MSM Participants

Name Project Email WGs
Geoffrey Abbott, Ph.D. Predictive MSM of Atrial Fibrillation for Therapy Development GWA2001@MED.CORNELL.EDU
Gary An, M.D. EMT/BSSE: Hierarchical Representation and Simulation of Modular Cellular Systems [1]
Kurt Anderson, Ph.D. Framework for the Adaptive Multiscale Modeling of Biopolymers anderk5@rpi.edu
Russ Altman, M.D., Ph.D. Physics-Based Simulation of Biological Structures russ.altman@stanford.edu
Portonovo Ayyaswamy Bridging multiple scales in modeling targeted drug nanocarrier delivery ayya@seas.upenn.edu
Victor Barocas, Ph.D. Multiscale Modeling of Facet Capsule Mechanobiology; Multiscale Mechanics of Bioengineered Tissues baroc001@umn.edu
James (Jim) Bassingthwaighte, M.D., Ph.D. Software Integration between JSim and Systems Biology Workbench; Modeling for Heart, Lung, and Blood: From Cell to Organ; Adaptive Multi-Scale Model Simulation, Reduction and Integration for Cardiac Muscle Physiology jbb2@u.washington.edu
Daniel Beard, Ph.D. Multi-Scale Modeling of the Heart in Metabolic Syndrome and Cardiovascular Disease, Mechanisms of Metabolic Dysfunction in Heart Disease beardda@umich.edu
Scott Berceli, M.D., Ph.D. Multiscale Network Modeling of Hemodynamically-Driven Vascular Adaptation bercesa@surgery.ufl.edu
Theodore Berger Predictive modeling of bioelectric activity on mammalian multilayered neuronal structures in the presence of supraphysiological electric fields berger@bmsr.usc.edu
Jeff Bischoff, Ph.D. Research Interests: Multiscale Joint Biomechanics jeff.bischoff@zimmer.com
Michael Blinov National Resource for Cell Analysis and Modeling; www.ccam.uchc.edu; vcell.org blinov@uchc.edu  
Danny Bluestein, Ph.D. Optimizing Cardiovascular Device Thromboresistance for Eliminating Anticoagulants dbluestein@ms.cc.sunysb.edu
Georgiy Bobashev Researching Social Dynamics of Local Methamphetamine Market bobashev@rti.org
James Bower, Ph.D. GENESIS BOWER@uthscsa.edu
James Brasseur, Ph.D. Micro-scale Transport as a Critical Link between Molecular-Scale Absorption and Macro-Scale Mixing in Gut Physiology and Function brasseur@engr.psu.edu
Markus Buehler, Ph.D. Models to predict protein biomaterial performance mbuehler@MIT.EDU
David Cai Collaborative Research: Cortical Processing across Multiple Time- and Space-Scales http://www.cims.nyu.edu/~yisun/publication.html http://www.rpi.edu/~kovacg/ http://www.math.nyu.edu/~cai/Publications/index.html cai@cims.nyu.edu
William Cannon, Ph.D. Hierarchical, Multi-Objective Optimization of Microbial Community Proteomic Systems william.cannon@pnl.gov
Xiaolin Cheng, Ph.D. Multiscale Mathematics and Simulations of Complex Biological Systems chengx@ornl.gov
Howard Chizeck, Sc.D. Adaptive Multi-Scale Model Simulation, Reduction and Integration for Cardiac Muscle Physiology http://nsr.bioeng.washington.edu chizeck@u.washington.edu
Yoonsuck Choe, Ph.D. Multi-Scale Imaging, Analysis, and Integration of Brain Networks choe@tamu.edu
Sharon Crook, Ph.D. NeuroML Standards and Tools for Multiscale Model Specification and Exchange Sharon.Crook@asu.edu
David Christini, Ph.D. Predictive MSM of Atrial Fibrillation for Therapy Development dchristi@med.cornell.edu
Ming Dao, Ph.D. Multiscale Modeling and Parallel Simulations of Blood Flow in Cerebral Malaria and Sickle Cell Diseases mingdao@mit.edu
David D'Argenio, Ph.D. Biomedical Simulations Resource: Core Project #1 - Pharmacokinetic/Pharmacodynamic Systems Analysis dargenio@bmsr.usc.edu
