可扩展多输入多输出信道高效模拟器研制

针对现有信道模拟器通道规模受限、扩展性差等缺陷,设计实现了一种可扩展的多输入多输出(multiply-input multiply-output, MIMO)信道高效模拟器。 该模拟器采用改进的坐标旋转数字计算(coordinate rotation digital computer, CORDIC)算法,只 需较少硬件资源便可实现大规模多支路的随机信道衰落精确模拟。 基于 MIMO 信道离散化模型提出了一种可扩展的硬件模拟 架构,并结合现场可编程门阵列(field-programmable gate array, FPGA)的并行处理优势,进行硬件实现及实测验证。 针对 3GPP 标准扩展车载 A 信道模型(extended vehicular A model, EVA)静态场景和时变场景的实测结果表明,所研制的 MIMO 信道模拟 器输出时延功率谱和多普勒功率谱等统计特性均与理论值吻合,可用于无线通信设备的方案验证、算法优化和性能分析。     

Self-consistent ion transport simulation in carbon nanotube channels

We propose a method to self-consistently deal with polarisation effects in Monte Carlo particle simulations of charge transport. The systems of interest were membrane structures with a narrow (4–8 Å) carbon nanotube (CNT) channel in an aqueous environment. Due to computational limitations for Molecular Dynamics (MD) simulations, we extended the Transport Monte Carlo known from semiconductor simulations to ionic transport in water as a background medium. This method has been used successfully to compute transport rates of ions in biological channels but polarization effects on protein walls cannot be easily included self-consistently, due to the complexity of the structure. Since CNTs have a regular structure, it is practical to employ a self-consistent scheme that accounts for the charge redistribution on the channel wall when an external bias is applied or when the electrical field of a passing ion is screened out. Previous work has shown that this is necessary and the computationally efficient tight-binding (TB) approach developed there [1] is combined with transport Monte Carlo simulations in this work.     

面向新一代能量管理系统的集群计算中间件

介绍了一种面向新一代能量管理系统（EMS）的集群计算环境的中间件（WLGrid）。该中间件被设计成一个容器,可以为不同功能的插件提供网络通信、资源定位、失败处理等高性能服务。由于采用了组件化开发策略,该中间件具有解耦的可插入式软件结构。通过屏蔽Socket通信、多任务处理等实现细节,使用该中间件的开发者可专注于业务逻辑的实现,从而降低了新一代EMS中分布式应用的开发难度。现场运行结果表明,基于WLGrid开发的预警系统,具有良好的可维护性和可扩展性,且计算速度能够满足实用要求。     

BioMOCA: A Transport Monte Carlo Model for Ion Channels

Ion channels are proteins that form natural water-filled nanotubes in the membranes of all biological cells. They regulate ion transport in and out of the cell thereby maintaining the correct internal ion composition that is crucial to cell survival and function. Every channel carries a strong permanent charge, which plays a critical role in the conduction mechanisms of the open channel. Many channels can selectively transmit or block a particular ion species and most have switching properties similar to electronic devices. These device-like features are appealing to the electronics community for their possible application in the design of novel bio-devices. Here we describe a three-dimensional (3-D) transport Monte Carlo ion channel simulation, BioMOCA, based on the approach taken in semiconductor device simulations. Since ion diameters are comparable with channel dimensions a physical model of the volume of the ions must also be included.     

Simulation of charge transport in ion channels and nanopores with anisotropic permittivity

