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15 projects in result set.
IA-FEMesh
- In an effort to facilitate anatomic FE model development, we introduce IA-FE Mesh (Iowa FE Mesh), a freely available software toolkit. IA-FEMesh employs a multiblock meshing scheme aimed at hexahedral mesh generation. An emphasis has been placed on making the tools interactive, in an effort to create a user-friendly environment. The goal is to provide an efficient and reliable method for model development, visualization, and mesh quality evaluation. While these tools have been developed, initially, in the context of skeletal structures, they can be applied to a virtually endless number of modeling applications. | |
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Activity Percentile: 89.31 Registered: 2008-08-29 02:59 |
Normal human left ventricular myofiber stress
- Ventricular wall stress is believed to be responsible for many physical mechanisms taking place in the human heart, including ventricular remodeling, which is frequently associated with heart failure. Therefore, normalization of ventricular wall stress is the cornerstone of many existing and new treatments for heart failure. In this paper, we sought to construct reference maps of normal ventricular wall stress in humans that could be used as a target for in silico optimization studies of existing and potential new treatments for heart failure. To do so, we constructed personalized computational models of the left ventricles of five normal human subjects using magnetic resonance images and the finite element method. These models were calibrated using left ventricular volume data extracted from magnetic resonance imaging (MRI) and validated through comparison with strain measurements from tagged MRI (950 ± 170 strain comparisons/subject). The calibrated passive material parameter values were C0 = 0.115 ± 0.008 kPa and B0 = 14.4 ± 3.18; the active material parameter value was Tmax = 143 ± 11.1 kPa. These values could serve as a reference for future construction of normal human left ventricular computational models. The differences between the predicted and the measured circumferential and longitudinal strains in each subject were 3.4% ± 6.3% and 0.5% ± 5.9%, respectively. The predicted end-diastolic and end-systolic myofiber stress fields for the five subjects were 2.21 ± 0.58 kPa and 16.54 ± 4.73 kPa, respectively. Thus, these stresses could serve as targets for in silico design of heart failure treatments. | |
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Registered: 2014-06-04 18:58 |
BioGears: An open source mathematical model of the human physiology.
- BioGears is an open source, comprehensive, extensible human physiology engine that will drive medical education, research, and training technologies. BioGears enables accurate and consistent physiology simulation across the medical community. The engine can be used as a standalone application or integrated with simulators, sensor interfaces, and models of all fidelities. | |
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Activity Percentile: 0.00 Registered: 2014-10-09 18:12 |
HemoSim
- This Project is an analysis tool for blood flow modelling in arterial or venous trees. | |
Activity Percentile: 0.00 Registered: 2008-09-25 21:24 |
The Reference Model for Disease Progression
- The Reference Model is now:
• <a href="http://dx.doi.org/10.7759/cureus.9455" target="_blank"> COVID-19 model for US states and territories </a>
• <a href="https://jacob-barhak.github.io/InteractivePoster_MSM_IMAG_2019.html" target="_blank"> The Most Validated Cardiovascular (CVD) Diabetes Model known </a>
• <a href="https://patents.google.com/patent/US20140297241A1/en" target="_blank"> United States Patent 9,858,390</a>
• <a href="https://patents.google.com/patent/US20170286627A1/en" target="_blank"> United States Patent Number 10,923,234</a>
The Reference Model can now:
• Attempt to explain COVID-19 for US states
• Determine CVD models that significantly behave better on several diabetic populations
• Deduce that CVD probability halves every 5 years due to medicine improving - according to information from the last 3 decades
• Calculate life tables for diabetics
• Interface with ClinicalTrials.Gov
• Include human interpretation in the model
• Create an interactive map of our <a href="https://jacob-barhak.github.io/InteractivePoster_MSM_IMAG_2019.html" target="_blank"> <b> cumulative computational knowledge gap</b>
<a href="http://dx.doi.org/10.7759/cureus.9455" target="_blank"> <b> COVID-19 MODEL</b> </a>
The interactive plot below shows our cumulative knowledge gap by showing the error in the vertical axis for US states and territories listed on the horizontal axis. Circles at the bottom have a better fit between observed COVID-19 results and model results. Results are for normalized population of size 10,000 individuals. Hover over the circles to see additional details about each state. The slider determines the model optimization iteration. User can explore the map by changing size and color attributes.
