Related papers: pH modulates friction memory effects in protein fo…
In spite of decades of research, much remains to be discovered about folding: the detailed structure of the initial (unfolded) state, vestigial folding instructions remaining only in the unfolded state, the interaction of the molecule with…
Hydrogel consists of a crosslinked polymer matrix imbibed with a solvent such as water at volume fractions that can exceed 90\%. They are important in many scientific and engineering applications due to their tunable physiochemical…
A minimal off-lattice model for alpha-helical proteins is presented. It is based on hydrophobicity forces and sequence independent local interactions. The latter are chosen so as to favor the formation of alpha-helical structure. They model…
We construct a theoretical model for the dynamics of a microscale colloidal particle, modeled as an interval, moving horizontally on a DNA-coated surface, modelled as a line coated with springs that can stick to the interval. Averaging over…
We consider nonequilibrium transport in a simple chain of identical mechanical cells in which particles move around. In each cell, there is a rotating disc, with which these particles interact, and this is the only interaction in the model.…
A theoretical framework is developed to study the dynamics of protein folding. The key insight is that the search for the native protein conformation is influenced by the rate r at which external parameters, such as temperature, chemical…
Significant progress in computer hardware and software have enabled molecular dynamics (MD) simulations to model complex biological phenomena such as protein folding. However, enabling MD simulations to access biologically relevant…
The dissipative dynamics of a vortex line in a superfluid is investigated within the frame of a non-Markovian quantal Brownian motion model. Our starting point is a recently proposed interaction Hamiltonian between the vortex and the…
We propose a simple microscopic model of molecular dynamics simulation to study orientational glass in three dimensions. We present simulation results for mixtures of mildly anisotropic particles and spherical impurities. We realize fcc…
De novo prediction of protein folding is an open scientific challenge. Many folding models and force fields have been developed, yet all face difficulties converging to native conformations. Hydrophobicity scales (HSs) play a crucial role…
It is quite clear from a wide range of experiments that gating phenomena of ion channels is inherently stochastic. It has been discussed using BD simulations in a recent paper that memory effects in ion transport is negligible, unless the…
We propose a system identification method, Non-Markovian Optimization-based Modeling for Approximate Dynamics with Spatially-homogeneous memory (NOMADS), for identifying linear dynamical systems from a set of multi-dimensional time-series…
We derive a kinetic equation with a non-Markovian collision term which includes a memory effect, from Kadanoff-Baym equations in $\phi^4$ theory within the three-loop level for the two-particle irreducible (2PI) effective action. The memory…
A protein is a linear chain containing a set of amino acids, which folds on itself to create a specific native structure, also called the minimum energy conformation. It is the native structure that determines the functionality of each…
Molecular dynamic (MD) simulations are applied to investigate the dependency of the kinetic friction coefficient on the temperature at the nano-scale. The system is comprised of an aluminum spherical particle consisting of 32000 atoms in an…
Protein function does not solely depend on structure but often relies on dynamical transitions between distinct conformations. Despite this fact, our ability to characterize or predict protein dynamics is substantially less developed…
Folding protein dynamics has been an area of high interest for quite some time, especially given the increased focus on the field of Biophysics. Because folding dynamics occur on such short time scales, empirical techniques developed for…
Macroscopic parameters as well as precise information on the random force characterizing the Langevin type description of the nuclear fusion process around the Coulomb barrier are extracted from the microscopic dynamics of individual…
Kinetics of biological motors such as kinesin or dynein is notably influenced by viscoelastic intracellular environment. The characteristic relaxation time of the cytosol is not separable from the colloidal timescale and therefore their…
Inspired by one--dimensional light--particle systems, the dynamics of a non-Hamiltonian system with long--range forces is investigated. While the molecular dynamics does not reach an equilibrium state, it may be approximated in the…