Suvranu De, Sc.D. A Self-Consistent Multiscale Method for Modeling the Effects of Neutron Irradiation on the Mechanical Properties of BCC and FCC Metals; Nonlinear Multiscale Modeling of 3D Woven Fiber Composites Under Ballistic Loading; Development of a Self-Consistent Multiscale Method for Coupled Nonlinear Micro Macro Analysis of Heterogeneous Explosives; http://acor.rpi.edu/, http://www.springer.com/engineering/biomedical+eng/book/978-90-481-3574-5 des@rpi.edu
Thomas Deisboeck, M.D. Center for the Development of a Virtual Tumor, CViT https://www.cvit.org deisboec@helix.mgh.harvard.edu
Scott Delp, Ph.D. Physics-Based Simulation of Biological Structures delp@stanford.edu
Yasin Dhaher A Multi-Scale Modeling Construct of Knee Mechanics following ACL Reconstruction y-dhaher@northwestern.edu
Thomas Diacovo, M.D. Model of Platelet Adhesion and Thrombus Formation td2142@columbia.edu
Scott Diamond, Ph.D. (Talid Sinno, Lawrence (Skip) Brass) [ www.bloodsystemsbiology.org Blood Systems Biology] SLD@SEAS.UPENN.EDU Theoretical and Computational Methods; Clinical and Translational Issues Working Group
David Eckmann, M.D., Ph.D. Bridging multiple scales in modeling targeted drug nanocarrier delivery // Targeted Microcarrier Design and Optimization David.Eckmann@uphs.upenn.edu
Uri Tzvi Eden Multiscale analysis and modeling of spatiotemporal dynamics in human epilepsy tzvi@bu.edu
Daniel Einstein 3D Imaging & Computer Model of the Respiratory Tract daniel.einstein@pnl.gov
Mounya Elhilali Overcoming the Cocktail Party Problem: a Multi-Scale Perspective on the Neurobiology of Auditory Scene Analysis mounya@jhu.edu
Ahmet Erdemir, Ph.D. Efficient Methods for Multi-Domain Biomechanical Simulations, Predicting Cell Deformation from Body Level Mechanical Loads, Open Knee: A Three-Dimensional Finite Element Representation of the Knee Joint erdemira@ccf.org Biomechanics Working Group, Model and Data Sharing Working Group
Stephen Eubank, Ph.D. Modeling Immunity to Enteric Pathogens (MIEP) seubank@vbi.vt.edu
Ronan Fleming, Ph.D. Numerical Optimization Algorithms and Software for Systems Biology ronan.mt.fleming@gmail.com
Joanne Flynn, Ph.D. A multi-scale model to predict outcomes of immuno- modulation and drug therapy during TB joanne@pitt.edu
Alison Galvani Evaluating the social influences that impact vaccination decisions; Impacts of Individual and Social Behavior on Influenza Dynamics and Control; http://galvani.medicine.yale.edu/index.aspx ALISON.GALVANI@YALE.EDU
Marc Garbey Multiscale Network Modeling of Hemodynamically-Driven Vascular Adaptation garbey@cs.uh.edu
Guy Genin Cross-scale interactions between mineral and collagen for tendon-bone attachment genin@wustl.edu IMuBEAM
Frank Gertler Modeling bi-directional signaling and cytoskeletal dynamics in 3D cell migrations fgertler@mit.edu
James Glazier CompuCell3D glazier@indiana.edu
Mark Gordon, Ph.D. Multiscale Mathematics and Simulations of Complex Biological Systems gordon@ameslab.gov mark@si.msg.chem.iastate.edu
Trent Guess, Ph.D. Dynamic Simulation of Joints Using Multi-Scale Modeling guesstr@umkc.edu
Randy Heiland, M.S. CompuCell3D heiland@indiana.edu
John Higgins Multiscale Modeling of Sickle Cell Anemia: Methods and Validation Higgins.John@mgh.harvard.edu  
Anthony Hunt, Ph.D. Media:Research_Description_for_MSM04May10.pdf http://biosystems.ucsf.edu/index.htm a.hunt@ucsf.edu
Jay Humphrey, Ph.D. Evolving Mechanics of Intraluminal Thrombus: From Formation to Organization jay.humphrey@yale.edu
Peter Hunter, Ph.D. International Union of Physiological Sciences Council Member p.hunter@auckland.ac.nz
Dov Jaron Multiscale, Transport-Dependent NO Signaling: Cells to Vascular Networks djaron@coe.drexel.edu
Paul Jasper Numerical Tools for Analyzing Cell Signaling Circuits in Normal and Tumor Cells pjasper@numericatech.com
Karl Jepsen Genetic Determination of Skeletal Fragility  
