Related papers: CSAW: a dynamical model of protein folding

Totally asymmetric exclusion processes (TASEP) with open boundaries are known to exhibit moving shocks or delocalised domain walls (DDW) for sufficiently small equal injection and extraction rates. In contrast TASEPs in an inhomogeneous…

Simulating large-scale protein dynamics using traditional all-atom molecular dynamics (MD) remains computationally prohibitive. We present a unified, universal framework for coarse-grained molecular dynamics (CG-MD) that achieves…

Cellular automata (CA) is an important modelling paradigm for complex systems. In the design of cellular automata, the most difficult task is to find the transformation rules that describe the temporal evolution or pattern of a modelled…

We investigate the dynamics of a particle executing a general Continuous Time Random Walk (CTRW) in three dimensions under the influence of arbitrary time-varying external fields. Contrary to the general approach in recent works, our method…

We consider the phase diagram of self-avoiding walks (SAW) on the simple cubic lattice subject to surface and bulk interactions, modeling an adsorbing surface and variable solvent quality for a polymer in dilute solution, respectively. We…

A one-dimensional system of nonintersecting Brownian particles is constructed as the diffusion scaling limit of Fisher's vicious random walk model. $N$ Brownian particles start from the origin at time $t=0$ and undergo mutually avoiding…

We propose a protein model based on a hierarchy of constraints that force the protein to follow certain pathways when changing conformation. The model exhibits a first order phase transition, cooperativity and is exactly solvable. It also…

We consider activated random walk (ARW), an interacting particle system and prototypical model of self-organized criticality in a setting which combines mean-field behavior with the geometry of an arbitrary graph, which we call the village…

We study continuous time random walks (CTRW) with power law distribution of waiting times under resetting which brings the walker back to the origin, with a power-law distribution of times between the resetting events. Two situations are…

We show that, in a broad class of continuous time random walks (CTRW), a small external field can turn diffusion from standard into anomalous. We illustrate our findings in a CTRW with trapping, a prototype of subdiffusion in disordered and…

Simplified Go models, where only native contacts interact favorably, have proven useful to characterize some aspects of the folding of small proteins. The success of these models is limited by the fact that all residues interact in the same…

Charge transport processes in disordered complex media are accompanied by anomalously slow relaxation for which usually a broad distribution of relaxation times is adopted. To account for those properties of the environment, a standard…

The slow dynamics in a glassy hard-sphere system is dominated by cage breaking events, i.e., rearrangements where a particle escapes from the cage formed by its neighboring particles. We study such events for an overdamped colloidal system…

We study a restricted class of self-avoiding walks (SAW) which start at the origin (0, 0), end at $(L, L)$, and are entirely contained in the square $[0, L] \times [0, L]$ on the square lattice ${\mathbb Z}^2$. The number of distinct walks…

Using molecular simulations, we identify microscopic relaxation events of individual particles in ageing structural glasses, and determine the full distribution of relaxation times. We find that the memory of the waiting time $t_w$ elapsed…

We investigate the dynamics and the pathways of the collapse of a single, semiflexible polymer in a poor solvent via 3-D Brownian Dynamics simulations. Earlier work indicates that the condensation of semiflexible polymers generically…

We develop a continuous time random walk (CTRW) approach for the evolution of Lagrangian velocities in steady heterogeneous flows based on a stochastic relaxation process for the streamwise particle velocities. This approach describes…

Improved communication systems, shrinking battery sizes and the price drop of tracking devices have led to an increasing availability of trajectory tracking data. These data are often analyzed to understand animal behavior. In this work, we…

We propose a new generative model, Cramer-Wold Autoencoder (CWAE). Following WAE, we directly encourage normality of the latent space. Our paper uses also the recent idea from Sliced WAE (SWAE) model, which uses one-dimensional projections…

Bovine heart cytochrome c has been immobilized into the mesoporous silica host material SBA-15 in both its native folded and urea-unfolded state. The comparison of the two folding states' behavior casts doubt on the commonly used…