相关论文: Side-chain and backbone ordering in Homopolymers

We have performed Monte Carlo simulations to investigate the temperature dependence of the ordering of the side chains of the X-shape liquid crystal molecules which are arranged in a hexagonal array. Each hexagon contains six side chains,…

Using molecular dynamics and thermodynamic integration, we report on the solvation process in water and in cyclohexane of seven polypeptides (GLY, ALA, ILE, ASN, LYS, ARG, GLU). The polypeptides are selected to cover the full hydrophobic…

We have studied folding mechanisms of three small globular proteins: crambin (CRN), chymotrypsin inhibitor 2 (CI2) and the fyn Src Homology 3 domain (SH3) which are modelled by a Go-like Hamiltonian with the Lennard-Jones interactions. It…

Using multicanonical simulations, the authors study the effect of charged end groups on helix formation in alanine based polypeptides. They confirm earlier reports that neutral polyalanine exhibits a pronounced helix-coil transition in gas…

The conformation and the phase diagram of a membrane protein are investigated via grand canonical ensemble approach using a homopolymer model. We discuss the nature and pathway of $\alpha$-helix integration into the membrane that results…

I propose a variation of the standard worm--like chain model to account for internal order parameter (helix/coil) fields on the polymer chain. This internal order parameter field influences polymer conformational statistics by locally…

We study numerically the dynamics of acetanilide (ACN) molecules placed on a flat surface of a multilayer hexagonal boron nitride structure. We demonstrate that the ACN molecules, being achiral in three dimensions, become chiral after being…

The coil-globule transition of hetero-polymer chains is studied here. By means of extensive Molecular Dynamics simulations, we show that the transition is directly linked to the complexity of the chain, which depends on the number of…

After a discussion of the definition and number of pseudoknots, we reconsider the self-attracting homopolymer paying particular attention to the scaling of the number of pseudoknots at different temperature regimes in two and three…

In standard molecular junctions, a molecular structure is placed between and connected to metal leads. Understanding how mechanical tuning in such molecular junctions can change heat conductance has interesting applications in nanoscale…

We have performed multicanonical Monte Carlo simulations of C-peptide of ribonuclease A. It is known by CD and NMR experiments that this peptide has high alpha-helix content in aqueous solution and that the side-chain charges of residues…

By taking into account base-base stacking interactions we improve the Generalized Model of Polypeptide Chain (GMPC). Based on a one-dimensional Potts-like model with many-particle interactions, the GMPC describes the helix-coil transition…

The melting transition in solid monolayers of a series of short-chained n-alkanes, n-octane (n-C8H18), n-decane (n-C10H22), and n-dodecane (n-C12H26) physisorbed onto the graphite basal plane are studied through use of molecular dynamics…

We present results for a lattice model of bio-polymers where the type of $\beta$-sheet formation can be controlled by different types of hydrogen bonds depending on the relative orientation of close segments of the polymer. Tuning these…

We have investigated the potential energy surfaces for glycine chains consisting of three and six amino acids. For these molecules we have calculated potential energy surfaces as a function of the Ramachandran angles phi and psi, which are…

For a model deca-alanine peptide the cavity (ideal hydrophobic) contribution to hydration favors the helix state in the coil-to-helix transition and the paired helix bundle in the assembly of two helices. The energetic contributions of…

In simple models side chains are often represented implicitly (e.g., by spin-states) or simplified as one atom. We study side chain effects using square lattice and tetrahedral lattice models, with explicitly side chains of two atoms. We…

We report a joint experimental and theoretical study of the structural, vibrational, and electronic properties of layered monoclinic arsenic sulfide (alpha-As2S3), aka mineral orpiment, under compression. X-ray diffraction and Raman…

The conformational complexity of linear polymers far exceeds that of point-like atoms and molecules. Polymers can bend, twist, even become knotted. Thus they may also display a much richer phase structure than point particles. But it is not…

We present simulations on a binary blend of bead-spring polymer chains. The introduction of monomer size disparity yields very different relaxation times for each component of the blend. Competition between two different arrest mechanisms,…