Yufang Jin, Ph.D. Mathematical Modeling of Matrix Metalloproteinase-9 Driven Left Ventricular Remodeling Post Myocardial Infarction Yufang.Jin@utsa.edu
Wolfgang Kainz, PhD Development of a functional ultra-high resolution head model Wolfgang.Kainz@fda.hhs.gov  
Roger Kamm, Ph.D. Modeling bi-directional signaling and cytoskeletal dynamics in 3D cell migrations Multi-Scale Analysis of Cellular Force Transmission and Biochemical Activation rdkamm@mit.edu
David Kaplan, Ph.D. Models to Predict Protein Biomaterial Performance David.Kaplan@tufts.edu] IMuBEAM
George Karniadakis, Ph.D. A Stochastic Molecular Dynamics Method for Multiscale Modeling of Blood Platelet Phenomena george_karniadakis@brown.edu
Roy Kerckhoffs The Role of Transmural Gradients of Excitation-Contraction Coupling in the Ventricularly Paced Normal and Failing Heart roy@eng.ucsd.edu
Michael King Model of Platelet Adhesion and Thrombus Formation mike.king@cornell.edu
Denise Kirschner, Ph.D. A multi-scale model to predict outcomes of immuno- modulation and drug therapy during TB kirschne@umich.edu Multiscale Systems Biology Working Group
Gregor Kovacic, Ph.D. Collaborative Research: Cortical Processing across Multiple Time- and Space-Scales http://www.cims.nyu.edu/~yisun/publication.html http://www.rpi.edu/~kovacg/ kovacg@rpi.edu
Mark Kramer Multiscale analysis and modeling of spatiotemporal dynamics in human epilepsy mak@bu.edu
Joy Ku, Ph.D. Physics-Based Simulation of Biological Structures; https://simtk.org/xml/index.xml joyku@stanford.edu Model and Data Sharing Working Group
Rob Kunz, Ph.D. Multi-Scale Human Respiratory System Simulations to Study the Health Effects of Aging, Disease and Inhaled Substances rfk102@only.arl.psu.edu
Anthony (Tony) Ladd, Ph.D. Multi-Scale Modeling of Chemical-to-Mechanical Energy Conversion in Actin-Based Motility tladd@che.ufl.edu
Nicola Lai, Ph.D. (in place of Marco Cabrera) Time Course of Metabolic Adaptations During Loading and Unloading nicola.lai@case.edu
Gianluca Lazzi Predictive modeling of bioelectric activity on mammalian multilayered neuronal structures in the presence of supraphysiological electric fields lazzi@utah.edu
Peter Laz A Multi-Scale Finite Element Musculoskeletal Modeling Framework Applied to Current Issues in Joint Replacement Peter.Laz@du.edu
Jonathan Lederer Calcium Entrained Arrhythmias jlederer@umaryland.edu
Ching-Long Lin, Ph.D. An integrative statistics-guided image-based multi-scale lung model; Multiscale Simulation of Gas Flow Distribution in the Human Lung ching-long-lin@uiowa.edu Cell-to-Macroscale Working Group
Jennifer Linderman, Ph.D. A multi-scale model to predict outcomes of immuno- modulation and drug therapy during TB linderma@umich.edu
Yaling Liu, Ph.D. Modeling Particle Shape Effect in Nanomedicine yal310@Lehigh.EDU
Leslie Loew National Resource for Cell Analysis and Modeling; www.ccam.uchc.edu; vcell.org les@volt.uchc.edu Multiscale Systems Biology Working Group
Georg Luebeck, Ph.D. Scales of Carcinogenesis: Cells, Crypts and Cancer; Controlling Esophageal Cancer in the US.: A Colloraborative Modeling Project gluebeck@fhcrc.org
Bill Lytton, M.D. Extension of NEURON Simulator for Simulation of Reaction-Diffusion in Neurons ; NEURON Simulator billl@neurosim.downstate.edu Clinical & Translational; Computational Neuroscience
Carlo Maley, Ph.D. Scales of Carcinogenesis: Cells, Crypts and Cancer cmaley@wistar.org
Parag Mallick Multi-scale Complex Systems Transdisciplinary Analysis of Response to Therapy paragm@stanford.edu
Madhav Marathe, Ph.D. Modeling Immunity to Enteric Pathogens (MIEP) mmarathe@vbi.vt.edu
Roger Mark, M.D., Ph.D. Physionet rgmark@mit.edu
