Skip to content

Publications

2025

  • Compositional Execution Motifs for Quantum-HPC Systems
    Authors: Nishant Saurabh, Pradeep Mantha, Shantenu Jha, Andre Luckow
    DOI: https://doi.org/10.1109/ipdpsw66978.2025.00181

  • Pilot-Quantum: A Middleware for Quantum-HPC Resource, Workload and Task Management
    Authors: Pradeep Mantha, Florian J. Kiwit, Nishant Saurabh, Shantenu Jha, Andre Luckow
    DOI: https://doi.org/10.1109/ccgrid64434.2025.00070

  • Scalable Runtime Architecture for Data-driven, Hybrid HPC and ML Workflow Applications
    Authors: Andre Merzky, Mikhail Titov, Matteo Turilli, Ozgur Kilic, Tianle Wang, Shantenu Jha
    DOI: https://doi.org/10.1109/ipdpsw66978.2025.00150

  • Adaptive Protein Design Protocols and Middleware
    Authors: Aymen Alsaadi, Jonathan Ash, Mikhail Titov, Matteo Turilli, Andre Merzky, Shantenu Jha, Sagar Khare
    DOI: https://doi.org/10.1109/ipdpsw66978.2025.00157

  • Comparative Performance Evaluation of Large Language Models for Extracting Molecular Interactions and Pathway Knowledge
    Authors: Gilchan Park, Byung-Jun Yoon, Xihaier Luo, Vanessa López-Marrero, Shinjae Yoo, Shantenu Jha
    DOI: https://doi.org/10.1089/cmb.2025.0078

  • PaleoSTeHM v1.0: a modern, scalable spatiotemporal hierarchical modeling framework for paleo-environmental data
    Authors: Yucheng Lin, Robert E. Kopp, Alexander Reedy, Matteo Turilli, Shantenu Jha, Erica L. Ashe
    DOI: https://doi.org/10.5194/gmd-18-2609-2025

2024

  • Hydra: Brokering Cloud and HPC Resources to Support the Execution of Heterogeneous Workloads at Scale
    Authors: Aymen Alsaadi, Shantenu Jha, Matteo Turilli
    DOI: https://doi.org/10.1145/3659995.3660040

  • Quantum Mini-Apps: A Framework for Developing and Benchmarking Quantum-HPC Applications
    Authors: Nishant Saurabh, Pradeep Mantha, Florian J. Kiwit, Shantenu Jha, Andre Luckow
    DOI: https://doi.org/10.1145/3659996.3660036

  • PaleoSTeHM v1.0-rc: a modern, scalable spatio-temporal hierarchical modeling framework for paleo-environmental data
    Authors: Yucheng Lin, Robert E. Kopp, Alexander Reedy, Matteo Turilli, Shantenu Jha, Erica L. Ashe
    DOI: https://doi.org/10.5194/egusphere-2024-2183

  • An Active Learning-Based Streaming Pipeline for Reduced Data Training of Structure Finding Models in Neutron Diffractometry
    Authors: Tianle Wang, Jorge Ramirez, Cristina Garcia-Cardona, Thomas Proffen, Shantenu Jha, Sudip K. Seal
    DOI: https://doi.org/10.1109/bigdata62323.2024.10825990

  • Enabling Performance Observability for Heterogeneous HPC Workflows with SOMA
    Authors: Dewi Yokelson, Mikhail Titov, Srinivasan Ramesh, Ozgur Kilic, Matteo Turilli, Shantenu Jha, Allen Malony
    DOI: https://doi.org/10.1145/3673038.3673100

  • Workflow Mini-Apps: Portable, Scalable, Tunable & Faithful Representations of Scientific Workflows
    Authors: Ozgur O. Kilic, Tianle Wang, Matteo Turilli, Mikhail Titov, Andre Merzky, Line Pouchard, Shantenu Jha
    DOI: https://doi.org/10.1109/ccgrid59990.2024.00059