Ion channels are part of nature’s solution for regulating biological environments. Every ion channel consists of a chain of amino acids carrying a strong and sharply varying permanent charge, folded in such a way that it creates a nanoscopic aqueous pore spanning the otherwise mostly impermeable membranes of biological cells. These naturally occurring proteins are particularly interesting to device engineers seeking to understand how such nanoscale systems realize device-like functions. Availability of high-resolution structural information from X-ray crystallography, as well as large-scale computational resources, makes it possible to conduct realistic ion channel simulations. In general, a hierarchy of simulation methodologies is needed to study different aspects of a biological system like ion channels. Biology Monte Carlo (BioMOCA), a three-dimensional coarse-grained particle ion channel simulator, offers a powerful and general approach to study ion channel permeation. BioMOCA is based on the Boltzmann Transport Monte Carlo (BTMC) and Particle-Particle-Particle-Mesh (P³M) methodologies developed at the University of Illinois at Urbana-Champaign. In this paper we briefly discuss the various approaches to simulating ion flow in channel systems that are currently being pursued by the biophysics and engineering communities, and present the effect of having anisotropic dielectric constants on ion flow through a number of nanopores with different effective diameters.     

An Application of the Recombination and Generation Theory by Shockley, Read and Hall to Biological Ion Channels

We have applied the Shockley-Read-Hall (SRH) model for the generation and recombination of charged carriers to biological ion channels. We show how to include this important effect in the traditional PNP model. The idea is to use the software of computational electronics that has been developed to solve Shockley’s equations. In particular we have used the simulator PROPHET to simulate biological ion channels and to include particle like properties and dynamics such as the capture and release of ions. The considerable reduction of effective diffusion coefficients can be well simulated. The saturation effect observed in current-concentration curves, which is not predicted by the conventional PNP model, has been successfully reproduced in our simulation. We also show that PROPHET can be used to perform both steady state and time dependent simulations for ion channels. The timescale can be microseconds, far beyond the range of molecular dynamics simulations. Our results demonstrate the useful role of PROPHET simulations in a multi-scale simulation approach.     

Generic Particle-Mesh Framework for the Simulation of Ionic Channels

The simulation of biological systems such as ion channels is a challenging task. Due to the low mobilities of ions and the long times required to resolve processes of biological importance current particle based methods of simulation have restricted applicability. We present a flexible Brownian framework designed for the simulation of Ion channels (although applicable to other problems). By using two implementations of the Langevin equation coupled in particle-mesh simulations it will be capable of resolving details of channel behavior from atomic scales up.     

Mapped Clock Oscillators as Ring Devices and Their Application to Neuronal Electrical Rhythms

The mapped clock oscillator (MCO) is a second-order, Winfree-type oscillator generating two instantaneous clock variables (amplitude and phase) that are mapped to an observable output variable (voltage) via a static nonlinearity. Two fundamental classes of ring devices are presented. Their respective dynamics give rise to two oscillator forms-the labile clock and the clock-which can be coupled together in various configurations to create higher-order systems with sufficient complexity to capture the dynamics of neuronal assemblies. To demonstrate the applicability of MCOs in modelling neuronal rhythms, a hippocampal network model of four coupled oscillators was constructed and shown to exhibit rhythmic activity of varying complexity, depending on model parameters. The dynamics of the network were quantified through estimation of the maximum lyapunov exponent and the correlation dimension. Synthesis of complex neuronal rhythms may have therapeutic implications. The modular and efficient design of the MCO should facilitate the process of implementing coupled MCO networks in electronic hardware as potential neural prostheses for treating dynamic diseases such as epilepsy.     

Computational Issues in Modeling Ion Transport in Biological Channels: Self-Consistent Particle-Based Simulations

In this work, a self-consistent Langevin dynamics simulator will be presented, and computational issues unique to the simulation of charge transport through ion channels will be addressed. The simulation approach is divided into two parts; the first is the development of an efficient model to account for the charge transport in bulk electrolyte solutions, while the second is the accurate representation of the channel protein and lipid structure. A cavity is made in the interior of a phospholipid bilayer and an ion channel is inserted, where the atomic coordinates of the protein are obtained from experimental work. The electrostatic potential felt by a potassium ion along the center of the channel is then calculated and comparisons are made between two types of potassium channels, KcsA and MthK.     

