Related papers: Excluded Volume in Protein Sidechain Packing
In the past years, the folding kinetics of many small single-domain proteins has been characterized by mutational Phi-value analysis. In this article, a simple, essentially parameter-free model is introduced which derives folding routes…
Entropic repulsion between DNA ring polymers under confinement is the key mechanism governing the spatial segregation of bacterial chromosomes, although it remains incompletely understood how proteins aid the process of entropic…
The native conformation of structured proteins is stabilized by a complex network of interactions. We analyzed the elementary patterns that constitute such network and ranked them according to their importance in shaping protein sequence…
We introduce a simple geometrical construction similar to covariant holographic entanglement entropy but with the addition of a new term proportional to boundary region volume. This new procedure has properties strongly resembling classical…
We investigate experimentally the distribution of configurations of a ring with an elementary topological constraint, a ``figure-8'' twist. Using vibrated granular chains, which permit controlled preparation and direct observation of such a…
Computer simulation was used to study the random sequential adsorption of identical discorectangles onto a continuous plane . The problem was analyzed for a wide range of discorectangle aspect ratios ($\varepsilon \in [1;100]$). We studied…
In this work we examine how volume exclusion caused by regions of high chromatin density might influence the time required for proteins to find specific DNA binding sites. The spatial variation of chromatin density within mouse olfactory…
This study focuses on comparing the individual polymer chain dynamics in an entangled polymeric liquid under different shear and extension rates. Polymer chains under various shear rates and extension rates were simulated using a…
The conformational states of a semiflexible polymer enclosed in a compact domain of typical size $a$ are studied as stochastic realizations of paths defined by the Frenet equations under the assumption that stochastic "curvature" satisfies…
We introduce a model for stochastic transport on a one-dimensional substrate with particles assuming different conformations during their stepping cycles. These conformations correspond to different footprints on the substrate: in order to…
Experiments using nanofluidic devices have proven effective in characterizing the physical properties of polymers confined to small cavities. Two recent studies using such methods examined the organization and dynamics of two DNA molecules…
In polymer physics it is typically assumed that excluded volume interactions are effectively screened in polymer melts. Hence, chains could be described by an effective random walk without excluded volume interactions. In this letter, we…
Estimating a fractal dimension from a finite stochastic trajectory is a finite-size scaling problem: the apparent box-counting exponent is shaped by an occupancy crossover between the resolved range of scales and the finite number of…
This paper explores methods for estimating or approximating the total variation distance and the chi-squared divergence of probability measures within topological sample spaces, using independent and identically distributed samples. Our…
We investigate the influence of varying confinement on the dynamics of polymer translocation through a cone shaped channel. For this, a linear polymer chain is modeled by a self voiding walks (SAWs) on a square lattice. The cis-side of a…
Colloid or nanoparticle mobility under confinement is of central importance to a wide range of physical and biological processes. Here, we introduce a minimal model of particles in a hydrodynamic continuum to examine how particle shape and…
In this paper we revisit the problem of a (non self-avoiding) polymer chain in a random medium which was previously investigated by Edwards and Muthukumar (EM). As noticed by Cates and Ball (CB) there is a discrepancy between the…
We present a novel Monte Carlo simulation of protein folding, in which all heavy atoms are represented as interacting hard spheres. This model includes all degrees of freedom relevant to folding - all sidechain and backbone torsions - and…
Entanglement entropy obeys area law scaling for typical physical quantum systems. This may naively be argued to follow from locality of interactions. We show that this is not the case by constructing an explicit simple spin chain…
A microscopic theory of the free energy barriers and folding routes for minimally frustrated proteins is presented, greatly expanding on the presentation of the variational approach outlined previously [J. J. Portman, S. Takada, P. G.…