There is, I think, something ethereal about i —the square root of minus one. I remember first hearing about it at school. It seemed an odd beast at that time—an intruder hovering on the edge of reality.

Usually familiarity dulls this sense of the bizarre, but in the case of i it was the reverse: over the years the sense of its surreal nature intensified. It seemed that it was impossible to write mathematics that described the real world in …

I and i

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

http://kth.diva-portal.org/smash/get/diva2:1303357/FULLTEXT01

GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers

[신간의 별자리x] 우리/미술, 그리고 ‘슬픔의 박물관’

PbTe and PbSe are among the most promising thermoelectric materials used in the mid-temperature (400–900 K) power generation range. In these materials the efficiency increase in thermoelectric performance is critically related to the lowering of lattice thermal conductivity (κL), without compromising the electronic power factor. By means of state-of-the-art equilibrium molecular dynamics (EMD), we investigate heat transport in several nanostructured PbTe/PbSe models as a function of material morphology. Layered composites show a reduction of the average κL of about 35 % with respect to the bulk. The insertion of PbSe nanoparticles into a PbTe matrix, or viceversa PbTe into PbSe reduces κL by up to 45 % while in more anisotropic nanocomposites the reduction exceeds PbSe/PbTe alloys. Layered composites show the lowest lattice thermal conductivity in the direction of layer stacking, for which an optimal thickness is identified. Along this line we provide a full account of the impact of alloying and (sub)nanostructuring on heat transport for this important class of materials. Particularly anisotropic nano-dot morphologies and layered (sub)nanocomposites emerge as a paradigm for outstanding thermoelectric materials. 

/pdf/pbte-pbse-thermoelectric-nanocomposites-the-impact-of-length-1ejh5anx.pdf

PbTe/PbSe Thermoelectric Nanocomposites: The Impact of Length Modulations on Lowering Thermal Conductivity

/pdf/ab-initio-investigation-of-the-melting-line-of-molecular-2113c8qvhw.pdf

Ab initio investigation of the melting line of molecular nitrogen at high pressure

We characterise the structural properties of the quasi-liquid layer (QLL) at two low-index ice surfaces in the presence of sodium chloride (Na+/Cl-) ions by molecular dynamics simulations. We find that the presence of a high surface density of Na+/Cl- pairs changes the surface melting behaviour from step-wise to gradual melting. The ions lead to an overall increase of the thickness and the disorder of the QLL, and to a low-temperature roughening transition of the air-ice interface. The local molecular structure of the QLL is similar to that of liquid water, and the differences between the basal and primary prismatic surface are attenuated by the presence of Na+/Cl- pairs. These changes modify the crystal growth rates of different facets and the solvation environment at the surface of sea-water ice with a potential impact on light scattering and environmental chemical reactions.

Effect of sodium chloride adsorption on the surface premelting of ice.

We have characterized the frictional properties of nanostructured (ns) carbon films grown by Supersonic Cluster Beam Deposition (SCBD) via an Atomic Force-Friction Force Microscope (AFM-FFM). The experimental data are discussed on the basis of a modified Amonton's law for friction, stating a linear dependence of friction on load plus an adhesive offset accounting for a finite friction force in the limit of null total applied load. Molecular Dynamics simulations of the interaction of the AFM tip with the nanostructured carbon confirm the validity of the friction model used for this system. Experimental results show that the friction coefficient is not influenced by the nanostructure of the films nor by the relative humidity. On the other hand the adhesion coefficient depends on these parameters.

https://arxiv.org/pdf/cond-mat/0208167.pdf

Nanofriction behavior of cluster-assembled carbon films

http://absimage.aps.org/image/MAR08/MWS_MAR08-2007-000339.pdf

Davide Donadio

Papers

PbTe/PbSe Thermoelectric Nanocomposites: The Impact of Length Modulations on Lowering Thermal Conductivity

Ab initio investigation of the melting line of molecular nitrogen at high pressure

Effect of sodium chloride adsorption on the surface premelting of ice.

Nanofriction behavior of cluster-assembled carbon films

The effect of temperature and anisotropic pressure on the phase transitions in $\alpha$-cristobalite