Three-Dimensional Continuum Simulations of Ion Transport Through Biological Ion Channels: Effect of Charge Distribution in the Constriction Region of Porin

Drift-diffusion models are useful for studying ion transport in open protein channel systems over time scales that cannot be resolved practically by detailed molecular dynamics or quantum approaches. Water is treated as a uniform background medium with a specific dielectric constant and macroscopic current flow is resolved by assigning an appropriate mobility and diffusivity to each ionic species. The solution of Poisson's equation over the entire domain provides a simple way to include external boundary conditions and image force effects at dielectric discontinuities. Here we present a 3-D drift-diffusion model of ion (K⁺ and Cl^–) permeation through the porin channel ompF, and its mutant G119D, implemented using the computational platform PROPHET.     

A Coupled 3-D PNP/ECP Model for Ion Transport in Biological Ion Channels

The Poisson-Nernst-Planck (PNP) or Drift-Diffusion theory can be used to compute macroscopic current in ion channels in an efficient manner. The major drawback of the standard PNP theory is that it is based on a continuum model for the charge flow, therefore it models ions as a gas of point particles. Water is also not simulated explicitly, but introduced as a background medium with a given permittivity. The PNP model can be modified to include effects of finite ion size and water occupation by including a correction term, the Excess Chemical Potential (ECP), in the standard model. Gillespie et al. [1] developed a model for ECP correction, based on Density Functional theory, which is introduced in an existing 3-D PNP solver for ion transport in biological ion channels realized using the numerical computational platform PROPHET. Since incorporation of the ECP correction directly into the PNP matrix formulation is not an easy task, for demonstration purposes we developed a relatively simple decoupled relaxed iteration algorithm. Preliminary tests were conducted on idealized channel geometries, showing how the adopted ECP correction model alters significantly the ion densities inside the channel from those predicted by the conventional PNP theory alone.     

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.     

Error Analysis of the Poisson P3M Force Field Scheme for Particle-Based Simulations of Biological Systems

The ability to accurately simulate electrolyte solutions is a strong requirement for the modeling of charge transport in ion channels. In this work, a Particle-Particle–Particle-Mesh (P³M) algorithm is used to model the electrostatic interactions governing the physics of electrolyte solutions. The goal of this study is to define the parameters relevant for this force field, and their respective influence on the accuracy of the simulation. Simulations have been performed for extended ranges of these parameters and the results are compared to theoretical models. Finally, the trade-offs between optimal algorithmic efficiency and accuracy are analyzed.     

Electro-Chemical Modeling Challenges of Biological Ion Pumps

We outline the basic operational, structural and functional features of ion motive ATPases: trans-membrane proteins central to biological functions of all animal cells. As an example we discuss the modeling problems associated with the operation of the surface membrane Na⁺,K⁺-ATPase and skeletal muscle sarcoplasmic reticulum Ca²⁺-ATPase and focus on the frameworks required for their solution. There are three basic problems: identification of the pathway for ion permeation, prediction of ion binding rate coefficients and affinities based on the structure of the protein, and prediction of conformational changes of protein structure and the associated movement of charges within the membrane dielectric. A solution strategy useful in approaching the first two problems and preliminary results obtained using molecular dynamics simulations are also presented.Supported by NIH grant NS22979.     

Parallel Approaches for Particle-Based Simulation of Charge Transport in Semiconductors

The aim of this contribution is to discuss possible algorithmic choices and hardware configurations for the implementation of efficient particle-based simulation programs. By using a population decomposition scheme, we modified the scalar version of the algorithm in order to improve the efficiency of our hybrid particle-based simulation engine. Using a Beowulf-class computer cluster, we measured parallel speed-up with different algorithmic configurations, and related it to the inter-process communication hardware.     

Fullband Particle-Based Simulation of High-Field Transient Transport in III–V Semiconductors

Motivated by recent experimental measurements (A. Leitenstorfer et al., 2000. Physical Review B 61(24): 16642–16652), this work presents the transient analysis of photogenerated electron-hole pairs in GaAs and InP pin diodes (S. M. Sze, 1981. Physics of Semiconductor Devices, 2nd edn., John Wiley) using a fullband particle-based simulator (M. Saraniti and S. Goodnick, 2000. IEEE Transactions on Electron Devices 47(10): 1909–1915). The fullband simulation tool is based on a particle-based technique that has been developed to reduce the computational time required for modeling charge transport phenomena in semiconductors. Excellent agreement is found between experiment and simulation of transient acceleration and velocity overshoot in GaAs and InP pin diodes due the femto-second optical excitation of carriers.     

Electrodiffusion Model Simulation of Ionic Channels: 1D Simulations

The drift-diffusion (Poisson-Nernst-Planck) model is applied to ionic channels in biological membranes plus surrounding solution baths. Simulations of the K channel in KCl solutions using the TRBDF2 method are presented which show significant boundary layers at the ends of the channel. The computed current-voltage curve for the K channel shows excellent agreement with experimental measurements.     

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.     

平原河渠过水能力的直接算法

遵从平原河网地区河渠抽水水力特性,从基本的能量方程入手,导出明渠渐变流基本微分方程,进而将该方程改写为水位沿程变化的微分式,再变微分为差分,推演出平原河渠过水流量的直接计算方式,该公式对棱柱体或非棱柱体河渠以及任一种底坡均可适用,且具有计算方便、成果精确且符合抽水流态特性等优点。对习惯算法的由来也作了简要叙述并与直接算法进行了比较。     

Robust Computational Models of Quantum Transport in Electronic Devices

A family of efficient quantum transport models for simulation of modern nanoscale devices is presented. These models are used for quantitative calculations of quantum currents in nanoscale electronic devices within our device simulator software. Specifically, we used them to simulate the tunneling current through thin barrier in vertical-cavity surface-emitting laser (VCSEL), direct and reverse tunnel currents through the tunnel junction, Schottky contact characteristics, and gate induced drain leakage (GIDL).     

