Publications
Below are selected publications by Cornell
researchers who have conducted research using Center or Center-supported resources.
2008
Cyberscholarship: High Performance Computing meets Digital Libraries
W. Arms
Journal of Electronic Publishing
High-Resolution Spatial Interpolation of Weather Generator Parameters Using Local Weighted Regressions
D. Wilks
Agricultural and Forest Meteorology
Modeling Diffusion in Random Heterogeneous Media: Data-Driven Models, Stochastic Collocation and the Variational Multiscale Method
B. Ganapathysubramanian, N. Zabaras
Physical Reviews B (in preparation)
Modeling the Response of HCP Polycrystals Deforming by Slip and Twinning Using a Finite Element Representation of the Orientation Space
B. Kouchmeshky, N. Zabaras
International Journal of Plasticity (submitted)
Non-Linear Dimension Reduction Methodology for Generating Data-Driven Stochastic Input Models
B. Ganapathysubramanian, N. Zabaras
Journal of Computational Physics (submitted)
Sensitivity Calculations in PDF Modelling of Turbulent Flames
Z. Ren, S. Pope
Proceedings of the Combustion Institute (submitted)
Turbulent Dispersion Behind Line Sources in Grid Turbulence
S. Viswanathan, S. Pope
Physics of Fluids (submitted)
2007
A Non-Intrusive Stochastic Galerkin Approach for Modeling Uncertainty Propagation in Deformation Processes
S. Acharjee, N. Zabaras
Computational Stochastic Mechanics
A Seamless Approach Towards Stochastic Modeling: Sparse Grid Collocation and Data Driven Input Models
B. Ganapathysubramanian, N. Zabaras
Finite Elements in Analysis and Design
A Tomato Endo-ß-1, 4-glucanase, SlCel9C1, Represents a Distinct Subclass with a New Family of Carbohydrate Binding Modules
B.R. Urbanowicz, C. Catala, D. Irwin, D.B. Wilson, D.R. Ripoll, J.K.C. Rose
Journal of Biological Chemistry
Cayuga: A General Purpose Event Monitoring System
A. Demers, J. Gehrke, B. Panda, M. Riedewald, V. Sharma, W. White
Conference on Innovative Data Systems Research (CIDR 2007)
Computational Fracture Mechanics of Concrete Structures: A Retrospective through Multiple Lenses
J. Emery, J. Hochhalther, A. Ingraffea
Cornell University Technical Report
Digital Material: A Flexible Atomistic Simulation Code
N. Bailey, T. Cretegny, J. Sethna, V. Coffman, A. Dolgert, C. Myers, J. Schiotz, J. Mortensen
Cornell Technical Report
Dynamically Dimensioned Search
Algorithm for Computationally Efficient Watershed Model Calibration
B. Tolson, C.A. Shoemaker
Water Resources Research
Evolutionary and Biomedical Insights from the Rhesus Macaque Genome
A.G. Clark and the Rhesus Macaque Genome Sequencing and Analysis Consortium
Science
Extracting Falsifiable Predictions from Sloppy Models
R. Gutenkunst, F. Casey, J. Waterfall, C. Myers, J. Sethna
Annals of the New York Academy of Science
Modeling the Response of HCP Polycrystals Deforming by Slip and Twinning Using a Finite Element Representation of the Orientation Space
B. Kouchmeshky, N. Zabaras
Cornell University Technical Report
Multiscale Modeling of Alloy Solidification Using a Database Approach
L. Tan, N. Zabaras
Journal of Computational Physics
Optimal Experimental Design in an EGFR Signaling and Down-Regulation Model
F. Casey, D. Baird, Q. Feng, R. Gutenkunst, J. Waterfall, C Myers, K. Brown, R. Cerione, J. Sethna
IET Systems Biology
Optimization of Quantum Monte
Carlo Wave Functions by Energy Minimization
J. Toulouse, C. Umrigar
Journal of Chemical Physics
Protistan Diversity in the Arctic: A Case of Paleoclimate Shaping Modern Biodiversity?
