Search results for "molecular dynamics"
showing 10 items of 1075 documents
Polymer brushes on flat and curved surfaces: How computer simulations can help to test theories and to interpret experiments
2012
Theoretical descriptions of static properties of polymer brushes are reviewed, with an emphasis on monodisperse macromolecules grafted to planar, cylindrical, or spherical substrates. Blob concepts and resulting scaling relations are outlined, and various versions of the self-consistent field theory are summarized: the classical approximation and the strong stretching limit, as well as the lattice formulation. The physical justification of various inherent assumptions is discussed, and computer simulation results addressing the test of the validity of these approximations are reviewed. Also, alternative theories, such as the single chain mean field theory and the density functional theory, …
Local Viscosity in the Vicinity of a Wall Coated by Polymer Brush from Green-Kubo Relations
2008
When fluids are confined in slit pores between parallel walls, their static structures and their dynamical properties exhibit inhomogeneity in the z-direction perpendicular to the wall. Of particular interest are local bulk viscosity η b (z) and shear viscosity η s (z). Here, we discuss an algorithm to estimate these quantities from Green-Kubo relations using equilibrium molecular dynamics. As an application example, a polymer brush (macromolecules end-grafted to a substrate at z= 0) interacting with a solvent formed from point-like particles is given.
Solvent-induced free energy landscape and solute-solvent dynamic coupling in a multielement solute
1999
AbstractMolecular dynamics simulations using a simple multielement model solute with internal degrees of freedom and accounting for solvent-induced interactions to all orders in explicit water are reported. The potential energy landscape of the solute is flat in vacuo. However, the sole untruncated solvent-induced interactions between apolar (hydrophobic) and charged elements generate a rich landscape of potential of mean force exhibiting typical features of protein landscapes. Despite the simplicity of our solute, the depth of minima in this landscape is not far in size from free energies that stabilize protein conformations. Dynamical coupling between configurational switching of the syst…
Monte Carlo simulations of polymer dynamics: Recent advances
1997
A brief review is given of applications of Monte Carlo simulations to study the dynamical properties of coarse-grained models of polymer melts, emphasizing the crossover from the Rouse model toward reptation, and the glass transition. The extent to which Monte Carlo algorithms can mimic the actual chain dynamics is critically examined, and the need for the use of coarse-grained rather than fully atomistic models for such simulations is explained. It is shown that various lattice and continuum models yield qualitatively similar results, and the behavior agrees with the findings of corresponding molecular dynamics simulations and experiments, where available. It is argued that these simulatio…
Solution NMR structure of aD,L-alternating oligonorleucine as a model of ?-helix
2001
beta-Helix structures are of particular interest due to their capacity to form transmembrane channels with different transport properties. However, the relatively large number of beta-helices configurations does not allow a direct conformational analysis of beta-helical oligopeptides. A synthetic alternating D,L-oligopeptide with twelve norleucines (XIIMe) has been used as a model to get insight in the conformational features of beta-helix structures. The spatial configuration of XIIMe in solution has been determined by NMR. An extensive set of distances (nuclear Overhauser effect) and dihedral (J coupling constants) constraints have been included in molecular dynamics calculations. The NMR…
Molecular-dynamics simulation of a glassy polymer melt: Rouse model and cage effect
1999
We report results of molecular-dynamics simulations for a glassy polymer melt consisting of short, linear bead-spring chains. It was shown in previous work that this onset of the glassy slowing down is compatible with the predictions of the mode coupling theory. The physical process of `caging' of a monomer by its spatial neighbors leads to a distinct two step behavior in the particle mean square displacements. In this work we analyze the effects of this caging process on the Rouse description of the melt's dynamics. We show that the Rouse theory is applicable for length and time scales above the typical scales for the caging process. Futhermore, the monomer displacement is compared with si…
Molecular modelling and QSAR in the discovery of HIV-1 integrase inhibitors
2007
The treatment regimens for the HIV-1 have mainly included reverse transcriptase or protease inhibitors but their long-term clinical utility is limited by severe side effects and viral drug resistance. A new attractive target for chemotherapeutic intervention can be the Integrase enzyme, that mediates the integration of HIV-1 DNA into a host chromosome, for which there is no known counterparts in the host cell. A number of derivatives have been found to inhibit IN in in vitro assays, but no successful drug based on them has emerged so far, although many compounds have been proposed. Moreover most of the inhibitors do not belong to a very precise structural class: this fact makes these compou…
Quantum Chemical-Based Protocol for the Rational Design of Covalent Inhibitors.
2016
We propose a structure-based protocol for the development of customized covalent inhibitors. Starting from a known inhibitor, in the first and second steps appropriate substituents of the warhead are selected on the basis of quantum mechanical (QM) computations and hybrid approaches combining QM with molecular mechanics (QM/MM). In the third step the recognition unit is optimized using docking approaches for the noncovalent complex. These predictions are finally verified by QM/MM or molecular dynamic simulations. The applicability of our approach is successfully demonstrated by the design of reversible covalent vinylsulfone-based inhibitors for rhodesain. The examples show that our approach…
Structure evolution and reaction mechanism in the Ni/Al reactive multilayer nanofoils
2014
Abstract The extremely rapid gasless reactions in binary Ni/Al reactive multilayer nanofoils (RMNFs) are investigated both experimentally and theoretically. The quenching technique is used to study the dynamics of structural transformation on the micro- and nanoscales. The experimentally obtained patterns of structural evolution related to the heterogeneous reactions are compared with the results of molecular dynamics simulations carried out for the same reactive system. Based on the obtained data, the intrinsic mechanism of the reaction in Ni/Al RMNF is considered, which adequately explains the unusual parameters of a gasless combustion wave in such a system.
A combined molecular dynamics and Monte Carlo study of the approach towards phase separation in colloid-polymer mixtures.
2011
A coarse-grained model for colloid-polymer mixtures is investigated where both colloids and polymer coils are represented as point-like particles interacting with spherically symmetric effective potentials. Colloid-colloid and colloid-polymer interactions are described by Weeks-Chandler-Andersen potentials, while the polymer-polymer interaction is very soft, of strength k(B)T/2 for maximum polymer-polymer overlap. This model can be efficiently simulated both by Monte Carlo and molecular dynamics methods, and its phase diagram closely resembles that of the well-known Asakura-Oosawa model. The static and dynamic properties of the model are presented for systems at critical colloid density, va…