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Research Output 2003 2019

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2019
2 Citations (Scopus)

CoCo-MD: A Simple and Effective Method for the Enhanced Sampling of Conformational Space

Shkurti, A., Styliari, I. D., Balasubramanian, V., Bethune, I., Pedebos, C., Jha, S. & Laughton, C. A., Apr 9 2019, In : Journal of Chemical Theory and Computation. 15, 4, p. 2587-2596 10 p.

Research output: Contribution to journalArticle

sampling
Sampling
Principal component analysis
principal components analysis
Maltose-Binding Proteins

Computational reproducibility of scientific workflows at extreme scales

Pouchard, L., Baldwin, S., Elsethagen, T., Jha, S., Raju, B., Stephan, E., Tang, L. & Van Dam, K. K., Sep 1 2019, In : International Journal of High Performance Computing Applications. 33, 5, p. 763-776 14 p.

Research output: Contribution to journalArticle

Scientific Workflow
Provenance
Reproducibility
Hybrid systems
Molecular dynamics

Middleware Building Blocks for Workflow Systems

Turilli, M., Balasubramanian, V., Merzky, A., Paraskevakos, I. & Jha, S., Jul 1 2019, In : Computing in Science and Engineering. 21, 4, p. 62-75 14 p., 8726147.

Research output: Contribution to journalArticle

Middleware
2018
1 Citation (Scopus)

A parallel unidirectional coupled DEM-PBM model for the efficient simulation of computationally intensive particulate process systems

Sampat, C., Bettencourt, F., Baranwal, Y., Paraskevakos, I., Chaturbedi, A., Karkala, S., Jha, S., Ramachandran, R. & Ierapetritou, M., Nov 2 2018, In : Computers and Chemical Engineering. 119, p. 128-142 15 p.

Research output: Contribution to journalArticle

Granulation
Computer simulation
Physics
4 Citations (Scopus)

A systematic framework for data management and integration in a continuous pharmaceutical manufacturing processing line

Cao, H., Mushnoori, S., Higgins, B., Kollipara, C., Fermier, A., Hausner, D., Jha, S., Singh, R., Ierapetritou, M. & Ramachandran, R., May 1 2018, In : Processes. 6, 5, 53.

Research output: Contribution to journalArticle

Data visualization
Data integration
Drug products
Information management
Processing
1 Citation (Scopus)

High-throughput binding affinity calculations at extreme scales

Dakka, J., Turilli, M., Wright, D. W., Zasada, S. J., Balasubramanian, V., Wan, S., Coveney, P. V. & Jha, S., Dec 21 2018, In : BMC Bioinformatics. 19, 482.

Research output: Contribution to journalArticle

High Throughput
Affine transformation
Extremes
Throughput
Calculator
14 Citations (Scopus)

Perspective: Computational chemistry software and its advancement as illustrated through three grand challenge cases for molecular science

Krylov, A., Windus, T. L., Barnes, T., Marin-Rimoldi, E., Nash, J. A., Pritchard, B., Smith, D. G. A., Altarawy, D., Saxe, P., Clementi, C., Crawford, T. D., Harrison, R. J., Jha, S., Pande, V. S. & Head-Gordon, T., Nov 14 2018, In : Journal of Chemical Physics. 149, 18, 180901.

Research output: Contribution to journalArticle

Intrinsically Disordered Proteins
Computational chemistry
computational chemistry
Supercomputers
Software design
1 Citation (Scopus)

Synapse: Synthetic application profiler and emulator

Merzky, A., Ha, M. T., Turilli, M. & Jha, S., Jul 2018, In : Journal of Computational Science. 27, p. 329-344 16 p.

Research output: Contribution to journalArticle

Synapse
Workload
Resources
Emulation
Profiling
2017
2 Citations (Scopus)

Introducing distributed dynamic data-intensive (D3) science: Understanding applications and infrastructure

Jha, S., Katz, D. S., Luckow, A., Chue Hong, N., Rana, O. & Simmhan, Y., Apr 25 2017, In : Concurrency Computation. 29, 8, e4032.

