Related papers: Conformational changes in glycine tri- and hexapep…
We have simulated, as a showcase, the pentapeptide Met-enkephalin (Tyr-Gly-Gly-Phe-Met) to visualize the energy landscape and investigate the conformational coverage by the multicanonical method. We have obtained a three-dimensional…
The number of protein structures is far less than the number of sequences. By imposing simple generic features of proteins (low energy and compaction) on all possible sequences we show that the structure space is sparse compared to the…
Structure, function and dynamics of many biomolecular systems can be characterized by the energetic variational principle and the corresponding systems of partial differential equations (PDEs). This principle allows us to focus on the…
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 describe and test an implicit solvent all-atom potential for simulations of protein folding and aggregation. The potential is developed through studies of structural and thermodynamic properties of 17 peptides with diverse secondary…
We present a continuum model for symmetry-breaking phase transformations in intercalation compounds, based on Ericksen's multi-well energy formulation. The model predicts the nucleation and growth of crystallographic microstructures in…
We introduce a simple and predictive model for determining the phase stability of ternary phospholipid-cholesterol mixtures. Assuming that competition between the liquid and gel order of the phospholipids is the main driving force behind…
Monte Carlo computer simulations are used to study the conformational free energy of a folded polymer confined to a long cylindrical tube. The polymer is modeled as a hard-sphere chain. Its conformational free energy $F$ is measured as a…
Many commonly used force fields for protein systems such as AMBER, CHARMM, GROMACS, OPLS, and ECEPP have amino-acid-independent force-field parameters of main-chain torsion-energy terms. Here, we propose a new type of amino-acid-dependent…
A general theoretical framework is developed using free energy functional methods to understand the effects of heterogeneity in the folding of a well-designed protein. Native energetic heterogeneity arising from non-uniformity in native…
For the contact of two finite portions of interacting rigid crystalline surfaces, we compute the dependence of the pinning energy barrier on the misfit angle and contact area. The resulting data are used to investigate the distribution of…
In this paper we study the phenomenon of kinetic partitioning when a polypeptide chain has two ground state conformations one of which is more kinetically reachable than the other. This question is relevant to understand the phenomenology…
We study the phase behavior of a symmetric binary polymer blend which is confined into a thin film. The film surfaces interact with the monomers via short range potentials. We calculate the phase behavior within the self-consistent field…
Molecular dynamics simulation is employed to understand the thermodynamic behavior of cuboctahedron (cub) and icosahedron (ico) nanoparticles with 2-20 number of shells (55-28741 atoms). The embedded atom method was used to describe the…
Energetic correlations due to polymeric constraints and the locality of interactions, in conjunction with the apriori specification of the existence of a particularly low energy state, provides a method of introducing the aspect of minimal…
It was recently discovered that friction between surfaces bearing phosphatidylcholine (PC) lipid bilayers can be increased by two orders of magnitude or more via an externally-applied electric field, and that this increase is fully…
Energies of graphene nanocones with 1 to 5 pentagonal disclinations are studied on an atomically detailed level. The numerical results are interpreted in terms of three different contributions to the cone energy: the core disclination…
We perform Monte Carlo simulations to study the elastic properties of the helix-coil worm-like chain model of alpha-helical polypeptides. In this model the secondary structure enters as a scalar (Ising like) variable that controls the local…
By simulating the first order globule-crystal transition of a flexible homopolymer chain, both by collision dynamics and Monte Carlo with non-kinetic moves, we show that the effective and the thermodynamic transition temperatures are…
We investigate the near-surface relaxation of freestanding atactic \glsdesc{ps} films with molecular dynamics simulations. As in previous coarse-grained simulations, relaxation times for backbone segments and phenyl rings are linked to…