New techniques for enhancing accuracy of EMTP/TSP hybrid simulation

This paper proposes a new hybrid approach, which integrates the simulation of electromagnetic transient program (EMTP) for waveform solutions to concerned electrical components, such as FACTS devices and HVDC etc. and the simulation of transient stability program (TSP) for phasor solutions to the rest of power systems. In the interface between the two simulations, new techniques considering the effect of frequency deviation due to disturbances are proposed for improving accuracy of the hybrid simulation. A case study is performed on the IEEE 10-generator New England systems. The results show that simulation accuracy of conventional EMTP/TSP hybrid methods has been evidently improved. The proposed new method would thus provide an efficient tool in the design and analysis of behaviors of FACTS devices in power system dynamics.     

A Simulative Model for the Analysis of Conduction Properties of Ion Channels Based on First-Principle Approaches

A physical model and a simulation framework are proposed for the analysis of conduction properties of ion channels. The permeation path of ions along the channel is defined through the simultaneous occupancy of a set of individual ion binding sites within the pore identified from structural X-ray data and Molecular Dynamics (MD) simulations. All permitted elementary transitions between different channel configurations and their rate constants can be evaluated from the atomistic structure and MD data and are implemented into a statistical model which is then coded in a Monte Carlo simulator. Results for K ions permeating the KcsA channel are shown.     

Digital multiplier-less implementation of high-precision SDSP and synaptic strength-based STDP

Spiking neural networks (SNNs) can achieve lower latency and higher efficiency compared with traditional neural networks if they are implemented in dedicated neuromorphic hardware. In both biological and artificial spiking neuronal systems, synaptic modifications are the main mechanism for learning. Plastic synapses are thus the core component of neuromorphic hardware with on-chip learning capability. Recently, several research groups have designed hardware architectures for modeling plasticity in SNNs for various applications. Following these research efforts, this paper proposes multiplier-less digital neuromorphic circuits for two plasticity learning rules: the spike-driven synaptic plasticity (SDSP) and synaptic strength–based spike timing–dependent plasticity (SSSTDP). The proposed architectures have increased the precision of the plastic synaptic weights and are suitable for spiking neural network architectures with more precise calculations. The proposed models are validated in MATLAB simulations and physical implementations on a field-programmable gate array (FPGA).     

Temporal analysis of valence & electrostatics in ion-motive sodium pump

The present work establishes a unique framework for the simulation study of ion-motive pumps in general and the Na⁺/K⁺-ATPase, or Na⁺ pump, in particular. We shall discuss the implications of electrostatic analysis, valence calculations, and protein cavity data, each carried over data extracted from molecular dynamics (MD) simulations, on the structure-function relationship of Na⁺/K⁺-ATPase. This diverse set of tools will be used to investigate atomic-level characteristics that remain undetermined such as ion binding and accessibility.     

Biophysical Neural Spiking, Bursting, and Excitability Dynamics in Reconfigurable Analog VLSI

We study a range of neural dynamics under variations in biophysical parameters underlying extended Morris-Lecar and Hodgkin-Huxley models in three gating variables. The extended models are implemented in NeuroDyn, a four neuron, twelve synapse continuous-time analog VLSI programmable neural emulation platform with generalized channel kinetics and biophysical membrane dynamics. The dynamics exhibit a wide range of time scales extending beyond 100 ms neglected in typical silicon models of tonic spiking neurons. Circuit simulations and measurements show transition from tonic spiking to tonic bursting dynamics through variation of a single conductance parameter governing calcium recovery. We similarly demonstrate transition from graded to all-or-none neural excitability in the onset of spiking dynamics through the variation of channel kinetic parameters governing the speed of potassium activation. Other combinations of variations in conductance and channel kinetic parameters give rise to phasic spiking and spike frequency adaptation dynamics. The NeuroDyn chip consumes 1.29 mW and occupies 3 mm × 3 mm in 0.5 μm CMOS, supporting emerging developments in neuromorphic silicon-neuron interfaces.     