Vasilis Marmarelis, Ph.D. Biomedical Simulations Resource (BMSR) vzm@usc.edu [Mathematical & Computational Methods]
Andrew McCulloch, Ph.D. Multi-Scale Modeling of the Mouse Heart: From Genotype to Phenotype http://cmrg.ucsd.edu, Multi-Scale Modeling of the Failing Heart for Cardiac Rysynchronization Therapy amcculloch@ucsd.edu
Jill McNitt-Gray, Ph.D. http://www.asbweb.org/index.html ; http://dornsife.usc.edu/cf/faculty-and-staff/faculty.cfm?pid=1003520&CFID=1692145&CFTOKEN=13548813 mcnitt@usc.edu
Michael Meyer-Hermann, Ph.D. Mathematical Modeling of the Migration in Germinal Centres m.meyer-hermann@fias.uni-frankfurt.de
George Moody Physionet george@MIT.edu
James Moore, Ph.D. Lymphatic Fluid Flow Modeling with Active Network Components james.moore.jr@imperial.ac.uk Biomechanics Working Group
Ion Moraru National Resource for Cell Analysis and Modeling; www.ccam.uchc.edu; vcell.org moraru@panda.uchc.edu  
Wendy Murray Prosthesis Control by Forward Dynamic Simulation of the Intact Biomedical System w-murray@northwestern.edu  
Mark Musen, M.D., Ph.D. The National Center for Biomedical Ontology musen@stanford.edu
Sriram Neelamegham Systems Biology of Glycosylation neel@buffalo.edu
Peter Ortoleva Intercellular Genomics of Subsurface Microbial Colonies ortoleva@indiana.edu
Manish Parashar http://nsfcac.rutgers.edu/people/parashar/ parashar@rutgers.edu
Abani Patra, Ph.D. http://www.mae.buffalo.edu/people/full_time/a_patra.php abani@buffalo.edu
Bernhard Palsson Numerical Optimization Algorithms and Software for Systems Biology palsson@ucsd.edu
Linda Petzold, Ph.D. Stochastic Simulation Service: A Cloud Computing Framework for Modeling and Simulation petzold@cs.ucsb.edu
Teresa Pitts, Ph.D. Regulation of Airway Protection tepitts@ufl.edu Computational Neuroscience Working Group
Sylvia Plevritis http://rsl.stanford.edu/plevritis/ Comparative Modeling of Lung Cancer Control Policies sylvia.plevritis.edu
Aleksander Popel Predictive Experiment-Based Multiscale Models of Angiogenesis in Breast Cancer apopel@jhu.edu
Vito Quaranta Image Driven Multi-Scale Modeling to Predict Treatment Response in Breast Cancer vito.quaranta@vanderbilt.edu Multiscale Systems Biology Working Group
Ravi Radhakrishnan Bridging multiple scales in modeling targeted drug nanocarrier delivery // Lab URL rradhak@seas.upenn.edu Multiscale Systems Biology Working Group; Theoretical and Computational Methods; High Performance Computing Working Group
Peter Richardson A Stochastic Molecular Dynamics Method for Multiscale Modeling of Blood Platelet Phenomena Peter_Richardson@brown.edu
Paul Rullkoetter A Multi-Scale Finite Element Musculoskeletal Modeling Framework Applied to Current Issues in Joint Replacement Paul.Rullkoetter@du.edu
Ilya Rybak, Ph.D. Multiscale Model of Neural Control of Breathing ilya.rybak@drexelmed.edu
Gerald Saidel, Ph.D. (in place of Marco Cabrera) Time Course of Metabolic Adaptations During Loading and Unloading gerald.saidel@case.edu
Edward Sander, Ph.D. Controlling the Mechanobiology of Cutaneous Wounds to Reduce Hypertrophic Scar edward-sander@uiowa.edu Biomechanics Working Group
Terence Sanger, M.D., Ph.D. High Speed Simulation of Developmental Motor Disorders tsanger@usc.edu
Michael Saunders Numerical Optimization Algorithms and Software for Systems Biology saunders@stanford.edu
Herbert Sauro, Ph.D. Software Integration between JSim and Systems Biology Workbench, Modeling for Heart, Lung, and Blood: From Cell to Organ hsauro@u.washington.edu
Jay Schieber CISE: Multiscale Modeling to Develop a Cyberinfrastructure for the Dynamics of Flexible and Stiff Entangled Macromolecules http://polyhub.org/bin/view sjs49@engr.psu.edu
