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Building a nanoHUB Graphical Interface for Exploring Protein Dynamics and Spectroscopy: the PigmentHunter App
Online Presentations | 18 Apr 2024 | Contributor(s):: Safa Ahad
Running and analyzing protein molecular dynamics (MD) simulations can be time consuming and tedious. In this webinar, we introduce PigmentHunter , an online nanoHUB tool that enables “point-and-click” MD-based simulation of excitonic spectra of chlorophyll proteins based on PDB...
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NanoHUB Jupyter Notebooks for Research and Education
Online Presentations | 15 Jun 2023 | Contributor(s):: Michael Earl Reppert
Prof. Reppert presents and over view of using nanoHUB Jupyter Notebooks to create applications for teaching chemistry. Also presented is a summary of the notebooks developed by his group.
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Photosynthetic Protein Spectroscopy Lab
Tools | 19 Oct 2020 | Contributor(s):: Safa Ahad, Chientzu Lin, Michael Earl Reppert
This tool parses PDB structures of photosynthetic proteins to identify pigments, calculate inter-pigment interactions, and simulate optical spectra for the complex.
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3 min. Research Talk: The Exciton Spectra Simulator of Photosynthetic Protein-pigment Complex
Online Presentations | 04 Feb 2019 | Contributor(s):: Qifeng Chen
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DNA and Protein Analysis using Nanotechnology I
Online Presentations | 19 Mar 2018 | Contributor(s):: Terry Kuzma, NACK Network
OutlinePart 1: This lectureMicroarrayTechnologyMicrofluidicsOverviewPart 2: Can be viewed hereCommon Materials and Processes
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DNA and Protein Analysis using Nanotechnology II
Online Presentations | 19 Mar 2018 | Contributor(s):: Terry Kuzma, NACK Network
OutlinePart 1: Can be viewed hereMicroarrayTechnologyMicrofluidicsOverviewPart 2: This lectureCommon Materials and Processes
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Biocompatibility and Cellular Overview II: Role of Proteins and Cellular Junctions
Online Presentations | 28 Nov 2017 | Contributor(s):: Terry Kuzma, NACK Network
Outline:BiocompatibilityQuick overview of cellular interactionscale, size, generic animal cellNanoscale materials for biological interactionLiposomesMetal NanoparticlesNanoshellsExamples of bionano applicationsLectures:Biocompatibility and Cellular Overview IBiocompatibility and Cellular Overview...
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DNA to Protein Overview Learning Module
Teaching Materials | 28 Aug 2017 | Contributor(s):: Southwest Center for Microsystems Education (SCME)
This learning module provides information needed to understand how the digitally encoded information in DNA is translated into a functional protein that can be used for biomedical applications. Activities delve deeper into protein structure and function as well as gene transcription.
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DNA to Protein Overview Learning Module - Instructor Guides
Teaching Materials | 28 Aug 2017 | Contributor(s):: Southwest Center for Microsystems Education (SCME)
This learning module provides information needed to understand how the digitally encoded information in DNA is translated into a functional protein that can be used for biomedical applications. Activities delve deeper into protein structure and function as well as gene transcription.
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Demo of Loading and Visualizing Proteins from the RCSB Protein Data Bank
Tools | 14 Dec 2016 | Contributor(s):: Martin Hunt
Demo of Loading and Visualizing Proteins from the RCSB Protein Data Bank
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[Illinois] Biophysics 401 Lecture 9: Protein Folding
Online Presentations | 20 Oct 2015 | Contributor(s):: Paul R Selvin
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[Illinois] Biomaterials to Replicate the Form and Function of Inhomogeneous Structures in the Body
Online Presentations | 25 Apr 2014 | Contributor(s):: Brendan Harley
The extracellular matrix (ECM) is a complex organization of structural proteins such as collagens and proteoglycans. Understanding that the ECM is dynamic and often spatially patterned or heterogeneous over the length-scale of traditional biomaterials, we are developing instructive biomaterials...
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cadnano to PDB File Converter
Tools | 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.
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Tensile Mechanics of alpha-Helical Polypeptides
Tools | 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.
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[Illinois] CNST 2013: Development of a Click Chemistry Approach to Evaluate the Effect of Protein Corona on Active Targeting Yield
Online Presentations | 31 May 2013 | Contributor(s):: Vahid Mirshafiee
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[Illinois] ECE 416 Avidin-Biotin and Surface Functionalization I
Online Presentations | 24 Apr 2013 | Contributor(s):: Brian Cunningham
In this lecture, we start off by taking a look at X-Ray Crystallography and how it is used to understand how biomolecules binding works. The x-ray data is processed by computer algorithms to determine coordinates of all atoms in...
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Carbon Dioxide Gating in Silk Cocoon
Papers | 18 Aug 2012 | Contributor(s):: sunil kumar meena
Silk is the generic name given to the fibrous proteins spun by a number of arthropods. During metamorphosis, the larva of the silk producing arthropods excrete silk-fiber from its mouth and spun it around the body to form a protective structure called cocoon. An adult moth emerges out from the...
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Appreciating Nature's Antibiotics as Chemical Treasures
Online Presentations | 21 Jun 2011 | Contributor(s):: Christopher T. Walsh
This lecture is part of the 28th Annual H.C. Brown Lectures in Organic Chemistry.
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Stretching simulation of an alpha-helical protein domain
Tools | 10 Jan 2011 | 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)
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BioInspired Solutions to Engineering Problems
Online Presentations | 17 Feb 2011 | Contributor(s):: Carlo Montemagno
Carlo Montemagno presented a research seminar to the BioEnegineering and MEMS programs at the University of Louisville on February 16, 2011. The talk is available as steaming video athttp://louisville.edu/television/bioengineering.021611.asxwith permission granted by C. Montemagno, R. Cohn and...