  • Frontiers in Scientific Workflows: Pervasive Integration With High-Performance Computing
    Authors: Rafael Ferreira da Silva, Rosa M. Badia, Deborah Bard, Ian T. Foster, Shantenu Jha, Frédéric Suter
    DOI: https://doi.org/10.1109/mc.2024.3401542

2023

  • AI-coupled HPC Workflows
    Authors: Shantenu Jha, Vincent Pascuzzi, Matteo Turilli
    DOI: https://doi.org/10.1142/9789811265679_0028

  • A Conceptual Architecture for a Quantum-HPC Middleware
    Authors: Nishant Saurabh, Shantenu Jha, Andre Luckow
    DOI: https://doi.org/10.1109/qsw59989.2023.00023

  • Asynchronous Execution of Heterogeneous Tasks in ML-Driven HPC Workflows
    Authors: Vincent R. Pascuzzi, Ozgur O. Kilic, Matteo Turilli, Shantenu Jha
    DOI: https://doi.org/10.1007/978-3-031-43943-8_2

  • A scalable solution for running ensemble simulations for photovoltaic energy
    Authors: Weiming Hu, Guido Cervone, Matteo Turilli, Andre Merzky, Shantenu Jha
    DOI: https://doi.org/10.1130/2022.2558(08)

  • RADICAL-Pilot and PMIx/PRRTE: Executing Heterogeneous Workloads at Large Scale on Partitioned HPC Resources
    Authors: Mikhail Titov, Matteo Turilli, Andre Merzky, Thomas Naughton, Wael Elwasif, Shantenu Jha
    DOI: https://doi.org/10.1007/978-3-031-22698-4_5

  • A Parallel Machine Learning Workflow for Neutron Scattering Data Analysis
    Authors: Tianle Wang, Sudip K. Seal, Ramakrishnan Kannan, Cristina Garcia-Cardona, Thomas Proffen, Shantenu Jha
    DOI: https://doi.org/10.1109/ipdpsw59300.2023.00133

  • Pipelines for automating compliance-based elimination and extension (PACE2): a systematic framework for high-throughput biomolecular materials simulation workflows
    Authors: Srinivas C Mushnoori, Ethan Zang, Akash Banerjee, Mason Hooten, Andre Merzky, Matteo Turilli, Shantenu Jha, Meenakshi Dutt
    DOI: https://doi.org/10.1088/2515-7639/ad08d0

  • Optimal decision-making in high-throughput virtual screening pipelines
    Authors: Hyun-Myung Woo, Xiaoning Qian, Li Tan, Shantenu Jha, Francis J. Alexander, Edward R. Dougherty, Byung-Jun Yoon
    DOI: https://doi.org/10.1016/j.patter.2023.100875

2022

2021

  • Dynamic and Adaptive Monitoring and Analysis for Many-task Ensemble Computing
    Authors: Shantenu Jha, Allen D. Malony
    DOI: https://doi.org/10.1109/cluster48925.2021.00095

  • Pilot-Edge: Distributed Resource Management Along the Edge-to-Cloud Continuum
    Authors: Andre Luckow, Kartik Rattan, Shantenu Jha
    DOI: https://doi.org/10.1109/ipdpsw52791.2021.00130

  • Exploring Task Placement for Edge-to-Cloud Applications using Emulation
    Authors: Andre Luckow, Kartik Rattan, Shantenu Jha
    DOI: https://doi.org/10.1109/icfec51620.2021.00019

  • Big PanDa Workflow Management on Titan for High Energy and Nuclear Physics and for Future Extreme Scale Scientific Application
    Authors: Kaushik De, Alexei Klimentov, Shantenu Jha, Jack Wells
    DOI: https://doi.org/10.2172/1765084

  • Comparing workflow application designs for high resolution satellite image analysis
    Authors: Aymen Al-Saadi, Ioannis Paraskevakos, Bento Collares Gonçalves, Heather J. Lynch, Shantenu Jha, Matteo Turilli
    DOI: https://doi.org/10.1016/j.future.2021.04.023

