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

Responsive polymer materials can adapt to surrounding environments, regulate transport of ions and molecules, change wettability and adhesion of different species on external stimuli, or convert chemical and biochemical signals into optical, electrical, thermal and mechanical signals, and vice versa. These materials are playing an increasingly important part in a diverse range of applications, such as drug delivery, diagnostics, tissue engineering and 'smart' optical systems, as well as biosensors, microelectromechanical systems, coatings and textiles. We review recent advances and challenges in the developments towards applications of stimuli-responsive polymeric materials that are self-assembled from nanostructured building blocks. We also provide a critical outline of emerging developments.

Emerging applications of stimuli-responsive polymer materials

Stimuli-responsive polymersomes for programmed drug delivery.

Emerging Applications of Polymersomes in Delivery: from Molecular Dynamics to Shrinkage of Tumors.

A DPD model of PEO-based block copolymer vesicles in water is developed by introducing a new density based coarse graining and by using experimental data for interfacial tension. Simulated as a membrane patch, the DPD model is in excellent agreement with experimental data for both the area expansion modulus and the scaling of hydrophobic core thickness with molecular weight. Rupture simulations of polymer vesicles, or “polymersomes”, are presented to illustrate the system sizes feasible with DPD. The results should provide guidance for theoretical derivations of scaling laws and also illustrate how spherical polymer vesicles might be studied in simulation.

/pdf/dissipative-particle-dynamics-simulations-of-polymersomes-3ia5ullxgi.pdf

Dissipative particle dynamics simulations of polymersomes.

https://www.utdallas.edu/~son051000/my_publications/perturb_biophysj2005.pdf

Lipid Bilayer Perturbations around a Transmembrane Nanotube: A Coarse Grain Molecular Dynamics Study

https://www.seas.upenn.edu/%7Edischer/pdfs/AFM+SpectrinLinker_SMD.pdf

Unfolding a linker between helical repeats.

Much work has been done in the past decade to quantify the phenomenon of allosteric communication in proteins. Every new study unveils an extra piece of the puzzle in our search for an understanding of allostery that allows us to make predictions on the response of a protein to medically relevant stimuli such as pathological mutations or drug binding. This review summarizes recent advances in the analysis of mechanisms of allosteric communication in proteins, and combines this new knowledge to offer a perspective of allostery which is consistent with chemical views of molecular processes. First, we review recent work, particularly computational, on the characterization of signal propagation and conformational changes in allosteric proteins. We then compare different models of allostery, and discuss the significance of the concept of an allosteric pathway. We argue that allostery can be rationalized in terms of pathways of residues that efficiently transmit energy between different binding sites. We then p...

Vanessa Ortiz

Papers

Emerging Applications of Polymersomes in Delivery: from Molecular Dynamics to Shrinkage of Tumors.

Dissipative particle dynamics simulations of polymersomes.

Lipid Bilayer Perturbations around a Transmembrane Nanotube: A Coarse Grain Molecular Dynamics Study

Unfolding a linker between helical repeats.

A Chemical Perspective on Allostery.