Passivity–preserving interpolation‐based parameterized model order reduction of PEEC models based on scattered grids

The increasing operating frequencies and decreasing IC feature size call for 3‐D electromagnetic (EM) methods, such as the Partial Element Equivalent Circuit (PEEC) method, as necessary tools for the analysis and design of high‐speed systems. Very large systems of equations are often generated by 3‐D EM methods and model order reduction (MOR) techniques are commonly used to reduce such a high model complexity. A typical design process includes optimization and design space exploration, and hence requires multiple simulations for different design parameter values. Traditional MOR techniques perform model reduction only with respect to frequency and such design activities call for parameterized MOR (PMOR) methods that can reduce large systems of equations with respect to frequency and other design parameters of the circuit, such as geometrical layout or substrate characteristics. We present a novel PMOR technique applicable to the PEEC method that provides parametric reduced order models, stable and passive by construction, over a user defined design space. We treat the construction of parametric reduced order models on scattered design space grids. Pertinent numerical examples validate the proposed approach. Copyright © 2010 John Wiley & Sons, Ltd.     

System-on-a-programmable-chip development platforms in the classroom

This paper describes the authors' experiences using a system-on-a-programmable-chip (SOPC) approach to support the development of design projects for upper-level undergraduate students in their electrical and computer engineering curriculum. Commercial field-programmable gate-array (FPGA)-based SOPC development boards with reduced instruction set computer (RISC) processor cores are used to support a wide variety of student design projects. A top-down rapid prototyping approach with commercial FPGA computer-aided design tools, a C compiler targeted for the RISC soft-processor core, and a large FPGA with memory is used and reused to support a wide variety of student projects.     

Causes of Transient Instabilities in the Dynamic Clamp

The dynamic clamp is a widely used method for integrating mathematical models with electrophysiological experiments. This method involves measuring the membrane voltage of a cell, using it to solve computational models of ion channel dynamics in real-time, and injecting the calculated current(s) back into the cell. Limitations of this technique include those associated with single electrode current clamping and the sampling effects caused by the dynamic clamp. In this study, we show that the combination of these limitations causes transient instabilities under certain conditions. Through physical experiments and simulations, we show that dynamic clamp instability is directly related to the sampling delay and the maximum simulated conductance being injected. It is exaggerated by insufficient electrode series resistance and capacitance compensation. Increasing the sampling rate of the dynamic clamp system increases dynamic clamp stability; however, this improvement, is constrained by how well the electrode series resistance and capacitance are compensated. At present, dynamic clamp sampling rates are justified solely on the temporal dynamics of the models being simulated; here we show that faster rates increase the stable range of operation for the dynamic clamp system. In addition, we show that commonly accepted levels of resistance compensation nevertheless significantly compromise the stability of a dynamic clamp system.     

Shot noise in single open ion channels: A computational approach based on atomistic simulations

This paper presents a computational analysis of the noise associated with ion current in single open ion channels. The study is performed by means of a coupled Molecular Dynamics/Monte Carlo approach able to simulate the conduction process on the basis of all microscopic information today available from protein structural data and atomistic simulations. The case of potassium ions permeating the KcsA channel is considered in the numerical calculations. Results show a noise spectrum different from what is theoretically predicted for uncorrelated ion-exit events (Poisson noise), confirming the existence of correlation in ion motion within the channel, already evinced by atomistic structural analyses.     

配电网信息管理系统的组件化设计与实现

基于组件对象模型(COM）的组件化软件设计方法继承并发展了面向对象程序设计方法。阐述了其概念、特点、原理和应用,并由此引出建立在COM基础上的3层客户／服务器软件结构。结合抚顺市配电网信息管理系统的研制与开发,介绍了该类软件的组件化设计与实现的新思路,指出在实际配电网信息管理系统的开发中,需要在统一规划的基础上,使用组件化软件设计方法,将整个系统分层、分块、分步实践。实践证明该方法有效地提高了软件的可重用性和可扩充性,改善了系统的可靠性和可维护性、节省了开发时间、提高了软件的生产效率。