  • Adaptive Ensemble Refinement of Protein Structures in High Resolution Electron Microscopy Density Maps with Radical Augmented Molecular Dynamics Flexible Fitting
    Authors: Daipayan Sarkar, Hyungro Lee, John W. Vant, Matteo Turilli, Josh V. Vermaas, Shantenu Jha, Abhishek Singharoy
    DOI: https://doi.org/10.1101/2021.12.07.471672

2020

  • Methods and Experiences for Developing Abstractions for Data-intensive, Scientific Applications
    Authors: Andre Luckow, Shantenu Jha
    DOI: https://doi.org/10.1109/ipdpsw50202.2020.00106

  • ICEBERG: Imagery Cyber-infrastructure and Extensible Building blocks to Enhance Research in the Geosciences. (A Research Programmer’s Perspective)
    Authors: Bradley D. Spitzbart, Heather J. Lynch, Matteo Turilli, Shantenu Jha
    DOI: https://doi.org/10.1145/3311790.3396640

  • Extensible and Scalable Adaptive Sampling on Supercomputers
    Authors: Eugen Hruska, Vivekanandan Balasubramanian, Hyungro Lee, Shantenu Jha, Cecilia Clementi
    DOI: https://doi.org/10.1021/acs.jctc.0c00991

  • Parallel performance of molecular dynamics trajectory analysis
    Authors: Mahzad Khoshlessan, Ioannis Paraskevakos, Geoffrey C. Fox, Shantenu Jha, Oliver Beckstein
    DOI: https://doi.org/10.1002/cpe.5789

  • Adaptive Ensemble Biomolecular Applications at Scale
    Authors: Vivek Balasubramanian, Travis Jensen, Matteo Turilli, Peter Kasson, Michael Shirts, Shantenu Jha
    DOI: https://doi.org/10.1007/s42979-020-0081-1

  • An ICEBERG Update and Request for Community Input
    Authors: Bradley Spitzbart, Heather Lynch, Shantenu Jha, Matteo Turilli, Ioannis Paraskevakos, Aymen Alsaadi, Mark Salvatore, Samira Daneshgar Asl, Bento Goncalves, Helen Eifert, Brian Szutu
    DOI: https://doi.org/10.1002/essoar.10503479.1

2019

2018

  • Adaptive ensemble simulations of biomolecules
    Authors: Peter M Kasson, Shantenu Jha
    DOI: https://doi.org/10.1016/j.sbi.2018.09.005

  • Pilot-Streaming: A Stream Processing Framework for High-Performance Computing
    Authors: Georgios Chantzialexiou, Andre Luckow, Shantenu Jha
    DOI: https://doi.org/10.1109/escience.2018.00033

  • A Comprehensive Perspective on Pilot-Job Systems
    Authors: Matteo Turilli, Mark Santcroos, Shantenu Jha
    DOI: https://doi.org/10.1145/3177851

  • Building Blocks for Workflow System Middleware
    Authors: Matteo Turilli, Andre Merzky, Vivek Balasubramanian, Shantenu Jha
    DOI: https://doi.org/10.1109/ccgrid.2018.00051

  • HPC enabled parallel, multi-scale & mechanistic model for high shear granulation using a coupled DEM-PBM framework
    Authors: Chaitanya Sampat, Yukteshwar Baranwal, Ioannis Paraskevakos, Shantenu Jha, Marianthi Ierapetritou, Rohit Ramachandran
    DOI: https://doi.org/10.1016/b978-0-444-64241-7.50238-x

  • Concurrent and Adaptive Extreme Scale Binding Free Energy Calculations
    Authors: Jumana Dakka, Kristof Farkas-Pall, Matteo Turilli, David W. Wright, Peter V. Coveney, Shantenu Jha
    DOI: https://doi.org/10.1109/escience.2018.00034

