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

다중혈관 관상동맥 환자에서 y-문합을 이용하여 양쪽 내흉동맥만을 사용한 우회술의 조기 성적

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

Deposits of clastic carbonate-dominated (calciclastic) sedimentary slope systems in the rock record have been identified mostly as linearly-consistent carbonate apron deposits, even though most ancient clastic carbonate slope deposits fit the submarine fan systems better. Calciclastic submarine fans are consequently rarely described and are poorly understood. Subsequently, very little is known especially in mud-dominated calciclastic submarine fan systems. Presented in this study are a sedimentological core and petrographic characterisation of samples from eleven boreholes from the Lower Carboniferous of Bowland Basin (Northwest England) that reveals a >250 m thick calciturbidite complex deposited in a calciclastic submarine fan setting. Seven facies are recognised from core and thin section characterisation and are grouped into three carbonate turbidite sequences. They include: 1) Calciturbidites, comprising mostly of highto low-density, wavy-laminated bioclast-rich facies; 2) low-density densite mudstones which are characterised by planar laminated and unlaminated muddominated facies; and 3) Calcidebrites which are muddy or hyper-concentrated debrisflow deposits occurring as poorly-sorted, chaotic, mud-supported floatstones. These

Phd by thesis

Microfabricated integrated circuits revolutionized computation by vastly reducing the space, labor, and time required for calculations. Microfluidic systems hold similar promise for the large-scale automation of chemistry and biology, suggesting the possibility of numerous experiments performed rapidly and in parallel, while consuming little reagent. While it is too early to tell whether such a vision will be realized, significant progress has been achieved, and various applications of significant scientific and practical interest have been developed. Here a review of the physics of small volumes (nanoliters) of fluids is presented, as parametrized by a series of dimensionless numbers expressing the relative importance of various physical phenomena. Specifically, this review explores the Reynolds number Re, addressing inertial effects; the Peclet number Pe, which concerns convective and diffusive transport; the capillary number Ca expressing the importance of interfacial tension; the Deborah, Weissenberg, and elasticity numbers De, Wi, and El, describing elastic effects due to deformable microstructural elements like polymers; the Grashof and Rayleigh numbers Gr and Ra, describing density-driven flows; and the Knudsen number, describing the importance of noncontinuum molecular effects. Furthermore, the long-range nature of viscous flows and the small device dimensions inherent in microfluidics mean that the influence of boundaries is typically significant. A variety of strategies have been developed to manipulate fluids by exploiting boundary effects; among these are electrokinetic effects, acoustic streaming, and fluid-structure interactions. The goal is to describe the physics behind the rich variety of fluid phenomena occurring on the nanoliter scale using simple scaling arguments, with the hopes of developing an intuitive sense for this occasionally counterintuitive world.

/pdf/microfluidics-fluid-physics-at-the-nanoliter-scale-4bpahtd8qa.pdf

Microfluidics: Fluid physics at the nanoliter scale

It is well known that, at a macroscopic level, the boundary condition for a viscous fluid at a solid wall is one of ``no slip.'' The liquid velocity field vanishes at a fixed solid boundary. We consider the special case of a liquid that partially wets the solid (i.e., a drop of liquid, in equilibrium with its vapor on the solid substrate, has a finite contact angle). Using extensive molecular dynamics simulations, we show that when the contact angle is large enough, the boundary condition can drastically differ (at a microscopic level) from a no-slip condition. Slipping lengths exceeding 30 molecular diameters are obtained for a contact angle of 140\ifmmode^\circ\else\textdegree\fi{}, characteristic of mercury on glass. This finding may have important implications for the transport properties in nanoporous media under such ``nonwetting'' conditions.

Large Slip Effect at a Nonwetting Fluid-Solid Interface

With the important development of microfluidic systems, miniaturization of flow devices has become a real challenge. Microchannels, however, are characterized by a large surface-to-volume ratio, so that surface properties strongly affect flow resistance in submicrometre devices. We present here results showing that the concerted effect of wetting properties and surface roughness may considerably reduce friction of the fluid past the boundaries. The slippage of the fluid at the channel boundaries is shown to be greatly increased by using surfaces that are patterned on the nanometre scale. This effect occurs in the regime where the surface pattern is partially dewetted, in the spirit of the 'superhydrophobic' effects that have been discovered at macroscopic scales1. Our results show for the first time that, in contrast to common belief, surface friction may be reduced by surface roughness. They also open the possibility of a controlled realization of the 'nanobubbles'2 that have long been suspected to play a role in interfacial slippage3,4.

https://hal.archives-ouvertes.fr/hal-00000275/document

Low-friction flows of liquid at nanopatterned interfaces.

The development of microfluidic devices has recently revived the interest in “old” problems associated with transport at, or across, interfaces. As the characteristic sizes are decreased, the use of pressure gradients to transport fluids becomes problematic, and new, interface driven, methods must be considered. This has lead to new investigations of flow near interfaces, and to the conception of interfaces engineered at various scales to reduce flow friction. In this review, we discuss the present theoretical understanding of flow past solid interfaces at different length scales. We also briefly discuss the corresponding phenomenon of heat transport, and the influence of surface slip on interface driven (e.g. electro-osmotic) flows.

http://ilm-perso.univ-lyon1.fr/~lbocquet/soft-matter-2007.pdf

Flow boundary conditions from nano- to micro-scales

1. An introduction to liquid matter Part I. Thermodynamics, Structure and Fluctuations: 2. A reminder of thermodynamics 3. Equilibrium fluctuations Part II. Phase Transitions: 4. Mean field approaches 5. Critical fluctuations and scaling Part III. Interfaces and Inhomogeneous Fluids: 6. Macroscopic description of interfaces 7. The density functional approach 8. Curvature and fluctuations Part IV. Dynamics: 9. Phenomenological description of transport processes 10. Brownian motion, diffusion and the Langevin equation 11. Response and correlation functions 12. Slow relaxations.

Basic Concepts for Simple and Complex Liquids: Frontmatter

The development of microfluidic devices has recently revived the interest in "old" problems associated with transport at, or across, interfaces. As the characteristic sizes are decreased, the use of pressure gradients to transport fluids becomes problematic, and new, interface driven, methods must be considered. This has lead to new investigations of flow near interfaces, and to the conception of interfaces engineered at various scales to reduce flow friction. In this review, we discuss the present theoretical understanding of flow past solid interfaces at different length scales. We also briefly discuss the corresponding phenomenon of heat transport, and the influence of surface slip on interface driven (e.g. electro-osmotic) flows.

Jean-Louis Barrat

Papers

Large Slip Effect at a Nonwetting Fluid-Solid Interface

Low-friction flows of liquid at nanopatterned interfaces.

Flow boundary conditions from nano- to micro-scales

Basic Concepts for Simple and Complex Liquids: Frontmatter

Flow boundary conditions from nano- to micro-scales