Scales Covered MSM Method Group Poster Number Title Last Name First Name Abstract/Poster File
Credibile practice guideline applicable to all scales of modeling and simulation The Committee on Credibe Practice of Modeling and Simulation in Healthcare:
1. Conducted an internal survey of Committee members via discussion within task teams
2. Sythecized to yeild the Committee has drafted its perspectives on “The Ten Simple Rules of Credible Practice of M&S in Healthcare
3. Solicited input from the broader M&S community through an online survey
4. Consolidating the Committee's perspective and community survey results to establish "Guidelines for Credible Practice of Modeling and Simulation in Healthcare"



Guidelines for Credible Practice of Modeling and Simulation in Healthcare

Mulugeta Lealem Poster: 
    1 47

Modeling osmotic transients during exercise

Bassingthwaite James
    1 75

Impact of Compartmentalization and Cell Shape on Signaling Pathways in Cancer

Spill Fabian
molecular General-purpose constrained optimization using quadruple-precision floating-point arithmetic 1 83 General-purpose Software for Systems Biology Saunders Michael
enzyme, pathway, cellular, consortia genome scale metabolic models, temporally resolved reaction diffusion PDEs, enzyme kinetics, agent based cellular models 2 84

in silico and in vitro analysis of resource allocation in a chronic wound biofilm consortia

Carlson Ross
    2 6

Multiscale Modeling of Blood Flow and Platelet Mediated Thrombosis

Bluestein Danny
    1 7

Computational Game Theory for Antibody Design



molecular, pathway, organelle PDE, ODE, image anaysis and segmentation, electron microscopy 2 8

Understanding the Role of Mitochondrial Cristae Structure on Energy Metabolism through Simulation

Afzal Nasrin
molecular, supramolecular, cellular PDEs, spatial stochastic 1 9

Multiscale Modeling of Wound Healing

Haugh Jason

molecules (1e-2 Da to 1e6 Da), cell

General-purpose constrained optimization using quadruple-precision floating-point arithmetic 2 10

A multiscale model of metabolism and protein expression predicts the response of E. coli to oxidative stress

Yang Laurence
molecular, cellular, network Uncertain ODEs 1 11 Multiscale Modeling of the Mammalian Circadian Clock: The Role of GABA Signaling Henson Michael


cell, tissue & hours to weeks agent-based and finite element analysis 2 12

Spatial Scaling in Multiscale Models: A Method for Coupling Agent-based and Finite-element Models of Tissue Remodeling

Lee Jia-Jye
Any All 1 13

Mechanistic Models, Model Mechanisms, and Computational Models of Explanation for Biological Phenomena

Hunt Anthony
molecular, cellular, tissue,
organ, mice, strains;
in vivo & in vitro
software objects & logic mapped explicitly to
biological behavior & structure through DES
2 14

Is the Mechanism of APAP Toxicity In Vivo & In Vitro really the same?  A model mechanism based explanation of the in vitro–in vivo disconnect

Smith Andrew
cell, tissue, system  finite element analysis, lumped parameter circulation model 1 15 Computational model of heart remodeling following relief of hemodynamic overload in a biventricular canine heart model Yoshida Kyoko
    2 16 Nonlinear mechanics of fibrin networks Alber Mark
    1 17

Structural biomechanics of platelet-driven clot contraction

Kim Oleg
    2 18 Multiscale models of blood clotting Xu Zhiliang
Genetic, cellular, tissue ODE,genetic algorithm 1 19 Linking Gene Dynamics to Intimal Hyperplasia – A Predictive Model of Vein Graft Adaptation Casarin Stefano
Cellular, Breast tissue Finite Element Analysis, agent-based model 2 20 Clinical study and multiscale modeling to predict the esthetic outcome of Breast Conservative Therapy Lesage Anne-Cecile
    1 21

High-Fidelity Controlled-Resolution Atlas and Deformable Model-based Anatomical Modeling for Medical Simulation and Therapy Planning

Audette Michel
Individual + Population Object Oriented, Microsimulation, Database interface 2 22

The Reference Model Interface with ClinicalTrials.Gov

Barhak Jacob
Cellular, Large-Scale Network, Bulk Tissue NEURON, Admittance Method 1 23

Improving Cortical Electrode Placement and Stimulation via Co-Simulation of Large-Scale Compartmental Neuronal and Multi-Resolution Admittance Method Models

