fr\"ohlich-type systems. Our results demonstrate that biologically relevant condensates can emerge at room temperature under appropriate nonlinear coupling schemes. The condensation mechanism remains robust also when the original Fr\"ohlich resonance conditions are relaxed.

physics.bio-ph↗

arXiv2024

Unveiling Long-Range Forces in Light Harvesting Proteins: Pivotal Roles of Temperature and Light

Electrodynamic interactions between biomolecules are of potential biological interest for signaling warranting investigation of their activation through various mechanisms in living systems. Here, using as model system a light harvesting protein within the phycobilisome antenna system of red algae, we proved that not only light exposure but also thermal energy alone can trigger attractive electrodynamic interactions up to hundreds of nanometer. The latter are sustained by low frequency collective modes and while the second mode appears only upon illumination, the fundamental one can be activated by temperature alone. Activation of such collective modes and ED interactions might influence conformational rearrangements and energy transport within the phycobilisome antenna system. This is a paradigm-shift that underscores the immense potential of biological systems in exploiting different forms of input energy to achieve optimal energy transfer.

physics.bio-ph↗

arXiv2023

Clustering in quasi-two-dimensional dispersions of Brownian particles with competitive interactions: Phase diagram and structural properties

Competing short-range attractive (SA) and long range repulsive (LR) interactions have been invoked to describe colloid or protein solutions, as well as membrane proteins interactions mediated by lipid molecules. Using Langevin dynamics simulations, we determine the generalized phase diagram, the cluster shapes and size distributions of a generic Q2D dispersion of spherical SALR particles confined to in-plane motion. SA and LR interactions are modelled by a generalized Lenard-Jones potential and a screened Coulomb potential, respectively. The microstructures of the various equilibrium and non-equilibrium phases turn out to be distinctly different from the ones observed in three-dimensional (3D) SALR systems. We discuss perturbation theory predictions for the metastable binodal line of a reference system of particles with SA interactions only, which in the Q2D-SALR phase diagram separates cluster from non-cluster phases. The transition from the high-temperature (low SA) dispersed fluid phase to the lower-temperature equilibrium cluster phase is characterised by a low-wavenumber peak of the static structure factor (corresponding to a thermal correlation length of about twice the particle diameter) featuring a distinctly smaller height ($\approx1.4$) than in 3D SALR systems. By further decreasing the temperature (increasing SA), the cluster morphology changes from disk-like shapes in the equilibrium cluster phase, to double-stranded anisotropic hexagonal cluster forms in the cluster-percolated gel phase. This transition is quantified by the hexagonal order parameter distribution function. The mean cluster size and coordination number of particles in the gel phase are insensitive to changes in the attraction strength.

cond-mat.soft↗

arXiv2021

Hydrodynamics of Immiscible Binary Fluids with Viscosity Contrast: A multiparticle collision dynamics approach

We present a multiparticle collision dynamics (MPC) implementation of layered immiscible fluids $A$ and $B$ of different shear viscosities separated by planar interfaces. The simulated flow profile for imposed steady shear motion and the time-dependent shear stress functions are in excellent agreement with our continuum hydrodynamics results for the composite fluid. The wave-vector dependent transverse velocity auto-correlation functions (TVAF) in the bulk-fluid regions of the layers decay exponentially, and agree with those of single-phase isotropic MPC fluids. In addition, we determine the hydrodynamic mobilities of an embedded colloidal sphere moving steadily parallel or transverse to a fluid-fluid interface, as functions of the distance from the interface. The obtained mobilities are in good agreement with hydrodynamic force multipoles calculations, for a no-slip sphere moving under creeping flow conditions near a clean, ideally flat interface. The proposed MPC fluid-layer model can be straightforwardly implemented, and it is computationally very efficient. Yet, owing to the spatial discretization inherent to the MPC method, the model can not reproduce all hydrodynamic features of an ideally flat interface between immiscible fluids.

cond-mat.soft↗

arXiv2020

Subdiffusive-Brownian crossover in membrane proteins: a Generalized Langevin Equation-based approach

In this paper, we propose a Generalized Langevin Equation (GLE)-based model to describe the lateral diffusion of a protein in a lipid bilayer. The memory kernel is represented in terms of a viscous (instantaneous) and an elastic (non instantaneous) component modeled respectively through a Dirac delta function and a three-parameter Mittag-Leffler type function. By imposing a specific relationship between the parameters of the three-parameters Mittag-Leffler function, the different dynamical regimes, namely ballistic, subdiffusive and Brownian, as well as the crossover from one regime to another, are retrieved. Within this approach, the transition time from the ballistic to the subdiffusive regime and the distribution of relaxation times underlying the transition from the subdiffusive to the Brownian regime are given. The reliability of the model is tested by comparing the Mean Squared Displacement (MSD) derived in the framework of this model and the MSD of a protein diffusing in a membrane calculated through molecular dynamics (MD) simulations.

physics.bio-ph↗

arXiv2017

Open Boundary Simulations of Proteins and Their Hydration Shells by Hamiltonian Adaptive Resolution Scheme

The recently proposed Hamiltonian Adaptive Resolution Scheme (H-AdResS) allows to perform molecular simulations in an open boundary framework. It allows to change on the fly the resolution of specific subset of molecules (usually the solvent), which are free to diffuse between the atomistic region and the coarse-grained reservoir. So far, the method has been successfully applied to pure liquids. Coupling the H-AdResS methodology to hybrid models of proteins, such as the Molecular Mechanics/Coarse-Grained (MM/CG) scheme, is a promising approach for rigorous calculations of ligand binding free energies in low-resolution protein models. Towards this goal, here we apply for the first time H-AdResS to two atomistic proteins in dual-resolution solvent, proving its ability to reproduce structural and dynamic properties of both the proteins and the solvent, as obtained from atomistic simulations.

physics.chem-ph↗