The user community for SIMTK is large. The DBPs during our first five years demonstrate the breadth of problems for which physics-based modeling and simulation are critical. The RNA folding and protein folding/misfolding DBPs included structural biologists, physical chemists, physicists, molecular biologists, physicians and biochemists. The myosin dynamics DBP included biochemists, biomechanical engineers, geneticists, chemists, biophysicists, and structural biologists. The neuromuscular dynamics DBP included orthopedic surgeons, biomechanical engineers, neurologists, and physical therapists. The cardiovascular fluid dynamics DBP included vascular surgeons, cardiologists, vascular biologists, and bioengineers. The three new DBPs, summarized under Core 2 similarly engage a broad spectrum of scientists, including structural biologists, neurologists, electrical engineers, biochemists, pharmaceutical chemists, physicians, computer scientists and biomedical engineers. These users will again provide appropriate "pull" on SIMTK to ensure that it has relevant and useful capabilities. We have disseminated the fruits of Simbios research and development through traditional publications (over 150 papers), presentations at conferences, workshops, and via the materials on our simtk.org website.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Specialized Center--Cooperative Agreements (U54)
Project #
5U54GM072970-09
Application #
8534883
Study Section
Special Emphasis Panel (ZRG1-BST-K)
Project Start
Project End
Budget Start
2013-09-01
Budget End
2014-08-31
Support Year
9
Fiscal Year
2013
Total Cost
$274,248
Indirect Cost
$113,933
Name
Stanford University
Department
Type
DUNS #
009214214
City
Stanford
State
CA
Country
United States
Zip Code
94305
Sack, Kevin L; Baillargeon, Brian; Acevedo-Bolton, Gabriel et al. (2016) Partial LVAD restores ventricular outputs and normalizes LV but not RV stress distributions in the acutely failing heart in silico. Int J Artif Organs 39:421-430
Shukla, Diwakar; Peck, Ariana; Pande, Vijay S (2016) Conformational heterogeneity of the calmodulin binding interface. Nat Commun 7:10910
Araya, Carlos L; Cenik, Can; Reuter, Jason A et al. (2016) Identification of significantly mutated regions across cancer types highlights a rich landscape of functional molecular alterations. Nat Genet 48:117-25
Uchida, Thomas K; Hicks, Jennifer L; Dembia, Christopher L et al. (2016) Stretching Your Energetic Budget: How Tendon Compliance Affects the Metabolic Cost of Running. PLoS One 11:e0150378
Seth, Ajay; Matias, Ricardo; Veloso, António P et al. (2016) A Biomechanical Model of the Scapulothoracic Joint to Accurately Capture Scapular Kinematics during Shoulder Movements. PLoS One 11:e0141028
Sahli Costabal, Francisco; Hurtado, Daniel E; Kuhl, Ellen (2016) Generating Purkinje networks in the human heart. J Biomech 49:2455-65
Dodani, Sheel C; Kiss, Gert; Cahn, Jackson K B et al. (2016) Discovery of a regioselectivity switch in nitrating P450s guided by molecular dynamics simulations and Markov models. Nat Chem 8:419-25
Eastman, Peter; Pande, Vijay S (2015) OpenMM: A Hardware Independent Framework for Molecular Simulations. Comput Sci Eng 12:34-39
Wisdom, Katrina M; Delp, Scott L; Kuhl, Ellen (2015) Use it or lose it: multiscale skeletal muscle adaptation to mechanical stimuli. Biomech Model Mechanobiol 14:195-215
Dorn, Tim W; Wang, Jack M; Hicks, Jennifer L et al. (2015) Predictive simulation generates human adaptations during loaded and inclined walking. PLoS One 10:e0121407

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