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

Electrospinning: a fascinating fiber fabrication technique.

Collagen is the most abundant protein in animals. This fibrous, structural protein comprises a right-handed bundle of three parallel, left-handed polyproline II-type helices. Much progress has been made in elucidating the structure of collagen triple helices and the physicochemical basis for their stability. New evidence demonstrates that stereoelectronic effects and preorganization play a key role in that stability. The fibrillar structure of type I collagen—the prototypical collagen fibril—has been revealed in detail. Artificial collagen fibrils that display some properties of natural collagen fibrils are now accessible using chemical synthesis and self-assembly. A rapidly emerging understanding of the mechanical and structural properties of native collagen fibrils will guide further development of artificial collagenous materials for biomedicine and nanotechnology.

/pdf/collagen-structure-and-stability-4a8qztbno6.pdf

Collagen Structure and Stability

Nature’s hierarchical materials

https://www.cell.com/biophysj/pdf/S0006-3495(07)71383-8.pdf

Mechanical Properties of Collagen Fibrils

Biomineralization is a dynamic, complex, lifelong process by which living organisms control precipitations of inorganic nanocrystals within organic matrices to form unique hybrid biological tissues, for example, enamel, dentin, cementum, and bone. Understanding the process of mineral deposition is important for the development of treatments for mineralization-related diseases and also for the innovation and development of scaffolds. This review provides a thorough overview of the up-to-date information on the theories describing the possible mechanisms and the factors implicated as agonists and antagonists of mineralization. Then, the role of calcium and phosphate ions in the maintenance of teeth and bone health is described. Throughout the life, teeth and bone are at risk of demineralization, with particular emphasis on teeth, due to their anatomical arrangement and location. Teeth are exposed to food, drink, and the microbiota of the mouth; therefore, they have developed a high resistance to localized demineralization that is unmatched by bone. The mechanisms by which demineralization-remineralization process occurs in both teeth and bone and the new therapies/technologies that reverse demineralization or boost remineralization are also scrupulously discussed. Technologies discussed include composites with nano- and micron-sized inorganic minerals that can mimic mechanical properties of the tooth and bone in addition to promoting more natural repair of surrounding tissues. Turning these new technologies to products and practices would improve health care worldwide.

/pdf/demineralization-remineralization-dynamics-in-teeth-and-bone-4qz7fpfvch.pdf

Demineralization–remineralization dynamics in teeth and bone

Collagen--emerging collagen based therapies hit the patient.

https://www.cell.com/biophysj/pdf/S0006-3495(07)70805-6.pdf

Collagen Fibrils: Nanoscale Ropes

High-speed atomic force microscopy (AFM) is important for following processes that occur on sub-second timescales for studies both in biology and materials science, and also for the ability to examine large areas of a specimen at high resolution in a practical length of time. Further developments of the previously reported high-speed contact-mode AFM are described. Two instruments are presented: (i) a high-speed flexure stage arrangement capable of imaging at a video rate of 30 fps, and (ii) an ultra-high speed instrument using a combined tuning fork and flexure-stage scanning system capable of ultra-high-speed imaging in excess of 1000 fps. Results of imaging collagen fibres under ambient conditions at rates of up to 1300 frames s−1 are presented. Despite tip–specimen relative velocities of up to 200 mm s−1, no significant damage to the collagen specimen was observed even after tens of thousands of frames were acquired in the same area of the specimen.

/pdf/breaking-the-speed-limit-with-atomic-force-microscopy-5dvasaxdrm.pdf

Laurent Bozec

Papers

Mechanical Properties of Collagen Fibrils

Demineralization–remineralization dynamics in teeth and bone

Collagen--emerging collagen based therapies hit the patient.

Collagen Fibrils: Nanoscale Ropes

Breaking the speed limit with atomic force microscopy