相关论文: Side-chain and backbone ordering in Homopolymers
Homogeneous nucleation of a new phase near a second, continuous, transition, is considered. The continuous transition is in the metastable region associated with the first-order phase transition, one of whose coexisting phases is…
The thermodynamic behavior and structural properties of hydrophobic-polar (HP) lattice proteins interacting with attractive surfaces are studied by means of Wang-Landau sampling. Three benchmark HP sequences (48mer, 67mer, and 103mer) are…
Poly($para$-phenylene) has been recognized as one important family of conducting polymers upon doping with donors or acceptors. This system possesses a chain-like structure with infinite benzene rings linked with the single C-C bond.…
Microphase separated structure consisting of the periodic alternation of the layers of stretched homopolymer chains surrounded by perpendicularly oriented oligomeric tails is studied for both, strongly bonded (ionic) systems and weakly…
We study random heteropolymer chain with gaussian distribution of kinds of monomers. The long-range correlations between kinds of monomers were introduce. The mean-field analysis of such heteropolymer indicates the existence of infinite…
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…
The statistical mechanics of a ribbon polymer made up of two semiflexible chains is studied using both analytical techniques and simulation. The system is found to have a crossover transition at some finite temperature, from a type of short…
The ability to accurately predict the finite temperature properties of realistic quantum solids is central to uncovering new phases and engineering materials with novel properties. Nonetheless, there remain comparatively few many-body…
We studied by molecular dynamics simulations the relation existing between the lifetime of hydrogen bonds, the tetrahedral order and the diffusion coefficient of model water. We tested four different models: SPC/E, TIP4P-Ew, TIP5P-Ew and…
HCl, a 'textbook' example of a polar covalent molecule, is a well-known compound of hydrogen and chlorine. Inspired by the discovery of unexpected stable stoichiometries of sodium chlorides, we performed systematic searches for all stable…
The thermodynamic behavior of collapse transition in a fully flexible coarse-grained model of energy polydisperse polymer (EPP), a statistical model of random heteropolymer, is investigated in an implicit solvent by means of molecular…
We investigate the fine structure of the sp3 hybridized covalent bond geometry that governs the tetrahedral architecture around the central C$_\alpha$ carbon of a protein backbone, and for this we develop new visualization techniques to…
We use Wang-Landau and replica exchange techniques to study the effect of an increasing stiffness on the formation of secondary structures in protein-like systems. Two possible models are considered. In both models, a polymer chain is…
Employing high-vacuum electrospray deposition and scanning tunneling microscopy, we investigated how individual poly(3-hexylthiophene) (P3HT) chains navigated on the periodic energy landscape of a reconstructed Au(111) surface. The…
We study the conformational properties of heteropolymers containing two types of monomers A and B, modeled as self-avoiding random walks on a regular lattice. Such a model can describe in particular the sequences of hydrophobic and…
We present the exact solution of a microscopic statistical mechanical model for the transformation of a long polypeptide between an unstructured coil conformation and an $\alpha$-helix conformation. The polypeptide is assumed to be adsorbed…
In order to inquire the microscopic origin of observed multiple time scales in solvation dynamics we carry out several computer experiments. We perform atomistic molecular dynamics simulations on three protein-water systems namely,…
We introduce a polymer model where the transition from swollen to compact configurations is due to interactions between the monomers and the solvent. These interactions are the origin of the effective attractive interactions between…
Hydrogen bonds are a common feature in protein folding and aggregation. Due to their chemical peculiarities in terms of strength and directionality, a particular attention must be paid to the definition of the hydrogen bond potential…
We study folding in 16-monomer heteropolymers on the square lattice. For a given sequence, thermodynamic properties and stability of the native state are unique. However, the kinetics of folding depends on the model of dynamics adopted for…