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

Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

Physical Review B

The concept of parity-time symmetric systems is rooted in non-Hermitian quantum mechanics where complex potentials obeying this symmetry could exhibit real spectra. The concept has applications in many fields of physics, e.g., in optics, metamaterials, acoustics, Bose-Einstein condensation, electronic circuitry, etc. The inclusion of nonlinearity has led to a number of new phenomena for which no counterparts exist in traditional dissipative systems. Several examples of nonlinear parity-time symmetric systems in different physical disciplines are presented and their implications discussed.

Nonlinear waves in PT -symmetric systems

Fundamentals of Molecular Evolution Dan Graur, Wen ... Bio 113/244 Fundamentals of Molecular Evolution Fundamentals of Molecular Evolution | Briefings in ... Fundamentals of Molecular Evolution by Dan Graur Fundamentals of Molecular Evolution: 9780878932665 ... Fundamentals of Molecular Evolution | Dan Graur, Wen ... (PDF) Fundamentals of molecular evolution Fundamentals Of Molecular Evolution Fundamentals of Molecular Evolution Dan Graur; Wen ... eBook [PDF] Fundamentals Of Molecular Evolution Download ... Fundamentals of molecular evolution Fundamentals Of Molecular Evolution FUNDAMENTALS OF MOLECULAR EVOLUTION Fundamentals of Molecular Evolution: Amazon.co.uk: Graur D ... Fundamentals of Molecular Evolution, 2nd Edition FUNDAMENTALS OF MOLECULAR EVOLUTION Fundamentals of molecular evolution : Li, Wen-Hsiung ... Molecular evolution Wikipedia

Fundamentals of molecular evolution

Next-generation-sequencing (NGS) has revolutionized the field of genome assembly because of its much higher data throughput and much lower cost compared with traditional Sanger sequencing. However, NGS poses new computational challenges to de novo genome assembly. Among the challenges, GC bias in NGS data is known to aggravate genome assembly. However, it is not clear to what extent GC bias affects genome assembly in general. In this work, we conduct a systematic analysis on the effects of GC bias on genome assembly. Our analyses reveal that GC bias only lowers assembly completeness when the degree of GC bias is above a threshold. At a strong GC bias, the assembly fragmentation due to GC bias can be explained by the low coverage of reads in the GC-poor or GC-rich regions of a genome. This effect is observed for all the assemblers under study. Increasing the total amount of NGS data thus rescues the assembly fragmentation because of GC bias. However, the amount of data needed for a full rescue depends on the distribution of GC contents. Both low and high coverage depths due to GC bias lower the accuracy of assembly. These pieces of information provide guidance toward a better de novo genome assembly in the presence of GC bias.

/pdf/effects-of-gc-bias-in-next-generation-sequencing-data-on-de-52egak3rp3.pdf

Effects of GC Bias in Next-Generation-Sequencing Data on De Novo Genome Assembly

Tetraena mongolica (Zygophyllaceae), an endangered endemic species in western Inner Mongolia, China. For endemic species with a limited geographical range and declining populations, historical patterns of demography and hierarchical genetic structure are important for determining population structure, and also provide information for developing effective and sustainable management plans. In this study, we assess genetic variation, population structure, and phylogeography of T. mongolica from eight populations. Furthermore, we evaluate the conservation and management units to provide the information for conservation. Sequence variation and spatial apportionment of the atp B-rbc L noncoding spacer region of the chloroplast DNA were used to reconstruct the phylogeography of T. mongolica. A total of 880 bp was sequenced from eight extant populations throughout the whole range of its distribution. At the cpDNA locus, high levels of genetic differentiation among populations and low levels of genetic variation within populations were detected, indicating that most seed dispersal was restricted within populations. Demographic fluctuations, which led to random losses of genetic polymorphisms from populations, due to frequent flooding of the Yellow River and human disturbance were indicated by the analysis of BEAST skyline plot. Nested clade analysis revealed that restricted gene flow with isolation by distance plus occasional long distance dispersal is the main evolutionary factor affecting the phylogeography and population structure of T. mongolica. For setting a conservation management plan, each population of T. mongolica should be recognized as a conservation unit.

/pdf/conservation-genetics-and-phylogeography-of-endangered-and-3bapxrzfea.pdf

Conservation genetics and phylogeography of endangered and endemic shrub Tetraena mongolica (Zygophyllaceae) in Inner Mongolia, China.

http://lab.es.ncku.edu.tw/hwangcc/t/paper/paper-pdf/090.pdf

Globally exponential stability of generalized Cohen–Grossberg neural networks with delays

This paper deals with the synchronization problem of a class of chaotic neural networks with or without delays. This class of chaotic neural networks covers several well-known neural networks, such as Hopfield neural networks, cellular neural networks, and bidirectional associative memory networks with or without delays. Using the drive-response concept, a control law is derived to achieve the state synchronization of two identical chaotic neural networks. Furthermore, based on the Lyapunov stability method and the Halanay inequality lemma, a delay independent sufficient exponential synchronization condition is derived. The synchronization condition is easy to verify and relies on the connection matrix in the driven networks and the suitable designed controller gain matrix in the response networks. Finally, some illustrative examples are given to demonstrate the effectiveness of the presented synchronization scheme.

Exponential synchronization of a class of chaotic neural networks

The $\ensuremath{\pi}$-electronic excitations are studied for the AA- and AB-stacked bilayer graphites within the linear self-consistent-field approach. They are strongly affected by the stacking sequence, the interlayer atomic interactions, the interlayer Coulomb interactions, and the magnitude of the transferred momentum. However, they hardly depend on the direction of the transferred momentum and the temperature. There are three low-frequency plasmon modes in the AA-stacked system but not the AB-stacked system. The AA- and AB-stacked plasmons exhibit the similar $\ensuremath{\pi}$ plasmons. The first low-frequency plasmon behaves as an acoustic plasmon, and the others belong to optical plasmons. The bilayer graphites quite differ from the monolayer graphite and the AB-stacked bulk graphite, such as the low-frequency plasmons and the small-momentum $\ensuremath{\pi}$ plasmons.

/pdf/coulomb-excitations-in-aa-and-ab-stacked-bilayer-graphites-41z0kncn7g.pdf

Chi-Chuan Hwang

Papers

Effects of GC Bias in Next-Generation-Sequencing Data on De Novo Genome Assembly

Conservation genetics and phylogeography of endangered and endemic shrub Tetraena mongolica (Zygophyllaceae) in Inner Mongolia, China.

Globally exponential stability of generalized Cohen–Grossberg neural networks with delays

Exponential synchronization of a class of chaotic neural networks

Coulomb excitations in AA- and AB-stacked bilayer graphites