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We study the effect of temporal correlation in a Langevin equation describing non-adiabatic dynamics at metal surfaces. For a harmonic oscillator the Langevin equation preserves the quantum dynamics exactly and it is demonstrated that…
The hydrophobic effect is the dominant force which drives a protein towards its native state, but its physics has not been thoroughly understood yet. We introduce an exactly solvable model of the solvation of non-polar molecules in water,…
Non-equilibrium molecular dynamics simulations, of crucial importance in sliding friction, are hampered by arbitrariness and uncertainties in the way Joule heat is removed. We implement in a realistic frictional simulation a parameter-free,…
Protein folding is one of the age-old biological problems that refers to the mechanism of understanding and predicting how a protein's linear sequence of amino acids folds into its specific three dimensional structure.This structure is…
Protein folding produces characteristic and functional three-dimensional structures from unfolded polypeptides or disordered coils. The emergence of extraordinary complexity in the protein folding process poses astonishing challenges to…
The understanding of memory effects arising from the interaction between system and environment is a key for engineering quantum thermodynamic devices beyond the standard Markovian limit. We study the performance of measurement-based…
A reasonable description of the degradation process is essential for credible reliability assessment in accelerated degradation testing. Existing methods usually use Markovian stochastic processes to describe the degradation process.…
In this work, we study the dynamics of complex systems with time-dependent transition rates, focusing on $p$-adic analysis in modeling such systems. Starting from the master equation that governs the stochastic dynamics of a system with a…
We present a simple route to obtain large quantities of suspensions of non-Brownian particles with stimuli-responsive surface properties to study the relation between their flow and interparticle interactions. We perform an alkaline…
We have performed a multicanonical molecular dynamics simulation on a simple model protein.We have studied a model protein composed of charged, hydrophobic, and neutral spherical bead monomers.Since the hydrophobic interaction is considered…
An analytical expression is derived for the transition path time distribution for a one-dimensional particle crossing of a parabolic barrier. Two cases are analyzed: (i) A non-Markovian process described by a generalized Langevin equation…
Frictional forces affect the rheology of hard-sphere colloids, at high shear rate. Here we demonstrate, via numerical simulations, that they also affect the dynamics of active Brownian particles, and their motility induced phase separation.…
This paper presents a theoretical analysis of the closure kinetics of a polymer with hydrodynamic interactions. This analysis, which takes into account the non-Markovian dynamics of the end-to-end vector and relies on the preaveraging of…
A molecular gas system in three dimensions is numerically studied by the energy conserving molecular dynamics (MD). The autocorrelation functions for the velocity and the force are computed and the friction coefficient is estimated. From…
Many aspects of the study of protein folding and dynamics have been affected by the recent advances in machine learning. Methods for the prediction of protein structures from their sequences are now heavily based on machine learning tools.…
The thermodynamic behavior of a three-dimensional off-lattice model for protein folding is probed. The model has only two types of residues, hydrophobic and hydrophilic. In absence of local interactions, native structure formation does not…
A reliable prediction of 3D protein structures from sequence data remains a big challenge due to both theoretical and computational difficulties. We have previously shown that our kinetostatic compliance method (KCM) implemented into the…
We assume that the protein folding process follows two autonomous steps: the conformational search for the native, mainly ruled by the hydrophobic effect; and, the final adjustment stage, which eventually gives stability to the native. Our…
Among the various features of amino acids, the hydrophobic property has most visible impact on stability of a sequence folding. This is mentioned in many protein folding related work, in this paper we more elaborately discuss the…
Hydrophobicity is thought to be one of the primary forces driving the folding of proteins. On average, hydrophobic residues occur preferentially in the core, whereas polar residues tends to occur at the surface of a folded protein. By…