Tags: nano/bio

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  1. Virtual Tissue Computer Simulation of Development, Homeostasis and Disease using CompuCell3D

    22 Sep 2022 | | Contributor(s):: James A Glazier, Trinity Chung

  2. Building & Testing a Component of Synthetic Genetic Circuit in Mammalian Cells

    20 Aug 2022 | | Contributor(s):: Ariel Delos Reyes, Rice University

    Oscillations in protein levels within cells help facilitate a variety of biological processes, from circadian rhythm to cell cycle progression. This research focuses on developing a platform for creating oscillatory circuits in mammalian cells by using several interrelated DNA constructs....

  3. Nanotechnolgy: The Future of Medicine?

    28 Jul 2022 | | Contributor(s):: Jared Ashcroft

  4. Antibody Engineers - Antibody Hackathon

    15 Jul 2022 |

  5. Nanomedicine for Drug Delivery, Controlled Release and Targeted Therapy

    17 Jun 2022 | | Contributor(s):: Neda Habibi

  6. CompuCell3D - Simulation of cell crawling in 3D

    03 Feb 2022 |

    Deploys the CompuCell3D simulation of cell crawling in 3D by Fortuna et al. 2020 https://doi.org/10.1016/j.bpj.2020.04.024

  7. Designing Machine Learning Surrogates for Molecular Dynamics Simulations

    25 Nov 2021 | | Contributor(s):: JCS Kadupitiya

    Molecular dynamics (MD) simulations accelerated by high-performance computing (HPC) methods are powerful tools for investigating and extracting the microscopic mechanisms characterizing the properties of soft materials such as self-assembled nanoparticles, virus capsids, confined electrolytes,...

  8. 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...

  9. Fun Experiments You Can Only Do With Frogs

    08 Jul 2021 | | Contributor(s):: Rebecca W. Heald

    Our studies aim to reveal underlying principles of spindle assembly and biological size control, as well as the molecular basis of variation that contributes to genomic instability and evolution. This talk will focus on the nano-scale aspects and include some single molecule experiments our lab...

  10. Rebecca W. Heald

    Rebecca Heald is a cell biologist recognized for her work on cell division and biological size control. In particular, she is known for her use of cytoplasmic extracts prepared from eggs of the...


  11. Tuberculosis Model Incorporating Treatment, Vaccination, and Antibiotic Resistance

    27 May 2021 | | Contributor(s):: Antonio Zdanis Neher

    Run though an interactive application to learn more about the consequences of antibiotic resistant pathogens through the lens of Tuberculosis.

  12. Cancer Evolution in CompuCell3D

    27 May 2021 | | Contributor(s):: Juliano Ferrari Gianlupi, James A Glazier

    Demonstrates implemetation of cancer evolution in CompuCell3D

  13. FocalPointPlasticity Plugin Demo

    19 May 2021 | | Contributor(s):: Juliano Ferrari Gianlupi, T.J. Sego

    This simple demo shows basic functionality of FocalPointPlasticity and how link rigidity affects cell behaviors.

  14. PhysiCell simulation of GBM tumour under oHSV1 treatment

    28 Mar 2021 | | Contributor(s):: Adrianne Jenner, Randy Heiland, Paul Macklin

    Simulation for GBM fragment growth under oHSV1 treatment published in Jenner et al. (2021)

  15. 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.

  16. Deep Learning for Time Series Illustrated by COVID-19 Infection Studies

    04 Feb 2021 | | Contributor(s):: Geoffrey C. Fox

    We show that one can study several sets of sequences or time-series in terms of an underlying evolution operator which can be learned with a deep learning network.

  17. 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...

  18. Cancer Games: Interactive Simulation of the Effect of Resource Limitation on Cancer Somatic Evolution using nanoHUB CompuCell3D

    04 Feb 2021 | | Contributor(s):: James A Glazier

    In this interactive mini-workshop we will use a very simple model of cancer somatic evolution and resource limitation based on one originally proposed by Heiko Enderling.

  19. Shape-changing Nanoparticles for Nanomedicine Applications

    04 Feb 2021 | | Contributor(s):: Vikram Jadhao

    I will describe the nanoHUB tool “Nanoparticle Shape Lab” that enables simulations of the shape deformation of charged nanoparticles for a broad variety of nanoparticle material properties including nanoparticle surface charge, pattern, elasticity and solution conditions such...

  20. 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.