Search results for "Biomolecules"
showing 10 items of 549 documents
Intramolecular proton transfer of serine in aqueous solution. Mechanism and energetics
2000
Serine amino acid in aqueous solution is theoretically studied at the B3PW91/6-31+G** level using a dielectric continuum solvent model. Neutral and zwitterionic structures in the gas phase and in solution are described and the proton-transfer mechanism is discussed. A neutral conformation in which the carboxyl hydrogen atom is already oriented toward the amino group seems to be the absolute energy minimum in the gas phase and the most stable neutral form in solution. The absolute energy minimum in solution is a zwitterionic form. The energy barrier for proton transfer is predicted to be very small, in particular when zero-point-energy contributions are added. Our calculations allow the dyna…
Self-assembly of a bioelastomeric structure: solution dynamics and the spinodal and coacervation lines.
1990
The stability, metastability, and instability regions of aqueous solutions of a representative synthetic bioelastomeric polymer, poly (Val-Pro-Gly-Val-Gly), were determined by a combined use of elastic and quasi-elastic light scattering experiments. The approach followed here offers the attractive advantage of singling out the relevant contributions to the total scattering even in the presence of traces of noninteracting larger sized impurities. Conclusions so reached were checked by means of independent experiments. The present results provide descriptions of the very early events in the physics of bioelastogenesis in terms of general polymer science and phase transitions, and in terms of …
Non-Equilibrium Markov State Modeling of the Globule-Stretch Transition
2016
We describe a systematic approach to construct coarse-grained Markov state models from molecular dynamics data of systems driven into a nonequilibrium steady state. We apply this method to study the globule-stretch transition of a single tethered model polymer in shear flow. The folding and unfolding rates of the coarse-grained model agree with the original detailed model. We demonstrate that the folding and unfolding proceeds through the same narrow region of configuration space but along different cycles.
Unfolding dynamics of small peptides biased by constant mechanical forces
2018
We show how multi-ensemble Markov state models can be combined with constant-force equilibrium simulations. Besides obtaining the unfolding/folding rates, Markov state models allow gaining detailed insights into the folding dynamics and pathways through identifying folding intermediates and misfolded structures. For two specific peptides, we demonstrate that the end-to-end distance is an insufficient reaction coordinate. This problem is alleviated through constructing models with multiple collective variables, for which we employ the time-lagged independent component analysis requiring only minimal prior knowledge. Our results show that combining Markov state models with constant-force simu…
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…
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. …