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57 projects in result set. Displaying 20 per page. Projects sorted by alphabetical order.
<1> <2> <3>
Open Knee(s): Virtual Biomechanical Representations of the Knee Joint
- Open Knee(s) was aimed to provide free access to three-dimensional finite element representations of the knee joint (<A HREF="https://doi.org/10.1007/s10439-022-03074-0">https://doi.org/10.1007/s10439-022-03074-0</A>). The development platform remains open to enable any interested party to use, test, and edit the model; in a nut shell get involved with the project.
This study was primarily funded by the National Institute of General Medical Sciences, National Institutes of Health (R01GM104139) and in part by National Institute of Biomedical Imaging and Bioengineering (R01EB024573 and R01EB025212). Previous activities leading towards this project had been partially funded by the National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health (R01EB009643).
Open Knee(s) by Open Knee(s) Development Team is licensed under a <A HREF="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International License</A>.
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Registered: 2010-02-18 20:41 |
Whole-Cell Computational Model of Mycoplasma genitalium
- The goal of this project was to develop the first detailed, "whole-cell" computational model of the entire life cycle of living organism, <i>Mycoplasma genitalium</i>. The model describes the dynamics of every molecule over the entire life cycle and accounts for the specific function of every annotated gene product.
We anticipate that whole-cell models will be critical for synthetic biology and personalized medicine. Please see the project website <a href="http://wholecell.org">wholecell.org</a> and the Downloads page to explore the whole-cell knowledge base and simulations and obtain the model code. | |
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Registered: 2012-01-24 03:21 |
Are subject-specific musculoskeletal models robust to parameter identification?
- This study analyzed the sensitivity of the predictions of an MRI-based musculoskeletal model (i.e., joint angles, joint moments, muscle and joint contact forces) during walking to the unavoidable uncertainties in parameter identification, i.e., body landmark positions, maximum muscle tension and musculotendon geometry. To this aim, we created an MRI-based musculoskeletal model of the lower limbs, defined as a 7-segment, 10-degree-of-freedom articulated linkage, actuated by 84 musculotendon units. We then performed a Monte-Carlo probabilistic analysis perturbing model parameters according to their uncertainty, and solving a typical inverse dynamics and static optimization problem using 500 models that included the different sets of perturbed variable values. Model creation and gait simulations were performed by using freely available software that we developed to standardize the process of model creation, integrate with OpenSim and create probabilistic simulations of movement. | |
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Activity Percentile: 92.37 Registered: 2014-11-10 15:19 |
Predicting Cell Deformation from Body Level Mechanical Loads
- This project is a NIBIB/NIH funded study (1R01EB009643-01) to establish models and computational platforms to predict cellular deformations from joint level mechanical loading.
Collaborators:
Ahmet Erdemir (PI), Amit Vasanji, Jason Halloran (Cleveland Clinic)
Cees Oomens, Frank Baaijens (Eindhoven University of Technology)
Jeff Weiss (University of Utah)
Farshid Guilak (Duke University)
Summary (from grant proposal):
Cells of the musculoskeletal system are known to have a biological response to deformation. Deformations, when abnormal in magnitude, duration, and/or frequency content, can lead to cell damage and possible disruption in homeostasis of the extracellular matrix. These mechanisms can be studied in an isolated fashion but connecting mechanical cellular response to organ level mechanics and human movement requires a multiscale approach. At the organ level, physicians perform surgical procedures, investigators try to understand risk of injury, and clinicians prescribe preventive and therapeutic interventions. Many of these operations are aimed at management and prevention of cell damage, and to associate joint level mechanical markers of failure to cell level failure mechanisms. Through human movement, one explores neuromuscular control mechanisms and the influence of physical activity on musculoskeletal tissue properties. At a lower level, mechanical sensation of cell deformations regulate movement control. Physical rehabilitation and exercise regimens are prescribed to promote tissue healing and/or strengthening through cellular regeneration. The knowledge of the mechanical pathway, through which the body level loads are distributed between organs, then within the tissues and further along the extracellular matrix and the cells, is critical for the success of various interventions. However, this information is not established. The goal of this research proposal is to portray that prediction of cell deformations from loads acting on the human body, therefore a clear depiction of the mechanical pathway, is possible, if a multiscale simulation approach is used. Multiresolution models of the knee joint, representative of joint, tissue and cell structure and mechanics, will