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

The density-matrix renormalization group method (DMRG) has established itself over the last decade as the leading method for the simulation of the statics and dynamics of one-dimensional strongly correlated quantum lattice systems. In the further development of the method, the realization that DMRG operates on a highly interesting class of quantum states, so-called matrix product states (MPS), has allowed a much deeper understanding of the inner structure of the DMRG method, its further potential and its limitations. In this paper, I want to give a detailed exposition of current DMRG thinking in the MPS language in order to make the advisable implementation of the family of DMRG algorithms in exclusively MPS terms transparent. I then move on to discuss some directions of potentially fruitful further algorithmic development: while DMRG is a very mature method by now, I still see potential for further improvements, as exemplified by a number of recently introduced algorithms.

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The density-matrix renormalization group in the age of matrix product states

基礎講座 電気泳動(Electrophoresis)

We present an algorithm to study mixed-state dynamics in one-dimensional quantum lattice systems. The algorithm can be used, e.g., to construct thermal states or to simulate real time evolution given by a generic master equation. Its two main ingredients are (i) a superoperator renormalization scheme to efficiently describe the state of the system and (ii) the time evolving block decimation technique to efficiently update the state during a time evolution. The computational cost of a simulation increases significantly with the amount of correlations between subsystems, but it otherwise depends only linearly on the system size. We present simulations involving quantum spins and fermions in one spatial dimension.

/pdf/mixed-state-dynamics-in-one-dimensional-quantum-lattice-28u8e5cdc8.pdf

Mixed-state dynamics in one-dimensional quantum lattice systems: A time-dependent superoperator renormalization algorithm

With the continued improvement of sequencing technologies, the prospect of genome-based medicine is now at the forefront of scientific research. To realize this potential, however, a revolutionary sequencing method is needed for the cost-effective and rapid interrogation of individual genomes. This capability is likely to be provided by a physical approach to probing DNA at the single-nucleotide level. This is in sharp contrast to current techniques and instruments that probe (through chemical elongation, electrophoresis, and optical detection) length differences and terminating bases of strands of DNA. Several physical approaches to DNA detection have the potential to deliver fast and low-cost sequencing. Central to these approaches is the concept of nanochannels or nanopores, which allow for the spatial confinement of DNA molecules. In addition to their possible impact in medicine and biology, the methods offer ideal test beds to study open scientific issues and challenges in the relatively unexplored area at the interface between solids, liquids, and biomolecules at the nanometer length scale. This Colloquium emphasizes the physics behind these methods and ideas, critically describes their advantages and drawbacks, and discusses future research opportunities in the field.

/pdf/colloquium-physical-approaches-to-dna-sequencing-and-apsgzh060l.pdf

Colloquium: Physical approaches to DNA sequencing and detection

A rapid and low-cost method to sequence DNA would usher in a revolution in medicine. We propose and theoretically show the feasibility of a protocol for sequencing based on the distributions of transverse electrical currents of single-stranded DNA while it translocates through a nanopore. Our estimates, based on the statistics of these distributions, reveal that sequencing of an entire human genome could be done with very high accuracy in a matter of hours without parallelization, that is, orders of magnitude faster than present techniques. The practical implementation of our approach would represent a substantial advancement in our ability to study, predict, and cure diseases from the perspective of the genetic makeup of each individual.

/pdf/fast-dna-sequencing-via-transverse-electronic-transport-2wosh22qor.pdf

Fast DNA sequencing via transverse electronic transport.

We report theoretical studies of charge transport in single-stranded DNA in the direction perpendicular to the backbone axis. We find that, if the electrodes which sandwich the DNA have the appropriate spatial width, each nucleotide carries a unique signature due to the different electronic and chemical structure of the four bases. This signature is independent of the nearest-neighbor nucleotides. Furthermore, except for the nucleotides with guanine and cytosine bases, we find that the difference in conductance of the nucleotides is large for most orientations of the bases with respect to the electrodes. By exploiting these differences it may be possible to sequence single-stranded DNA by scanning its length with conducting probes.

Electronic signature of DNA nucleotides via transverse transport

Thermodynamic methods based on conductor-like screening models (COSMO) originated from the use of solvation thermodynamics and computational quantum mechanics. These methods rely on sigma profiles specific to each molecule. A sigma profile is the probability distribution of a molecular surface segment having a specific charge density. Two COSMO-based thermodynamic models are COSMO-RS (realistic solvation) developed by Klamt and his colleagues, and COSMO-SAC (segment activity coefficient) published by Lin and Sandler. Quantum mechanical calculations for generating the sigma profiles represent the most time-consuming and computationally expensive aspect of using COSMO-based methods. A growing number of scientists and engineers are interested in the COSMO-based thermodynamic models but are intimidated by the complexity of performing quantum mechanical calculations. This paper presents the first free, web-based sigma profile database of 1432 compounds. We describe the procedure for sigma profile generation, and we have validated our database by comparing COSMO-based predictions of activity coefficients, normal boiling point and solubility with experimental data and thermodynamic property database. We discuss improvements which include using supplemental geometry optimization software packages to provide good initial guesses for molecular conformations as a precursor to the COSMO calculation. Finally, this paper provides a FORTRAN program and a procedure to generate additional sigma profiles, as well as a FORTRAN program to generate binary phase-equilibrium predictions using the COSMO-SAC model. Our sigma profile database will facilitate predictions of thermodynamic properties and phase behaviors from COSMO-based thermodynamic models.

Michael Zwolak

Papers

Mixed-state dynamics in one-dimensional quantum lattice systems: A time-dependent superoperator renormalization algorithm

Colloquium: Physical approaches to DNA sequencing and detection

Fast DNA sequencing via transverse electronic transport.

Electronic signature of DNA nucleotides via transverse transport

Sigma-Profile Database for Using COSMO-Based Thermodynamic Methods