<iframe width="1000" height="400" src="https://jacob-barhak.netlify.app/thereferencemodel/results_covid19_2020_06_27/populationplot" frameborder="0" > </iframe>
<a href="https://simtk.org/projects/mist" target="_blank"> <b> TECHNOLOGY </b> </a>
The Reference Model is a good way to cross reference information to find out pieces of information and assumptions that fit together, and allow competition against accumulated known data to guide our perception. High Performance Computing is a key to those capabilities and it provided using capabilities of the <a href="https://simtk.org/projects/mist" target="_blank"> MIcro Simulation Tool (MIST) </a> .
MIST also provides advance population generation techniques using Evolutionary computation. The Reference Model uses publicly available data such as clinical trial publications. This allows it to access more information since it allows accessing data that otherwise will be restricted from sharing. The Reference Model has an interface that allows it to read information from <a href="https://clinicaltrials.gov/" target="_blank" > ClinicalTrials.Gov</a> while maintaining tractability and reproducibility.
<b> <a href="https://simtk.org/plugins/simtk_news/index.php?group_id=1286" target="_blank"> PUBLICATIONS: </a> </b>
The Reference Model was created in 2012 and evolved since then. You can find key developments and publications by year in the <a href="https://simtk.org/plugins/simtk_news/index.php?group_id=1286" target="_blank"> news section </a>.
Here are some videos describing the Model:
This video gives a brief introduction
<iframe width="800" height="450" src="https://www.youtube.com/embed/s9L-qFF84Ew" title="The Reference Model for Disease Progression: Explaining COVID-19" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
This video will shows recent results of explaining COVID-19 using USA data:
<iframe width="800" height="450" src="https://www.youtube.com/embed/1M645o5gWrc" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
This video will show a breakthrough of becoming the first multiscale ensemble model for COVID-19:
<iframe width="800" height="450" src="https://www.youtube.com/embed/-z8N40TdKDk?start=1860" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
This video explains the model in a larger context as presented in AnacondaCon 2019:
<iframe width="800" height="450" src="https://www.youtube.com/embed/fQIYMf5wKGE" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
This video explains how human interpretation can be used as presented in the Multiscale Viral Pandemics working group webinar:
<iframe width="800" height="450" src="https://www.youtube.com/embed/aTB8-XEZheU" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
This video summarizes a decade of work as presented in PyTexas 2017:
<iframe width="800" height="450" src="https://www.youtube.com/embed/Pj_N4izLmsI?list=PL0MRiRrXAvRiwQUUwTTh5g8rhbQyYlubo" frameborder="0" gesture="media" allow="encrypted-media" allowfullscreen></iframe>
This describes the evolution of the model up to 2016 presented in PyTexas:
<iframe width="800" height="450" src="https://www.youtube.com/embed/htGRRjia-QQ" frameborder="0" allowfullscreen></iframe>
This describes the work presented in PyData in 2014:
<iframe width="800" height="450" src="https://www.youtube.com/embed/vyvxiljc5vA" frameborder="0" allowfullscreen></iframe> | |
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Registered: 2017-05-09 05:34 |
Python tools for Markov state models
- This project is a collection of Python modules for generating, analyzing, and interpreting Markov state models. Some features: objects to represent and sample from transition matrices, Singhal's sensitivity analysis, clustering on arbitrary data objects. | |
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Activity Percentile: 0.00 Registered: 2007-12-19 01:22 |
Hierarchical Human Biomechanics Framework
- This project intends to build a virtual anatomical object library to hierarchiclally implement human biomechanics simulators used to improve clinical approaches and human biotech products. | |
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Activity Percentile: 0.00 Registered: 2008-04-25 12:23 |
CFD analysis of Arterial flow in Thromboembolism
- To evaluate "52" dimensionless CFD numbers (akin to 'deck' of French-Playing cards):-
