Benchmark of Schemes for Multiscale Molecular Dynamics Simulations.

In multiscale molecular dynamics simulations the accuracy of detailed models is combined with the efficiency of a reduced representation. For several applications - namely those of sampling enhancement - it is desirable to combine fine-grained (FG) and coarse-grained (CG) approaches into a single hybrid approach with an adjustable mixing parameter. We present a benchmark of three algorithms that use a mixing of the two representation layers using a Lagrangian formalism. The three algorithms use three different approaches for keeping the particles at the FG level of representation together: 1) addition of forces, 2) mass scaling, and 3) temperature scaling. The benchmark is applied to liquid hexadecane and includes an evaluation of the average configurational entropy of the FG and CG subsystems. The temperature-scaling scheme achieved a 3-fold sampling speedup with little deviation of FG properties. The addition-of-forces scheme kept FG properties the best but provided little sampling speedup. The mass-scaling scheme yielded a 5-fold speedup but deviated the most from FG properties.

Efficient Algorithms for Langevin and DPD Dynamics.

In this article, we present several algorithms for stochastic dynamics, including Langevin dynamics and different variants of Dissipative Particle Dynamics (DPD), applicable to systems with or without constraints. The algorithms are based on the impulsive application of friction and noise, thus avoiding the computational complexity of algorithms that apply continuous friction and noise. Simulation results on thermostat strength and diffusion properties for ideal gas, coarse-grained (MARTINI) water, and constrained atomic (SPC/E) water systems are discussed. We show that the measured thermal relaxation rates agree well with theoretical predictions. The influence of various parameters on the diffusion coefficient is discussed.

Inhibition of cell-mediated immune reactions by an aqueous extract of normal human skin.

An aqueous extract of normal human skin has been shown to contain an inhibitor of certain cell mediated immune reactions. In this report, the effect of the inhibitor on cell membrane markers and antibody dependent cellular cytotoxicity was determined. Significant diminution of E rosette formation was demonstrated using as little as 0.6 microgram of the skin fraction (p less than .02). Fc receptors for both IgG and IgM were reduced by 46-96% of controls in the presence of the skin inhibitor. On the other hand, no effect on the detection of the complement receptor or surface immunoglobulin was observed, indicating some specificity of binding. In addition, the antibody dependent cell-mediated cytotoxic reaction was inhibited on the skin extract. It was shown that the inhibitor interacted with the lymphocytes, not the antibody or target cells. No effect was detectable when the skin fraction was added after the interactions of effector cells, antibody, and target cells had occurred. This was in contrast to PHA-induced cytotoxicity which could be inhibited following the preincubation of the lymphocytes with the mitogen. Thus there appears to be 2 mechanisms by which the skin fraction interferes with cellular responses: inhibition of antibody binding to Fc receptors, and interference with a step in cellular activation following mitogen stimulation. Analysis of the extract showed the inhibitor was inactivated by trypsin, and did not contain sialic acid, 5'-nucleotidase of beta-N-acetylglucosaminidase, and thus was not associated with membrane or lysosomal enzymes.

Inhibition of lymphocyte cytotoxicity and mitogen-induced transformation of lymphocytes by human skin homogenates.

Limitation of the inflammatory cascade has been demonstrated in man by an inhibitor(s) of the prostaglandin system and by inhibitor(s) for chemotaxis of leukocytes. Other factors may exist in vivo that inhibit other inflammatory sequences. In this report, homogenates from human skin interfered with 2 standard assays of lymphocyte function, mitogen-induced transformation and cytotoxicity while homogenates of human placenta did not. Differential centrifugation studies located inhibitory factor(s) primarily in the nuclear fractions. Therefore, reversible transitory depressions of the cell-mediated immune response that are observed concomitantly with chronic dermatoses may reflect release of inhibitory material dermatitic skin in vivo.