T. Stoeck, J. Kasper, J. Bunge, C. Leslin, V. Ilyin, S. Epstein
PLoS ONE
Python for Education: Computational Methods for Nonlinear Systems
C. Myers, J. Sethna
Computing for Science and Engineering
Python Unleashed on Systems Biology
C. Myers, R. Gutenkunst, J. Sethna
Computing in Science and Engineering
Satisfiability, Sequency Niches, and Molecular Codes in Cellular Signaling
C. Myers
Cornell University Technical Report
Scalable Framework for the Solution of Stochastic Inverse Problems Using a Sparse Grid Collocation Approach
N. Zabaras, B. Ganapathysubramanian
Cornell University Technical Report
Support Vector Training of
Protein Alignment Models
R. Elber, T. Joachims, J. Pillardy,
C. Yu
Research in Computational Molecular
Biology
Topology of Type II REases Revisted; Structural Classes and the Common Conserved Core
M. Niv, D. Ripoll, J. Vila, A. Liwo, E. Vanamee, A. Aggarwal, H. Weinstein, H. Scheraga
Nucleic Acids Research
Universally Sloppy Parameter
Sensitivities in Systems Biology
R. N. Gutenkunst, J.J. Waterfall,
F.P. Casey, K.S. Brown, C.R. Myers, J.P. Sethna
Cornell University Technical Report
2006
A Localized Specific Interaction
Alters the Unfolding Pathways of Structural Homologues
G. Xu, M. Narayan, I. Kurinov, D.R. Ripoll, E.
Welker, M. Khalili, S.E. Ealick, H.A. Scheraga
Journal of American Chemical Society
A
Research Library Based
on the Historical Collections of the Internet Archive
W. Arms, S. Aya, P Dmitriev, B. Kot,
R. Mitchell, L. Walle
D-Lib Magazine
Advanced Computational Techniques
for Materials-by-Design
N. Zabaras
Cornell University Technical Report
ALPS: A Software Framework
for Parallel Space-Time Adaptive Processing
K. Lee, A.W. Bojanczyk
Applied Parallel Computing
Bayesian Calibration of Computationally
Expensive Models Using Optimization and Radial Basic Function Approximation
N. Blizniouk, P. Mugunthan, R. Regis,
D. Ruppert, C. Shoemaker, S. Wild
Cornell University Technical Report
Building a Research Library
for the History of the Web
W. Arms, S. Aya, P. Dmitriey, B.
Kot, R. Mitchell, L Walle
Joint Conference on Digital Libraries
Cluster Assimilation and Collisional
Filtering on Metal-Oxide Surfaces
D.A. Freedman, T.A. Arias
Physical Review Letters
Comment on
“Computational Improvements Reveal Great Bacterial Diversity and High
Metal Toxicity in Soil”
J. Bunge, S.S. Epstein, D.G. Peterson
Science
Efficient Computation of the
First Passage Time Distribution of the Generalized Master Equation by
Steady-State Relaxation
D. Shalloway, A. Faradkijan
Journal of Chemical Physics
Development and Characterization
of a Normalized Canine Retinal cDNA Library for Genomic and Expression
Studies
B. Zangerl, Q. Sun, J. Pillardy,
J. Johnson, P. Schweitzer, A. Hernandez, L. Liu, G. Acland, G. Aguirre
Investigative Ophthalmology and
Visual Science
Distributed System Based on
Web Services for Computational Science Simulations
K. Pingali, P. Stodghill
Proceedings of the International
Conference on Supercomputing
Efficient Query Processing
on Unstructured Tetrahedral Meshes
S. Papadomanolakis, A. Ailamaki,
J. Lopez, T. Tu, D.R. O’Hallaron, G. Heber
Proceedings of ACM SIGMOD
Evaluation of the PNM Model
for Simulating Drain Flow Nitrate-N Concentration Under Manure-Fertilized
Maize
J.M. Sogbedji, H.M. van Es, J.J.
