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The dynamics of units (molecules) with slowly relaxing internal states is studied as an iterated function system (IFS) for the situation common in e.g. biological systems where these units are subjected to frequent collisional interactions.…
We implement molecular dynamics simulations in canonical ensemble to study the effect of confinement on a $2d$ crystal of point particles interacting with an inverse power law potential proportional to $r^{-12}$ in a narrow channel. This…
The appealing feature of molecular electronics is the possibility of exploiting functionality built within a single molecule. This functionality can be employed, for example, for sensing or switching purposes. Thus, ideally, the associated…
Protein structure generative models excel at predicting single protein static structures from sequence, but routinely fail to capture the correct conformational state of protein complexes, critical for protein design and induced proximity…
Computation of biological processes creates great promise for everyday life and great challenges for physical scientists. Simulations of molecular dynamics appeal to biologists as a natural extension of structural biology. Once biologists…
Proteins constitute a large group of macromolecules with a multitude of functions for all living organisms. Proteins achieve this by adopting distinct three-dimensional structures encoded by the sequence of their constituent amino acids in…
Protein dynamics is a fundamental element to comprehend their biological functions. However, a theoretical picture providing microscopic-detail explanation of its relevant features is still missing. One of the outmost relevant properties…
Inspired by active shape morphing in developing tissues and biomaterials, we investigate two generic mechanochemical models where the deformations of a thin elastic sheet are driven by, and in turn affect, the concentration gradients of a…
A series of simulations aimed at elucidating the self-assembly dynamics of spherical virus capsids is described. This little-understood phenomenon is a fascinating example of the complex processes that occur in the simplest of organisms.…
Cells control the size and organization of biomolecular condensates formed by liquid-liquid phase separation (LLPS), but multiple mechanisms likely contribute to this control and remain to be fully elucidated. Here we propose a…
Mechanics has an important role during morphogenesis, both in the generation of forces driving cell shape changes and in determining the effective material properties of cells and tissues. Drosophila dorsal closure (DC) has emerged as a…
The evolution of porous structure and mechanical properties of binary glasses under tensile loading were examined using molecular dynamics simulations. We consider vitreous systems obtained in the process of phase separation after a rapid…
The dynamic interplay between collective cell movement and the various molecules involved in the accompanying cell signalling mechanisms plays a crucial role in many biological processes including normal tissue development and pathological…
We study the role of active coupling on the transport properties of homogeneously charged macromolecules in an infinitely dilute solution. An enzyme becomes actively bound to a segment of the macromolecule, exerting an electrostatic force…
We propose a mechanism of cell motility which is based on contraction and does not require protrusion. The contraction driven translocation of a cell is due to internal flow of the cytoskeleton generated by molecular motors. Each motor…
Self-organized pattern formation is vital for many biological processes. Reaction-diffusion models have advanced our understanding of how biological systems develop spatial structures, starting from homogeneity. However, biological…
Biomolecular condensates help organize the cell cytoplasm and nucleoplasm into spatial compartments with different chemical compositions. A key feature of such compositional patterning is the local enrichment of enzymatically active…
The motility of a fish keratocyte on a flat substrate exhibits two distinct regimes: the non-migrating and the migrating one. In both configurations the shape is fixed in time and, when the cell is moving, the velocity is constant in…
The motion involved in barrier crossing for protein folding are investigated in terms of the chain dynamics of the polymer backbone, completing the microscopic description of protein folding presented in the previous paper. Local reaction…
Taking the two-dimensional Ising model for example, short-time behavior of critical dynamics with a conserved order parameter is investigated by Monte Carlo simulations. Scaling behavior is observed, but the dynamic exponent $z$ is updating…