CORE 2: DRIVING BIOLOGICAL PROBLEMS Three driving biological problems will focus our biocomputation research. A macroscale DBP focused on neuroprosthetic dynamics, a mesoscale DBP focused on viral and cellular dynamics, and a molecular scale DBP focused on drug target dynamics. We use seven criteria to select our Driving Biological Problems (DBPs): Canonical: The problem should be an archetype of problems in an entire field of inquiry to guarantee broad applicability of the tools we develop. ? Collectively cover a range of scales: It is critical that activities of the center cover scales from molecular through cellular to organismal levels. ? Physics-based: The DBP should present a problem that can be addressed by representing and analyzing the geometry and physics of the biological system. ? Data rich: Biology is dominated by experimental data. These data provide the real-world constraints that drive and validate models and simulations. ? World-class, engaged experimentalists: We seek close integration and deep interactions among the biological and computational participants. ? Have important implications for disease: We ensure that our DBPs are related to disease processes or treatments to ensure that they contribute to the advancement of human health. Our past DBPs met these criteria and enabled us to develop software that is now used by a very broad community of researchers. Our next three DBPs also satisfy these criteria and are briefly reviewed below.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Specialized Center--Cooperative Agreements (U54)
Project #
5U54GM072970-08
Application #
8382383
Study Section
Special Emphasis Panel (ZRG1-BST-K)
Project Start
Project End
Budget Start
2012-09-01
Budget End
2013-08-31
Support Year
8
Fiscal Year
2012
Total Cost
$401,372
Indirect Cost
$162,833
Name
Stanford University
Department
Type
DUNS #
009214214
City
Stanford
State
CA
Country
United States
Zip Code
94305
DeMers, Matthew S; Hicks, Jennifer L; Delp, Scott L (2017) Preparatory co-activation of the ankle muscles may prevent ankle inversion injuries. J Biomech 52:17-23
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
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
Meng, Yilin; Shukla, Diwakar; Pande, Vijay S et al. (2016) Transition path theory analysis of c-Src kinase activation. Proc Natl Acad Sci U S A 113:9193-8
Sahli Costabal, Francisco; Hurtado, Daniel E; Kuhl, Ellen (2016) Generating Purkinje networks in the human heart. J Biomech 49:2455-65
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
Schwantes, Christian R; Shukla, Diwakar; Pande, Vijay S (2016) Markov State Models and tICA Reveal a Nonnative Folding Nucleus in Simulations of NuG2. Biophys J 110:1716-1719
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

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