Related papers: CSAW: a dynamical model of protein folding
We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a…
We study a lattice model of a magnetic polymer where the XY spin variables are located on a self-avoiding walk (SAW) on a regular lattice in two and three dimensions. We consider the regime where both spins and conformations are dynamic,…
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…
The combined Continuous Time Random Walk (CTRW) in position and momentum space is introduced, in the form of two coupled integral equations that describe the evolution of the probability distribution for finding a particle at a certain…
We formulate an irreversible Markov chain Monte Carlo algorithm for the self-avoiding walk (SAW), which violates the detailed balance condition and satisfies the balance condition. Its performance improves significantly compared to that of…
Using Wang-Landau sampling with suitable Monte Carlo trial moves (pull moves and bond-rebridging moves combined) we have determined the density of states and thermodynamic properties for a short sequence of the HP protein model. For free…
Quantum walks exhibit many unique characteristics compared to classical random walks. In the classical setting, self-avoiding random walks have been studied as a variation on the usual classical random walk. Classical self-avoiding random…
We have analyzed geometric and topological features of self-avoiding walks. We introduce a new kind of walk: the loop-deleted self-avoiding walk (LDSAW) motivated by the interaction of chromatin with the nuclear lamina. Its critical…
Active matter systems - such as a collection of active colloidal particles - operate far from equilibrium with complex inter-particle interactions that govern their collective dynamics. Predicting the collective dynamics of such systems may…
Many of the concepts which are at the basis of the development associated with a quantitative treatment of the variety of phenomena associated with the spontaneous breaking of gauge symmetry in nuclei have been instrumental in connection…
The smart kinetic self-avoiding walk (SKSAW) is a random walk which never intersects itself and grows forever when run in the full-plane. At each time step the walk chooses the next step uniformly from among the allowable nearest neighbors…
Wavefunction collapse models modify Schr\"odinger's equation so that it describes the collapse of a superposition of macroscopically distinguishable states as a dynamical process. This provides a basis for the resolution of the quantum…
To determine the 3D conformation of proteins is a necessity to understand their functions or interactions with other molecules. It is commonly admitted that, when proteins fold from their primary linear structures to their final 3D…
Let D be a domain in the plane containing the origin. We are interested in the ensemble of self-avoiding walks (SAW's) in D which start at the origin and end on the boundary of the domain. We introduce an ensemble of SAW's that we expect to…
We consider two types of Go models of a protein (crambin) and study their kinetics through molecular dynamics simulations. In the first model, the residue -- residue contact interactions are selected based on a cutoff distance, $R_c$,…
Pedestrian trajectory prediction is a key technology in many applications such as video surveillance, social robot navigation, and autonomous driving, and significant progress has been made in this research topic. However, there remain two…
It is quite possible that the Technicolor problems are related to the poorly known self-energy expression, or the way chiral symmetry breaking (CSB) is realized in non-abelian gauge theories. Actually, the only known laboratory to test the…
We consider the continuous time random walk model (CTRW) of tracer's motion in porous medium flows based on the experimentally determined distributions of pore velocity and pore size reported in Holzner et al. Phys. Rev. E 92, 013015…
This paper is dedicated to the investigation of a $1+1$ dimensional self-interacting and partially directed self-avoiding walk, usually referred to by the acronym IPDSAW and introduced in \cite{ZL68} by Zwanzig and Lauritzen to study the…
We study the first passage dynamics of an ageing stochastic process in the continuous time random walk (CTRW) framework. In such CTRW processes the test particle performs a random walk, in which successive steps are separated by random…