Research output: Contribution to journalArticle

Infrastructure
Engineering Application
Software System
Availability
Scenarios
2 Citations (Scopus)

On the complexities of utilizing large-scale lightpath-connected distributed cyberinfrastructure

Maassen, J., van Werkhoven, B., van Meersbergen, M., Bal, H. E., Kliphuis, M., Brunnabend, S. E., Dijkstra, H. A., van Malenstein, G., de Vos, M., Kuijpers, S., Boele, S., Wolfrat, J., Hill, N., Wallom, D., Grimm, C., Kranzlmüller, D., Ganpathi, D., Jha, S., Khamra, Y. E., Bryan, F. O. & 2 others, Kirtman, B. & Seinstra, F. J., Jan 25 2017, In : Concurrency Computation. 29, 2, e3853.

Research output: Contribution to journalArticle

Infrastructure
E-Science
Climate Models
Human Resources
Supercomputer
2016
2 Citations (Scopus)

Application skeletons: Construction and use in eScience

Katz, D. S., Merzky, A., Zhang, Z. & Jha, S., Jun 2016, In : Future Generation Computer Systems. 59, p. 114-124 11 p.

Research output: Contribution to journalArticle

Tuning
Systems analysis
Scheduling
Testing
Experiments

Integration of Panda Workload Management System with supercomputers

De, K., Jha, S., Klimentov, A., Maeno, T., Mashinistov, R., Nilsson, P., Novikov, A., Oleynik, D., Panitkin, S., Poyda, A., Read, K. F., Ryabinkin, E., Teslyuk, A., Velikhov, V., Wells, J. C. & Wenaus, T., Sep 1 2016, In : Physics of Particles and Nuclei Letters. 13, 5, p. 647-653 7 p.

Research output: Contribution to journalArticle

supercomputers
management systems
Workload
Saturn
Titan
2015
9 Citations (Scopus)

Characterization of the three-dimensional free energy manifold for the uracil ribonucleoside from asynchronous replica exchange simulations

Radak, B. K., Romanus, M., Lee, T-S., Chen, H., Huang, M., Treikalis, A., Balasubramanian, V., Jha, S. & York, D., Feb 10 2015, In : Journal of Chemical Theory and Computation. 11, 2, p. 373-377 5 p.

Research output: Contribution to journalArticle

Ribonucleosides
uracil
Uracil
replicas
Free energy
8 Citations (Scopus)

Pilot-Data: An abstraction for distributed data

Luckow, A., Santcroos, M., Zebrowski, A. & Jha, S., Jun 3 2015, In : Journal of Parallel and Distributed Computing. 79-80, p. 16-30 15 p.

Research output: Contribution to journalArticle

Scheduling
Interoperability
Placement
Abstraction
Distributed Environment
15 Citations (Scopus)

SAGA: A standardized access layer to heterogeneous distributed computing infrastructure

Merzky, A., Weidner, O. & Jha, S., Jan 1 2015, In : SoftwareX. 1-2, p. 3-8 6 p.

Research output: Contribution to journalArticle

Distributed computer systems
Interfaces (computer)
2014
4 Citations (Scopus)

Advancing next-generation sequencing data analytics with scalable distributed infrastructure

Kim, J., Maddineni, S. & Jha, S., Mar 25 2014, In : Concurrency Computation Practice and Experience. 26, 4, p. 894-906 13 p.

Research output: Contribution to journalArticle

Sequencing
Infrastructure
Pipelines
Genes
Chromatin
17 Citations (Scopus)

Comparative analysis of nucleotide translocation through protein nanopores using steered molecular dynamics and an adaptive biasing force

Martin, H. S. C., Jha, S. & Coveney, P. V., Apr 5 2014, In : Journal of Computational Chemistry. 35, 9, p. 692-702 11 p.

Research output: Contribution to journalArticle

Nanopore
Nanopores
Translocation
Nucleotides
Comparative Analysis
67 Citations (Scopus)

Computing clinically relevant binding free energies of HIV-1 protease inhibitors

Wright, D. W., Hall, B. A., Kenway, O. A., Jha, S. & Coveney, P. V., Mar 11 2014, In : Journal of Chemical Theory and Computation. 10, 3, p. 1228-1241 14 p.

Research output: Contribution to journalArticle

protease
human immunodeficiency virus
Molecular mechanics
Protease Inhibitors
inhibitors
7 Citations (Scopus)

Developing eThread pipeline using SAGA-pilot abstraction for large-scale structural bioinformatics

Ragothaman, A., Boddu, S. C., Kim, N., Feinstein, W., Brylinski, M., Jha, S. & Kim, J., 2014, In : BioMed Research International. 2014, 348725.

