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Effect of distribution of stickers along the backbone on structural properties in associating polymer solutions is studied using self-consistent field lattice model. Only two inhomogeneous morphologies, i.e., microfluctuation homogenous…
We study active agents embedded in bulk or in confinement explicitly considering hydrodynamics and simulating the swimmers via an implementation inspired by the squirmer model. We develop a Dissipative Particle Dynamics scheme for the…
Silicene, a two-dimensional (2D) allotrope of silicon, has attracted significant interest for its electronic and mechanical properties, alongside its compatibility with various substrates. In this study, we investigate the structural and…
Via molecular dynamics simulation with Langevin thermostat we study the structure and dynamics of a flexible bead-spring active polymer model after a quench from good to poor solvent conditions. The self propulsion is introduced via a…
The question of if silica nanoparticles can enhance the ionic conductivity of a polymer electrolyte above its crystallization temperature has remained unclear for the two decades following the first experiments on these systems. We use…
We report the results of Monte Carlo simulations investigating the effect of a spherical confinement within a simple model for a flexible homopolymer. We use the parallel tempering method combined with multi-histogram reweighting analysis…
Solutions of semiflexible polymers confined by repulsive planar walls are studied by density functional theory and Molecular Dynamics simulations, to clarify the competition between the chain alignment favored by the wall and the depletion…
The formation of (bio)molecular condensates via liquid-liquid phase separation in cells has received increasing attention, as these coacervates play important functional and regulatory roles within biological systems. However, the majority…
Thermal conductivity of aligned polymer molecules can be exceptionally high along the alignment direction due to energy transport through strong covalent bonds. At the same time, it is highly sensitive to molecular conformation, varying by…
Dense packings composed of irregular polyhedral particles are investigated by numerical simulations under quasistatic triaxial compression. The Contact Dynamics method is used for this investigation with 40 000 particles. The effect of…
We present a detailed description of biopolymer translocation through a nanopore in the presence of a solvent, using an innovative multi-scale methodology which treats the biopolymer at the microscopic scale as combined with a…
First shells of hydration and bulk solvent plays a crucial role in the folding of proteins. Here, the role of water in the dynamics of proteins has been investigated using a theoretical protein-solvent model and a statistical physics…
We perform molecular-dynamics simulations of a molecular system in supercooled states for different values of inertia parameters to provide evidence that the long-time dynamics depends only on the equilibrium structure. This observation is…
Properties of 1,4-\textit{trans} poly (isoprene) at ambient conditions are determined by simulations on two length scales based on two different models: a full-atomistic and a mesoscopic one. The models are linked via a mapping scheme such…
Configurational fluctuations of conducting polymers in solution can bring into proximity monomers which are distant from each other along the backbone. Electrons can hop between these monomers across the "bridges" so formed. We show how…
The effect of sequence heterogeneity on polynucleotide translocation across a pore and on simple models of molecular motors such as helicases, DNA polymerase/exonuclease and RNA polymerase is studied in detail. Pore translocation of RNA or…
We study the dynamics of a polymer that is pulled by a constant force through a viscoelastic medium. This is a model for a polymer being pulled through a cell by an external force, or for an active biopolymer moving due to a self generated…
The authors study the short-time dynamics of helix-forming polypeptide chains using an all-atom representation of the molecules and an implicit solvation model to approximate the interaction with the surrounding solvent. The results confirm…
In the present paper, using a molecular dynamics simulation, we study a nature of melting of a two-dimensional ($2D$) system of classical particles interacting through a purely repulsive isotropic core-softened potential which is used for…
We perform molecular dynamics simulations using the extended simple point charge SPC/E water model in order to investigate the dynamical behavior of supercooled-stretched water. We focus on the behavior of the translational diffusion…