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pc4nanobio: cancer nanotherapy simulator
19 Apr 2018 | Contributor(s):: Randy Heiland, Paul Macklin
Simulate cancer response to shape-changing nanoparticles conjugated to novel therapeutics
The Effective Fragment Potential Method Calculation Tool
out of 5 stars
07 Jun 2017 | | Contributor(s):: Hanjing Xu, Pradeep Kumar Gurunathan
LIBEFP facilitates extension of unique electronic structure methodologies designed for accurate simulations in the gas phase to condensed phases via QM/EFP. This tool provides a easy-to-use GUI for input generation and output visualization.
Ions in Nanoconfinement
06 Dec 2017 | | Contributor(s):: Kadupitige Kadupitiya, Suresh Marru, Fox, Geoffrey C., Vikram Jadhao
The Ions in Nanoconfinement app empowers users to simulate ions confined between material surfaces that are nanometers apart, and extract the associated ionic structure.
Atomistic Polymer Workflow Notebook
19 Oct 2017 | | Contributor(s):: Benjamin P Haley
Run PolymerModeler and nuSIMM tools to create atomistic polymer systems
Mechanics of Crystalline Nano Cellulose Nanofilm
06 Jul 2017 | | Contributor(s):: Joshua Leonardo, Mehdi Shishehbor, Pablo Daniel Zavattieri
Simulation of tensile tests on your own Crystalline Nano Cellulose structures.
Fundamental Limits to the Precision of Multicellular Sensing
26 Jun 2017 | | Contributor(s):: Andrew Mugler
Here we address, with both theory and experiments, whether cell-cell communication improves concentration- and gradient-sensing precision. We develop a minimal model of collective sensing by cells that communicate via juxtacrine signaling, in which a small molecule is exchanged between...
Glass transition temperature notebook
22 May 2017 | | Contributor(s):: Benjamin P Haley, Lorena Alzate-Vargas
Calculate the glass transition temperature of an atomistic, amorphous system by running MD simulations in a notebook
A profile of a Nano EPICS High School - Agawam High School
10 May 2017 | | Contributor(s):: Tamecia Raishaun Jones
This is a short profile of an EPICS High School that has found a way to integrate nano into its curriculum. The profile describes how the teacher used her specialized background in marine biology to create a plan for nano project in a marine biology classroom. At the time, this...
[Illinois] NanoBIO Interfaces
13 Apr 2017 | | Contributor(s):: Aleksei Aksimentiev
11/29/2016Light/Matter Interactions at the Nano-Bio Interface Workshop
Unsupervised Learning to Unravel Differential Cell Fate Outcomes
09 Dec 2016 | | Contributor(s):: Kristen Naegle
Cells are constantly receiving cues from the outside world and responding to them by altering their physiological fate by transducing this signal via intracellular biochemical networks. An important mechanism that many cell networks utilize to transduce these signals is the regulation of protein...
DNA Origami Visualization Tools
12 Sep 2016 | | Contributor(s):: Jessica Nash
Visualize DNA origami designs
Tracking the Maturation of Organelles and Signaling Cluster with Quantitative Super-Resolution Microscopy
09 Dec 2016 | | Contributor(s):: Elias M. Puchner
Quantitative Super-Resolution Microscopy is evolving into a powerful technique to study biological processes below the optical diffraction limit. However, a deeper understanding of the biological structures under investigation is often limited by the inability to quantify their molecular...
Characterizing Noise in a Mathematical Model of the Adipogenic Transcriptional Network
09 Dec 2016 | | Contributor(s):: Alexandra Jilkine
For each model, we first characterized overall susceptibility to noise by calculating the relative local sensitivity of AdipoQ and fat to various parameters. We then simulated the experiment done by Loo et al. with 30% added noise to determine if our system could replicate their data. Our...
Population Density Modulates Antibiotic Efficacy, Treatment Bistability, and the Evolution of Resistance in Bacteria
09 Dec 2016 | | Contributor(s):: Kevin Wood
In this talk, I will discuss our recent work to address these questions by measuring real-time per capita growth of Enterococcus faecalis populations at fixed population densities using multiplexed computer-automated culture devices. We show that density-dependent growth inhibition is pervasive...
Atomic Resolution Brownian Dynamics
09 Nov 2016 | | Contributor(s):: Chris Maffeo
GPU-accelerated Brownian dynamics simulation tool for biomolecular and nanotechnological systems
Tissue-Level Communication Through Patterning Of Intercellular Ca2+ Wave Dynamics
21 Nov 2016 | | Contributor(s):: Jeremiah J. Zartman
Here we characterize periodic intercellular Ca2+ waves (ICWs) in a model organ system of epithelial growth and patterning—the Drosophila wing imaginal disc. We developed a novel regulated environment for micro-organs (REM-Chip) device that enable a broad range of genetic, chemical and...
Decoding the Epigenetic Language of Life
15 Nov 2016 | | Contributor(s):: Jian-Kang Zhu
I will describe work in my lab that has shed light on how DNA methyltransferases and demethylases are guided to specific sequences, and how the antagonistic actions of the enzymes are coordinated to generate proper DNA methylation patterns. I will also describe some of our recent work on how DNA...
Coarse Graining of Crystalline Cellulose
29 Jul 2016 | | Contributor(s):: Kuo Tian, Mehdi Shishehbor, Pablo Daniel Zavattieri
Bio-inspired Crystalline Nano-Cellulose coarse graining toolkit
MidQBio 2016: 4th Midwest Quantitative Biology Symposium
22 Oct 2016 | | Contributor(s):: Srividya Iyer-Biswas, Tamara L. Kinzer-Ursem, Andrew Mugler
The MidQBio Symposium aims to bring together research groups from around the Midwest with a shared interest in quantitative biology, and to help build a community of these researchers. The symposium provides researchers opportunities to meet periodically to disseminate recent results; network...
The Epithelial-Mesenchymal Transition Its role in metastasis? Can Theory Help Cancer Biology?
19 Oct 2016 | | Contributor(s):: Herbert Levine
In order to spread from the primary tumor to distant sites, cancer cells must undergo a coordinated change in their phenotypic properties referred to as the "epithelial-to-mesenchymal" transition. We have studied the nonlinear genetic circuits that are responsible for this...