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Agent Based Active Matter Simulations with Mechanica
14 Nov 2021 | | Contributor(s):: Somogyi, Andy T
Mechanica is an interactive mesh-free, chemistry and biology simulation environment, with an emphasis towards enabling users to model and simulate complex sub-cellular and cellular biological physics problems. Mechanica is designed first and foremost to enable users to work interactively...
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Winter Interactive nanoBIO Workshop
04 Feb 2021 | | Contributor(s):: Ballard, Joshua Brendan (editor)
The Winter Interactive nanoBIO Workshop will walk students and researchers through how to understand a variety of biological problems using simulations based on cloud-based tools on nanoHUB or other easy to use platforms.
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How Simple Cell-Cell Interactions Lead to Complex Multicellular Dynamics
04 Feb 2021 | | Contributor(s):: Paul Macklin
In this talk, we use agent-based simulation models to simulate (1) individual cell behaviors, (2) cell-cell interactions, and (3) cell-environment interactions to show how simple rules can give rise to complex multicellular phenomena. We showcase and explore free, interactive online tools to...
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Biology of COVID-19 Attack on Epithelial Cells, understood from a Modeling and Simulation Perspective
04 Feb 2021 | | Contributor(s):: Paul Macklin
n this session, we describe a community-driven effort to iteratively develop a multiscale, spatially-resolved open source model of SARS-CoV-2 dynamics and immune response in tissues.
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PhysiCell model for tumor hypoxia
07 Aug 2020 | | Contributor(s):: Lima Da Rocha, Heber, Paul Macklin, Furkan Kurtoglu
Multicellular simulation in 2-D of tumor hypoxia.
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CompuCell3D v4 Main Tool
08 Jun 2020 | | Contributor(s):: Juliano Ferrari Gianlupi, T.J. Sego
Base tool for CompuCell3D version 4 and greater. Allows running any of the demos included with CC3D (/CompuCell3D_Demos/Demos)
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Understanding Movement of Molecules across the Cell Membrane
17 Apr 2020 | | Contributor(s):: Brandi Childress, NNCI Nano
This lesson uses a macro-model to demonstrate the diffusion of molecules across the cell membrane. A deshelled egg serves as the cell model to observe movement in and out of the “cell”. Students will learn that the cell membrane is composed of a complex nano-structured...
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Linear Diffusion and Cell Signaling
17 Apr 2020 | | Contributor(s):: NNCI Nano
In this activity, students explore the concept of diffusion as a component of cell communication. Specifically, students will explore how the rate of diffusion varies with distance and concentration gradient. They will use a pipet with water and dye to observe a macro-model of diffusion....
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Soft Materials for Studying Hard Biological Problems
15 Oct 2019 | | Contributor(s):: Kristi S. Anseth
This talk will illustrate how we leverage these and other reversible chemistries to create biologically responsive hydrogel matrices, and employ them to study the effects of matricellular signaling on diverse cellular functions and processes. For example, we exploit...
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Replication Competent Oncolytic Virus in Epithelial cell layer
18 Apr 2019 | | Contributor(s):: Adrianne Jenner, Paul Macklin
PhysiCell simulation of a replication competent oncolytic virus release from two veins, diffusing through a layer of epithelial cells.
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CELL-MET Thrust Area 2: Nanomechanics: Mechanical Properties of Materials, Scaffolds and Cardiac Tissues
04 Apr 2019 | | Contributor(s):: Pranjal Nautiyal
In this presentation, FIU graduate student Pranjal Nautiyal explains his work on Nanomechanics in Arvind Agarwal's Lab.
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CELL-MET Thrust Area 2 - Nanomechanics: Cell-Integrated Surface Plasmon Resonance
08 Feb 2019 | | Contributor(s):: Maedeh Mozneb, CELL-MET ERC
In this presentation, FIU graduate student Maedeh Mozneb explains her work on Nanomechanics in Chen-Zhong Li’s lab.
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Cells: The Building Blocks of Life Learning Module
28 Aug 2017 | | Contributor(s):: Southwest Center for Microsystems Education (SCME)
This learning module provides a review of "cells", the smallest unit exhibiting the properties of life. It discusses how these cells are being used in bioMEMS as well as other micro and nano-sized devices. A research activity provides the opportunity to further explore how...
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Cells: The Building Blocks of Life Learning Module - Instructor Guides
28 Aug 2017 | | Contributor(s):: Southwest Center for Microsystems Education (SCME)
This learning module provides a review of "cells", the smallest unit exhibiting the properties of life. It discusses how these cells are being used in bioMEMS as well as other micro and nano-sized devices. A research activity provides the opportunity to further explore how...
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Inference from Single Molecules to Cells
19 Jan 2017 | | Contributor(s):: Steve Pressé
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Nanoparticle Pollutants
17 Jan 2017 | | Contributor(s):: Darren Hayes, Nancy Healy, NNCI Nano
Many plastics are in our oceans due to pollution, including ocean dumping and land runoff. Sunlight and alkaline ocean water break these plastics down into small particles, many are nanoscale in size. These nanoparticles can easily enter our cells. Students examine if and how these...
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Pulsed Power as an Enabling Technology for Cellular Manipulation and Cancer Treatment
02 Dec 2016 | | Contributor(s):: Allen Garner
Ongoing research explores the application of pulsed power for biomedical applications, including athermal sterilization of milk, water, and juices, cancer treatment, permeabilization of cells and tissues for drug delivery, and even wound healing. This lecture will provide a general overview...
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Tissue-Level Communication Through Patterning Of Intercellular Ca2+ Wave Dynamics
22 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...
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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...
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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...