Research output: Contribution to journalArticle

Bioinformatics
Computational Biology
Pipelines
Genes
Genome
3 Citations (Scopus)

Numerical methodologies for investigation of moderate-velocity flow using a hybrid computational fluid dynamics - molecular dynamics simulation approach

Ko, S. H., Kim, N., Jha, S., Nikitopoulos, D. E. & Moldovan, D., Jan 1 2014, In : Journal of Mechanical Science and Technology. 28, 1, p. 245-253 9 p.

Research output: Contribution to journalArticle

Flow velocity
Molecular dynamics
Computational fluid dynamics
Computer simulation
Sampling
2013
14 Citations (Scopus)

Distributed computing practice for large-scale science and engineering applications

Jha, S., Cole, M., Katz, D. S., Parashar, M., Rana, O. & Weissman, J., Aug 10 2013, In : Concurrency Computation Practice and Experience. 25, 11, p. 1559-1585 27 p.

Research output: Contribution to journalArticle

Distributed Applications
Distributed computer systems
Distributed Computing
Engineering Application
Infrastructure
15 Citations (Scopus)

The Impact of a Ligand Binding on Strand Migration in the SAM-I Riboswitch

Huang, W., Kim, J., Jha, S. & Aboul-ela, F., May 1 2013, In : PLoS computational biology. 9, 5, e1003069.

Research output: Contribution to journalArticle

Riboswitch
Helix
RNA
Methionine
ligand
2012
9 Citations (Scopus)

Conformational heterogeneity of the SAM-I riboswitch transcriptional on state: A chaperone-like role for S-adenosyl methionine

Huang, W., Kim, J., Jha, S. & Aboul-Ela, F., May 18 2012, In : Journal of molecular biology. 418, 5, p. 331-349 19 p.

Research output: Contribution to journalArticle

Riboswitch
Methionine
Biosynthetic Pathways
Ligands
Base Pairing
24 Citations (Scopus)

Distributed Application Runtime Environment (DARE): A Standards-based Middleware Framework for Science-Gateways

Maddineni, S., Kim, J., El-Khamra, Y. & Jha, S., Dec 1 2012, In : Journal of Grid Computing. 10, 4, p. 647-664 18 p.

Research output: Contribution to journalArticle

Middleware
User interfaces
2 Citations (Scopus)

Quantized water access to the HIV-1 protease active site as a proposed mechanism for cooperative mutations in drug affinity

Hall, B. A., Wright, D. W., Jha, S. & Coveney, P. V., Aug 21 2012, In : Biochemistry. 51, 33, p. 6487-6489 3 p.

Research output: Contribution to journalArticle

Catalytic Domain
Lopinavir
Ritonavir
Mutation
Water
2011
44 Citations (Scopus)

Autonomic management of application workflows on hybrid computing infrastructure

Kim, H., El-Khamra, Y., Rodero, I., Jha, S. & Parashar, M., Jan 1 2011, In : Scientific Programming. 19, 2-3, p. 75-89 15 p.

Research output: Contribution to journalArticle

Conservation
Scheduling
Oils
10 Citations (Scopus)

Efficient large-scale replica-exchange simulations on production infrastructure

Thota, A., Luckow, A. & Jha, S., Aug 28 2011, In : Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences. 369, 1949, p. 3318-3335 18 p.

Research output: Contribution to journalArticle

Replica
replicas
Infrastructure
Exchange Algorithm
Simulation
7 Citations (Scopus)

Energy landscape analysis for regulatory RNA finding using scalable distributed cyberinfrastructure

Kim, J., Huang, W., Maddineni, S., Aboul-Ela, F. & Jha, S., Dec 10 2011, In : Concurrency Computation Practice and Experience. 23, 17, p. 2292-2304 13 p.

Research output: Contribution to journalArticle

Energy Landscape
RNA
Ludwig Boltzmann
Ensemble
Folding
17 Citations (Scopus)

Understanding application-level interoperability: Scaling-out MapReduce over high-performance grids and clouds

Sehgal, S., Erdelyi, M., Merzky, A. & Jha, S., May 1 2011, In : Future Generation Computer Systems. 27, 5, p. 590-599 10 p.

Research output: Contribution to journalArticle

Interoperability
Level control
Application programming interfaces (API)
2010
11 Citations (Scopus)

Large scale computational science on federated international grids: The role of switched optical networks

Coveney, P. V., Giupponi, G., Jha, S., Manos, S., MacLaren, J., Pickles, S. M., Saksena, R. S., Soddemann, T., Suter, J. L., Thyveetil, M. & Zasada, S. J., Jan 1 2010, In : Future Generation Computer Systems. 26, 1, p. 99-110 12 p.

