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

Spintronics, or spin electronics, involves the study of active control and manipulation of spin degrees of freedom in solid-state systems. This article reviews the current status of this subject, including both recent advances and well-established results. The primary focus is on the basic physical principles underlying the generation of carrier spin polarization, spin dynamics, and spin-polarized transport in semiconductors and metals. Spin transport differs from charge transport in that spin is a nonconserved quantity in solids due to spin-orbit and hyperfine coupling. The authors discuss in detail spin decoherence mechanisms in metals and semiconductors. Various theories of spin injection and spin-polarized transport are applied to hybrid structures relevant to spin-based devices and fundamental studies of materials properties. Experimental work is reviewed with the emphasis on projected applications, in which external electric and magnetic fields and illumination by light will be used to control spin and charge dynamics to create new functionalities not feasible or ineffective with conventional electronics.

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Spintronics: Fundamentals and applications

I have developed "tennis elbow" from lugging this book around the past four weeks, but it is worth the pain, the effort, and the aspirin. It is also worth the (relatively speaking) bargain price. Including appendixes, this book contains 894 pages of text. The entire panorama of the neural sciences is surveyed and examined, and it is comprehensive in its scope, from genomes to social behaviors. The editors explicitly state that the book is designed as "an introductory text for students of biology, behavior, and medicine," but it is hard to imagine any audience, interested in any fragment of neuroscience at any level of sophistication, that would not enjoy this book. The editors have done a masterful job of weaving together the biologic, the behavioral, and the clinical sciences into a single tapestry in which everyone from the molecular biologist to the practicing psychiatrist can find and appreciate his or

Principles of Neural Science

Demand has never been greater for revolutionary technologies that deliver fast, inexpensive and accurate genome information. This challenge has catalysed the development of next-generation sequencing (NGS) technologies. The inexpensive production of large volumes of sequence data is the primary advantage over conventional methods. Here, I present a technical review of template preparation, sequencing and imaging, genome alignment and assembly approaches, and recent advances in current and near-term commercially available NGS instruments. I also outline the broad range of applications for NGS technologies, in addition to providing guidelines for platform selection to address biological questions of interest.

/pdf/sequencing-technologies-the-next-generation-599pyrfdla.pdf

Sequencing technologies-the next generation

A memristor is a two-terminal electronic device whose conductance can be precisely modulated by charge or flux through it. Here we experimentally demonstrate a nanoscale silicon-based memristor device and show that a hybrid system composed of complementary metal−oxide semiconductor neurons and memristor synapses can support important synaptic functions such as spike timing dependent plasticity. Using memristors as synapses in neuromorphic circuits can potentially offer both high connectivity and high density required for efficient computing.

/pdf/nanoscale-memristor-device-as-synapse-in-neuromorphic-1sl2njhdyu.pdf

Nanoscale Memristor Device as Synapse in Neuromorphic Systems

A pulsed technique for electrons in 2D systems, in some ways analogous to spin echo in nuclear magnetic resonance, is discussed. We show that a sequence of optical below-band gap pulses can be used to suppress the electron spin relaxation due to the D'yakonov-Perel' spin relaxation mechanism. The spin relaxation time is calculated for several pulse sequences within a Monte Carlo simulation scheme. The maximum of spin relaxation time as a function of magnitude/width of the pulses corresponds to $\pi$-pulse. It is important that even relatively distant pulses efficiently suppress spin relaxation.

/pdf/optically-induced-suppression-of-spin-relaxation-in-two-3z5kwsp3mq.pdf

Optically Induced Suppression of Spin Relaxation in Two-Dimensional Electron Systems with Rashba Interaction

Recently, it was shown that the amoebalike cell Physarum polycephalum when exposed to a pattern of periodic environmental changes learns and adapts its behavior in anticipation of the next stimulus to come. Here we show that such behavior can be mapped into the response of a simple electronic circuit consisting of a LC contour and a memory-resistor (a memristor) to a train of voltage pulses that mimic environment changes. We also identify a possible biological origin of the memristive behavior in the cell. These biological memory features are likely to occur in other unicellular as well as multicellular organisms, albeit in different forms. Therefore, the above memristive circuit model, which has learning properties, is useful to better understand the origins of primitive intelligence.

/pdf/memristive-model-of-amoeba-learning-1emo5b0lki.pdf

Memristive model of amoeba learning

We suggest a novel methodology to obtain a digital representation of analog signals and to perform its back-conversion using memristive devices. In the proposed converters, the same memristive systems are used for two purposes: as elements performing conversion and elements storing the code. This approach to conversion is particularly relevant for interfacing analog signals with memristive digital logic/computing circuits.

Analog-to-Digital and Digital-to-Analog Conversion with Memristive Devices

The article focuses on the development of electronic components in memcomputing, which is the use of computers containing superfast memory processing hardware. Topics include the development of processors that store computer memory, technological advancement in electronics, and the development of 'mem' components such as meminductors and memcapacitors.

just add memory.

Photocurrent generation is studied in a system composed of a quantum wire with side-coupled quantum rings. The current generation results from the interplay of the particular geometry of the system and the use of circularly polarized radiation. We study the energy-momentum conservation for optical transitions involving electrons moving forwards and backwards in the wire. Due to the lack of time-reversal symmetry in the radiation, the optical transitions depend on the direction of motion of the electrons, leading to a current at zero bias voltage. The photocurrent increases with the number of rings within a wide range of physical parameters. A weak non-linear dependence of the current in the number of rings, related to quantum interference effects, is also predicted. This geometry suggests a scalable method for the generation of sizeable photocurrents based on nanoscale components.

/pdf/radiation-induced-current-in-quantum-wires-with-side-coupled-292uf4kwpr.pdf

Yuriy V. Pershin

Papers

Optically Induced Suppression of Spin Relaxation in Two-Dimensional Electron Systems with Rashba Interaction

Memristive model of amoeba learning

Analog-to-Digital and Digital-to-Analog Conversion with Memristive Devices

just add memory.

Radiation-Induced Current in Quantum Wires with Side-Coupled Nanorings