BioMOCA Demo

30 May 2006 | Tools | Contributor(s): Reza Toghraee, Umberto Ravaioli

Transport Monte Carlo simulation of conduction in biological Ionic Channels.

https://nanohub.org/resources/biomoca

BioMOCA Suite

04 Feb 2008 | Tools | Contributor(s): David Papke, Reza Toghraee, Umberto Ravaioli, Ankit Raj

Simulates ion flow through a channel.

https://nanohub.org/resources/BMCsuite

Computing the Horribleness of Soft Condensed Matter

19 Oct 2007 | Online Presentations | 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 …

https://nanohub.org/resources/3424

Discussion about Ion Channels Using Reduced Model Approaches

21 Sep 2011 | Online Presentations | 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.

https://nanohub.org/resources/12120

From Research to Learning in Chemistry through Visualization and Computation

17 May 2007 | Online Presentations | 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 …

https://nanohub.org/resources/2725

Hierarchy of Simulation Approaches for Charge Transport Simulation

01 Aug 2008 | Online Presentations | Contributor(s): Omar N Sobh, Umberto Ravaioli

General considerations Model simulation hierarchy Continuum model Particle Transport Monte Carlo model Examples of simulations Umberto Ravaioli - University of Illinois, Urbana-ChampaignNCN@Purdue …

https://nanohub.org/resources/5175

Illinois iOptics Lecture 1: Super Accuracy and Super-Resolution of Molecular Motors and Ion Channels

15 Apr 2010 | Online Presentations | 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 …

https://nanohub.org/resources/8853

Ionic Selectivity in Channels: complex biology created by the balance of simple physics

05 Jun 2008 | Online Presentations | 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 …

https://nanohub.org/resources/4726

Lecture 21: Nerves

24 Apr 2008 | Online Presentations | Contributor(s): Paul R Selvin

Ion Channels,Ionic current, Gating current, Digital Ion Channels, Structural studies, X-ray Crystallography

https://nanohub.org/resources/4425

Lecture 22: Conformational Changes in Ion Channels

24 Apr 2008 | Online Presentations | Contributor(s): Paul R Selvin

Voltage dependence, Spontaneous shut-off, Nerve Impulse propagation, Structure Pore Domain, Voltage Sensor

https://nanohub.org/resources/4429

P-N Semiconductor Membranes for Ion Filtering and Rectification

06 Apr 2008 | Online Presentations | Contributor(s): J. P. Leburton

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 …

https://nanohub.org/resources/4245

PNP Cyclic Peptide Ion Channel Model

04 Apr 2007 | Tools | Contributor(s): Brian Radak, Hyonseok Hwang, George C. Schatz, Mark A. Ratner

This tool simulates ion flow in a system modeled after cyclic peptide ion channels using Poisson-Nernst-Planck (PNP) theory.

https://nanohub.org/resources/pnppeptide

Potassium Channels: Conduction, Selectivity, Blockage, Inactivation, and Gating

03 Nov 2006 | Online Presentations | Contributor(s): Benoit Roux, NCN SLC@Northwestern

The determination of the structure of the KcsA K+ channel from Streptomyces lividan has made it possible to investigate the function of a biological channel at the atomic level. Because of its …

https://nanohub.org/resources/1959

Review of Several Quantum Solvers and Applications

11 Jun 2004 | Online Presentations | Contributor(s): Umberto Ravaioli

Review of Several Quantum Solvers and Applications

https://nanohub.org/resources/413

Spectroscopy and Modeling to Infer Channel Structure and Function

23 Mar 2008 | Online Presentations | 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> …

https://nanohub.org/resources/4173

Structure and Ion Permeation of the Gramicidin Channel using Molecular Dynamics

12 Apr 2004 | Online Presentations | Contributor(s): Toby Allen

Molecular dynamics (MD) has become an essential tool for obtaining microscopic insight into biological function. The gramicidin channel as an excellent benchmark system for this purpose. Using …

https://nanohub.org/resources/161

[Illinois] Coarse-grained Simulation of Ion Channels

29 Dec 2012 | Online Presentations | Contributor(s): Umberto Ravaioli

…

https://nanohub.org/resources/16157

[Illinois] Coarse-grained Simulation of Ion Channels

19 Jun 2012 | Online Presentations | 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, …

https://nanohub.org/resources/14321