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

https://www.seas.upenn.edu/%7Edischer/pdfs/Cell_on_Gel-CELLpaper.pdf

Matrix elasticity directs stem cell lineage specification.

/pdf/self-assembled-monolayers-of-thiolates-on-metals-as-a-form-1neb0hj3k4.pdf

Self-assembled monolayers of thiolates on metals as a form of nanotechnology.

Normal tissue cells are generally not viable when suspended in a fluid and are therefore said to be anchorage dependent. Such cells must adhere to a solid, but a solid can be as rigid as glass or softer than a baby's skin. The behavior of some cells on soft materials is characteristic of important phenotypes; for example, cell growth on soft agar gels is used to identify cancer cells. However, an understanding of how tissue cells-including fibroblasts, myocytes, neurons, and other cell types-sense matrix stiffness is just emerging with quantitative studies of cells adhering to gels (or to other cells) with which elasticity can be tuned to approximate that of tissues. Key roles in molecular pathways are played by adhesion complexes and the actinmyosin cytoskeleton, whose contractile forces are transmitted through transcellular structures. The feedback of local matrix stiffness on cell state likely has important implications for development, differentiation, disease, and regeneration.

/pdf/tissue-cells-feel-and-respond-to-the-stiffness-of-their-6dx0rumap6.pdf

Tissue Cells Feel and Respond to the Stiffness of Their Substrate

Increased Upper Airway Resistance Prolongs Mechanical Inspiratory Time Independent Of Changes In Respiratory Motor Output During Sleep In Patients With Obstructive Sleep Apnea

Correction of a recurrent error.

Mechanical impedance of activated human airway smooth from muscle cells from 0.05 to 0.2 Hz

Measurement of Surface Area to Volume Ratio with 129Xe Exchange

where: SIlung = signal from ROI of lung before the contrast agent SIlung + Fe = signal from ROI of lung after contrast agent SIblood = signal from control blood, without contrast agent SIblood + Fe = signal from control blood with contrast agent Vb is the mean volume occupied by the blood within a voxel Accurate Quantification of Fractional Blood Volume in Lung Tissue G. P. Topulos1, S. Patz2, J. P. Butler3, L. L. Tsai4, R. W. Mair4, M. S. Rosen4, R. L. Walsworth4 1 Department of Anaesthesia, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA 2 Department of Radiology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA 3 Harvard School of Public Health, Boston, MA, USA 4 Harvard-Smithsonian Center for Astrophysics, Cambridge, MA, USA

James P. Butler

Papers

Increased Upper Airway Resistance Prolongs Mechanical Inspiratory Time Independent Of Changes In Respiratory Motor Output During Sleep In Patients With Obstructive Sleep Apnea

Correction of a recurrent error.

Mechanical impedance of activated human airway smooth from muscle cells from 0.05 to 0.2 Hz

Measurement of Surface Area to Volume Ratio with 129Xe Exchange

Accurate Quantification of Fractional Blood Volume in Lung Tissue.