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The authors study the short-time dynamics of helix-forming polypeptide chains using an all-atom representation of the molecules and an implicit solvation model to approximate the interaction with the surrounding solvent. The results confirm…
The formation of fibrillar aggregates seems to be a common characteristic of polypeptide chains, although the observation of these aggregates may depend on appropriate experimental conditions. Partially folded intermediates seem to have an…
We study the spin-dependent stereodynamics of the S + H2 -> SH + H reaction using full-dimensional quantum dynamics calculations with zero total nuclear angular momentum along the triplet 3A" states and singlet 1A' states. We find that the…
We address the well-known limitation of the Huxley and Simmons 1971 (HS) model. It is a statement that at physiological value of stiffness in the actomyosin complex, the distribution of the myosin motors becomes microscopically uniform (all…
The cooperative effect plays a significant role in understanding the intermolecular donor-acceptor interactions of hydrogen bonds (H-bonds, D-H...A). Herein, using the benchmark method of high-precision ab initio, the well-known cooperative…
The thermodynamic properties for three different types of off-lattice four-strand beta-sheet protein models interacting via a hybrid Go-type potential have been investigated. Discontinuous molecular dynamic simulations have been performed…
Analysis of the electron density distribution in clusters composed of hydrogen fluoride, water, and ammonia molecules, especially within the hydrogen-bond domains, reveals the existence of both \sigma- and \pi-binding between molecules. The…
Accurate intermolecular potential-energy surfaces (IPESs) for the ground and first excited states of the Sr-H$_2$ and Yb-H$_2$ complexes were calculated. After an extensive methodological study, the CCSD(T) method with the…
Sr_2CuO_3 and Ca_2CuO_3 are considered to be model systems of strongly anisotropic, spin-1/2 Heisenberg antiferromagnets. We report on the basis of a band-structure analysis within the local density approximation and on the basis of…
Protein electrostatics have been demonstrated to play a vital role in protein functionality, with many functionally important amino acid residues exhibiting an electrostatic state that is altered from that of a normal amino acid residue.…
The present paper is aimed to developing an effective field theory in the GeV region to describe consistently both elastic and inelastic NN-scattering in a fully covariant way. In this development we employ our novel s-channel mechanism of…
Electronic stopping cross sections (SCS) of nickel, silicon and nickel-silicon alloys for protons and helium (He) ions are studied in the regime of medium and low energy ion scattering, i.e., for ion energies in the range from 500 eV to 200…
We inquire how structure emerges during the process of protein folding. For this we scrutinise col- lective many-atom motions during all-atom molecular dynamics simulations. We introduce, develop and employ various topological techniques,…
The measured low initial sticking probability of oxygen molecules at the Al(111) surface that had puzzled the field for many years was recently explained in a non-adiabatic picture invoking spin-selection rules [J. Behler et al., Phys. Rev.…
A comprehensive study is presented on the short-time dynamics in suspensions of charged colloidal spheres. The explored parameter space covers the major part of the fluid-state regime, with colloid concentrations extending up to the…
Theoretical characterizations of the various intermediates in the proton pump cycle of the retinal Schiff base in the Halobacterium salinarium have been performed. Contrary to the general belief over the years that the most stable…
Nearly a quarter of genomic sequences and almost half of all receptors that are likely to be targets for drug design are integral membrane proteins. Understanding the detailed mechanisms of the folding of membrane proteins is a largely…
The low-frequency collective vibrational modes in proteins as well as the protein-water interface have been suggested as dominant factors controlling the efficiency of biochemical reactions and biological energy transport. It is thus…
Imidazole and 1,2,3-triazole are promising hydrogen-bonded heterocycles that conduct protons via a structural mechanism and whose derivatives are present in systems ranging from biological proton channels to proton exchange membrane fuel…
Intermediate energy (p,p$'$x) reaction is studied with antisymmetrized molecular dynamics (AMD) in the cases of $^{58}$Ni target with $E_p = 120$ MeV and $^{12}$C target with $E_p = $ 200 and 90 MeV. Angular distributions for various…