Steven Schiff CRCNS Collaborative Research: Model-Based Control of Spreading Depression schieber@iit.edu
Bill Schultz http://www-personal.umich.edu/~schultz/ schultz@umich.edu
James Schwaber http://www.dbi.tju.edu james.schwaber@jefferson.edu
Daniel Segre An Open Source Platform for Multi-Scale Spatially Distributed Simulations of Microbial Ecosystems dsegre@bu.edu
Terrence (Terry) Sejnowski, Ph.D. Integrated Empirical and Multiscale Modeling of Human Sleep Spindles sejnowski@salk.edu
Kevin Shelburne A Multi-Scale Finite Element Musculoskeletal Modeling Framework Applied to Current Issues in Joint Replacement, http://www.du.edu/biomechanics kevin.shelburne@comcast.net
Yohannes Shiferaw MSM of Calcium Mediated Triggered Activity in the Heart yohannes.shiferaw@csun.edu
Jeff Smith, Ph.D. Multiscale Model of Neural Control of Breathing jsmith@helix.nih.gov
Jeremy Smith Multiscale Mathematics and Simulations of Complex Biological Systems smithjc@ornl.gov
Subra Suresh, Sc.D. Multiscale Modeling and Parallel Simulations of Blood Flow in Cerebral Malaria and Sickle Cell Diseases ssuresh@mit.edu
Maciej Swat, Ph.D. Multiscale Studies of Segmentation in Vertebrate Embryos mswat@indiana.edu
Dalin Tang, Ph.D. In Vivo IVUS Image-Based Modeling for Human Coronary Plaque Assessment dtang@wpi.edu
Michela Taufer, Ph.D. DAPLDS: A Dynamically Adaptive Protein-Ligand Docking System Based on Multi-Scale Modeling taufer@acm.org
Merryn Tawhai, Ph.D. Airway Hyperresponsiveness: From Molecule to Organ m.tawhai@auckland.ac.nz
Darryl Thelen A Multi-Scale Modeling Construct of Knee Mechanics following ACL Reconstruction THELEN@ENGR.WISC.EDU
Ines Thiele Numerical Optimization Algorithms and Software for Systems Biology ines.thiele@googlemail.com
Stavros Thomopoulos Cross-scale interactions between mineral and collagen for tendon-bone attachment thomopouloss@wudosis.wustl.edu IMuBEAM
Natalia Trayanova Resynchronizing the Failing Heart: Insights from a Multiscale Cardiac Model ntrayanova@jhu.edu
Raj Vadigepalli "Modeling Central Autonomic Regulatory Network Adaptation to Hypertension” and “Integrated Modeling of Adaptive Neuronal Regulation” Rajanikanth.Vadigepalli@jefferson.edu
Peter Vekilov Multiscale Modeling of Sickle Cell Anemia: Methods and Validation pgvekilo@Central.UH.EDU
Marco Viceconti Insigneo Institute m.viceconti@sheffield.ac.uk
Paolo Vicini, Ph.D. Research Interests: Pharmacokinetics, Pharmacodynamics, Biotherapeutics, Translational Research, Model Identification and Parameter Estimation paolo.vicini@pfizer.com
Yoram Vodovotz, Ph.D. Mathematical Modeling of Inflammation in ARDS vodovotzy@upmc.edu Multiscale Systems Biology Working Group; Clinical and Translational Issues
Jeff Weiss, Ph.D. FEBio-Finite Elements for Biomechanics and Biophysics jeff.weiss@utah.edu
Ron White, Ph.D. http://sdmines.sdsmt.edu/sdsmt/directory/personnel/rwhite Ronald.White@sdsmt.edu
Bridget Wilson, Ph.D. Mapping and Modeling ErbB Receptor Membrane Topography bwilson@salud.unm.edu
Beth Winkelstein Multiscale Modeling of Facet Capsule Mechanobiology winkelst@seas.upenn.edu
Joyce Wong, Ph.D. Models to predict protein biomaterial performance jywong@bu.edu IMuBEAM
Tom Yankeelov Image Driven Multi-Scale Modeling to Predict Treatment Response in Breast Cancer thomas.yankeelov@vanderbilt.edu Clinical and Translational Issues Working Group
Kaiming Ye   kye@binghamton.edu
Muhammad Zaman Modeling bi-directional signaling and cytoskeletal dynamics in 3D cell migrations zaman@bu.edu
Yanhang Zhang Multi-Scale Integration of Extracellular Matrix Mechanics in Vascular Remodeling yanhang@bu.edu Biomechanics Working Group
Xiaobo Zhou, Ph.D. Modeling the Growth of the MIC Niche at the System Level xizhou@wakehealth.edu