相关论文: Differences in Solution Behavior among Four Semico…

We study the thermodynamic behavior of a simple off-lattice model for protein folding. The model is two-dimensional and has two different ``amino acids''. Using numerical simulations of all chains containing eight or ten monomers, we…

Acid solutions exhibit a variety of complex structural and dynamical features arising from the presence of multiple interacting reactive proton defects and counterions. However, disentangling the transient structural motifs of proton…

Using density functional theory the atomic and electronic structure of sodium are predicted to depart substantially from those expected of simple metals for $r_s <$ 2.48 ($p > 130$ GPa). Newly-predicted phases include those with low…

We report a molecular dynamics simulation of selenium, described by a three-body interaction. The temperatures T_g and T_c and the structural properties are in agreement with experiment. The mean nearest neighbor coordination number is 2.1.…

The solvent quality determines the collapsed or the expanded state of a polymer. For example, a polymer dissolved in a poor solvent collapses, whereas in a good solvent it opens up. While this standard understanding is generally valid,…

In this study, a possible non-quasiparticle glue for superconductivity of both conventional and unconventional superconductors is explored in a pure electron picture. It is shown clearly that the moving electrons due to the electromagnetic…

Combining the principal component analysis (PCA) of X-ray spectrum with MD simulations, we experimentally reveal the existence of three basic components in water. These components exhibit distinct structures, densities, and temperature…

We combine small angle scattering experiments and simulations to investigate the internal structure and interactions of composite Poly(N-isopropylacrylamide)-Poly(ethylene glycol) (PNIPAM-PEG) microgels. At low temperatures the…

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…

We consider a fluid of hard spheres bearing one or two uniform circular adhesive patches, distributed so as not to overlap. Two spheres interact via a ``sticky'' Baxter potential if the line joining the centers of the two spheres intersects…

We examine five different popular rigid water models (SPC, SPCE, TIP3P, TIP4P and TIP5P) using MD simulations in order to investigate the hydrophobic hydration and interaction of apolar Lennard-Jones solutes as a function of temperature in…

The interplay of nematic order and phase separation in solutions of semiflexible polymers in solvents of variable quality is investigated by density functional theory (DFT) and molecular dynamics (MD) simulations. We studied coarse-grained…

Semiflexible polymers are widely used as a paradigm for understanding structural phases in biomolecules including folding of proteins. Here, we compare bead-spring and bead-stick variants of coarse-grained semiflexible polymer models that…

We present a study of the solvation properties of model aqueous electrode interfaces. The exposed electrodes we study strongly bind water and have closed packed crystalline surfaces, which template an ordered water adlayer adjacent to the…

Based on a newly developed contact-density chain-growth algorithm, we have simulated a nongrafted peptide in the vicinity of different attractive substrates. We analyzed the specificity of the peptide adsorption by focussing on the…

The mechanics of complex soft matter often cannot be understood in the classical physical frame of flexible polymers or rigid rods. The underlying constituents are semiflexible polymers, whose finite bending stiffness ($\kappa$) leads to…

The aqueous solvent profoundly influences protein folding, yet its effects are relatively poorly understood. In this study, we investigate the impact of solvation on the folding of lattice proteins by using Monte Carlo simulations. The…

We present the results of a molecular dynamics simulation study of thermodynamic and structural properties upon supercooling of a low concentration sodium chloride solution in TIP4P water and the comparison with the corresponding bulk…

Using molecular dynamics simulations we study the thermodynamic behavior of a single-component covalent material described by the recently proposed Environment-Dependent Interatomic Potential (EDIP). The parameterization of EDIP for silicon…

Synthetic copolymers and biopolymers, such as polypeptides and double-stranded DNA, often exhibit strong variations in bending stiffness along their contour, which can significantly impact conformational behavior at larger scales. To…