Related papers: Collective Molecular Dynamics in Proteins and Memb…
Water and water-mediated interactions determine thermodynamic and kinetics of protein folding, protein aggregation and self-assembly in confined spaces. To obtain insights into the role of water in the context of folding problems, we…
The coupled in-plane diffusion dynamics between point-particles embedded in stacked fluid membranes are investigated. We calculate the contributions to the coupling longitudinal and transverse diffusion coefficients due to particle motion…
The evolution of mesoscopic structure for cement-water mixtures turning into colloidal gels remains far from being understood. Recent neutron scattering investigations (Phys. Rev. Lett. 93, 255704 (2004); Phys. Rev. B. 72, 224208 (2005);…
Particles diffusing near interfaces face anisotropic resistance to motion due to hydrodynamic interactions. While this has been extensively studied near \textit{hard} interfaces since the works of Lorentz and Brenner, our understanding of…
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…
Electrostatic forces play many important roles in molecular biology, but are hard to model due to the complicated interactions between biomolecules and the surrounding solvent, a fluid composed of water and dissolved ions. Continuum model…
Elastic network models (ENM) and constraint-based, topological rigidity analysis are two distinct, coarse-grained approaches to study conformational flexibility of macromolecules. In the two decades since their introduction, both have…
In recent years molecular elasticity has emerged as an active area of research: there are experiments that probe mechanical properties of single biomolecules such as DNA and Actin, with a view to understanding the role of elasticity of…
Protein dynamics form a critical bridge between protein structure and function, yet the impact of evolution on ultrafast processes inside proteins remains enigmatic. This study delves deep into nanosecond-scale protein dynamics of a…
We study the electromagnetic contribution to elastic neutrino-proton and neutrino-neutron scattering processes. The neutrino electromagnetic charge, magnetic, electric, and anapole form factors of both diagonal and transition types in the…
The dynamic behavior of a partially wetting polymer droplet driven over a nanostructured interface is studied using molecular dynamics simulations. We consider the bead-spring model to represent a polymeric liquid that partially wets a…
All-atom and coarse-grained molecular dynamics are two widely used computational tools to study the conformational states of proteins. Yet, these two simulation methods suffer from the fact that without access to supercomputing resources,…
Single molecule and NMR measurements of protein dynamics increasingly uncover the complexity of binding scenarios. Here we describe an extended conformational selection model which embraces a repertoire of selection and adjustment…
We study the non-equilibrium dynamics of lipid membranes with proteins that actively pump ions across the membrane. We find that the activity leads to a fluctuating force distribution due to electrostatic interactions arising from variation…
The principles underlying protein folding remains one of Nature's puzzles with important practical consequences for Life. An approach that has gathered momentum since the late 1990's, looks at protein hetero-polymers and their folding…
The structure and dynamics of fluids confined in nanoporous media differ from those in bulk, which can be probed using NMR relaxation measurements. We here show, using atomistic molecular dynamics simulations of water in a slit nanopore,…
1. Role of inter-domain water clusters in large-scale dynamics of proteins; 2. Description of large-scale dynamics of proteins based on generalized Stokes-Einstein and Eyring-Polany equation; 3. Dynamic model of protein-ligand complexes…
For the first time an analytic expression was obtained for the inelastic neutron scattering law with an isotropic neutron source within the gas model, considering moderating medium temperature as a parameter. The inelastic scattering law is…
Interactions mediated by the cell membrane between inclusions, such as membrane proteins or antimicrobial peptides, play important roles in their biological activity. They also constitute a fascinating challenge for physicists, since they…
Motor proteins are active enzymatic molecules that drive a variety of biological processes, including transfer of genetic information, cellular transport, cell motility and muscles contraction. It is known that these biological molecular…