Insights Into the Amazing World of RNA Catalysis from Hybrid QM/MM Simulations
07 Nov 2017 | Online Presentations | Contributor(s): Darrin M. York
The present talk will focus on the use of computational enzymology approaches to gain a unified interpretation of experimental data and a detailed, predictive understanding of catalytic mechanism. Molecular simulation models, including from ab initio combined quantum mechanical/molecular...
Atomistic Polymer Workflow Notebook
19 Oct 2017 | Tools | Contributor(s): Benjamin P Haley
Run PolymerModeler and nuSIMM tools to create atomistic polymer systems
Mechanics of Crystalline Nano Cellulose Nanofilm
06 Jul 2017 | Tools | 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
27 Jun 2017 | Online Presentations | 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 | Tools | 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 | Papers | 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 | Online Presentations | Contributor(s): Aleksei Aksimentiev
11/29/2016Light/Matter Interactions at the Nano-Bio Interface Workshop
Unsupervised Learning to Unravel Differential Cell Fate Outcomes
17 Jan 2017 | Online Presentations | 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 | Tools | Contributor(s): Jessica Nash
Visualize DNA origami designs
Tracking the Maturation of Organelles and Signaling Cluster with Quantitative Super-Resolution Microscopy
15 Dec 2016 | Online Presentations | 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
15 Dec 2016 | Online Presentations | 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
13 Dec 2016 | Online Presentations | 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 | Tools | 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
22 Nov 2016 | Online Presentations | 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
22 Nov 2016 | Online Presentations | 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 | Tools | 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 | Workshops | 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 | Online Presentations | 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...
18 Jul 2016 | Tools | Contributor(s): Aldi Hoxha, Paolo Scarbolo, Andrea Cossettini, Federico Pittino, Luca Selmi
A tool to simulate Ion Sensitive Field Effect Transistors in two dimensions
Collective Sensing by Communicating Cells
22 Sep 2016 | Online Presentations | Contributor(s): Andrew Mugler
In this talk I will describe recent theoretical and experimental results in which this question is explored in several contexts, including gradient detection by groups of epithelial cells. I will show how communication allows cells to perform qualitatively new behaviors that single cells cannot...