Melkonian, R.R. Schindelbeck
Plant and Soil
From Wayback Machine to Yesternet:
New Opportunities for Social Science
W. Arms, D. Huttenlocher, J. Kleinberg,
M. Macy, D Strang
Second International Conference
on e-Social Science
Ground State of the Pseudogap
in Cuprate Superconductors
T. Valla, A.V. Fedorov, Jinho Lee,
J.C. Davis, G.D. Gu
Science
Microfluidic Biomaterials
A.D. Stroock, M. Cabodi
M.R.S. Bulletin
Mobile MPI Programs in Computational
Grids
R. Fernandes, K. Pingali, P. Stodghill
ACM 2006 Symposium on Principles
and Practice of Parallel Computing
“Propeller” Regime of
Disk Accretion to Rapidly Rotating Stars
G.V. Ustyugova, A.V. Kodoba, M.M.
Romanova, R.V.E. Lovelace
The Astrophysical Journal
Protein Translocation Through
a Tunnel Induces Changes in Folding Kinetics: A Lattice Model Study
L.M. Contreras Martinez, F.J. Martinez-Verachoechea,
P. Pohkarel, A.D. Stroock, F.A. Escobedo, M.P. DeLisa
Biotechnology & Bioengineering
Reported Anatomical Variability
Naturally Leads to Multimodal Distributions of Denavit-Hartenberg
V. Santos, F. Valero-Cuevas
IEEE Transactions of Biomedical
Engineering
Risk Neutral Compatibility
with Option Prices
J. Jacod, P. Protter
Cornell University Technical Report
Spatial Interpolation of Daily
Maximum and Minimum Air Temperature Based on Meteorological Model Analysis
and Independent Observation
A.T. DeGaetano, B.N. Belcher
Cornell University Technical Report
Strategic Design of Distribution
Systems with Economies of Scale in Transportation
J.R. Lin, L.K. Nozick, M.A. Turnquist
Annals of Operation Research
Supporting Finite Element
Analysis with a Relational Database Backend; Part III
G. Heber, C. Pelkie, A. J. Dolgert.
J. Gray, D. Thompson
Microsoft
Research Technical Report
Supporting Finite Element
Analysis with a Relational Database Backend; Part II
G. Heber, J. Gray
Microsoft Research Technical Report
Synthetic Statistical Approach
Reveals a High Degree of Richness of Microbial Eukaryotes in an Anoxic
Water Column
S.-O. Jean, J. Bunge, T. Stoeck,
K.J.-A. Barger, S.-H. Hong, S.S. Epstein
Applied and Environmental Microbiology
The Sloppy Model Universality
Class and Vandermonde Matrix
J.J. Waterfall, F.P. Casey, R.N.
Gutenkunst, K.S. Brown, C.R. Myers, P.W. Brouwer, V. Elser, J.P. Sethna
Physical Review Letters
Three Case Studies of Large-Scale
Data Flows
W. Arms, S. Aya, M. Calimlim, J.
Cordes, P. Deneva, P. Dmitriev, J. Gehrke, L. Gibbons, C.D. Jones, V.
Kuznetsov, D. Lifka, M. Riedewald, D. Riley, A. Ryd, G.J. Sharp
IEEE Proceedings on Workflow and
Dataflow for Scientific Applications
Whole-Genome
Expression Profiling Defines the HrpL Regulon of Pseudomonas syringae
pv. Tomato DC3000
A.O. Ferreira, C.R. Myers, J.S. Gordon,
G.B. Martin, M. Vencato, A. Collmer, M.D. Wehling, J.R. Alfano, G. Moreno-Hagelsieb,
W.F. Lamboy, G. DeClerck, D.J. Schneider, S.W. Cartinhour
Molecular Plant-Microbe Interactions
2005
A Method to Infer Time of
Observation at U.S. Cooperative Observer Network Stations Using Model
Analyses
B.N. Belcher, A.T. DeGaetano
Cornell University Technical Report
A Surface Loop of the Potato
Leafroll Virus Coat Protein is Involved in Virion Assembly, Systemic
Movement, and Aphid Transmission
L. Lee, I.B. Kaplan, D.R. Ripoll,
D. Liang, P. Palukaitis, S.M. Gray
Journal of Virology
A Variable Temperature EPR
Study of Mn2+
-doped NH4C10.9I0.1
Single Crystal at 170 GHz: Zero-Field Splitting Parameter and its
Absolute Sign
S. K. Misra, S.I. Andronenko, P.
Chand, K.A. Earle, S.V. Paschenko, J.H. Freed
Journal of Magnetic Resonance
Coupling Between Conformation
and Proton Binding in Proteins
J.
