[Show abstract][Hide abstract]ABSTRACT: Ion channels, as natures' solution to regulating biological environments, are particularly interesting to device engineers seeking to understand how natural molecular systems realize device-like functions, such as stochastic sensing of organic analytes. What's more, attaching molecular adaptors in desired orientations inside genetically engineered ion channels, enhances the system functionality as a biosensor. 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 (P(3)M) methodologies developed at the University of Illinois at Urbana-Champaign. In this paper, we have employed BioMOCA to study two engineered mutations of α-HL, namely (M113F)(6)(M113C-D8RL2)(1)-β-CD and (M113N)(6)(T117C-D8RL3)(1)-β-CD. The channel conductance calculated by BioMOCA is slightly higher than experimental values. Permanent charge distributions and the geometrical shape of the channels gives rise to selectivity towards anions and also an asymmetry in I-V curves, promoting a rectification largely for cations.
Full-text · Article · Dec 2010 · Journal of Computational and Theoretical Nanoscience
[Show abstract][Hide abstract]ABSTRACT: As part of nature's solution for regulating biological environments, ion channels are particularly interesting to device engineers seeking to understand how nanoscale molecular systems realize device-like functions, such as biosensing of organic analytes. By attaching molecular adaptors inside genetically engineered ion channels, it's possible to further enhance this biosensor functionality.
No preview · Article · Mar 2010 · Computing in Science and Engineering
[Show abstract][Hide abstract]ABSTRACT: This paper proposes and investigates a short-channel MOSFET model down to a 0.1-μm regime for the frequency-domain analysis of the device operation through the harmonic balance technique. The efficiency and the preciseness of our method are validated by comparison of simulation results with the two-dimensional time-domain simulation tool, MEDICI. Along with the carrier transport model, the displacement current components are included in the terminal current equations for the extended analysis under external circuit environments.
Full-text · Article · Jul 2005 · IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems
[Show abstract][Hide abstract]ABSTRACT: In this paper, we present a full three-dimensional simulation of the ompF porin channel using BioMOCA, a self-consistent particle-based ion channel simulation tool, based on the Boltzmann Transport Monte Carlo methodology widely used to simulate conduction in the solid-state device. Significant computational speed-up over atomistic Molecular Dynamics simulations is achieved by treating protein, membrane and water as continuum dielectric background media and computing only the trajectories of mobile ions in solution. A realistic channel structure with permanent fixed charges is mapped onto a finite mesh using the Cloud-in-Cell scheme. Electrostatic forces, computed by solving Poisson equation at regular intervals, are added to a pair-wise ion-ion interaction, which is necessary to prevent the unphysical coalescence of finite-sized ions. The interaction between ions and water is modeled as a random scattering process that thermalizes the ion. Using this tool we computed the complete current-voltage characteristic of the porin channel in approximately one week using ten IBM p690 processors. We also present steady-state ion channel occupancies and compare them with results obtained from recent drift-diffusion based simulations.
No preview · Article · Mar 2005 · Journal of Computational Electronics
[Show abstract][Hide abstract]ABSTRACT: In this paper, we propose an efficient method for the harmonic balance analysis of the short channel MOSFET including the non-quasistatic effect Our method is based on the charge-sheet model in the linear region and assumes that the saturation region is modulated by the external voltage instantaneously. By comparing with the current responses under large signal conditions obtained from the time-dependent two-dimensional simulator (MEDICI), it is confirmed that the proposed method is efficient and accurate for the frequency-domain analysis of the short channel MOSFET in the 0.1 μm regime.
[Show abstract][Hide abstract]ABSTRACT: We propose a harmonic balance technique for the frequency-domain
analysis of the metal-oxide-semiconductor field-effect transistor
(MOSFET) operation. The MOSFET model in our approach is based on the
charge-sheet and the nonquasi-static MOSFET models in the channel region
with a harmonic balance technique applied to the channel charges. It is
shown that the proposed method renders a computationally efficient tool
to analyze the harmonic distortion occurrence in the MOSFET device due
to the nonlinear response of the channel charges
No preview · Article · Aug 2001 · IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems