Simbios Collaborations

Simbios Scientific Advisory Board
NIH Program and Science Officers (SO)

Andrew McCammon, Ph.D., UC San Diego
Chris Johnson, Ph.D., University of Utah
Klaus Schulten, Ph.D., University of Illinois
Richard Friesner, Ph.D., Columbia University
Ton van den Bogert, Ph.D., Cleveland State University, Ohio
Brian Gerkey, Ph.D., Open Source Robotics Foundation
Victor Ng-Thow-Hing, Ph.D., Honda Research Institute
Christopher Bayly, Ph.D., OpenEye Scientific Software
Grace Peng, Ph.D., NIH

Peter Lyster, Ph.D. (NIGMS), Program Officer
Grace Peng, Ph.D. (NIBIB), Lead SO
Jennie Larkin, Ph.D. (NHLBI), SO
Semahat Demir, Ph.D. (NSF), SO
Jim Gnadt, Ph.D. (NINDS), SO
Peter Highnam, Ph.D. (NCRR), SO
Jerry Li, M.D., Ph.D. (NIGMS), SO
Yuan Liu, Ph.D. (NINDS), SO
Richard Morris, Ph.D. (NIAID), SO
David Thomassen, Ph.D. (DOE), SO
Jane Ye, Ph.D. (NLM), SO
Nancy Shinowara, Ph.D. (NICHD), SO

Collaborators through the collaborating R01/R21 program

Antonie van den Bogert
Department of Biomedical Engineering, Lerner Research Institute, Cleveland Clinic
Project: Efficient Methods for Multi-Domain Biomechanical Simulations (2006)

Patrice Koehl
Department of Computer Science, Genome Center, University of California Davis
Project: Geometric-based and Physics-based Simulations of RNA Folding (2007)

Richard Neptune
Cockrell School of Engineering, University of Texas at Austin
Project: Development of a SimTK-based framework for hemiparetic walking assessment (2007)

Silvia Salinas Blemker
Departments of Mechanical, Aerospace and Biomedical Engineering, University of Virginia
Darryl Thelen
Department of Mechanical Engineering, University of Wisconsin-Madison
Project: Biocomputation of the Links Between Muscle Morphology, Coordination and Injury (2007)

Jay Humphrey
Department Biomedical Engineering, Texas A&M University
Project: Biomechanical Simulation of Evolving Aortic Aneurysms for Designing Intervention (2008)

Jill Higginson
Department of Mechanical Engineering, University of Delaware
Project: Muscle Morphology, Strength and Compensatory Strategies Following Stroke (2008)

Ivet Bahar
Department of Computational Biology, University of Pittsburgh at Pittsburgh
Project: Structural Dynamics of Biomolecular Systems (2009)

Julius Guccione
Department of Surgery, University of California San Francisco
Project: Simulation of Coronary Artery Bypass Graft and Surgical Ventricular Restoration (2009)

Collaborators through "Simbios's Seed Project Program" and NCBC collaborative Postdoc Program


Wendy Murray
Department of Biomedical Engineering, Northwestern University
Project: Forward Simulation and Endpoint Force Production in the Upper Limb – seed project collaborator

Jesús A. Izaguirre
Department of Computer Science and Engineering, University of Notre Dame
Project: Normal Model Langevin and OpenMM – seed project collaborator


Ellen Kuhl
Department of Mechanical Engineering, Stanford University
Project: SimGrowth – A virtual lab for myocardial infarction and restoration of cardiac function

Peter Ortoleva
Center for Cell and Virus Theory, Indiana University
Project: All-atom Multiscale Simulation of Virus, Ribosome and Other Bionanosystems, visit the Simtk project.

Jeff Weiss
Department of Biongineering, University of Utah
Project: Modeling of Skeletal Muscle with FEBio

Brian Garner
Department of Mechanical Engineering, Baylor University
Project: Improved Muscle-Path Modeling Tools Applied to the Male Upper Extremity, visit the Simtk project

Wah Chiu
National Center for Macromolecular imaging

Baylor College of Medicine
Project: Building Protein Models for Biological Machines by a Hybrid of CryoEM
and Physics-Based Simulations


Patrice Koehl
Department of Computer Science and Genome Center, UC Davis
Current R01 collaborator (see above)
Project: ElecTK: A Toolbox for Macromolecular Electrostatics

Jill Higginson
Department of Mechanical Engineering, University of Delaware
Current R01 collaborator (see above)
Project: Simulation of post-stroke hemiparetic gait: 2d vs 3d

Darryl Thelen
Department of Mechanical Engineering, University of Wisconsin-Madison
Current R01 collaborator (see above)
Project: The Incorporation of Ground Contact Models When Simulating Subject-Specific Gait

Pengyu Ren and Robin Gutell, Department of Biomedical Engineering, UT Austin
Project: Physical-based Coarse-Grain Modeling tool for RNA

Other Collaborative Grants

NeuroMusculoSkeletal Physiome: A cooperation between the Osteoporotic Virtual Physiological Human Integrated Project (VPHOP) and SIMBIOS to develop tools for the neuromusculoskeletal physiome, sponsored by the European Commission (website)

Other Collaborators and Advisors

Kim Branson
Vertex Pharmaceuticals

Michael Brenowitz
Department of Biochemistry
Albert Einstein School of Medicine

Rhiju Das
Department of Physics and Biochemistry
Stanford University

Julius Guccione
Department of Surgery
UC San Francisco

Alain Laederach
Computational & Structural Biology
Wadsworth Center/ School of Biomedical Sciences at SUNY Albany

Jung-Chi Liao
Department of Mechanical Engineering
Columbia University

Erik Lindahl
Department of Biochemistry & Biophysics
Center for Biomembrane Research
Stockholm University

Somdeb Mitra
Department of Biochemistry
Albert Einstein School of Medicine

Li Niu
Department of Chemistry
University of Albany

Jay Ponder
Department of Biochemistry & Molecular Biophysics

Washington University

Rick Russell
Department of Chemistry and Biochemistry
University of Texas at Austin

David Lloyd
School of Sport Science, Exercise, and Health
University of Western Australia

Glen Lichtwark
School of Physiotherapy and Exercise Science
Griffith University

Marcus Pandy
Department of Mechanical Engineering
The University of Melbourne

Marco Viceconti
Istituto Ortopedico Rizzoli di Bologna

Jeff Reinbolt
Mechanical, Aerospace and Biomedical Engineering Department
University of Tennessee, Knoxville

BJ Fregly
Department of Mechanical and Aerospace Engineering
University of Florida

Katherine Holzbaur
School of Biomedical Engineering and Sciences
Virginia Tech - Wake Forest University

John Hutchinson
Royal Veterinary College
University of London

Antonio Veloso
Human Kinetics
Technical University of Lisbon

Ilse Jonkers
Research Centre for Movement Control and Neuroplasticity
K.U. Leuven

Robert Siston
Department of Mechanical Engineering
Ohio State University

Ko Sasaki
Department of Mechanical Engineering
UT Austin

Adam Godzik
Infectious & Inflammatory Disease Center
Burnham Institute for Medical Research