• 1245 Citations
  • 19 h-Index
20012020

Research output per year

If you made any changes in Pure these will be visible here soon.

Research Output

Filter
Article
2020

Parallel performance of molecular dynamics trajectory analysis

Khoshlessan, M., Paraskevakos, I., Fox, G. C., Jha, S. & Beckstein, O., Jan 1 2020, (Accepted/In press) In : Concurrency Computation.

Research output: Contribution to journalArticle

2019

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

3 Scopus citations

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

2 Scopus citations

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

1 Scopus citations
2018

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

2 Scopus citations

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

6 Scopus citations

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

2 Scopus citations

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

20 Scopus citations

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

1 Scopus citations
2017

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

3 Scopus citations

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

2 Scopus citations
2016

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

2 Scopus citations

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

2015

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

9 Scopus citations

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

8 Scopus citations

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

18 Scopus citations
2014

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

4 Scopus citations

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

17 Scopus citations

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

72 Scopus citations

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

7 Scopus citations

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

3 Scopus citations
2013

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

14 Scopus citations

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

17 Scopus citations
2012

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

10 Scopus citations

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

24 Scopus citations

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

2 Scopus citations
2011

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

44 Scopus citations

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

10 Scopus citations

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

7 Scopus citations

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

18 Scopus citations
2010

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

11 Scopus citations

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

3 Scopus citations
2009

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

19 Scopus citations

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

39 Scopus citations

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

22 Scopus citations

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

3 Scopus citations
3 Scopus citations

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

51 Scopus citations
2007

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

18 Scopus citations

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

11 Scopus citations
2005

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

15 Scopus citations