Related papers: Effect of Sequence-Dependent Rigidity on Plectonem…
Obtaining reliable estimates of the statistical properties of complex macromolecules by computer simulation is a task that requires high computational effort as well as the development of highly efficient simulation algorithms. We present…
In protein folding the term plasticity refers to the number of alternative folding pathways encountered in response to free energy perturbations such as those induced by mutation. Here we explore the relation between folding plasticity and…
Many proteins interact with and deform double-stranded DNA in cells. Single-molecule experiments have studied the elasticity of DNA with helix-deforming proteins, including proteins that bend DNA. These experiments increase the need for…
The flexibility of short DNA chains is investigated via computation of the average correlation function between dimers which defines the persistence length. Path integration techniques have been applied to confine the phase space available…
Semiflexible polymers form central structures in biological material. Modeling approaches usually neglect influences of polymer-specific molecular features aiming to describe semiflexible polymers universally. Here, we investigate the…
Effects of sequence disorder on looping and cyclization of the double-stranded DNA are studied theoretically. Both random intrinsic curvature and inhomogeneous bending rigidity are found to result in a remarkably wide distribution of…
The highly distinctive phonon self-energy dependences on the wave vector, calculated respectively for the static and dynamic stripe phase models of the underdoped cuprates are presented. The negative values of the real part of the on-stripe…
The level of supercoiling in the chromosome can affect gene expression. To clarify the basis of supercoiling sensitivity, we analyzed the structural features of nucleotide sequences in the vicinity of promoters for the genes with expression…
To survive in harsh conditions, motile bacteria swim in complex environment and respond to the surrounding flow. Here we develop a PDE model describing how the flagella bending affects macroscopic properties of bacterial suspensions. First,…
We prove bounds on the variance of a function $f$ under the empirical measure of the samples obtained by the Sequential Monte Carlo (SMC) algorithm, with time complexity depending on local rather than global Markov chain mixing dynamics.…
Theories with compact extra spatial dimensions felt only by gravity are subject to direct experimental tests if the compactification volume is large. Estimates of high-energy collider observables induced by graviton radiation into extra…
In the process of translation, ribosomes read the genetic code on an mRNA and assemble the corresponding polypeptide chain. The ribosomes perform discrete directed motion which is well modeled by a totally asymmetric simple exclusion…
An ensemble of directed macromolecules on a lattice is considered, where the constituting molecules are chosen as a random sequence of N different types. The same type of molecules experiences a hard-core (exclusion) interaction. We study…
Tree models for rigidity percolation are introduced and solved. A probability vector describes the propagation of rigidity outward from a rigid border. All components of this ``vector order parameter'' are singular at the same rigidity…
We introduce a probabilistic model for protein sliding motion along DNA during the search of a target sequence. The model accounts for possible effects due to sequence-dependent interaction between the nonspecific DNA and the protein. As an…
Numerical simulations and finite-size scaling analysis have been carried out to study the percolation behavior of straight rigid rods of length $k$ ($k$-mers) on two-dimensional square lattices. The $k$-mers, containing $k$ identical units…
Context. The model of disc fragmentation due to gravitational instabilities offers an alternate formation mechanism for gas giant planets, especially those on wide orbits. Aims. Our goal is to determine the 3D structure of disc-instability…
As the chief informational molecule of life, DNA is subject to extensive physical manipulations. The energy required to deform double-helical DNA depends on sequence, and this mechanical code of DNA influences gene regulation, such as…
Functional data analysis has been a growing field of study in recent decades, and one fundamental task in functional data analysis is estimating the sample location. A notion called statistical depth has been extended from multivariate data…
Wall-based spanwise forcing has been experimentally used with success by Auteri et al. (Phys. Fluids vol. 22, 2010, 115103) to obtain large reductions of turbulent skin-friction drag and considerable energy savings in a pipe flow. The…