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13 Aug 2014 | | Contributor(s):: AbderRahman N Sobh, Sarah White, Jeremy Smith, Nahil Sobh, Prashant K Jain
Combines the Discrete Dipole Scattering (DDSCAT) tool with the DDAConvert tool for a single workflow for custom shapes.
09 Jun 2014 | | Contributor(s):: Mingxuan Lu, Chang Wan Han, Benjamin P Haley, Volkan Ortalan
Online IMOD tool for electron tomography
[Illinois] BioNanotechnology Summer Institute 2014
31 Jul 2014 | | Contributor(s):: NanoBio Node
Attendees participate in two weeks of lectures and hands-on training in engineering and physical science laboratory techniques by experts in the field. Topics include cancer nanotechnology, cell mechanics, molecular biology, micro fabrication, and NanoBio devices.Featuring invited...
[Illinois] DIY BIOSENSORS Day 3 Summer 2014 Workshop
26 Jun 2014 | | Contributor(s):: Kaustubh Bhalerao
In Day 3, the students continue building their first models of the biosensors. Once completed, they test out their newly-built biosensor with spoiled milk and evaluate their design. The students then start designing their second prototype. At the end, then discussed and reevaluated their...
[Illinois] DIY BIOSENSORS Day 4 Summer 2014 Workshop
In Day 4, the second prototype biosensors continued to be tested. The thought process of building an effective biosensor was then discussed. There were five steps taken: the design objective, design criteria, first prototype, lessons learned, and second prototype. Each of these steps was then...
[Illinois] DIY BIOSENSORS Day 5 Summer 2014 Workshop
In Day 5, each group gave a presentation about the biosensor they had created. They discussed the design objective, design criteria, first prototype, lessons learned, and the second prototype. In trying to depict their biosensor as the best, they learned what is sought from the market when...
[Illinois] DIY BIOSENSORS Day 2 Summer 2014 Workshop
In Day 2, the students start out by brainstorming a design for their biosensor and the shape that they will cut it in. The students start their first prototype and build throughout the video.This nanoBIO node workshop is a one week intensive high school Workshop on biosensors led by Kaustubh...
[Illinois] DIY BIOSENSORS Day 1 Summer 2014 Workshop
In Day 1, the lecture starts out by discussing the three definitions of a biosensor. These definitions are: something that measures a physical process, something that measures a molecular signature of a process, or a sensor that uses biological materials that may or may not measure biological...
[Illinois] Cooperation and Construction: From Multicellularity to Eusociality
28 Apr 2014 | | Contributor(s):: Corina Tarnita
The evolutionary trajectory of life on earth is one of increasing size and complexity. Yet the standard equations of evolutionary dynamics describe mutation and selection among similar organisms that compete on the same level of organization. I will try to outline a mathematical theory that...
28 Oct 2013 | | Contributor(s):: Taha Goudarzi, AbderRahman N Sobh, Kathy Walsh, Nahil Sobh, Iwona Jasiuk
Nanoindentation for Mechanical Characterization of Soft Materials
23 Apr 2013 | | Contributor(s):: Prashant K Jain, Nahil Sobh, Jeremy Smith, AbderRahman N Sobh, Sarah White, Jacob Faucheaux, John Feser
Calculate scattering and absorption of light by targets with arbitrary geometries and complex refractive index.
cadnano to PDB File Converter
13 Nov 2013 | | Contributor(s):: Jejoong Yoo, AbderRahman N Sobh, Chen-Yu Li, Aleksei Aksimentiev
Accepts CadNano files in the form of *.json and outputs a file in *.pdb which can be read by programs such as VMD.
30 Aug 2013 | | Contributor(s):: AbderRahman N Sobh, Chen-Yu Li, Nahil Sobh, Aleksei Aksimentiev
Using molecular dynamic simulation - explore the interactions between a molecular structure and substrate when they are linked together.
[Illinois] Graphene Synthesis from Biochar using Wet Chemical Treatment Process
27 Sep 2013 | | Contributor(s):: Sriraam Chandrasekaran
Biochar is a major by-product from pyrolysis and gasification of biomass. Biochar finds potential applications in soil amendment, carbon sequestration, super capacitors, adsorbents, etc. However, its applicability is limited by its properties such as low carbon content, low porosity, and surface...
Tensile Mechanics of alpha-Helical Polypeptides
30 Aug 2013 | | Contributor(s):: Korosh Torabi, George C. Schatz
This model is capable of making quantitatively accurate predictions of force-extension behavior of a given helix-forming polypeptide sequence including its dependence on pH, temperature and ionic strength.
Molecular Dynamics Showcase
06 Jul 2013 | | Contributor(s):: Michael McLennan, Chen-Yu Li, john stone, Aleksei Aksimentiev, George A. Howlett
View interesting features of a molecular dynamics trajectory file
[Illinois] Physics 550 Biomolecular Physics
03 Sep 2013 | | Contributor(s):: Klaus Schulten, Taekjip Ha
Physical concepts governing the structure and function of biological macromolecules; general properties, spatial structure, energy levels, dynamics and functions, and relation to other complex physical systems such as glasses; recent research in biomolecular physics; physical...
Neural Systems Modeling Ch10-13 Master Tool
02 Aug 2013 | | Contributor(s):: Jessica S Johnson, NanoBio Node
Combination of all tools used in Chapters 10-13 of Neural Systems Modeling by Anastasio
[Illinois]: Neural Systems Modeling Ch 6-9 Master Tool
26 Jul 2013 | | Contributor(s):: Jessica S Johnson, NanoBio Node
Combination of all tools used in Chapters 6-9 of Neural Systems Modeling by Anastasio
[Illinois]: Error Gradient Estimations Due to Parallel Perturbation of Weights
07 Jul 2013 | | Contributor(s):: AbderRahman N Sobh, Jessica S Johnson, NanoBio Node
This tool trains two-layered networks of sigmoidal units to associate patterns using simultaneous perturbation of weights.