  • Modeling Impact of Execution Strategies on Resource Utilization
    Authors: Alexey Poyda, Mikhail Titov, Alexei Klimentov, Jack Wells, Sarp Oral, Kaushik De, Danila Oleynik, Shantenu Jha
    DOI: https://doi.org/10.1109/escience.2018.00085

  • A parallel unidirectional coupled DEM-PBM model for the efficient simulation of computationally intensive particulate process systems
    Authors: Chaitanya Sampat, Franklin Bettencourt, Yukteshwar Baranwal, Ioannis Paraskevakos, Anik Chaturbedi, Subhodh Karkala, Shantenu Jha, Rohit Ramachandran, Marianthi Ierapetritou
    DOI: https://doi.org/10.1016/j.compchemeng.2018.08.006

  • Task-parallel Analysis of Molecular Dynamics Trajectories
    Authors: Ioannis Paraskevakos, Andre Luckow, Mahzad Khoshlessan, George Chantzialexiou, Thomas E. Cheatham, Oliver Beckstein, Geoffrey C. Fox, Shantenu Jha
    DOI: https://doi.org/10.1145/3225058.3225128

  • Harnessing the Power of Many: Extensible Toolkit for Scalable Ensemble Applications
    Authors: Vivek Balasubramanian, Matteo Turilli, Weiming Hu, Matthieu Lefebvre, Wenjie Lei, Ryan Modrak, Guido Cervone, Jeroen Tromp, Shantenu Jha
    DOI: https://doi.org/10.1109/ipdps.2018.00063

  • High-throughput binding affinity calculations at extreme scales
    Authors: Jumana Dakka, Matteo Turilli, David W. Wright, Stefan J. Zasada, Vivek Balasubramanian, Shunzhou Wan, Peter V. Coveney, Shantenu Jha
    DOI: https://doi.org/10.1186/s12859-018-2506-6

  • A Systematic Framework for Data Management and Integration in a Continuous Pharmaceutical Manufacturing Processing Line
    Authors: Huiyi Cao, Srinivas Mushnoori, Barry Higgins, Chandrasekhar Kollipara, Adam Fermier, Douglas Hausner, Shantenu Jha, Ravendra Singh, Marianthi Ierapetritou, Rohit Ramachandran
    DOI: https://doi.org/10.3390/pr6050053

  • Enabling Trade-offs Between Accuracy and Computational Cost: Adaptive Algorithms to Reduce Time to Clinical Insight
    Authors: Jumana Dakka, Kristof Farkas-Pall, Vivek Balasubramanian, Matteo Turilli, Shunzhou Wan, David W. Wright, Stefan Zasada, Peter V. Coveney, Shantenu Jha
    DOI: https://doi.org/10.1109/ccgrid.2018.00005

2017

  • Conceptualizing a Computing Platform for Science Beyond 2020: To Cloudify HPC, or HPCify Clouds?
    Authors: Geoffrey Fox, Shantenu Jha
    DOI: https://doi.org/10.1109/cloud.2017.120

  • AIMES Final Technical Report
    Authors: Shantenu Jha, ,
    DOI: https://doi.org/10.2172/1350148

  • Parallel Analysis in MDAnalysis using the Dask Parallel Computing Library
    Authors: Mahzad Khoshlessan, Ioannis Paraskevakos, Shantenu Jha, Oliver Beckstein
    DOI: https://doi.org/10.25080/shinma-7f4c6e7-00a

  • Exploring the Use of Hybrid HPC-Grids/Clouds Infrastru and Engineering
    Authors: Hyunjoo Kim, Yaakoub El-Khamra, Shantenu Jha, Manish Parashar
    DOI: https://doi.org/10.1201/b11149-25

  • Hacking at the Divide Between Polar Science and HPC: Using Hackathons as Training Tools
    Authors: Jane Wyngaard, Heather Lynch, Jaroslaw Nabrzyski, Allen Pope, Shantenu Jha
    DOI: https://doi.org/10.1109/ipdpsw.2017.177