# Reynolds number,
# Sherwood number,
# Schimdt number,
# Rayleigh number,
# Weber number,
# Capillary number,
# Bond number,
# Froude number,
# Nusselt number,
# Peclet number (for Mass diffusivity),
# Peclet number (for Heat diffusivity),
# Prandtl number,
# Grashof number, and
# Brinkman number,
# Cavitation number,
# Stanton number,
# [Mass -Transfer] Stanton number,
# Eckert number,
# Knudsen number,
# Graetz number,
# Lewis number,
# Mach number,
# Poiseuille number,
# Rossby number,
# Strouhal number; and
# Taylor number,
# Archimedes number,
# Arrhenius number,
# Bingham number,
# Biot number,
# [Mass-Transfer] Biot number,
# Blake number,
# Bondenstein number,
# Cauchy number,
# Coefficient of Frication (dimensionless number),
# Condensation number,
# Dean number,
# Drag-coefficient (dimensionless number),
# Elasticity number,
# Etovos number,
# Euler number,
# Fourier number,
# [Mass-Transfer] Fourier number,
# Friction factor (dimensionless number),
# Galileo number,
# Colburn "j" (Heat) factor,
# Colburn "j" (Mass) factor,
# Hodgson number,
# Jakob number,
# Ohnesorge number,
# Pipeline parameter (dimensionless number),
# Power number [possibly of 3D-printed Thrombotic human heart].
Ideally, we would very much like to Extend this "Wolfram Mathematica-11 Demonstration" under the simplistic consideration of a Single "Spherical Thromb", merely beyond the Re= Reynolds number - to ALL of the "52" CFD-'deck' numbers immediately post-Plaque Fissure around the instance of "Thrombotic-Thrombolytic Equilibrium" involved in Coronary Arterial flow.
DEMO:
- Mikhail Dimitrov Mikhailov
"Flow around a Sphere at Finite Reynolds Number by Galerkin Method"
http://demonstrations.wolfram.com/FlowAroundASphereAtFiniteReynoldsNumberByGalerkinMethod/
Wolfram Demonstrations Project
Published: January 2, 2013
REFERENCES:
[0] Coronary Plaque Disruption
Erling Falk, Prediman K. Shah, Valentin Fuster
https://doi.org/10.1161/01.CIR.92.3.657
Circulation. 1995;92:657-671
Originally published August 1, 1995.
[1] Lagrangian wall shear stress structures and near-wall transport in high-Schmidt-number aneurysmal flows.
Amirhossein Arzani (a1), Alberto M. Gambaruto (a2), Guoning Chen (a3) and Shawn C. Shadden (a1)
(a1) Mechanical Engineering, University of California Berkeley, Berkeley, CA 94720, USA
(a2) Mechanical Engineering, University of Bristol, University Walk, Bristol BS8 1TR, UK
(a3) Computer Science, University of Houston, Houston, TX 77204, USA
https://doi.org/10.1017/jfm.2016.6
[2] A reduced-dimensional model for near-wall transport in cardiovascular flows.
Kirk B. Hansen* , Shawn C. Shadden*
*Department of Mechanical Engineering, University of California, Berkeley, CA, USA.
PMID: 26298313 PMCID: PMC4764478 DOI: 10.1007/s10237-015-0719-4
^WIKI:
https://en.wikipedia.org/wiki/Dimensionless_numbers_in_fluid_mechanics
$OPEN ACCESS IMAGING DATASETS:
https://grand-challenge.org/
@OUR LAB HOMEPAGE:
http://www.triindia.org/
%RESOURCES:
http://www.cfd.life/
https://cfd.direct/
+CERTIFICATIONS:
https://onlinecourses.nptel.ac.in/noc17_ee01/preview
https://onlinecourses.nptel.ac.in/noc17_ch01/preview
~Inspiration: "CAF" (Cellular Automaton Fluids: Wolfram, 1986).
http://www.stephenwolfram.com/publications/cellular-automata-complexity/pdfs/cellular-automaton-fluids-theory.pdf | |
Registered: 2017-01-23 13:42 |
Open MM and Zephyr applications to XBOX360 platform.
- This project is intended to use the OpenMM and Zephyr source code for compilation upon the XBOX 360 platforms. An executable with the functionality of Zephyr is desired. | |
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Activity Percentile: 0.00 Registered: 2009-12-25 17:02 |
Cardiovascular Model Repository
- The geometric models in this repository are collected from past research projects in the Cardiovascular Biomechanics Research Laboratory at Stanford University. The geometric models in this repository are mostly built from imaging data of healthy and diseased individuals. For each of the models, a short description is given with a reference. Click on the model image for a larger image of the model. The geometric models are in VTK PolyData XML .vtp format. For information about this format see VTK.org.