Vila, D.R. Ripoll, Y.A. Arnautova, Y.N. Vorobjev, H.A. Scheraga
Proteins
Detection of Repolarization
Alternans With an Implantable Cardioverter Defibrillator Lead in a Porcine
Model
Maybhate, S.C. Hao, S. Iwai,
J.U. Lee, A.B. Guttigoli, K.Stein, B. Lerman,
D. Christini
IEEE Transactions on Biomedical
Engineering
Electric Organ Discharge Patterns
During Group Hunting by a Mormyrid Fish
M.E. Arnegard, B.A. Carlson
Proceedings of the Royal Society
Evolutionary Robotics and
Open-Ended Design Automation
H. Lipson
Biometrics
Functional Differentiation
of Bundle Sheath and Mesophyll Maize Chloroplasts Determined by Comparative
Proteomics
W. Majeran, Y. Cai, Q. Sun, K.J.
van Wijk
Plant Cell
High-Frequency ESR at ACERT
K.A. Earle, B. Dzikovski. W. Hofbauer,
J.K. Moscicki, J.H. Freed
Magnetic Resonance in Chemistry
Insights into Dark Energy:
Interplay Between Theory and Observation
R. Bean, S. Carroll, M. Trodden
Cornell University Technical Report
Lattice Strain Partitioning
in a Two-Phase Alloy and its Redistribution Upon Yielding
T.S. Han, Paul R. Dawson
Materials Science and Engineering
Measuring and Modeling the
Appearance of Finished Wood
S.R. Marchner, S.H. Westin, A. Arbree,
J.T. Moon
ACM Transactions on Graphics (SIGGRAPH
2005 Proceedings)
Minimizing CVaR and VaR for
a Portfolio of Derivatives
S. Alexander, T.F. Coleman, Y. Li
Journal of Banking and Finance
Modeling Nitrogen Dynamics
Under Maize on Ferralsols in Western Africa
J.M. Sogbedji, H.M. van Es, K.L.
Agbeko
Nutrient Cycling in Agroecosystems
Multivariate Optimization
of a High Brightness DC Gun Photoinjector
I. Bazarov, C.K. Sinclair
Physical Review
Nonlinear Spectroscopy of
Resonantly Coupled Classical Mechanical Molecular Vibrations
W.G. Noid, R.F. Loring
Molecular Physics
Predicting Microbial Species
Richness
S.-H. Hong, J. Bunge, S.-O. Jeon,
S.S. Epstein
National Academy of Science
Reducing Communication Time
Through Message Prefetching
J. Ke, M. Burscher, E. Speight
2005 International Conference
on Parallel and Distributed Processing
Structural Damage Identification
Using Co-Evolution and Frequency Response Functions
B. Kouchmeshky, W. Aquino
Cornell University Technical Report
Three-Dimensional, Parallel,
Finite Element Simulation of Fatigue Crack Growth in a Bevel Pinion
Gear
A. Ural, G. Heber, P.A. Wawrzynek,
A.R. Ingraffea, D.G Lewicki, Joaquim Neto
Engineering
Fracture Mechanics Journal
The Influence of Chemical
Mechanisms on PDF Calculations of Nonpremixed Piloted Jet Flames
R.R. Cao, S.B. Pope
Combustion and Flame Journal
The Maximum Density Droplet
to Lower Density Droplet Transition in Quantum Dots
A.D. Guclu, C.J. Umrigar
Physical Review
Physics-Based Protein-Structure
Prediction Using a Hierarchical Protocol Based on the UNRES Force Field:
Assessment in Two Blind Tests
S. Lodziej, C. Czaplewski, A. Liwo,
M. Chinchio, M. Nanias, JA Vila, M. Khalili, Y.A. Arnautova, A. Jagielska,
M. Makowski, H.D. Schafroth, R. Kazmierkiewicz, . D.R. Ripoll, J. Pillardy, J.A. Saunders, Y.K. Kang, K.D. Gibson, H.A. Scheraga
Proceedings of the National Academy
of Science
Reducing Communication Time
Through Message Prefetching
J. Ke, Martin Burtscher, E. Speight
Proceedings of International Conference
on Parallel and Distributed Processing
Scientific Data Management
in the Coming Decade
J. Gray, D.T. Liu, M.Nieto-Santisteban,
A. Szalay, D.J. DeWitt, G. Heber
ACM SIGMOD
Soil Test, Aerial Image and
Yield Data as Inputs for Site-specific Fertility and Hybrid Management
Under Maize
A.
