Related papers: Conformational changes in glycine tri- and hexapep…
A model to describe the mechanism of conformational dynamics in protein based on matter interactions using lagrangian approach and imposing certain symmetry breaking is proposed. Both conformation changes of proteins and the injected…
Experimental observations suggest that proteins follow different pathways under different environmental conditions. We perform molecular dynamics simulations of a model of the SH3 domain over a broad range of temperatures, and identify…
We study the conformational equilibria of two peptides using a novel statistical mechanics approach designed for calculating free energy differences between highly dis-similar conformational states. Our results elucidate the contrasting…
The prediction of the biologically active native conformation of a protein is one of the fundamental challenges of structural biology. This problem remains yet unsolved mainly due to three factors: the partial knowledge of the effective…
Ab initio calculations based on the density-functional pseudopotential approach have been used to study the fully relaxed structure, the electron distribution and the electronic density of states of (001) terraces, steps, corners and…
A new lattice protein model with a four-helix bundle ground state is analyzed by a parameter-space Monte Carlo histogram technique to evaluate the effects of an extensive variety of model potentials on folding thermodynamics. Cooperative…
We study the relation between $\alpha$-helix formation and folding for a simple artificial peptide, Ala$_{10}$-Gly$_5$-Ala$_{10}$. Our data rely on multicanonical Monte Carlo simulations where the interactions among all atoms are taken into…
The conformation space of a 20-residue antiparallel $\beta$-sheet peptide, sampled by molecular dynamics simulations, is mapped to a network. Conformations are nodes of the network, and the transitions between them are links. The…
We present a first principles-quality potential energy surface (PES) describing the inter-atomic forces for hydrogen atoms interacting with free-standing graphene. The PES is a high-dimensional neural network potential that has been…
We present a theoretical study of the unielectronic energy spectra, electron localization, and optical absorption of triangular core-shell quantum rings. We show how these properties depend on geometric details of the triangle, such as side…
In experiments and in simulations, the free energy of a state of a system can be determined from the probability that the state is occupied. However, it is often necessary to impose a biasing potential on the system so that high energy…
Theoretical studies of protein folding on lattice models relie on the assumption that water close to amino-acids is always in thermal equilibrium all along the folding pathway. Within this framework, it has always been considered that…
Protein folding, peptide aggregation and crystallization, as well as adsorption of molecules on soft or solid substrates have an essential feature in common: In all these processes, structure formation is guided by a collective, cooperative…
Surface energies for different GaAs surface orientations have been calculated as a function of the chemical potential. We use an energy density formalism within the first-principles pseudopotential density-functional approach. The…
A new chemical model is presented that simulates fully-coupled gas-phase, grain-surface and bulk-ice chemistry in hot cores. Glycine (NH2CH2COOH), the simplest amino acid, and related molecules such as glycinal, propionic acid and propanal,…
We present results of molecular simulations of a model protein whose hydrophobic collapse proceeds as a cascade of downhill transitions between distinct intermediate states. Different intermediates are stabilized by means of appropriate…
For the first time the potential energy surfaces of actinide nuclei in the $(\beta_{20}, \beta_{22}, \beta_{30})$ deformation space are obtained from a multi-dimensional constrained covariant density functional theory. With this newly…
Measurements of chain conformation in proteins/polyelectrolytes complexes (lysozyme and PSSNa) show that the crossover observed between an open structure -a chain network crosslinked by the proteins, and a globular one - dense globules of ~…
The folding pathway and rate coefficients of the folding of a knotted protein are calculated for a potential energy function with minimal energetic frustration. A kinetic transition network is constructed using the discrete path sampling…
In the current AFM experiments the distribution of unfolding times, P(t), is measured by applying a constant stretching force f_s from which the apparent unfolding rate is obtained. To describe the complexity of the underlying energy…