基于实验经济学仿真构建碳排放交易的多代理模型

碳排放交易的市场效率及减排效果受各类角色及大量参与者决策的影响,参与者特别是市场设计者及监管者必须掌握其行为及机理。实验经济学通过真实实验人参与的实验,反映参与者的有限理性。但其实验规模受限于合格实验者的数量,而多场景实验之间的可比性还受限于实验者的专注度。为此采用了一种混合交互仿真法,先通过实验提炼出真实实验人群在碳排放交易中的不确定行为的关键变量及规律,据此建立具有相同分布特性的多代理随机模型。此后就只需动用少量真实实验人来反映特殊的决策者,并与上述模型生成的大量多代理交互仿真。在保持实验经济学特点的同时,克服了其对实验规模的限制,并保证了重复实验的统计一致性。     

智能调度建模技术中若干问题的研究

分布式一体化建模技术是智能调度的核心技术之一。该技术基于"源端维护,全局共享"的原则,实现了跨层、跨区的分布式一体化建模。分析了分布式一体化建模技术应用中遇到的电网模型校验、模型边界维护等问题,并针对每个问题提出了解决方案,具体包括:提出了电网模型校验的有效方法,保证了源端模型的正确性;提出了智能边界维护的方法,彻底解决了模型边界维护繁琐的问题;提出了实现模型一体化在线同步的具体方法,解决了图、数、模无扰动投入在线系统的问题。这些问题的解决方案是对智能电网分布式一体化建模方案的完善和补充。     

Thirty Years of Monte Carlo Simulations of Electronic Transport in Semiconductors: Their Relevance to Science and Mainstream VLSI Technology

We review briefly some aspects of the history of Monte Carlo simulations of electronic transport in semiconductors. In the early days their heavy computational cost rendered them suitable only to study problems of pure physics, as simpler models provided the answers necessary to design ‘electrostatically good’ devices. Now that scaling has taken another meaning (i.e., looking for alternative materials, crystal orientations, device geometries, etc.), Monte Carlo simulations may gain popularity once more, since they allow an efficient and reliable evaluation of speculative ideas. We show examples of both aspects of the results of Monte Carlo work.     

Modeling and Characterization of Electrical Transport in Oxygen Conducting Solid Electrolytes

A model for the electrical conductivity in acceptor-doped oxides which involves an association between the acceptor-dopants and oxygen vacancies resulting in donor centers is considered. The model relates the behavior of the electrical conductivity with the temperature, ambient atmosphere and band structure. The predictions of the model are compared to experimental data for ZrO₂:16% Y and SrCeO₃:5% Yb oxygen conductors and some band structure parameters have been determined.     

Modeling and Characterization of Electrical Transport in Oxygen Conducting Solid Electrolytes

A model for the electrical conductivity in acceptor-doped oxides which involves an association between the acceptor-dopants and oxygen vacancies resulting in donor centers is considered. The model relates the behavior of the electrical conductivity with the temperature, ambient atmosphere and band structure. The predictions of the model are compared to experimental data for ZrO₂:16% Y and SrCeO₃:5% Yb oxygen conductors and some band structure parameters have been determined.     

Comparison Between Non-Equilibrium Green's Function and Monte Carlo Simulations for Transport in a Silicon Quantum Wire Structure

We present comparisons of simulations conducted with non-equilibrium Green's functions and Monte Carlo approaches. As prototype, we consider an idealized silicon quantum wire structure, consisting of a conduction channel of rectangular cross-section, terminated by two contacts. The Monte Carlo model treats the particles as semi-classical, but distributed over up to seven subbands and with scattering model similar to the one used for the Green's functions model. Results for drift velocity under various field conditions agree very closely using the two techniques, suggesting that particle simulation may continue to be a useful physical investigation tool at the nanoscale with an appropriate introduction of the most important quantum features of the transport.     

Modeling Spin-Dependent Transport in InAs/GaSb/AlSb Resonant Tunneling Structures

The Rashba effect resonant tunneling diode is a candidate for achieving spin polarizing under zero magnetic field using only conventional non-magnetic III–V semiconductor heterostructures. We point out the challenges involved based on simple arguments, and offer strategies for overcoming these difficulties. We present modeling results that demonstrate the benefits of the InAs/GaSb/AlSb-based asymmetric resonant interband tunneling diode (a-RITD) for spin filtering applications.     

Modeling of Transport Through Submicron Semiconductor Structures: A Direct Solution to the Coupled Poisson-Boltzmann Equations

We report on a computational approach based on the self-consistent solution of the steady-state Boltzmann transport equation coupled with the Poisson equation for the study of inhomogeneous transport in deep submicron semiconductor structures. The nonlinear, coupled Poisson-Boltzmann system is solved numerically using finite difference and relaxation methods. We demonstrate our method by calculating the high-temperature transport characteristics of an inhomogeneously doped submicron GaAs structure where the large and inhomogeneous built-in fields produce an interesting fine structure in the high-energy tail of the electron velocity distribution, which in general is very far from a drifted-Maxwellian picture.