Magri, H. M. van Es, M.A. Glos, W.J. Cox
Precision
Agriculture
Supporting Finite Element
Analysis with a Relational Database Backend; Part I
G. Heber, J. Gray
Microsoft Research Technical Report
2004
A Vision for PetaByte Data
Management and Analysis Services for the Arecibo Telescope
M. Calimlim, J. Cordes, A. Demers,
J. Deneva, J. Gehrke, D. Kifer, M. Riedewald, J. Shanmugasundaram
IEEE Computer Society
Accuracy and Power of Statistical
Methods for Detecting Adaptive Evolution Protein Coding Sequences and
for Identifying Positively Selected Sites
W. Wong, Z. Yang, N. Goldman, R. Nielsen
Genetics
Enriching the Sequence Substitution
Matrix by Structural Information
O. Teodorescu, T. Galor, J. Pillardy,
R. Elber
Protein
Hedging Guarantees in Variable
Annuities (Under Both Market and Interest Rate Risks)
T.F. Coleman, Y. Li, M.-C. Patron
Cornell University Technical Report
In-Depth Analysis of the Thylakoid
Membrane proteome of Arabidopsis thaliana Chloroplasts: New Proteins,
New Functions, and a Plastid Proteome Database
G. Frisco, L. Guacamole, A. J. Sternberg,
J.B. Pettier, A. Rubella, Q. Sun, K.J. van Wink
Plant Cell
Implementation and Evaluation
of a Scalable Application-Level Checkpoint-Recovery Scheme for MPI Programs
M. Schulz, G. Bronevetsky, R. Fernandes,
D. Marques, K. Pingali, P. Stodghill
Supercomputing 2004
Integrated Design, Deployment
and Inference for Robot Ecologies
J. Bongard, H. Lipson
Proceedings of Robosphere 2004
Novel Two-Dimensional Photonic
Crystals Designed by Evolutionary Algorithms
S.F. Preble, H. Lipson, M. Lipson
Proceedings of the International
Society for Optical Engineering 2004
PeerGAD: a Peer-Review-based
and Community-Centric Web Application for Viewing and Annotating Prokaryotic
Genome Sequences
M.D. D’Ascenzo, A. Collmer, G.B.
Martin
Nucleic Acids Research
Performance Analysis of the
Pipe Problem, a Multi-Physics Simulation Based on Web Services
P. Stodghill, R. Cronin, K. Pingali,
G. Heber
Cornell University Technical Report
Performance Modeling and Optimization
Framework for Space-Time Adaptive Processing (STAP)
K. Lee, A. Bojanczyk
IEEE International Parallel and
Distributed Processing Symposium
Robustly Hedging Variable
Annuities with Guarantees Under Jump and Volatility Risks
T. Coleman, Y. Kim, Y. Li, M.-C.
Patron
Cornell University Technical Report
Runtime Compression of MPI
Messages to Improve the Performance and Scalability of Parallel Applications
J. Ke, M. Burtscher, E. Speight
Supercomputing 2004
Sam68 Exerts Separable Effects
on Cell Cycle Progression and Apoptosis
S.J. Taylor, R.J. Resnick, D. Shalloway
BMC Cell Biology
The Protein Folding Problem:
Global Optimization of Force Fields
H.A. Scheraga, A. Liwo, S. Oldziej,
C. Czaplewski, J. Pillardy, D.R. Ripoll, J.A. Vila, R. Kazmierkiewicz,
J.A. Saunders, Y.A. Arnautova, A. Jagielska, M. Chinchio, M. Nanias
Frontiers of Biology Journal
Vortex-Induced Vibrations
C.H.K. Williamson, R. Govardhan
Annual Review of Fluid Mechanics
