相关论文: Coarse-grained lattice model for investigating the…

Bacterial colonies can form a wide variety of shapes and structures based on ambient and internal conditions. To help understand the mechanisms that determine the structure of and the diversity within these colonies, various numerical…

We extend a previously studied lattice model of particles with infinite repulsions to the case of finite energy interactions. The phase diagram is studied using grand canonical Monte Carlo simulation. Simulations of dynamical phenomena are…

Lattice models for the second-order strain-gradient models of elasticity theory are discussed. To combine the advantageous properties of two classes of second-gradient models, we suggest a new lattice model that can be considered as a…

We consider two- and three-dimensional lattice models of proteins which were characterized previously. We coarse grain their folding dynamics by reducing it to transitions between effective states. We consider two methods of selection of…

While generative models have recently become ubiquitous in many scientific areas, less attention has been paid to their evaluation. For molecular generative models, the state-of-the-art examines their output in isolation or in relation to…

We use a coarse grained molecular model of supported lipid bilayers to study the formation of adhesion domains. We find that this process is a first order phase transition, triggered by a combination of pairwise short range attractive…

We propose and illustrate an approach to coarse-graining the dynamics of evolving networks (networks whose connectivity changes dynamically). The approach is based on the equation-free framework: short bursts of detailed network evolution…

We present a coarse-grained model for evaluation of interactions of globular proteins with nanoparticles. The protein molecules are represented by one bead per aminoacid and the nanoparticle by a homogeneous sphere that interacts with the…

In the growth of bacterial colonies, a great variety of complex patterns are observed in experiments, depending on external conditions and the bacterial species. Typically, existing models employ systems of reaction-diffusion equations or…

Correlation of interacting particles is studied in their dynamics and localization in ideal and disordered lattice systems with the help of numerical tools. Both 1D and 2D systems are considered. In 1D lattices with long-range hopping,…

Machine-learned coarse-grained (CG) models have the potential for simulating large molecular complexes beyond what is possible with atomistic molecular dynamics. However, training accurate CG models remains a challenge. A widely used…

We present a ``coarse molecular dynamics'' approach and apply it to studying the kinetics and thermodynamics of a peptide fragment dissolved in water. Short bursts of appropriately initialized simulations are used to infer the deterministic…

We analyze response of a macromolecule near to a substrate; the substrate is tiled in the sequential and specific manner so that repeat units of the macromolecule may have different response on its adsorption in different directions onto…

Tissue dynamics and collective cell motion are crucial biological processes. Their biological machinery is mostly known, and simulation models such as the "active vertex model" (AVM) exist and yield reasonable agreement with experimental…

In my PhD thesis I studied cooperative phenomena arise in complex systems using the methods of statistical and computational physics. The aim of my work was also to study the critical behaviour of interacting many-body systems during their…

We investigate the cooperative behavior of regular monolayers of driven two-level dipoles, using classical electrodynamics simulations. The dipolar response results from the interference of many cooperative eigenmodes, each…

Using a coarse molecular-dynamics (CMD) approach with an appropriate choice of coarse variable (order parameter), we map the underlying effective free-energy landscape for the melting of a crystalline solid. Implementation of this approach…

Understanding the structure and dynamics of liquids is pivotal for the study of larger spatiotemporal processes, especially in glass-forming materials at low temperatures. Density scaling, observed in many molecular systems through…

Due to the subtle balance of intermolecular interactions that govern structure-property relations, predicting the stability of crystal structures formed from molecular building blocks is a highly non-trivial scientific problem. A…

I consider a generic coarse-grained model suitable for the study of bulk self-assembly of liquid crystal (LC) macromolecules. The cases include LC dendrimers, gold nanoparticles modified by polymer chains with terminating LC groups and…