  • Introducing distributed dynamic data‐intensive (D3) science: Understanding applications and infrastructure
    Authors: Shantenu Jha, Daniel S. Katz, Andre Luckow, Neil Chue Hong, Omer Rana, Yogesh Simmhan
    DOI: https://doi.org/10.1002/cpe.4032

  • Evaluating Distributed Execution of Workloads
    Authors: Matteo Turilli, Yadu Nand Babuji, Andre Merzky, Ming Tai Ha, Michael Wilde, Daniel S. Katz, Shantenu Jha
    DOI: https://doi.org/10.1109/escience.2017.41

  • High-Throughput Computing on High-Performance Platforms: A Case Study
    Authors: Danila Oleynik, Sergey Panitkin, Matteo Turilli, Alessio Angius, Sarp Oral, Kaushik De, Alexei Klimentov, Jack C. Wells, Shantenu Jha
    DOI: https://doi.org/10.1109/escience.2017.43

2016

  • Synapse: Synthetic Application Profiler and Emulator
    Authors: Andre Merzky, Shantenu Jha
    DOI: https://doi.org/10.1109/ipdpsw.2016.168

  • STREAM2016: Streaming Requirements, Experience, Applications and Middleware Workshop
    Authors: Geoffrey Fox, Shantenu Jha, Lavanya Ramakrishnan
    DOI: https://doi.org/10.2172/1344785

  • Hadoop on HPC: Integrating Hadoop and Pilot-Based Dynamic Resource Management
    Authors: Andre Luckow, Ioannis Paraskevakos, George Chantzialexiou, Shantenu Jha
    DOI: https://doi.org/10.1109/ipdpsw.2016.166

  • Ensemble Toolkit: Scalable and Flexible Execution of Ensembles of Tasks
    Authors: Vivekanandan Balasubramanian, Antons Treikalis, Ole Weidner, Shantenu Jha
    DOI: https://doi.org/10.1109/icpp.2016.59

  • Application skeletons: Construction and use in eScience
    Authors: Daniel S. Katz, Andre Merzky, Zhao Zhang, Shantenu Jha
    DOI: https://doi.org/10.1016/j.future.2015.10.001

  • Big Data, Simulations and HPC Convergence
    Authors: Geoffrey Fox, Judy Qiu, Shantenu Jha, Saliya Ekanayake, Supun Kamburugamuve
    DOI: https://doi.org/10.1007/978-3-319-49748-8_1

  • Application Skeleton: Generating Synthetic Applications for Infrastructure Research
    Authors: Zhao Zhang, Daniel S. Katz, Andre Merzky, Matteo Turilli, Shantenu Jha, Yadu Nand
    DOI: https://doi.org/10.21105/joss.00017

  • RepEx: A Flexible Framework for Scalable Replica Exchange Molecular Dynamics Simulations
    Authors: Antons Treikalis, Andre Merzky, Haoyuan Chen, Tai-Sung Lee, Darrin M. York, Shantenu Jha
    DOI: https://doi.org/10.1109/icpp.2016.78

  • A Scalable Pipeline for Transcriptome Profiling Tasks with On-Demand Computing Clouds
    Authors: Shayan Shams, Nayong Kim, Xiandong Meng, Ming Tai Ha, Shantenu Jha, Zhong Wang, Joohyun Kim
    DOI: https://doi.org/10.1109/ipdpsw.2016.129

  • ExTASY: Scalable and flexible coupling of MD simulations and advanced sampling techniques
    Authors: Vivekanandan Balasubramanian, Iain Bethune, Ardita Shkurti, Elena Breitmoser, Eugen Hruska, Cecilia Clementi, Charles Laughton, Shantenu Jha
    DOI: https://doi.org/10.1109/escience.2016.7870921

  • Integrating Abstractions to Enhance the Execution of Distributed Applications
    Authors: Matteo Turilli, Feng Liu, Zhao Zhang, Andre Merzky, Michael Wilde, Jon Weissman, Daniel S. Katz, Shantenu Jha
    DOI: https://doi.org/10.1109/ipdps.2016.64