You are free to download the geometric models and use them provided that you properly reference the source. The models are part of the academic output of the researcher cited and should be referred to as such. Permission is granted to use these models for research purposes, but not for commercial use.
<b>Note: This repository is no longer maintained. A more up-to-date repository of cardiovascular models can be found at http://www.vascularmodel.com/sandbox/doku.php. </b>
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Activity Percentile: 0.00 Registered: 2005-06-20 17:42 |
Simulation of Coronary Artery Bypass Graft and Surgical Ventricular Restoration
- This project is a virtual surgery tool for enabling clinicians to easily simulate the effects of coronary artery bypass graft (CABG) and surgical ventricular restoration (SVR) on patients with ischemic heart failure. | |
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Activity Percentile: 0.00 Registered: 2009-03-19 19:19 |
3D Numerical Investigation of Endothelial Shear Stress in Arteries
- 3D numerical investigation of endothelial shear stress in coronary arteries. | |
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Activity Percentile: 0.00 Registered: 2015-11-30 13:34 |
Infarcted human left ventricular myofiber stress
- Heart failure is increasing at an alarming rate, making it a worldwide epidemic. As the population ages and life expectancy increases, this trend is not likely to change. Myocardial infarction (MI)-induced adverse left ventricular (LV) remodeling is responsible for nearly 70% of heart failure cases. The adverse remodeling process involves an extension of the border zone (BZ) adjacent to an MI, which is normally perfused but shows myofiber contractile dysfunction. To improve patient-specific modeling of cardiac mechanics, we sought to create a finite element model of the human LV with BZ and MI morphologies integrated directly from delayed-enhancement magnetic resonance (DE-MR) images. Instead of separating the LV into discrete regions (e.g., the MI, BZ, and remote regions) with each having a homogeneous myocardial material property, we assumed a functional relation between the DE-MR image pixel intensity and myocardial stiffness and contractility--we considered a linear variation of material properties as a function of DE-MR image pixel intensity, which is known to improve the accuracy of the model''''s response. The finite element model was then calibrated using measurements obtained from the same patient--namely, 3D strain measurements-using complementary spatial modulation of magnetization magnetic resonance (CSPAMM-MR) images. This led to an average circumferential strain error of 8.9% across all American Heart Association (AHA) segments. We demonstrate the utility of our method for quantifying smooth regional variations in myocardial contractility using cardiac DE-MR and CSPAMM-MR images acquired from a 78-yr-old woman who experienced an MI approximately 1 yr prior. We found a remote myocardial diastolic stiffness of C(0) = 0.102 kPa, and a remote myocardial contractility of T(max) = 146.9 kPa, which are both in the range of previously published normal human values. Moreover, we found a normalized pixel intensity range of 30% for the BZ, which is consistent with the literature. Based on these regional myocardial material properties, we used our finite element model to compute patient-specific diastolic and systolic LV myofiber stress distributions, which cannot be measured directly. One of the main driving forces for adverse LV remodeling is assumed to be an abnormally high level of ventricular wall stress, and many existing and new treatments for heart failure fundamentally attempt to normalize LV wall stress. Thus, our noninvasive method for estimating smooth regional variations in myocardial contractility should be valuable for optimizing new surgical or medical strategies to limit the chronic evolution from infarction to heart failure. | |
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Activity Percentile: 0.00 Registered: 2015-04-16 18:15 |
2007BioE15 Bruns
- Project for class. Hey! Guess what! It is required to put a longer \"detailed\" description into this area by the set up form! The retarded error message just says \"longer\", so who knows how long I have to keep spitting up this junk to keep the darn thing happy? | |
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Activity Percentile: 0.00 Registered: 2007-04-11 01:29 |
Flow and Velocities in an Artery Bypass Model: Finite-Element Simulation vs. MRI
- The study described in this publication compared finite-element fluid dynamics simulation results of blood flow against measurements obtained using magnetic resonance imaging (MRI) techniques. The simulation used data acquired from an in vitro experiment with pulsatile flow (average Reynolds number of 770) through an idealized blood vessel model with a stenosis and a bypass graft. | |
Registered: 2008-12-16 23:22 |