Bingham Clayton
Large-Scale Network NEURON 2 24 Spatio-Temporal Patterns Revealed by a Large-Scale Model of the Hippocampal Entorhinal-Dentate-CA3 System: Emergence of Clustered Activity Yu Gene
Cellular, Population ODEs 1 25

Temporal Dynamics of Macrophage Plasticity in Bone Metastatic Prostate Cancer

Lynch Conor
Molecular, cellular, population Agent-based 2 26 Modeling the ecosystem of bone metastases: insights from a multi scale, multi modeling approach Basanta David
Molecules, Channels, Cells, Neural Network, Organ System Agent-based, ODEs 1 27

Integrating Microscopic Variability in Systems Modeling

Dick Thomas
    2 28 Multiscale modeling of the brain motor cortex circuits Dura-Bernal Salvador
Molecular scales (angstrom to nanometer) Full atomistic molecular simulation, Recombinant DNA technology 1 29

Design of Biomaterial Bioinorganic Interfaces Related to Mineralization

Ebrahimi Davoud
atomic to nm fully atomistic and coarse-grained molecular dynamics 2 30

Thermal Response of Silk-Elastin-Like Protein Hydrogels: Integrating Experiments and Multiscale Computational Modeling

Yeo Jingjie
    1 31 Multiscale Modeling of Collagen IV Network: Insights into the Structural Basis of Pathologies Sarkar Biplab
    2 32 Modeling of the relation between degradation and mechanical properties of a collagen fibril: A precursor examination towards understanding cartilage health Dhaher Yassin
    1 33

Prediction of EMG based on neural firing rates using stochastic dynamical operators

Sanger Terence
milliseconds to 24 hours Statistical thermodynamics 2 34

Multi-scale Modeling of Circadian Rhythms: From Metabolism to Regulation and Back in 24 hours

Cannon William
    1 35 Electrical Stimulation Waveform Design Towards Increasing the E ectiveness of Retina Prosthetic Devices Loizos Kyle
Tissue (250um) – Cell (20um), Time ranges from 0.01 second to minutes. Agent based, PDE & ODE 2 36

Comparison of Models of Hepatic Lobules at Varying Levels of Detail

Sluka James
Tissue (250um) – sub-Cell (5um), Time ranges from hours to months. Agent based, PDE & ODE 1 37

Coupled multiscale modeling and pathway analysis for prediction of drug efficacy in cystic kidney diseases

Glazier James

arterioles 20-80 um, NO 0-100 nM, PO2 0-100 torr, time 0.1 s to minutes

Statistical data analysis 2 38

Nitrite-mediated Vasodilation Quantified from In Vivo Studies in Rat Mesentery

Buerk Donald
Microcirculatory tissue and arteriole: 1-100 μm, Steady state Finite element analysis, mass transport ODEs, cellular reaction kinetics 1 39

A Mathematical Model for the Role of N2O3 in Enhancing Nitric Oxide Following Nitrite Infusion

Liu Yien
Nanoscale to Microscale (Surface Receptors, Calcium, Nanomotors, Neuron)

IEEE Std 1906.1TM-2015; and Reference Code NEMo, doi: 10.1109/TMBMC.2015.2465513


2 40

Applying Nanocommunication Modeling to Understand Calcium Ion Influx in Neurons and Impact on Kinesin Axonal Transport of BDNF Vesicles

Paluh Janet
    1 41

Modelling the Airway Epithelium to Facilitate Cystic Fibrosis Drug Development

Corcoran Timothy

Sub-cellular to whole body lymphatic system, 10^-3 sec to hours

PDEs, ODEs, ABM 2 42

Mass Transport in the Lymphatic Vessels and Nodes

Moore James
Mesoscale & Microscale ODEs, Discrete and Spatial Stochastic Simulation, 1 43

StochSS: An Integrated Development Environment for Simulation and Analysis of Discrete Stochastic Biochemical Models

Petzold Linda
    2 44

A multiscale systems biology model to characterize antitumor immunity and evaluate biomarkers for immunotherapeutics

Gong Chang
molecular, cellular, tissue, organ and systemic levels; days to years ODEs, algebraic equations, probabilities 1 45

Systems Pharmacology Multiscale Model to Optimize Mono- and Combination-Therapy Regimens for Immune Checkpoint Inhibitors and Identify Potential Biomarkers

Milberg Oleg
spatial/temporal agent-based, ODE/PDE 2 46

Multiscale modeling of vascularized bone regeneration in hybrid constructs of soft collagen gels and rigid scaffold

