Related papers: Excluded Volume in Protein Sidechain Packing
We propose a new sensitivity analysis methodology for complex stochastic dynamics based on the Relative Entropy Rate. The method becomes computationally feasible at the stationary regime of the process and involves the calculation of…
The entropy region is constructed from vectors of random variables by collecting Shannon entropies of all subvectors. Its shape is studied here by means of polymatroidal constructions, notably by convolution. The closure of the region is…
In this paper we generalise the main result of a recent work by J. L. Cardy and the present authors concerning the bi-partite entanglement entropy between a connected region and its complement. There the expression of the leading order…
Recent advances in single macromolecule experiments have sparked interest in the ensemble dependence of force-extension relations. The thermodynamic limit may not be attainable for such systems, that leads to inequivalence of the…
We have studied the conformational and scaling behaviors of a flexible dendrimer immersed in athermal or good solvents. A self-consistent field theory combined with a pre-averaged excluded volume potential representing the two-body…
A relation between the conformal anomaly and the logarithmic term in the entanglement entropy is known to exist for CFT's in even dimensions. In odd dimensions the local anomaly and the logarithmic term in the entropy are absent. As was…
Nested stochastic modeling has been on the rise in many fields of the financial industry. Such modeling arises whenever certain components of a stochastic model are stochastically determined by other models. There are at least two main…
The excluded area between a pair of two-dimensional hard particles with given relative orientation is the region in which one particle cannot be located due to the presence of the other particle. The magnitude of the excluded area as a…
We present a study of the bend angle distribution of semiflexible polymers of short and intermediate lengths within the wormlike chain model. This enables us to calculate the elastic response of a stiff molecule to a bending moment. Our…
Conformational changes upon protein-protein association are the key element of the binding mechanism. The study presents a systematic large-scale analysis of such conformational changes in the side chains. The results indicate that short…
The structure of random sphere packings in mechanical equilibrium in prescribed stress states, as studied by molecular dynamics simulations, strongly depends on the assembling procedure. Frictionless packings in the limit of low pressure…
Evolutionally conserved quantity that specifies folding nuclei is pursued by a case study for a small protein (PDB code: 1ten). First it is demonstrated that the sequences of amino acids at folding nuclei are not conserved. Then 3D…
Random packings of stiff rods are self-supporting mechanical structures stabilized by long range interactions induced by contacts. To understand the geometrical and topological complexity of the packings, we first deploy X-ray computerized…
In molecular dynamics simulations in the NPT ensemble at constant pressure, the size and shape of the periodic simulation box fluctuate with time. For particle images far from the origin, the rescaling of the box by the barostat results in…
Using small angle neutron scattering, we conducted a detailed structural study of poly(3-alkylthiophenes) dispersed in deuterated dicholorbenzene. The focus was placed on addressing the influence of spatial arrangement of constituent atoms…
We study theoretically the effects of finite volume for pipi scattering in order to extract physical observables for infinite volume from lattice QCD. We compare three different approaches for pipi scattering (lowest order Bethe-Salpeter…
Discrepancies play an important role in the study of uniformity properties of point sets. Their probability distributions are a help in the analysis of the efficiency of the Quasi Monte Carlo method of numerical integration, which uses…
Configurational entropy is an important factor in the free energy change of many macromolecular recognition and binding processes, and has been intensively studied. Despite great progresses that have been made, the global sampling remains…
We examine the phase transition of polymer adsorption as well as the underlying kinetics of polymer binding from dilute solutions on a structureless solid surface. The emphasis is put on the properties of regular multiblock copolymers,…
Define a chi-square random field on a multi-dimensional lattice points index set with a direct-product covariance structure, and consider the distribution of the maximum of this random field. We provide two approximate formulas for the…