Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

A critical review of adsorption methods that are currently used in the characterization of ordered organic−inorganic nanocomposite materials is presented, and the adsorption methodology that is potentially useful for this characterization, but has not yet been applied, is discussed. The ordered organic−inorganic nanocomposites include surface-functionalized ordered mesoporous materials (OMMs) with siliceous frameworks (synthesized either via postsynthesis surface modification or via direct co-condensation method), periodic mesoporous organosilicas, and surfactant-containing OMMs. This review covers the methods for determination of the specific surface area and pore volume. The available methods for mesopore size analysis are critically compared and evaluated, with special emphasis on the recent developments related to the application of advanced computational methods for studying adsorption in porous media and to the direct modeling of adsorption using highly ordered surface-functionalized OMMs as model a...

Gas adsorption characterization of ordered organic-inorganic nanocomposite materials

https://web.iitd.ac.in/~arunku/files/CEL311_Y13/Adsorption%20Theory%20to%20practice_Dabrowski.pdf

Adsorption — from theory to practice

Pore size determination in modified micro- and mesoporous materials. Pitfalls and limitations in gas adsorption data analysis

We present an improved method, based upon density functional theory, for the determination of the pore size distribution (PSD) of porous sorbents. The adsorption isotherms predicted by nonlocal mean field theory for individual slit pores are correlated as a function of pressure and pore width. The PSD is then calculated by fitting this correlation to the experimental adsorption isotherm of the sorbent. We apply the analysis method to adsorption data for nitrogen on several porous carbons. In this application, the porous network is modeled as a continuous size distribution of noninteracting slit-shaped graphitic pores. The PSDs obtained by using the Kelvin equation and using the local and nonlocal versions of the mean field density functional theory are compared and evaluated. The results demonstrate that nonlocal theory provides a more accurate interpretation of the PSD than previous methods have achieved, particularly when the analysis is applied to highly microporous sorbents.

/pdf/pore-size-distribution-analysis-of-microporous-carbons-a-4fxx8jjk32.pdf

Pore size distribution analysis of microporous carbons: a density functional theory approach

We present model isotherms predicted by nonlocal density functional theory for adsorption of simple fluids in carbon slit pores. The effects of pore size, temperature, and solid-fluid potential interaction strength are examined. Our results are summarized into a classification scheme based upon regimes of continuous pore filling, capillary condensation, and 0 1 layering transitions. The descriptions we have devised depart from the IUPAC convention in that the filling behavior, rather than the physical width of the pore, is used as a guide to classification. Our results suggest that while the magnitude of the solid-fluid interactions dictates the pressure at which pore filling occurs, the type of filling depends primarily upon the ratio of pore width to adsorbate molecular diameter. The critical pore widths that denote the boundaries between various regimes of filling behavior are strongly dependent upon the temperature. To confirm the accuracy of the theoretical results, we compare adsorption isotherms and density profiles calculated from nonlocal theory and Gibbs ensemble simulation. The results from theory and simulation are found to be in good agreement. We conclude with a discussion of the problems associated with estimating solid-fluid potential parameters from experiment for use in theoretical computations. A comparison of nonlocal theory model isotherms and experimental nitrogen uptake measurements on nonporous carbon is presented.

/pdf/pore-size-heterogeneity-and-the-carbon-slit-pore-a-density-1emnrpbgyf.pdf

Pore size heterogeneity and the carbon slit pore: a density functional theory model

The receptor for advanced glycation end products (RAGE) may promote diabetic vascular and renal disease through the activation of intracellular signaling pathways that promote oxidative stress. Oxidative stress is a mediator of hyperglycemia-induced cell injury and a unifying theme for all mechanisms of diabetic complications, but there are few studies on the expression and potential contribution of RAGE in diabetic neuropathy. The current study demonstrates that dorsal root ganglia neurons express functional RAGE and respond to the RAGE ligand S100 with similar downstream signaling, oxidative stress, and cellular injury as other diabetic complication-prone tissues. RAGE-induced phosphatidylinositol-3 kinase activity is associated with formation of reactive oxygen species, caspase-3 activation, and nuclear DNA degradation. These events are prevented by treatment with the antioxidant α-lipoic acid. Our data indicate that therapies aimed at decreasing RAGE ligands, blocking RAGE signaling, or preventing oxi...

Receptor for advanced glycation end products activation injures primary sensory neurons via oxidative stress.

We present isotherms calculated from density functional theory for the adsorption of argon in model slit-shaped carbon pores at 77 K. The model isotherms are used to interpret experimental argon uptake measurements and to obtain the pore size distributions of several porous carbons. A similar set of density functional theory isotherms, previously reported for nitrogen adsorption on carbon slit pores at 77 K, are used to determine pore size distributions for the same set of carbons. The pore size distribution maxima, mean pore widths, and specific pore volumes measured using the two different probe gases are all found to agree to within approximately 8% on average. Some of the differences in the pore size distributions obtained from argon and nitrogen porosimetry may be attributable to quadrupolar interactions of the nitrogen molecules with functional groups on the carbon surface.

/pdf/pore-size-analysis-of-activated-carbons-from-argon-and-5alna5rnnp.pdf

Pore size analysis of activated carbons from argon and nitrogen porosimetry using density functional theory

Capture of carbon dioxide from fossil fuel power plants via adsorption and sequestration of carbon dioxide in unmineable coal seams are achievable near-term methods of reducing atmospheric emissions of this greenhouse gas. To investigate the influence of surface heterogeneity upon predicted adsorption behavior in activated carbons and coal, isotherms were generated via grand canonical Monte Carlo simulation for CO 2 adsorption in slit-shaped pores with underlying graphitic structure and several variations of chemical heterogeneity (oxygen and hydrogen content), pore width, and surface functional group orientation. Adsorption generally increased with increasing surface oxygen content, although exceptions to this trend were observed on structurally heterogeneous surfaces with holes or furrows that yield strongly adsorbing preferred binding sites. Among the heterogeneous pore structures investigated, those with coal-like surfaces adsorbed carbon dioxide more strongly than planar, homogeneous graphitic slit pores of comparable width. Electrostatic adsorbate-adsorbent interactions significantly influenced adsorption onto model surfaces.

/pdf/molecular-simulation-of-carbon-dioxide-adsorption-in-5e5nb2u47i.pdf

Christian M. Lastoskie

Papers

Pore size distribution analysis of microporous carbons: a density functional theory approach

Pore size heterogeneity and the carbon slit pore: a density functional theory model

Receptor for advanced glycation end products activation injures primary sensory neurons via oxidative stress.

Pore size analysis of activated carbons from argon and nitrogen porosimetry using density functional theory

Molecular simulation of carbon dioxide adsorption in chemically and structurally heterogeneous porous carbons