相关论文: Effect of Sequence-Dependent Rigidity on Plectonem…
DNA is subject to large deformations in a wide range of biological processes. Two key examples illustrate how such deformations influence the readout of the genetic information: the sequestering of eukaryotic genes by nucleosomes, and DNA…
Synthetic copolymers and biopolymers, such as polypeptides and double-stranded DNA, often exhibit strong variations in bending stiffness along their contour, which can significantly impact conformational behavior at larger scales. To…
We report results of long timescale adaptive kinetic Monte Carlo simulations aimed at identifying possible molecular reordering processes on both proton-disordered and ordered (Fletcher) basal plane (0001) surfaces of hexagonal ice. The…
In composite materials composed of soft polymer matrix and stiff, high-aspect-ratio particles, the composite undergoes a transition in mechanical strength when the inclusion phase surpasses a critical density. This phenomenon (rheological…
In evolutionary dynamics, a key measure of a mutant trait's success is the probability that it takes over the population given some initial mutant-appearance distribution. This "fixation probability" is difficult to compute in general, as…
We present experimental measurements of the cholesteric-smectic phase transition of suspensions of charged semiflexible rods as a function of rod flexibility and surface charge. The rod particles consist of the bacteriophage M13 and closely…
The torsional dynamics of a semiflexible polymer with a contour length $L$ larger than its persistence length L_p that is rotated at fixed frequency omega_0 at one end is studied by scaling arguments and hydrodynamic simulations. We find a…
Chain molecules play important roles in industry and in living cells. Our focus here is on distinct ways of modeling the stiffness inherent in a chain molecule. We consider three types of stiffnesses -- one yielding an energy penalty for…
We report a novel simulation strategy that enables us to identify key parameters controlling the experimentally measurable characteristics of structural protein tags on dsDNA construct translocating through a double nanopore setup. First,…
Under many in vitro conditions, some small viruses spontaneously encapsidate a single stranded (ss) RNA into a protein shell called the capsid. While viral RNAs are found to be compact and highly branched because of long distance…
We study the deeply virtual Compton scattering cross-section in twist-two generalized parton distribution (GPD) approximation, and show that different choices of light-cone vectors and gauges for the final photon polarization will lead to…
We report a theoretical low-field magnetotransport study unveiling the effect of pseudospin in realistic models of weakly disordered graphene-based materials. Using an efficient Kubo computational method, and simulating the effect of…
We investigate the effects of crowding on the conformations and assembly of confined, highly charged, and thick polyelectrolyte brushes in the osmotic regime. Particle tracking experiments on increasingly dense suspensions of colloids…
Phenotypes of individuals in a population of organisms are not fixed. Phenotypic fluctuations, which describe temporal variation of the phenotype of an individual or individual-to-individual variation across a population, are present in…
This study investigates the radial densification of spruce wood using explicit Finite Element Method simulations, focusing on the effects of various densification protocols. These protocols include quasi-static compression, oscillatory…
Numerical simulations of concrete fracture performed with a probabilistic mesoscale discrete model are presented. The model represents a substantial part of material randomness by assigning random locations to the largest aggregates. The…
Polycrystalline graphene has an inherent tendency to buckle, i.e. develop out-of-plane, three-dimensional structure. A force applied to stretch a piece of polycrystalline graphene influences the out-of-plane structure. Even if the graphene…
Transcription factor binding sites vary in their specificity, both within and between species. Binding specificity has a strong impact on the evolution of gene expression, because it determines how easily regulatory interactions are gained…
In this paper, we have studied, within a discrete WLC model, the spatial constraints in magnetic tweezers used in single molecule experiments. Two elements are involved: first, the fixed plastic slab on which is stuck the initial strand,…
We present a new Monte Carlo algorithm for studying site or bond percolation on any lattice. The algorithm allows us to calculate quantities such as the cluster size distribution or spanning probability over the entire range of site or bond…