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

[신간의 별자리x] 우리/미술, 그리고 ‘슬픔의 박물관’

Li-ion battery materials: present and future

During charging or discharging of a lithium-ion battery, lithium is extracted from one electrode and inserted into the other. This extraction-insertion reaction causes the electrodes to deform. An electrode is often composed of small active particles in a matrix. If the battery is charged at a rate faster than lithium can homogenize in an active particle by diffusion, the inhomogeneous distribution of lithium results in stresses that may cause the particle to fracture. The distributions of lithium and stress in a LiCoO2 particle are calculated. The energy release rates are then calculated for the particle containing preexisting cracks. These calculations predict the critical rate of charging and size of the particle, below which fracture is averted.

/pdf/fracture-of-electrodes-in-lithium-ion-batteries-caused-by-59jrbykgzz.pdf

Fracture of electrodes in lithium-ion batteries caused by fast charging

Silicon can host a large amount of lithium, making it a promising electrode for high-capacity lithium-ion batteries. Recent experiments indicate that silicon experiences large plastic deformation upon Li absorption, which can significantly decrease the stresses induced by lithiation and thus mitigate fracture failure of electrodes. These issues become especially relevant in nanostructured electrodes with confined geometries. On the basis of first-principles calculations, we present a study of the microscopic deformation mechanism of lithiated silicon at relatively low Li concentration, which captures the onset of plasticity induced by lithiation. We find that lithium insertion leads to breaking of SiSi bonds and formation of weaker bonds between neighboring Si and Li atoms, which results in a decrease in Young's modulus, a reduction in strength, and a brittle-to-ductile transition with increasing Li concentration. The microscopic mechanism of large plastic deformation is attributed to continuous lithium-assisted breaking and re-forming of SiSi bonds and the creation of nanopores.

/pdf/lithium-assisted-plastic-deformation-of-silicon-electrodes-462j93wm0j.pdf

Lithium-Assisted Plastic Deformation of Silicon Electrodes in Lithium-Ion Batteries: A First-Principles Theoretical Study

Evidence has accumulated recently that a high-capacity electrode of a lithium-ion battery may not recover its initial shape after a cycle of charge and discharge. Such a plastic behavior is studied here by formulating a theory that couples large amounts of lithiation and deformation. The homogeneous lithiation and deformation in a small element of an electrode under stresses is analyzed within nonequilibrium thermodynamics, permitting a discussion of equilibrium with respect to some processes, but not others. The element is assumed to undergo plastic deformation when the stresses reach a yield condition. The theory is combined with a diffusion equation to analyze a spherical particle of an electrode being charged and discharged at a constant rate. When the charging rate is low, the distribution of lithium in the particle is nearly homogeneous, the stress in the particle is low, and no plastic deformation occurs. When the charging rate is high, the distribution of lithium in the particle is inhomogeneous, and the stress in the particle is high, possibly leading to fracture and cavitation.

/pdf/large-plastic-deformation-in-high-capacity-lithium-ion-jicd3fkaus.pdf

Large Plastic Deformation in High-Capacity Lithium-Ion Batteries Caused by Charge and Discharge

In an electrochemical cell, crystalline silicon and lithium react at room temperature, forming an amorphous phase of lithiated silicon. The reaction front—the phase boundary between the crystalline silicon and the lithiated silicon—is atomically sharp. Evidence has accumulated recently that the velocity of the reaction front is limited by the rate of the reaction at the front, rather than by the diffusion of lithium through the amorphous phase. This paper presents a model of concurrent reaction and plasticity. We identify the driving force for the movement of the reaction front, and accommodate the reaction-induced volumetric expansion by plastic deformation of the lithiated silicon. The model is illustrated by an analytical solution of the co-evolving reaction and plasticity in a spherical particle. We derive the conditions under which the lithiation-induced stress stalls the reaction. We show that fracture is averted if the particle is small and the yield strength of lithiated silicon is low. Furthermore, we show that the model accounts for recently observed lithiated silicon of anisotropic morphologies.

/pdf/concurrent-reaction-and-plasticity-during-initial-lithiation-3a7l75cxp5.pdf

Concurrent Reaction and Plasticity during Initial Lithiation of Crystalline Silicon in Lithium-Ion Batteries

Electrochemical experiments were conducted on {100}, {110}, and {111} silicon wafers to characterize the kinetics of the initial lithiation of crystalline Si electrodes. Under constant current conditions, we observed constant cell potentials for all orientations, indicating the existence of a phase boundary that separates crystalline silicon from the amorphous lithiated phase. For a given potential, the velocity of this boundary was found to be faster for {110} silicon than for the other two orientations. We show that our measurements of varying phase boundary velocities can accurately account for anisotropic morphologies and fracture developed in crystalline silicon nanopillars. We also present a kinetic model by considering the redox reaction at the electrolyte/lithiated silicon interface, diffusion of lithium through the lithiated phase, and the chemical reaction at the lithiated silicon/crystalline silicon interface. From this model, we quantify the rates of the reactions at the interfaces and estimate a lower bound on the diffusivity through the lithiated silicon phase.

/pdf/kinetics-of-initial-lithiation-of-crystalline-silicon-4qced15ohc.pdf

Kejie Zhao

Papers

Fracture of electrodes in lithium-ion batteries caused by fast charging

Lithium-Assisted Plastic Deformation of Silicon Electrodes in Lithium-Ion Batteries: A First-Principles Theoretical Study

Large Plastic Deformation in High-Capacity Lithium-Ion Batteries Caused by Charge and Discharge

Concurrent Reaction and Plasticity during Initial Lithiation of Crystalline Silicon in Lithium-Ion Batteries

Kinetics of initial lithiation of crystalline silicon electrodes of lithium-ion batteries.