Related papers: Coarse-grained molecular simulations of allosteric…
Three coarse-grained molecular dynamics (MD) models are investigated with the aim of developing and analyzing multiscale methods which use MD simulations in parts of the computational domain and (less detailed) Brownian dynamics (BD)…
Nanoscale polymeric thin films are widely used in diverse applications such as energy devices, flexible electronics and biosensors, where a satisfactory mechanical performance is of vital importance to realize their full functionality. It…
The actin cytoskeleton is composed of multiple networks which are specialized for several processes such as cell motility or cell division. Each of these networks are composed of organized actin microfilaments which are decorated with…
Although the importance of protein dynamics in protein function is generally recognized, the role of protein fluctuations in allosteric effects scarcely has been considered. To address this gap, the Kullback-Leibler divergence (Dx) between…
Molecular dynamics simulations provide theoretical insight into the microscopic behavior of materials in condensed phase and, as a predictive tool, enable computational design of new compounds. However, because of the large temporal and…
The phase behavior of charged rods in the presence of inter-rod linkers is studied theoretically as a model for the equilibrium behavior underlying the organization of actin filaments by linker proteins in the cytoskeleton. The presence of…
Increasing evidence suggests that chromosome folding and genetic expression are intimately connected. For example, the co-expression of a large number of genes can benefit from their spatial co-localization in the cellular space.…
We study the dynamics of intracellular calcium oscillations in the presence of proteins that bind calcium on multiple sites and that are generally believed to act as passive calcium buffers in cells. We find that multisite calcium-binding…
Allosteric interactions between molecules bound to DNA at distant locations have been known for a long time. The phenomenon has been studied via experiments and numerical simulations, but a comprehensive understanding grounded in a theory…
This work is motivated by the need for large-scale simulations to extract physical information on the iron-chromium system that is a binary model alloy for ferritic steels used or proposed in many nuclear applications. From first-principles…
The two key phenomena occurring in the process of ceramic powder compaction are the progressive gain in cohesion and the increase of elastic stiffness, both related to the development of plastic deformation. The latter effect is an example…
Elastic filaments are vital to biological, physical and engineering systems, from cilia driving fluid in the lungs to artificial swimmers and micro-robotics. Simulating slender structures requires intricate balance of elastic, body, active,…
Background: If biology is modular then clusters, or communities, of proteins derived using only protein interaction network structure should define protein modules with similar biological roles. We investigate the link between biological…
We develop a theoretical approach to the protein folding problem based on out-of-equilibrium stochastic dynamics. Within this framework, the computational difficulties related to the existence of large time scale gaps in the protein folding…
Structure based ligand discovery is one of the most successful approaches for augmenting the drug discovery process. Currently, there is a notable shift towards machine learning (ML) methodologies to aid such procedures. Deep learning has…
This paper compares simulation results and experimental published data concerning the interaction between $\alpha_2\beta_1$ integrin and collagen.This phenomenon is characterized by a competition among steric, reciprocal orientation…
The tight binding model is a minimal electronic structure model for molecular modelling and simulation. We show that the total energy in this model can be decomposed into site energies, that is, into contributions from each atomic site…
A statistical mechanical distance constraint model (DCM) is presented that explicitly accounts for network rigidity among constraints present within a system. Constraints are characterized by local microscopic free energy functions.…
The adhesion of cells is mediated by receptors and ligands anchored in apposing membranes. A central question is how to characterize the binding affinity of these membrane-anchored molecules. For soluble molecules, the binding affinity is…
The actin cytoskeleton in living cells has many types of crosslinkers. The mechanical interplay between these different crosslinker types is an open issue in cytoskeletal mechanics. We develop a framework to study the cooperativity and…