GranSim is a hybrid agent-based computational model (ABM) that describes the formation and function of a granuloma during Mycobacterium tuberculosis infection in the lung. Although granulomas are 3D entities, due to the high computational costs associated to simulate a 3D version, GranSim has been developed and curated since 2004 only in 2D.

Prostate cancer (PCa) is the most commonly diagnosed malignancy and the second leading cause of cancer-related death in American men. Androgen deprivation therapy (ADT) has become a standard treatment strategy for advanced PCa. Although a majority of patients initially respond to ADT well, most of them will eventually develop castration-resistant PCa (CRPC).

In a new linkage, we connected atomistic scale information to protein, cell and tissue scales by predicting drug binding affinities and rates from simulation of ion channel and drug structure interactions and then used these values to model drug effects on the hERG channel.

The auditory stream segregation model leverages the multiplexed and non-linear representation of sounds along an auditory hierarchy and learns local and global statistical structure naturally emergent in natural and complex sounds.

During early mammalian embryo development, a small number of cells make robust fate decisions at particular spatial locations in a tight time window to form inner cell mass (ICM), and later epiblast (Epi) and primitive endoderm (PE).

The main goal of this project is to develop a software based on a novel mathematical framework that uses individual COVID-19 patient data to obtain accurate personalized treatment strategies.

The respiratory control system produces the rhythm that underlies breathing. But this rhythm is not restricted to just the respiratory system.

The purpose of this resource is a computational framework of a machine learning technique to analyze multi-region electrophysiological recordings and learn electrical connectome networks that are related to outcomes of interest (e.g., mouse model of depression).  The learned networks are visualizable and explainable.

The lung model integrates mechanics and cell models. The mechanics model utilizes imaging-based, high-fidelity computational technologies for three-dimensional (3D) fluid and solid mechanical systems to predict airflow-induced shear stress, tissue stress and particle deposition at a local level in the realistic human lung models.

The D-REX model is designed for exploring the computational mechanisms in the brain involved in statistical regularity extraction from dynamic sounds.

GranSim, the Agent-based model (ABM) describing tuberculosis (TB) granuloma formation and function in the lung, was developed based on four basic concepts: an environment (section of the lung parenchyma), agents (immune cells), ABM rules that govern the agents and their interactions, and the time-step (Δt) used to update events.

The project is to develop a full-scale model of rat hippocampus using compartmental models of individual neurons. The code available can be used to construct the connectivity for an entorhinal-dentate network with lateral and medial entorhinal cortical cells as spike generators and compartmental models of dentate granule cells and basket cells.

The Innate Immune Response Agent-Based Model (IIRABM) is a two-dimensional abstract representation of the human endothelial-blood interface.  This abstraction is designed to model the endothelial-blood interface for a traumatic (in the medical sense) injury, and does so by representing this interface as the unwrapped internal vascular surface of a 2D projection of the termin

We developed a model of primary motor cortex (M1) microcircuits [1] with over 10,000 biophysically detailed neurons and 30

Silk project;
-Replica exchange molecular dynamics is used to develop a structure for the silk chimeras.
-MD is also used to explain the change in integrin folding associated with its activation due to interactions with inorganic surfaces

When completed, the model will have a web-based user interface that allows immunologists and other researchers to interact with the model, gain insights into the early stages of the infection and test potential alternative, host centric interventions.

Tissue growth and remodeling (G&R) has been modeled in a continuum mechanics framework with an approach similar to plasticity named 'finite growth model'. Computationally, G&R has been simulated with custom finite element implementations.

Hybrid multi-scale computational model that tracks whole-lung Mycobacterium tuberculosis infection and predicts factors that inhibit dissemination.  

MICA is an imaging clustering analysis method that employs imaging-based metrics at local and global scales of the human lungs constructed from 3D computed tomography (CT) lung images to identify homogeneous subgroups, known as clusters, in healthy, asthma and COPD populations.

We will use an integrated Dissipative Particle Dynamics (DPD) and Coarse Grained Molecular Dynamics (CGMD) approach that allows platelets to continuously change their shape and synergistically activate by a biomechanical transductive linkage chain, interact with other blood constituents and clotting factors, aggregate, and interact and adhere to the blood vessels and

The code and methodology presented here describe a computational model aimed at investigating the effects of current waveforms of electrical stimulation of the retina used in prosthetic devices aimed at restoring partial vision lost to retinal degenerative diseases.

Amyotrophic lateral sclerosis (ALS) is the most common Motor Neuron Disease. It is a progressive neurodegenerative disease that affects motor neurons in the brain and the spinal cord. The progressive degeneration of motor neurons in the spinal cord causes patients to lose their ability to control their muscle movement.

National Toxicology Program (NTP) Interagency Center for the Evaluation of Alternative Toxicological Methods (NICEATM)

This resource is a project website to provide free access to three-dimensional finite element representations of the knee joint and open development of knee models for collaborative testing and use.

This is a physics-based model of central metabolism of Neurospora crassa, a filamentous fungi, in which physiologically reasonable rate constants are inferred from data and physical principles.

These models are composed of partial differential equations and boundary conditions that model the receptor-mediated activation of phospholipase C (PLC) and protein kinase C (PKC) enzymes in mammalian cells. PLC hydrolyzes the membrane lipid, PIP2, to produce the lipid second messenger, diacylglycerol (DAG), which mediates PKC activation at the plasma membrane.

This resource is the project website to provide fundamental data, open and freely accessible databases of tissue mechanical and anatomical properties, models of multi-layer tissue structures of musculoskeletal extremities.

This project aims for understanding the influence of modelers’ approaches and decisions (essentially their art) throughout the lifecycle of modeling and simulation. It will demonstrate the uncertainty of delivering consistent simulation predictions when the founding data to feed into models remain the same.

The Reference Model is:

The