Related papers: Intramolecular distances and form factor of cyclic…
We perform direct numerical simulations of a bi-disperse suspension of heavy spherical particles in forced, homogeneous, and isotropic three-dimensional turbulence. We compute the joint distribution of relative particle distances and…
We present the simulation of the time evolution of the distance matrix. The result is the node-node distance distribution for various kinds of networks. For the exponential trees, analytical formulas are derived for the moments of the…
Conventional molecular dynamics simulations macromolecules require long computational times because the most interesting motions are very slow compared with the fast oscillations of bond lengths and bond angles that limit the integration…
In this paper, we show how different types of distributed mutual algorithms can be compared in terms of performance through simulations. A simulation-based approach is presented, together with an overview of the relevant evaluation metrics…
We consider the problem of statistical inference for the S distribution and introduce new minimum distance estimators for the four parameters of the S distribution using Kolmogorov-Smirnov, Cramer-von Mises and related distance metrics.…
A fundamental theory is presented for the mechanical response of polymer networks undergoing large deformation which seamlessly integrates statistical mechanical principles with macroscopic thermodynamic constitutive theory. Our formulation…
Complex biological and physical transport processes are often described through systems of interacting particles. Excluded-volume effects on these transport processes are well studied, however the interplay between volume exclusion and…
In recent past, experiments and simulations have suggested that apart from the solvent friction, friction arising from the protein itself plays an important role in protein folding by affecting the intra-chain loop formation dynamics. This…
We investigate the large-scale distribution of galaxy clusters taken from several X-ray catalogs. Different statistics of clustering like the conditional correlation function (CCF) and the minimal spanning tree (MST) as well as void…
The effect of molecule size (excluded volume) and the range of interaction on the surface tension, phase diagram and nucleation properties of a model globular protein is investigated using a combinations of Monte Carlo simulations and…
Because the constant extension ensemble of single chain molecule is not always equivalent with constant force ensemble, a model of double-stranded conformations, as in RNA molecules and $\beta$-sheets in proteins, with fixed extension…
We investigate the mechanism of chain exchange in diblock copolymer micelles using two distinct yet complementary simulation techniques. First, enhanced sampling method is combined with coarse-grained molecular dynamics to compute a…
In this work, it is suggested that the extremum complexity distribution of a high dimensional dynamical system can be interpreted as a piecewise uniform distribution in the phase space of its accessible states. When these distributions are…
Experimental data regarding auxin and venation formation exist at both macroscopic and molecular scales, and we attempt to unify them into a comprehensive model for venation formation. We begin with a set of principles to guide an abstract…
In the framework of Gibbs statistical theory, the issue of the distribution of particle sizes forming the statistical system and the moments of this distribution are considered. This task is relevant for a wide variety of applications. The…
A recent burst of dynamic single-cell growth-division data makes it possible to characterize the stochastic dynamics of cell division control in bacteria. Different modeling frameworks were used to infer specific mechanisms from such data,…
We study the flow of fluid in porous media in dimensions $d=2$ and 3. The medium is modeled by bond percolation on a lattice of $L^d$ sites, while the flow front is modeled by tracer particles driven by a pressure difference between two…
We discuss the extension of the empirical equation: $\left\langle s_{N}^{2}\right\rangle_{0}\propto g\,l^{2}$, where the subscript 0 denotes the ideal value with no excluded volume and $g$ the generation number from the root to the youngest…
Computation of biological processes creates great promise for everyday life and great challenges for physical scientists. Simulations of molecular dynamics appeal to biologists as a natural extension of structural biology. Once biologists…
In this paper we prove a nonautonomous chain rule formula for the distributional divergence of the composite function $\boldsymbol{v}(x)=\boldsymbol{B}(x,u(x))$, where $\boldsymbol{B}(\cdot,t)$ is a divergence--measure vector field and $u$…