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’

We have characterized the frictional properties of nanostructured carbon films grown by supersonic cluster beam deposition 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.

Nanofriction behavior of cluster-assembled carbon films.

Thermoelectric devices convert temperature gradients into electrical power and vice versa, thus enabling energy scavenging from waste heat, sensing and cooling. Yet, many of these attractive applications are hindered by the limited efficiency of thermoelectric materials, especially in the low temperature regime. This review provides a summary of the recent advances in the design of new efficient silicon--based thermoelectric materials through nanostructuring, alloying and chemical optimization, emphasizing the contribution from theory and atomistic modeling.

Advances in the optimization of silicon-based thermoelectrics: a theory perspective

Intercalation offers a promising way to alter the physical properties of two-dimensional (2D) layered materials. Here, we investigate the electronic and vibrational properties of 2D layered MoSe2 intercalated with atomic manganese at ambient and high pressure up to 7 GPa by Raman scattering and electronic structure calculations. The behavior of optical phonons is studied experimentally with a diamond anvil cell and computationally through density functional theory calculations. Experiment and theory show excellent agreement in optical phonon behavior. The previously Raman inactive A2u mode is activated and enhanced with intercalation and pressure, and a new Raman mode appears upon decompression, indicating a possible onset of a localized structural transition, involving the bonding or trapping of the intercalant in 2D layered materials. Density functional theory calculations reveal a shift of the Fermi level into the conduction band and spin polarization in MnxMoSe2 that increases at low Mn concentrations and low pressure. Our results suggest that intercalation and pressurization of van der Waals materials may allow one to obtain dilute magnetic semiconductors with controllable properties, providing a viable route for the development of new materials for spintronic applications.

/pdf/mn-intercalated-mose2-under-pressure-electronic-structure-4fd2hjh3ws.pdf

Mn-intercalated MoSe2 under pressure: Electronic structure and vibrational characterization of a dilute magnetic semiconductor.

/pdf/stability-of-hydrocarbons-at-deep-earth-pressures-and-2a2kjubf12.pdf

Stability of hydrocarbons at deep Earth pressures and temperatures

https://escholarship.org/content/qt8dz5k8cj/qt8dz5k8cj.pdf?t=o17i0b

Davide Donadio

Papers

Nanofriction behavior of cluster-assembled carbon films.

Advances in the optimization of silicon-based thermoelectrics: a theory perspective

Mn-intercalated MoSe2 under pressure: Electronic structure and vibrational characterization of a dilute magnetic semiconductor.

Stability of hydrocarbons at deep Earth pressures and temperatures

Adsorption of polyiodobenzene molecules on the Pt(111) surface using van der Waals density functional theory