Bimodal Polymer Nano Brush

12 Jul 2011 | Tools | Contributor(s): Rikkert Jan Nap, Fritzlaine Roche, Marcelo Carignano

Structure and Thermodynamics of Bimodal Polymer Nano Brushes

https://nanohub.org/resources/binbrush

Bio Composite Simulator

13 Oct 2011 | Tools | Contributor(s): Sebastian Lee, Pablo Daniel Zavattieri, Alejandro Strachan

Simulation mechanical response of bio composites using rigid particles

https://nanohub.org/resources/nacresimulator

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

BioSensorLab

14 Aug 2006 | Tools | Contributor(s): Pradeep R. Nair, Jonghyun Go, Graeme John Landells, Tejas Rajiv Pandit, Muhammad Alam

BioSensorLab is a tool to evaluate and predict the performance parameters of Biosensors.

https://nanohub.org/resources/senstran

Cyber-Infrastructure for Imaging and Simulation of Molecular and Cellular Mechanics (CISMCM)

27 Oct 2009 | Tools | Contributor(s): Raheem Syed, Umberto Ravaioli, Gabriel Popescu, Nahil Sobh

Simulation-Driven Science Project

https://nanohub.org/resources/cismcm

Exciton Dynamics Lab for Light-Harvesting Complexes (GPU-HEOM)

18 Dec 2012 | Tools | Contributor(s): Christoph Kreisbeck, Tobias Kramer

Non-Markovian calculation of absorption spectra, 2d echo-spectra, coherences and polulation dynamics for light-harvesting complexes.

https://nanohub.org/resources/gpuheompop

Forced Protein Unfolding

01 Jun 2009 | Tools | Contributor(s): Ashlie Martini, Benjamin Rafferty, Zachary Carl Flohr

Molecular dynamics simulation of forced protein unfolding

https://nanohub.org/resources/fpuf

Hydrophobicity Lab

24 Jul 2006 | Tools | Contributor(s): Eric F Darve, Artit Wangperawong, Kazutora Hayashida

Study hydrophobicity and how Lennard Jones particles cluster in a polar solvent

https://nanohub.org/resources/hydrolab

Illinois Tool: FIONA (Fluorescence Imaging with One Nanometer Accuracy)

01 Nov 2010 | Tools | Contributor(s): Paul R Selvin, Raheem Syed, Nahil Sobh

Fluorescence Imaging with One Nanometer Accuracy

https://nanohub.org/resources/fiona

Illinois Tools: NanoGromacsDemo

30 Oct 2006 | Tools | Contributor(s): Dairui Chen, Derrick Kearney, Jay Mashl, Nahil Sobh, Eric Jakobsson

Implementation of the popular molecular dynamics software suite GROMACS

https://nanohub.org/resources/nanogromacs

imageJ

03 Apr 2009 | Tools | Contributor(s): Raheem Syed, Nahil Sobh, Umberto Ravaioli, Gabriel Popescu, Mohamed Mohamed

It can display, edit, analyze, process, save and print 8-bit, 16-bit and 32-bit images. It can read many image formats.

https://nanohub.org/resources/imagej

Intercellular synthetic biology

03 May 2013 | Tools | Contributor(s): Ting Lu, Nahil Sobh, John Feser, Pratik Naik

Synthetic biology tool for engineering patterning systems.

https://nanohub.org/resources/patform

Nano-Bio-Photonics Simulator

17 Feb 2012 | Tools | Contributor(s): Zuhaib Bashir Sheikh, Nahil Sobh

Simulates passage of light through biological tissue having an embedded metallic nanoparticles using FDTD

https://nanohub.org/resources/nanobiophotsim

Nanoindentation close to an interface

06 May 2011 | Tools | Contributor(s): Alvian Siswoyo, Marisol Koslowski

Simulated the indentation force curve close to a perfectly bonded interface

https://nanohub.org/resources/nanoin

Nisin Diffusion Tool

08 Apr 2013 | Tools | Contributor(s): Andrew Blanchard

Simulate cell fluorescence based on nisin concentration

https://nanohub.org/resources/nisindiffusion

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

Polymer Modeler

28 Jun 2010 | Tools | Contributor(s): Benjamin P Haley, Nate Wilson, Chunyu Li, Andrea Arguelles, Eugenio Jaramillo, Alejandro Strachan

Build thermoplastic polymer chains and run LAMMPS to relax the chains and study mechanical properties

https://nanohub.org/resources/polymod

Protein Contact Maps

22 Oct 2010 | Tools | Contributor(s): Benjamin Rafferty, Zachary Carl Flohr, Ashlie Martini

Create and view protein contact maps and distance maps.

https://nanohub.org/resources/contactmaps

Stretching simulation of an alpha-helical protein domain

10 Jan 2011 | Tools | Contributor(s): Markus Buehler, Justin Riley, Joo-Hyoung Lee, Jeffrey C Grossman

Uses steered molecular dynamics (SMD) to apply a tensile load to the ends of a molecule (such as an alpha-helical protein domain)

https://nanohub.org/resources/stretchmol