Related papers: Interaction of proteins in solution from small ang…
Single Particle Imaging techniques at X-ray lasers have made significant strides, yet the challenge of determining the orientation of freely rotating molecules during delivery remains. In this study, we propose a novel method to partially…
Aligning protein-protein interaction (PPI) networks of different species has drawn a considerable interest recently. This problem is important to investigate evolutionary conserved pathways or protein complexes across species, and to help…
The interaction between surface patches of proteins with different surface properties has a vital role to play driving conformational changes of proteins in different salt solutions. We demonstrate the existence of ion-specific attractive…
The understanding of dynamics and functioning of biological membranes and in particular of membrane embedded proteins is one of the most fundamental problems and challenges in modern biology and biophysics. In particular the impact of…
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…
Thermal behaviors of hydroxypropyl cellulose dilute aqueous solutions with impurities of Group~I alkali metal ions (Li, Na, K, Rb and Cs chlorides) has been studied by means of static and dynamic light scattering measurements. From the…
We studied the possibility to approximate a Lennard Jones interaction by a pairwise contact potential. First we used a Lennard-Jones potential to design off-lattice, protein-like heteropolymer sequences, whose lowest energy (native)…
The interactions of a protein, its phase behavior, and ultimately, its ability to function, are all influenced by the interactions between the protein and its hydration waters. Here we study proteins with a variety of sizes, shapes,…
We derive a novel formulation for the interaction potential between deformable fibers due to short-range fields arising from intermolecular forces. The formulation improves the existing section-section interaction potential law for in-plane…
The effect of scattering with non-zero impact parameters between consituents in relativistic heavy ion collisions is investigated. In solving the relativistic Boltzmann equation, the characteristic range of the collision kernel is varied…
A novel combination of discontinuous molecular dynamics and the Langevin equation, together with an intermediate-resolution model, are used to carry out long (several $\mu$s) simulation and study folding transition and transport of proteins…
The correlations between the segments of a semidilute polymer solution are found to induce correlations in the positions of small particles added to the solution. Small means a diameter much less than the polymer's correlation length. In…
The folding vs. adsorption behaviour of a coarse-grained off-lattice protein model near an attractive surface is presented within the frame of a Multicanonical Monte Carlo simulations. In the polymer-surface model, the Lennard-Jones…
Molecular dynamics simulation is used for studying the contact angle of nanoscale sessile drops on a planar solid wall in a system interacting via the truncated and shifted Lennard-Jones potential. The entire range between total wetting and…
In this paper the normal collision of spherical particles is investigated. The particle interaction is modelled in a macroscopic way using the Hertzian contact force with additional linear damping. The goal of the work is to develop an…
Background:Typically, proteins perform key biological functions by interacting with each other. As a consequence, predicting which protein pairs interact is a fundamental problem. Experimental methods are slow, expensive, and may be error…
The paper presents a novel approach to the description of the nonrelativistic weak interaction of a massive neutral particle (lepton) and a nucleus, in which the latter retains its integrity. The cross section of such a process is a sum of…
Short-range repulsion within inter-molecular force fields is conventionally described by either Lennard-Jones (${A}/{r^{12}}$) or Born-Mayer ($A\exp(-Br)$) forms. Despite their widespread use, these simple functional forms are often unable…
In this article, we study a second-order expansion for the effect induced on a large quantum particle which undergoes a single scattering with a low-mass particle via a repulsive point interaction. We give an approximation with third-order…
In this paper, we study the large-scale protein interaction network of yeast uti lizing a stochastic method based upon percolation of random graphs. In order to find the global features of connectivities in the network, we introduce numeric…