相关论文: Ab initio study of alanine polypeptide chains twis…
We develop a methodology for the calculation of surface free energies based on the probability distribution of a wandering interface. Using a simple extension of the NpT sampling, we allow the interface area to randomly probe the available…
We implement the replica exchange molecular dynamics algorithm to study the interactions of a model peptide (WALP-16) with an explicitly represented DPPC membrane bilayer. We observe the spontaneous, unbiased insertion of WALP-16 into the…
We study the electronic properties of coupled parallel Polyyne chains in a couple of symmetric stacking arrangements, namely the AA stacking and the stacking AB, with the single and triple carbon bonds of one chain aligned (AA) and…
The proposal of this paper is to provide a simple angular random walk model to build up polypeptide structures, which encompass properties of dihedral angles of folded proteins. From this model, structures will be built with lengths ranging…
The folding of a peptide chain into a three dimensional structure is a thermodynamically driven process such that the chain naturally evolves to form domains of similar amino acids. The formation of this domain occurs by curling the one…
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…
We studied the electronic and the structural properties of amino acids (alanine, glycine, and histidine) attached to graphene oxide (GO) by peptide bonding, via plane wave pseudopotential total-energy calculations within the local spin…
Understanding and computing the entropic forces exerted by polymer chains under confinement is important for many reasons, from research to applications. However, extracting properties related to the free energy, such as the force (or…
We provide evidence that the energy landscapes of folded proteins do not shift with temperature, but the onset of functional dynamics is associated with its effective sampling. The motion of the backbone is described by three distinct…
Amphiphiles are molecules which have both hydrophilic and hydrophobic parts. In water- and/or oil-like solvent, they self-assemble into extended sheet-like structures due to the hydrophobic effect. The free energy of an amphiphilic system…
The anchor of most integral membrane proteins consists of one or several helices spanning the lipid bilayer. The WALP peptide, GWW(LA)$_n$(L)WWA, is a common model helix to study the fundamentals of protein insertion and folding, as well as…
Recent experimental studies have observed a surprisingly wide range of strengths in polycrystalline graphene. Previous computational investigations of graphene tilt boundaries have highlighted the role of interfacial topology in determining…
We have simulated 10-residue polyalanine chain by multicanonical method to visualize the 3D topographic picture of the free energy landscape over the whole range of temperatures, hence to show the funnel along the folding pathway…
The viscosity dependence of the folding rates for four sequences (the native state of three sequences is a beta-sheet, while the fourth forms an alpha-helix) is calculated for off-lattice models of proteins. Assuming that the dynamics is…
Exploring and understanding the protein-folding problem has been a long-standing challenge in molecular biology. Here, using molecular dynamics simulation, we reveal how parallel distributed adjacent planar peptide groups of unfolded…
Two-state cooperativity is an important characteristic in protein folding. It is defined by a depletion of states lying energetically between folded and unfolded conformations. While there are different ways to test for two-state…
We present a ``coarse molecular dynamics'' approach and apply it to studying the kinetics and thermodynamics of a peptide fragment dissolved in water. Short bursts of appropriately initialized simulations are used to infer the deterministic…
A central goal of protein-folding theory is to predict the stochastic dynamics of transition paths --- the rare trajectories that transit between the folded and unfolded ensembles --- using only thermodynamic information, such as a…
Recently, a new two-dimensional carbon allotrope, named biphenylene network (BPN) was experimentally realized. The BPN structure is composed of four-, six-, and eight-membered rings of sp$^2$-hybridized carbon atoms. In this work, we…
Employing ab-initio electronic structure calculations combined with the non-equilibrium Green's function technique, we study the dependence of the thermopower Q on the conformation in biphenyl-based single-molecule junctions. For the series…