be developed for this purpose. The knee endures high rates of traumatic injury to its soft tissue structures and it is predominantly affected by osteoarthritis, chronically induced by abnormalities in mechanical loading or how it is transferred to the cartilage. Through multiscale mechanical coupling of these models, a map of cellular deformation in cartilage, ligaments and menisci under a variety of tibiofemoral joint loads will be obtained. Comprehensive mechanical testing at joint, tissue and cell levels will be conducted for parameter estimation and validation, including in vitro loading of the knee joint representative of lifelike loading scenarios. In addition, imaging modalities will capture joint and tissue anatomy, and spatial and deformation related information from cell and extracellular matrix. Advanced computational approaches will be used to obtain model properties and to facilitate multiscale simulations. The approach will combine the expertise of many investigators experienced in biomechanical modeling and experimentation at various biological scales, some with clinical expertise. In future, the research team will utilize this platform to establish the relationship between the structural and loading state of the knee and chondrocyte stresses to explore potential mechanisms of cartilage degeneration. Through documented dissemination of data and models, simulations of other pathologies and translation of the methodology to other organs can be carried out by any interested investigator. | |
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Registered: 2009-07-23 17:33 |
Predicting allosteric communication in myosin via a conserved residue pathway
- This project contains the AlloPathFinder application that allows users to compute likely allosteric pathways in proteins. The underlying assumption is that residues participating in allosteric communication should be fairly conserved and that communication happens through residues that are close in space.
The initial application for the code provided was to study the allosteric communication in myosin. Myosin is a well-studied molecular motor protein that walks along actin filaments to achieve cellular tasks such as movement of cargo proteins.
It couples ATP hydrolysis to highly-coordinated conformational changes that result in a power-stroke motion, or ''walking'' of myosin. Communication between a set of residues must link the three functional regions of myosin and transduce energy: the catalytic ATP binding region, the lever arm, and the actin-binding domain. We are investigating which residues are likely to participate in allosteric communication pathways. | |
Registered: 2007-01-09 18:30 |
Musculoskeletal Model of the Lumbar Spine
- The work here features a number of different OpenSim models of the lumbar spine developed to study lumbar kinematics and dynamics.
Briefly, the models consist of the following bodies:
# rigid pelvis and sacrum
# five lumbar vertebrae (separated by joints with three rotational degrees of freedom)
# torso (thoracic spine + ribcage)
The motion of the individual joints are defined using constraint functions specifying the motion of the lumbar vertebra as functions of the net lumbar motion (flexion-extension, lateral bending and axial rotation). Future models will incorporate joints with stiffness properties to more accurately mimic the action of the intervertebral joints.
The most complex of these models also feature the 238 muscle fascicles associated with the 8 main muscle groups of the lumbar spine necessary to study the contribution of the lumbar spinal musculature to spinal motion. Simpler models incorporating two and seven of the main muscle groups of the lumbar spine are provided as well for completeness.
Read more about the model in the paper, freely downloadable at http://link.springer.com/article/10.1007%2Fs10237-011-0290-6.
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September 2011 Addendum
Click on the "Downloads" link to the left for downloads related to more recent work.
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September 2012 Addendum
The Constrained Lumbar Spine Model does not require any of the files uploaded after the creation of the Constrained Lumbar Spine Model project. The .vtp files (and descriptions) are included here for the benefit of those of you who wish to create your own model that has origins shifted to the center of the bones since this typically saves a number of transformations. Many apologies for any confusion(!).
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March 2014 Addendum
(1)
This model was build with OpenSim 2+. Version 3+ will not allow you to use periods (.) in your variable names. Unfortunately, a bunch of the variables used (muscles mainly) have periods in the names so it will throw an error if you try and run it in OpenSim version 3+. To fix this, either use version 2+, OR, rename the variables appropriately.
(2)
We have all graduated and are no longer actively working on this project (we haven't been working on it since the end of 2011 actually). At this point, you probably know more than us about OpenSim so we apologize in advance if our support is subpar.
(3)
The complex mode is not meant to be run straight out of the box. It has almost 250 muscles after all and unless you have a super computer, running CMC, or FD on it is going to bring up the rainbow ball of death on your computer.
