Related papers: CSAW: a dynamical model of protein folding
Uncovering the mechanism behind the scaling law in human trajectories is of fundamental significance in understanding many spatio-temporal phenomena. In combination of the exploration and the preferential returns, we propose a simple…
Transport properties of a hard-sphere colloidal fluid are investigated by Brownian dynamics simulations. We implement a novel algorithm for the time-dependent velocity-autocorrelation function (VACF) essentially eliminating the noise of the…
Sliced-Wasserstein Flow (SWF) is a promising approach to nonparametric generative modeling but has not been widely adopted due to its suboptimal generative quality and lack of conditional modeling capabilities. In this work, we make two…
In many physical, social or economical phenomena we observe changes of a studied quantity only in discrete, irregularly distributed points in time. The stochastic process used by physicists to describe this kind of variables is the…
Scaled Brownian motion (SBM) is widely used to model anomalous diffusion of passive tracers in complex and biological systems. It is a highly non-stationary process governed by the Langevin equation for Brownian motion, however, with a…
We consider the dynamics of a separable Continuous Time Random Walk (CTRW) when the random walker is biased by a velocity field in a uniformly growing domain. Concrete examples for such domains include growing biological cells or lipid…
Path sampling allows the study of rare events like chemical reactions, nucleation and protein folding via a Monte Carlo (MC) exploration in path space. Instead of configuration points, this method samples short molecular dynamics (MD)…
Under supercoiling constraints, naked DNA, such as a large part of bacterial DNA, folds into braided structures called plectonemes. The double-helix can also undergo local structural transitions, leading to the formation of denaturation…
Continuous-time random walk (CTRW) is a model of anomalous sub-diffusion in which particles are immobilized for random times between successive jumps. A power-law distribution of the waiting times, $\psi(\tau) \tau^{-(1+\alpha)}$, leads to…
Subordinating a random walk to a renewal process yields a continuous time random walk (CTRW) model for diffusion, including the possibility of anomalous diffusion. Transition densities of scaling limits of power law CTRWs have been shown to…
Consistently predicting biopolymer structure at atomic resolution from sequence alone remains a difficult problem, even for small sub-segments of large proteins. Such loop prediction challenges, which arise frequently in comparative…
In two dimensions polymer collapse has been shown to be complex with multiple low temperature states and multi-critical points. Recently, strong numerical evidence has been provided for a long-standing prediction of universal scaling of…
We present the Monte Carlo with Absorbing Markov Chains (MCAMC) method for extremely long kinetic Monte Carlo simulations. The MCAMC algorithm does not modify the system dynamics. It is extremely useful for models with discrete state spaces…
The conjecture that the scaling limit of the two-dimensional self-avoiding walk (SAW) in a half plane is given by the stochastic Loewner evolution (SLE) with $\kappa=8/3$ leads to explicit predictions about the SAW. A remarkable feature of…
We present a quantum-dynamical framework for identifying structurally important residues in proteins based on continuous time quantum walks (CTQWs) on weighted residue interaction networks constructed from experimentally resolved…
Graph convolutional networks have been widely applied in skeleton-based gait recognition. A key challenge in this task is to distinguish the individual walking styles of different subjects across various views. Existing state-of-the-art…
We study the dynamics of a radioactive species flowing through a porous material, within the Continuous-Time Random Walk (CTRW) approach to the modelling of stochastic transport processes. Emphasis is given to the case where radioactive…
We have investigated a polymer growth process on the triangular lattice where the configurations produced are self-avoiding trails. We show that the scaling behaviour of this process is similar to the analogous process on the square…
The determination of the folding mechanisms of proteins is critical to understand the topological change that can propagate Alzheimer and Creutzfeld-Jakobs diseases, among others. The computational community has paid considerable attention…
The conformational dynamics of a single protein molecule in a shear flow is investigated using Brownian dynamics simulations. A structure-based coarse grained model of a protein is used. We consider two proteins, ubiquitin and integrin, and…