Research output: Contribution to journalArticle

Switching networks
Fiber optic networks
Middleware
Quality of service
Visualization
3 Citations (Scopus)

Understanding performance of distributed data-intensive applications

Miceli, C., Miceli, M., Rodriguez-Milla, B. & Jha, S., Sep 13 2010, In : Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences. 368, 1926, p. 4089-4102 14 p.

Research output: Contribution to journalArticle

Data Placement
Infrastructure
Distributed File System
genome
Data Management
2009
19 Citations (Scopus)

Adaptive distributed replica exchange simulations

Luckow, A., Jha, S., Kim, J., Merzky, N. & Schnor, B., Jun 28 2009, In : Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences. 367, 1897, p. 2595-2606 12 p.

Research output: Contribution to journalArticle

Replica
replicas
Application programming interfaces (API)
Parallel algorithms
Scheduling
37 Citations (Scopus)

A mechanism for S-adenosyl methionine assisted formation of a riboswitch conformation: A small molecule with a strong arm

Huang, W., Kim, J., Jha, S. & Aboul-Ela, F., Nov 16 2009, In : Nucleic acids research. 37, 19, p. 6528-6539 12 p.

Research output: Contribution to journalArticle

Riboswitch
Methionine
S-Adenosylmethionine
RNA
Molecular Dynamics Simulation
20 Citations (Scopus)

Determination of free energy profiles for the translocation of polynucleotides through α-hemolysin nanopores using non-equilibrium molecular dynamics simulations

Martin, H. S. C., Jha, S., Howorka, S. & Coveney, P. V., Aug 1 2009, In : Journal of Chemical Theory and Computation. 5, 8, p. 2135-2148 14 p.

Research output: Contribution to journalArticle

polynucleotides
Polynucleotides
Porins
Hemolysin Proteins
Nanopores
3 Citations (Scopus)

Louisiana: A model for advancing regional e-research through cyberinfrastructure

Katz, D. S., Allen, G., Cortez, R., Cruz-Neira, C., Gottumukkala, R., Greenwood, Z. D., Guice, L., Jha, S., Kolluru, R., Kosar, T., Leger, L., Liu, H., McMahon, C., Nabrzyski, J., Rodriguez-Milla, B., Seidel, E., Speyrer, G., Stubblefield, M., Voss, B. & Whittenburg, S., Jun 28 2009, In : Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences. 367, 1897, p. 2459-2469 11 p.

Research output: Contribution to journalArticle

scientific visualization
Visualization
Data Storage
Storage System
data storage
3 Citations (Scopus)
resources
Resources
Molecular dynamics
Scheduling
distributing
50 Citations (Scopus)

Using clouds to provide grids with higher levels of abstraction and explicit support for usage modes

Jha, S., Merzky, A. & Fox, G., Jun 10 2009, In : Concurrency Computation Practice and Experience. 21, 8, p. 1087-1108 22 p.

Research output: Contribution to journalArticle

Grid
Terminology
Affine transformation
Distributed Applications
Abstraction
2007
18 Citations (Scopus)

NEKTAR, SPICE and Vortonics: Using federated grids for large scale scientific applications

Boghosian, B., Coveney, P., Dong, S., Finn, L., Jha, S., Karniadakis, G. & Karonis, N., Sep 1 2007, In : Cluster Computing. 10, 3, p. 351-364 14 p.

Research output: Contribution to journalArticle

SPICE
Middleware
Interoperability
Scheduling
11 Citations (Scopus)

Rapid, accurate, and precise calculation of relative binding affinities for the SH2 domain using a computational grid

Fowler, P. W., Geroult, S., Jha, S., Waksman, G. & Coveney, P. V., May 1 2007, In : Journal of Chemical Theory and Computation. 3, 3, p. 1193-1202 10 p.

Research output: Contribution to journalArticle

computational grids
affinity
Phosphopeptides
Free energy
free energy
2005
15 Citations (Scopus)

Force field validation for nucleic acid simulations: Comparing energies and dynamics of a DNA dodecamer

Jha, S., Coveney, P. V. & Laughton, C. A., Nov 30 2005, In : Journal of Computational Chemistry. 26, 15, p. 1617-1627 11 p.

Research output: Contribution to journalArticle

Nucleic acids
Force Field
Nucleic Acids
Molecular dynamics
DNA