Rather, it's meant to be a reference for those of you who intend to build up your own model. My advice would be to start with the simple 4 fascicle model, get it to work, then incrementally build up from there using the parameters provided in our model as a starting point. Copy-Paste is your friend here. :)
(4)
If this is your very first OpenSim project, I strongly _strongly_ *strongly* suggest that you go through the examples provided with the OpenSim version you just downloaded and understand how they work. This will save you months of pain down the road. | |
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Activity Percentile: 87.02 Registered: 2010-11-04 02:25 |
Force Field X
- Force Field X is a group of open source (GPL v. 3), platform independent (Java Runtime Environment) modules for molecular biophysics. Key methods include:
Polarizable AMOEBA force fields
Particle-mesh Ewald electrostatics
Generalized Kirkwood continuum electrostatics
X-ray and neutron crystallography refinement
Real space refinement for CryoEM
Methods for structure based drug design
for more information, see http://ffx.kenai.com | |
Activity Percentile: 86.26 Registered: 2012-02-04 21:49 |
Specimen-Specific Models of the Healthy Knee
- As part of research funded by the National Institutes of Health, National Institute of Biomedical Imaging and Bioengineering (NIBIB), investigators at the University of Denver Center for Orthopaedic Biomechanics have made available a repository of experimental, image, and computational modeling data from mechanical testing of natural human knee biomechanics. It is uncommon for such a comprehensive dataset to be obtained. Therefore, we have made this repository available to assist the greater research community interested in the complexities and pathologies of knee health and mechanical function. Data are provided for 7 human knees (5 cadaveric subjects) and fall under two categories:
Image Data and Experimental & Computational Modeling Data.
Additional details about the data can be found at:
http://ritchieschool.du.edu/research/centers-institutes/orthopaedic-biomechanics/downloads/natural-knee-data/
This repository of natural knee data has been made available thanks to funding from the National Institutes of Health through National Institute of Biomedical Imaging and Bioengineering R01-EB015497. | |
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Registered: 2008-06-12 23:15 |
Reference Models for Multi-Layer Tissue Structures
- This project aims to establish the founding knowledge, data and models for the mechanics of multi-layer tissue structures of the limbs, particularly of the lower and upper legs and arms. The activity is targeted to promote scientific research in layered tissue structures and allow reliable virtual surgery simulations for clinical training and certification.
This research and development project titled “Reference Models for Multi-Layer Tissue Structures" was conducted by the Cleveland Clinic Foundation and was made possible by a contract vehicle which was awarded and administered by the U.S. Army Medical Research & Materiel Command under award number: W81XWH-15-1-0232. The views, opinions and/or findings contained in this website are those of the authors and do not necessarily reflect the views of the Department of Defense and should not be construed as an official DoD/Army position, policy or decision unless so designated by other documentation. No official endorsement should be made. | |
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Registered: 2015-08-24 12:54 |
Simulation of Constrained Musculoskeletal Systems in Task Space
- Objective: This work proposes an operational task space formalization of constrained musculoskeletal systems, motivated by its promising results in the field of robotics.
Methods: The change of representation requires different algorithms for solving the inverse and forward dynamics simulation in the task space domain. We propose an extension to the Direct Marker Control and an adaptation of the Computed Muscle Control algorithms for solving the inverse kinematics and muscle redundancy problems respectively.
Results: Experimental evaluation demonstrates that this framework is not only successful in dealing with the inverse dynamics problem, but also provides an intuitive way of studying and designing simulations, facilitating assessment prior to any experimental data collection.
Significance: The incorporation of constraints in the derivation unveils an important extension of this framework towards addressing systems that use absolute coordinates and topologies that contain closed kinematic chains. Task space projection reveals a more intuitive encoding of the motion planning problem, allows for better correspondence between observed and estimated variables, provides the means to effectively study the role of kinematic redundancy and, most importantly, offers an abstract point of view and control, which can be advantageous towards further integration with high level models of the precommand level.
Conclusion: Task-based approaches could be adopted in the design of simulation related to the study of constrained musculoskeletal systems.
The source code of the project can be found at: https://github.com/mitkof6/opensim-task-space.git
The new API of task space and constraint projection for OpenSim V4.0 is available at: https://github.com/mitkof6/task-space
<iframe width="560" height="315" src="https://www.youtube.com/embed/jfE14iWRZDs" frameborder="0" allow="autoplay; encrypted-media" allowfullscreen></iframe> | |
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Registered: 2017-08-28 12:06 |
Topological Methods for Exploring Low-density States in Folding Pathways
- In this paper, we develop a computational approach to explore the relatively low populated transition or intermediate states in biomolecular folding pathways based on a topological data analysis tool, Mapper. We applied Mapper to simulation data from large-scale distributed computing to provide structural evidence on multiple intermediate states of the unfolding and refolding of an RNA hairpin with a GCAA tetraloop. This project contains Mapper, the RNA conformations (in contact map format), and instructions to reproduce results from this paper.