Tan Hua
    1 3 High-Performance and Quantum Computing for Solving Biological Problems Difelice Rosa
    2 48 Genome-wide prediction of minor groove electrostatics enables biophysical modeling of protein-DNA binding Chiu Tsu-Pei
    1 49 Autonomic, Metabolic, and Mechanical Control of Coronary Blood Flow Beard Daniel
molecular, cellular, tissue; seconds to years agent-based, ODE, PDE 2 50 A Multi-scale Systems Pharmacology Approach to TB Treatment Linderman Jennifer
Individial-Population scales Multiscale Imaging-based Cluster Analysis (MICA), Machine Learning 1 51 Multiscale imaging-based cluster analysis of a cohort of current smokers Lin Ching-Long
Spatial/Temporal Agent-based, ODE/PDE 2 52 Systematically understanding immunity leading to CRPC progression Ji Zhiwei
    1 53 Sugar-Sweetened Beverage Warning Labels in Baltimore, Philadelphia and San Francisco: A Simulation Study Ferguson Marie
    2 54 A Parallel Fluid Solid Coupling Tool Using Lammps and Palabos Tan Jifu
    1 55

Development of a multiscale skin barrier model for de novo, in silico prediction

Tasseff Ryan

From the minute to the year, from the individual staff/patient scale to the OR suite and peripheral area scale.

hybrid ABM - stochastic ODE



Multiscale Modeling of Surgical Flow in a Large Operating Room Suite: Understanding the Mechanism of Accumulation of Delays in Clinical Practice

Garbey Marc
    1 57 Multiscale Multiphysics Model of Thrombus Biomechanics Yazdani Alireza
molecular, cellular, tissue, organ animal models of pressure- and volum-overload, mathematical models of growth and remodeling, computational multiscale models 2 58 Multiscale modeling of myocardial growth and remodeling Kuhl Ellen
    1 59

Molecular Scale Prediction of Lidocaine Interaction with the Pore Domain of Human NaV1.5

DeMarco Kevin
    2 60

Multiscale Analysis of Trauma

Sinno Talid
    1 61

Emulating Body Tissue Architectures for Computer-controlled Smart Material Design and Manufacture

Knothe-Tate Melissa
    2 62 Motion of spheroidal nanoparticles in a cylindrical vessel flow: accurately resolving the hydrodynamic interactions and stochastic thermal motion Ayyaswamy Portonovo
    1 63

Biophysically inspired model for functionalized nanocarrier adhesion to cell surface and the development of next-generation pharmacokinetic models

Radhakrishnan Ravi
    2 64

A multiscale model for predicting margination effects and transport of nanogels in blood vasculature: comparison of Dynamical Density Functional Theory and Monte Carlo based approaches

Eckmann David
hundreds of microns to tens of cm (acinus to trachea) PDEs (wav eqn), 3D-to-1D coupling, fractal methods 1 65 The Multiscale Audible Human Project Royston Thomas
molecular to cellular PDEs, stochastic simulations 2 66 Catch bonds at T cell interfaces Abel Steven
    1 67

Cell Death as a Trigger for Morphogenesis of Bacterial Colonies

Aguilar Boris
Molecular, Cellular, Individual, Population Agent-based model, Genetic Algorithms, Random Dynamical Systems 2


Really Big Data from HPC-enabled biomedical agent-based modeling:
Pathways to Precision Medicine
An Gary
an_gary.pdf43.01 KB

sub-cellular, cellular, tissue

agent-based models, finite element models


1 69 Computational models predict the effect of anti-fibrotic therapies in Duchenne muscular dystrophy Kelley Virgilio
tissue, Cellular, sub-cellular Agent based model, ode, pde 2 70 A Hybrid Multiscale Tumor Growth Model Lima Ernesto
    1 71 Growth Control in Cancer: An Computational Model of YAP/TAZ Integrating cell-ECM Mechanosensing and Hippo pathway Sun Meng
    2 72 Stochastic Simulation of Functional Knee Mechanics Enabled via Statistical Shape Modeling and High Throughput Computing Smith Colin
    1 73 Multi-scale mechanics of the tendon-to-bone attachment Thomopoulos Stavros
    2 74 Analysis of Multielectrode Data from CPG Networks Using
a Stochastic Framework
Abolfath-Beygi Maryam
 body/organ/tissue/cell PDE / finite element analysis 2 2 Democratization of Modeling & Simulation in Biomechanics Erdemir Ahmet
2 76 Mesoscopic modeling of biomechanics and biorheology of red blood cells in type 2 diabetes mellitus Chang Hung-yu


