Related papers: Kinetic energy flows in activated dynamics of biom…
We investigate dynamical coupling between water and amino acid side-chain residues in solvation dynamics by selecting residues often used as natural probes, namely tryptophan, tyrosine and histidine, located at different positions on…
An all-atom model of proteins is used to show that the same sequence of amino acids can have many alternative structures, that are very distant from, and that can be as stable as, the corresponding native structure. Such alternative…
We propose a proof of convergence of an adaptive method used in molecular dynamics to compute free energy profiles. Mathematically, it amounts to studying the long-time behavior of a stochastic process which satisfies a non-linear…
In turbulent flows, energy flux refers to the transfer of kinetic energy across different scales of motion, a concept that is a cornerstone of turbulence theory. The direction of net energy flux is prescribed by the dimensionality of the…
The present work aims at exploring the scale-by-scale kinetic energy exchanges in multiphase turbulence. For this purpose, we derive the K\'arm\'an-Howarth-Monin equation which accounts for the variations of density and viscosity across the…
Important cellular processes, such as cell motility and cell division, are coordinated by cell polarity, which is determined by the non-uniform distribution of certain proteins. Such protein patterns form via an interplay of protein…
Our study unveils the precise role of the underlying potential in regulating the fundamental processes of dynamic hysteresis, which manifests in numerous natural and designed systems. We identify that it is possible to induce symmetry…
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…
We revisit the problem of how energy transfer through the turbulent cascade operates in compressible hydrodynamic turbulence. In general, there is no conservative compressible cascade since the kinetic and internal energy reservoirs can…
Various research studies indicate that action recognition performance highly depends on the types of motions being extracted and how accurate the human actions are represented. In this paper, we investigate different optical flow, and…
The observation of large azimuthal anisotropies $v_n$ in the particle spectra of proton-proton (pp) and proton-nucleus (pA) collisions challenges fluid dynamic interpretations of $v_n$, as it remains unclear how small collision systems can…
A simple model of the driven motion of interacting particles in a two dimensional random medium is analyzed, focusing on the critical behavior near to the threshold that separates a static phase from a flowing phase with a steady-state…
Unlike macroscopic engines, the molecular machinery of living cells is strongly affected by fluctuations. Stochastic Thermodynamics uses Markovian jump processes to model the random transitions between the chemical and configurational…
The folding dynamics of small single-domain proteins is a current focus of simulations and experiments. Many of these proteins are 'two-state folders', i.e. proteins that fold rather directly from the denatured state to the native state,…
The forces that mixtures of motorized and passive crosslinking proteins collectively generate between cytoskeletal filaments within our cells are the key drivers of active cellular mechanics. Despite their importance, a unified theory to…
A protein's function depends critically on its conformational ensemble, a collection of energy weighted structures whose balance depends on temperature and environment. Though recent deep learning (DL) methods have substantially advanced…
The classical theory of chemical reactions can be understood in terms of diffusive barrier crossing, where the rate of a reaction is determined by the inverse of the mean first passage time (FPT) to cross a free energy barrier. Whenever a…
Biomolecular machines transduce between different forms of energy. These machines make directed progress and increase their speed by consuming free energy, typically in the form of nonequilibrium chemical concentrations. Machine dynamics…
We propose a biochemical model providing the kinetic and energetic descriptions of the processivity dynamics of kinesin and dinein molecular motors. Our approach is a modified version of a well known model describing kinesin dynamics and…
A central goal of protein-folding theory is to predict the stochastic dynamics of transition paths --- the rare trajectories that transit between the folded and unfolded ensembles --- using only thermodynamic information, such as a…