<b> Motivation: </b> Characterization of transient intermediate or transition states is crucial for the description of biomolecular folding pathways, which is however difficult in both experiments and computer simulations. Such transient states are typically of low population in simulation samples. Even for simple systems such as RNA hairpins, recently there are mounting debates over the existence of multiple intermediate states.
<b> More about Mapper and the computational approach </b> The method is inspired by the classical Morse theory in mathematics which characterizes the topology of high dimensional shapes via some functional level sets. In this paper we exploit a conditional density filter which enables us to focus on the structures on pathways, followed by clustering analysis on its level sets, which helps separate low populated intermediates from high populated uninteresting structures.
The method is effective in dealing with high degree of heterogeneity in distribution, capturing structural features in multiple pathways, and being less sensitive to the distance metric than nonlinear dimensionality reduction or geometric embedding methods. The methodology described in this paper admits various implementations or extensions to incorporate more information and adapt to different settings, which thus provides a systematic tool to explore the low density intermediate states in complex biomolecular folding systems. | |
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Activity Percentile: 79.77 Registered: 2008-12-10 00:53 |
Stroke gait
- This project involves the generation of subject-specific simulations of a range of post-stroke hemiparetic gait patterns, contribution of parallel optimization techniques, comparison of control algorithms, and analysis of 2d and 3d results. | |
Activity Percentile: 62.60 Registered: 2006-08-23 17:28 |
HiTRACE: High-Throughput Robust Analysis for Capillary Electrophoresis
- This project contains the HiTRACE software that allows users to accurately and automatically perform key quantitative analysis tasks involved in high-throughput capillary electrophoresis (CE) of nucleic acids. CE has become a workhorse technology underlying high-throughput experimental methods such as high-speed genome sequencing and large-scale footprinting for nucleic acid structural inference. Despite the wide availability of CE-based equipment, there remain challenges in leveraging the full power of CE for quantitative analysis of RNA and DNA structure. We developed HiTRACE in order to address this issue. See <a href="http://arxiv.org/abs/1104.4337">Preprint</a> for more information. | |
Activity Percentile: 53.82 Registered: 2010-11-10 08:11 |
Evertor and invertor muscle co-activation prevents ankle inversion injury
- The study described in this publication used musculoskeletal simulations to compare the capacity of planned invertor/evertor co-activation versus stretch reflexes with physiologic delay to prevent ankle inversion injuries. To achieve this, developed a novel model, muscle stretch controllers, and muscle reflex controllers for simulating landing in OpenSim. By freely providing the models, software plugins defining the controllers, and the resulting simulations, we hope to enable others to answer questions about landing control and injuries using simulations.
All models, data, and simulation results are provided in the downloads area of this project.
For software and sourcecode defining the novel stretch feedback controller and stretch reflex controller, see the related repository on GitHub.
https://github.com/msdemers/opensim-reflex-controllers
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Activity Percentile: 48.85 Registered: 2015-07-20 20:18 |
Wrist Anatomy and Kinematics Data Collection
- <div align="justify">CT images of wrists from 90 healthy volunteers (43 males and 47 females) were acquired in various wrist positions. The outer cortical surfaces of the carpal bones, radius, and ulna in a 3D format, and each bone kinematics were calculated for each wrist position using a methodology described in the README file associated with the database. The database does not include soft tissue or the cartilage information of the wrist. Moreover, there is a MATLAB graphic user interface (GUI) available for you to observe the database. This dataset comes from four different NIH funding between 2001 and 2014.</div>
Please cite the work if you're using this database:
<div align="justify"><a href="https://onlinelibrary.wiley.com/doi/abs/10.1002/jor.24435">Akhbari, B., Moore, D. C., Laidlaw, D. H., Akelman, E., Weiss, A-P. C., Wolfe, S. W., Crisco, J. J., 2019. Predicting Carpal Bone Kinematics using an Expanded Digital Database of Wrist Carpal Bone Anatomy and Kinematics, Journal of Orthopaedic Research. DOI:10.1002/jor.24435</a></div>
If you want the pdf version of the manuscript, please send your request on <a href="http://bit.ly/2YU2tTh">ResearchGate</a>.