1 77

Patient-specific modeling of biomechanics and biorheology of red blood cells in sickle cell anemia

Li Xuejin
    2 78 Multiscale modeling of cardiac growth Lee Lik Chuan
cellular ~ tissue  agent-based & ODE/PDE 1 79 Multiscale Modeling of Multiple Myeloma Using Biocellion Framework Kang Chris
cellular ~ tissue agent-based & ODE/PDE 2 80

Biocellion: a large capacity modeling platform for multicellular biological systems

Kang Seunghwa
All scales Bayesian inference, probabilistic programming 1 81 Stan: A Platform for Scalable Bayesian Inference Betancourt Michael
molecular, subcellular, cellular, layer, column, area, multiarea ODE, event-driven 2 82 Embedded Ensemble Encoding - a new theory of brain cortex function Lytton William
molecular, subcellular, cellular and networks PDEs, Deterministic and Stochastic simulation 1 5 Expanding NEURON to bridge electrophysiology, chemical, and network scales: simulations of ischemic stroke Newton Adam
Multiple/All Scales Agent-based Modeling, Adaptive Model Exploration 2 4 From Desktop to Large-Scale Model Exploration with EMEWS Ozik Jonathan
    1 85 A detailed rule-based computational model for the interaction of VEGF pathway with thrombospondin-1 integrating multiple signaling modules: Implications for pro-angiogenic therapeutic interventions Bazzazi Hojjat
Behavioral, Population, International ODE, Deterministic 2 86

Effectiveness of UNAIDS targets and HIV vaccination across 127 countries

Fitzpatrick Meagan
Micro to Macro FDM of PDEs, DEM, CFD, Machine Learning 1 87

Hip Prostheses Lifetime Prediction via Simulation-based Engineering

Higgs C. Fred
    2 88

Parallel Discrete Event Simulation of Neurons

Tropper Carl
cellular, tissue  FEM, ODE  1 89 Comparison of cellular- and tissue-scale models of dynamic contrast-enhanced MRI Woodall Ryan
Spatial, Temporal, Population Multiscale statistical-based SolidWorks CAD modeling 2 90 Parametric Anatomical CAD Model Generation with Silicone Phantom Fabrication Tools for Validation Studies Bergeron Clint
Temporal, Population Event-driven, Matlab, Simulink Simscape, Finite State Modeling 2 91 Development of a Pulmonary Simulator Utilizing Windkessel Modeling Techniques for Simulating Various Patient Populations within a Mock Circulatory System King Jacob
Temporal, Population Event-driven, Matlab, Simulink Simscape 2 92 Evaluation of ventricular assist systems through target patient models Taylor Charles
    1 93 Exploring Polygenic Mechanisms of Pathogenesis and Treatment Resistance in Childhood Absence Epilepsy with a Multiscale Thalamocortical Model Knox Andrew
Molecualr, Subcellular MATLAB, NEURON 2 94

Modeling Postsynaptic Current at the Glutamatergic Synapse of a CA1 Pyramidal Neuron: Development and Adaptation for Multi-Scale Simulations

Hu Eric
Microscopic, Mesoscopic, Sub-macroscopic and Macroscopic Molecular Dynamic, Stochastic Simulations, Partial Differential Equation, and Bayesian scientific computing 1 95 Multi-scale Modeling of Gas Transport through Channels in Living Cells Occhipinti Rossana
    2 96

Multiscale Model of Facet Capsule Mechanobiology

Barocas Victor
Molecular, cellular ODE, standard format, SBML 1 97

Building Reproducible Dynamical Models with Tellurium 2.0: A Case Study using EGFR/Erk

Sauro Herbert
 Any/All  Applicability analysis 2 98 Applicability analysis of validation evidence for biomedical computational models Pathmanathan Pras
Cellular, tissue Event-driven 1 99 A Comparative Modeling Study on Intestinal Crypt Dynamics of Steady State and After Radiation Hu Shaowen
 Molecular, cellular Event-based 2


Calculation of deletion, inversion, and ring spectra using a computational model of the radiation-induced chromosome aberrations with stochastic and amorphous particle tracks Ponomarev Artem

Titles displayed in bold letters are those of posters from current U01 awardees.
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