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30 May 2006 | | Contributor(s):: Reza Toghraee, Umberto Ravaioli
Ion channel simulator
04 Feb 2008 | | Contributor(s):: David Papke, Reza Toghraee, Umberto Ravaioli, Ankit Raj
Simulates ion flow through a channel.
Computing the Horribleness of Soft Condensed Matter
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19 Oct 2007 | | Contributor(s):: Eric Jakobsson
A great triumph of computer simulations 40 years ago was to make the liquid state of matter understandable in terms of physical interactions between individual molecules. Prior to the first simulations of liquid argon and liquid water in the 1960's, there was no quantitatively rigorous molecular...
Discussion about Ion Channels Using Reduced Model Approaches
21 Sep 2011 | | Contributor(s):: James Fonseca
The seminar will cover the reasons how the channels are able to selectively permit the flow of certain species of ions while blocking other physiological cations.
From Research to Learning in Chemistry through Visualization and Computation
17 May 2007 | | Contributor(s):: Eric Jakobsson
Modern chemistry research and high school chemistry education are separated by institutional and geographical boundaries. As such, much of secondary chemistry education is still based on the periodic table instead of the computational methods that drive current chemistry research. In this talk,...
Hierarchy of Simulation Approaches for Charge Transport Simulation
01 Aug 2008 | | Contributor(s):: Omar N Sobh, Umberto Ravaioli
General considerationsModel simulation hierarchyContinuum modelParticle Transport Monte Carlo modelExamples of simulationsUmberto Ravaioli - University of Illinois, Urbana-ChampaignNCN@Purdue Student Leadership TeamNetwork for Computational NanotechnologyThe Institute for Nanoelectronics and...
Illinois iOptics Lecture 1: Super Accuracy and Super-Resolution of Molecular Motors and Ion Channels
15 Apr 2010 | | Contributor(s):: Paul R Selvin
The standard diffraction limit of light is about 250 nm, meaning that you cannot "resolve" objects closer than this distance. Despite this, we have come up with a method to measure individual biomolecules with 1.5 nm spatial localization in x-y plane and 1-500 msec temporal resolution, using a...
Ionic Selectivity in Channels: complex biology created by the balance of simple physics
05 Jun 2008 | | Contributor(s):: Bob Eisenberg
An important class of biological molecules—proteins called ionic channels—conduct ions (like Na+ , K+ , Ca2+ , and Cl− ) through a narrow tunnel of fixed charge (‘doping’). Ionic channels control the movement of electric charge and current across biological membranes and so play a role in...
Lecture 21: Nerves
24 Apr 2008 | | Contributor(s):: Paul R Selvin
Ion Channels,Ionic current, Gating current, Digital Ion Channels, Structural studies, X-ray Crystallography
Lecture 22: Conformational Changes in Ion Channels
Voltage dependence, Spontaneous shut-off, Nerve Impulse propagation, Structure Pore Domain, Voltage Sensor
P-N Semiconductor Membranes for Ion Filtering and Rectification
06 Apr 2008 |
Jean-Pierre Leburton's research at the Beckman Institute deals with transport and optical processes in semiconductor nanostructures such as quantum wires and quantum dots that exhibit a high degree of quantization dependent on the semiconductor materials and geometrical confinement. This...
PNP Cyclic Peptide Ion Channel Model
04 Apr 2007 | | Contributor(s):: Brian Radak, Hyonseok Hwang, George C. Schatz, Mark Ratner
This tool simulates ion flow in a system modeled after cyclic peptide ion channels using Poisson-Nernst-Planck (PNP) theory.
Potassium Channels: Conduction, Selectivity, Blockage, Inactivation, and Gating
03 Nov 2006 | | Contributor(s):: Benoit Roux, NCN at Northwestern University
The determination of the structure of the KcsA K+ channel fromStreptomyces lividan has made it possible to investigate the functionof a biological channel at the atomic level. Because of its structuralsimilarity with eukaryotic K-channels, investigations of KcsA areexpected to help understand a...
Review of Several Quantum Solvers and Applications
11 Jun 2004 | | Contributor(s):: Umberto Ravaioli
Review of Several Quantum Solvers and Applications
Spectroscopy and Modeling to Infer Channel Structure and Function
23 Mar 2008 | | Contributor(s):: Vishwanath Jogini
We are particularly interested in issues about ion permeation, ion selectivity, gating, and channel inhibitors. We are currently working on the KcsA channel, the OmpF porin, and the gramicidin A> channel. We are also spending our efforts in the development of new computational approaches for...
[Illinois] Biophysics 401 Lecture 23: Ion Channels II
06 Dec 2015 | | Contributor(s):: Paul R Selvin
[Illinois] Biophysics 401 Lecture 24: Ion Channels III
10 Dec 2015 | | Contributor(s):: Paul R Selvin
[Illinois] Coarse-grained Simulation of Ion Channels
19 Jun 2012 | | Contributor(s):: Umberto Ravaioli
29 Dec 2012 | | Contributor(s):: Umberto Ravaioli
This Summer School will train students in molecular simulation and simulation at multiple time and length scales. Instruction will be provided on quantum Monte Carlo simulation, molecular dynamics, coarse-grained simulations, and multiscale simulations with opportunities for hands-on experience...