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Registered: 2019-02-25 19:48 |
Data and Media Management for Biomechanics (DMMB)
- (written for biomechanics researchers interested in managing and distributing big data/ media)
This project will serve as a tool to help researchers categorize, organize, prioritize, and distribute big data collected specifically in biomechanical applications. Additionally, this project will serve as a project map a guide for how to streamline and distribute biomechanics-related media (photographs, videos, interactive modules, etc.). | |
Registered: 2014-02-04 18:53 |
STRUCTURAL INSIGHTS INTO PRE-TRANSLOCATION RIBOSOME MOTIONS
- This project distributes RNABuilder input files, structural coordinates, and trajectories advertised in our PSB 2011 paper. | |
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Activity Percentile: 22.52 Registered: 2010-07-14 22:01 |
Lower Extremity EMG-driven Modeling with Automated Adjustment of Geometry
- This project provides Matlab code for developing EMG-driven models of walking using scaled OpenSim lower extremity musculoskeletal models. The Matlab code adjusts not only traditional Hill-type muscle-tendon model parameters values (optimal muscle fiber length, tendon slack length) but also non-traditional musculoskeletal model parameter values (EMG scale factors, coefficients defining surrogate representations of muscle-tendon lengths, velocities, and moment arms). Along with the Matlab code, we provide sample walking data (marker, ground reaction, and EMG data) collected from a hemiparetic male subject and a sample scaled OpenSim musculoskeletal model of the subject. A README file provides instructions for how to perform the EMG-driven model calibration process using the provided Matlab code, walking data, and scaled OpenSim model. | |
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Registered: 2016-05-06 02:33 |
Neuromusculoskeletal Modeling (NMSM) Pipeline
- <div style="display:inline-block"><a href="https://nmsm.rice.edu"><img src="https://nmsm.rice.edu/img/nmsm-pipeline-social-card.jpg" style="float:left;max-width:calc(100% - 40px);"></a></div>
Full project information is available at: https://nmsm.rice.edu. Please direct any inquiries about the NMSM Pipeline to us by posting your questions on this SimTK project forum or emailing nmsm@rice.edu.
Neuromusculoskeletal Modeling (NMSM) Pipeline is a set of tools for personalizing models and designing treatments for movement impairments and other pathologies.
The NMSM Pipeline consists of two toolsets:
Model Personalization - Personalize joint, muscle-tendon, neural control, and ground contact model properties.
Treatment Optimization - Design treatments using personalized models and an optimal control methodology.
At this time, Treatment Optimization requires the use of <a href="https://www.gpops2.com/">GPOPS-II optimal control solver</a>.
The NMSM Pipeline is written in MATLAB to lower the barrier for entry and to facilitate accessibility to the core codebase. We encourage users to modify the code to meet their needs.
The core codebase and examples are available to download for use in research. At this time, we ask that you wait to publish any work that uses the NMSM Pipeline until the journal article reference for the software is available. Please get in touch with us if you have any questions.
If you need help or want to start a discussion, please use the SimTK forum for this project.
Note: This project is a living entity. Updates will be made available as the Pipeline, examples, and tutorials are developed further and improved. | |
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Registered: 2022-07-07 14:55 |
Modeling the Intervertebral Discs as a Stiffness Matrix: a SpineBushing element
- This project features a "SpineBushing" element that can be used to model the intervertebral disc as a 6x6 stiffness matrix. This permits the study of the disc's force-motion relationship for the case where the coordinates are coupled to each other.
The guiding equation is,
F_2 = -K * Delta_Q
where F_2 is the generalized 6x1 force vector acting on the upper vertebra, K is a stiffness matrix, and Delta_Q is the generalized 6x1 displacement vector specifying the change in position from neutral between the points of attachment of the stiffness element.
By Newton's 3rd law,
F_1 = - F_2.
The SpineBushing features two *key* differences from the existing bushing element:
(1) we incorporated a full 6x6 stiffness matrix instead of the current three translational and three rotational stiffnesses.
(2) the **change** in relative motion is used and not the relative motion itself. In 1-D, you can think of this as having a spring with a resting length equal to the distance between the specified attachment points on the two bodies in the neutral posture. (The typical bushing element, on the other hand would be analogous to a spring with zero resting length.)
Further details are provided in the accompanying documents. | |
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Activity Percentile: 1.15 Registered: 2011-10-12 05:41 |
57 projects in result set. Displaying 20 per page. Projects sorted by alphabetical order.
<1> <2> <3>