Search results for "Biomolecule"
showing 10 items of 666 documents
Noise driven translocation of short polymers in crowded solutions
2008
In this work we study the noise induced effects on the dynamics of short polymers crossing a potential barrier, in the presence of a metastable state. An improved version of the Rouse model for a flexible polymer has been adopted to mimic the molecular dynamics by taking into account both the interactions between adjacent monomers and introducing a Lennard-Jones potential between all beads. A bending recoil torque has also been included in our model. The polymer dynamics is simulated in a two-dimensional domain by numerically solving the Langevin equations of motion with a Gaussian uncorrelated noise. We find a nonmonotonic behaviour of the mean first passage time and the most probable tran…
Global stability of protein folding from an empirical free energy function
2013
The principles governing protein folding stand as one of the biggest challenges of Biophysics. Modeling the global stability of proteins and predicting their tertiary structure are hard tasks, due in part to the variety and large number of forces involved and the difficulties to describe them with sufficient accuracy. We have developed a fast, physics-based empirical potential, intended to be used in global structure prediction methods. This model considers four main contributions: Two entropic factors, the hydrophobic effect and configurational entropy, and two terms resulting from a decomposition of close-packing interactions, namely the balance of the dispersive interactions of folded an…
Triplet of cysteines – Coordinational riddle?
2020
Polythiol binding of metal ions plays crucial role in the proper functioning of cysteine-rich proteins that are responsible for metal homeostasis and defending processes against metal toxicity (including heavy metals detoxification). The coordination properties of cysteine residues involved in specific sequencional patterns in proteins (like those present in e.g. metallothioneins) are interesting not only from a chemical point of view but may also lead to a better understanding of the purpose and allocation of metal ions in various biomolecules. In this study, the interaction of Zn2+, Cd2+ and Ni2+ ions with four peptides containing cysteine triplet motif were studied by potentiometric and …
Polarization Force Fields for Peptides Implemented in ECEPP2 and MM2
2000
Abstract The empirical conformational energy program for peptides (ECEPP2) and molecular mechanics (MM2) have been used for the simulation of the For-Gly-NH2 backbone. I propose two different methods for the calculation of the polarization energy term: the polarization procedure by non-interacting induced dipoles (NID) which assumes scalar isotropic point polarizabilities and the polarization scheme by interacting induced dipoles (ID) which calculates tensor effective anisotropic point polarizabilities (method of Applequist). I present a comparative study of ECEPP2 and MM2 + polarization. I discuss molecular mechanics results including the total energy differences, partitional analyses of t…
On the Adsorption Process in Polymer Brushes: A Monte Carlo Study
1996
The adsorption process of the single polymer chain in a polymer brush of varying surface coverages is studied by means of Monte Carlo simulations of the bond-fluctuation lattice model. Only the end monomers can adsorb at the grafting surface, whereas inner monomers interact repulsively with it. The brush builds up a steric hindrance which forces the penetrating polymer to stretch strongly and which is responsible for small adsorption probabilities at surface coverages close to the overlap density. The final step of the adsorption process is determined by a fluctuation of the end monomer around its average position, which is comparable to the initial step of the desorption process.
Polymer Brushes on Flat and Curved Substrates: Scaling Concepts and Computer Simulations
2007
The scaling concepts for isolated flexible macromolecules in good solvent grafted with one chain end to a flat surface (polymer mushrooms) as well as for layers of many overlapping end-grafted chain molecules (polymer brushes) are introduced. Monte Carlo attempts to test these concepts are briefly reviewed. Then the extension of these concepts to polymer brushes grafted to the interior of a cylinder surface is discussed. Molecular Dynamics results on chain average linear dimensions in the direction normal to the grafting surface and in axial direction are described, as well as distribution functions for the density of end monomers and of all monomers of the chains. It is argued that under t…
Adsorption of Semiflexible Polymers in Cylindrical Tubes
2021
Conformations of wormlike chains in cylindrical pores with attractive walls are explored for varying pore radius and strength of the attractive wall potential by molecular dynamics simulations of a coarse-grained model. Local quantities such as the fraction of monomeric units bound to the surface and the bond-orientational order parameter as well as the radial density distribution are studied, as well as the global chain extensions parallel to the cylinder axis and perpendicular to the cylinder surface. A nonmonotonic convergence of these properties to their counterparts for adsorption on a planar substrate is observed due to the conflict between pore surface curvature and chain stiffness. …
Experimental and theoretical evidence of overcharging of calcium silicate hydrate
2007
International audience; Electrokinetic measurements such as electrophoresis may show an inversion of the effective surface charge of colloidal particle called overcharging. This phenomenon has been studied by various theoretical approaches but up to now very few attempts of confrontation between theory and experiment have been conducted. In this work we report electrophoretic measurements as well as Monte Carlo simulations of the electrokinetic potential for the surface of calcium silicate hydrate (Csingle bondSsingle bondH), which is the major constituent of hydrated cement. In the simulations, the surface charge of Csingle bondSsingle bondH nanoparticles in equilibrium with the ionic solu…
Robust three-dimensional best-path phase-unwrapping algorithm that avoids singularity loops.
2009
In this paper we propose a novel hybrid three-dimensional phase-unwrapping algorithm, which we refer to here as the three-dimensional best-path avoiding singularity loops (3DBPASL) algorithm. This algorithm combines the advantages and avoids the drawbacks of two well-known 3D phase-unwrapping algorithms, namely, the 3D phase-unwrapping noise-immune technique and the 3D phase-unwrapping best-path technique. The hybrid technique presented here is more robust than its predecessors since it not only follows a discrete unwrapping path depending on a 3D quality map, but it also avoids any singularity loops that may occur in the unwrapping path. Simulation and experimental results have shown that …
2,4-Di-tert-butyl-6-({[2-(di-methyl-amino)-eth-yl](2-hy-droxy-benz-yl)amino}-meth-yl)phenol.
2014
The title compound, C26H40N2O2, has both its N atoms in trigonal-pyramidal geometries. The molecular structure is stabilized by O—H...N and C—H...O hydrogen bonds. In the crystal, C—H...π interactions lead to the formation of a supramolecular helical chain along theb-axis direction.