2015

  • Session details: Session 3
    Authors: Shantenu Jha
    DOI: https://doi.org/10.1145/3261037

  • SAGA: A standardized access layer to heterogeneous Distributed Computing Infrastructure
    Authors: Andre Merzky, Ole Weidner, Shantenu Jha
    DOI: https://doi.org/10.1016/j.softx.2015.03.001

  • Pilot-Data: An abstraction for distributed data
    Authors: Andre Luckow, Mark Santcroos, Ashley Zebrowski, Shantenu Jha
    DOI: https://doi.org/10.1016/j.jpdc.2014.09.009

  • HPC-ABDS High Performance Computing Enhanced Apache Big Data Stack
    Authors: Geoffrey C. Fox, Judy Qiu, Supun Kamburugamuve, Shantenu Jha, Andre Luckow
    DOI: https://doi.org/10.1109/ccgrid.2015.122

  • Characterization of the Three-Dimensional Free Energy Manifold for the Uracil Ribonucleoside from Asynchronous Replica Exchange Simulations
    Authors: Brian K. Radak, Melissa Romanus, Tai-Sung Lee, Haoyuan Chen, Ming Huang, Antons Treikalis, Vivekanandan Balasubramanian, Shantenu Jha, Darrin M. York
    DOI: https://doi.org/10.1021/ct500776j

2014

  • Gateways to high-perfomance and distributed computing resources for global health challenges
    Authors: Sandra Gesing, Jarek Nabrzyski, Shantenu Jha
    DOI: https://doi.org/10.1109/ihtc.2014.7147530

  • Comparative analysis of nucleotide translocation through protein nanopores using steered molecular dynamics and an adaptive biasing force
    Authors: Hugh S. C. Martin, Shantenu Jha, Peter V. Coveney
    DOI: https://doi.org/10.1002/jcc.23525

  • Towards an Understanding of Facets and Exemplars of Big Data Applications
    Authors: Geoffrey C. Fox, Shantenu Jha, Judy Qiu, Andre Luckow
    DOI: https://doi.org/10.1145/2737909.2737912

  • A Tale of Two Data-Intensive Paradigms: Applications, Abstractions, and Architectures
    Authors: Shantenu Jha, Judy Qiu, Andre Luckow, Pradeep Mantha, Geoffrey C. Fox
    DOI: https://doi.org/10.1109/bigdata.congress.2014.137

  • Numerical methodologies for investigation of moderate-velocity flow using a hybrid computational fluid dynamics — molecular dynamics simulation approach
    Authors: Soon-Heum Ko, Nayong Kim, Shantenu Jha, Dimitris E. Nikitopoulos, Dorel Moldovan
    DOI: https://doi.org/10.1007/s12206-013-0962-5

  • Computing Clinically Relevant Binding Free Energies of HIV-1 Protease Inhibitors
    Authors: David W. Wright, Benjamin A. Hall, Owain A. Kenway, Shantenu Jha, Peter V. Coveney
    DOI: https://doi.org/10.1021/ct4007037

  • Developing eThread Pipeline Using SAGA-Pilot Abstraction for Large-Scale Structural Bioinformatics
    Authors: Anjani Ragothaman, Sairam Chowdary Boddu, Nayong Kim, Wei Feinstein, Michal Brylinski, Shantenu Jha, Joohyun Kim
    DOI: https://doi.org/10.1155/2014/348725

2013

  • Advancing next‐generation sequencing data analytics with scalable distributed infrastructure
    Authors: Joohyun Kim, Sharath Maddineni, Shantenu Jha
    DOI: https://doi.org/10.1002/cpe.3013

  • The Impact of a Ligand Binding on Strand Migration in the SAM-I Riboswitch
    Authors: Wei Huang, Joohyun Kim, Shantenu Jha, Fareed Aboul-ela
    DOI: https://doi.org/10.1371/journal.pcbi.1003069

  • Scalable online comparative genomics of mononucleosomes
    Authors: Jack A. Smith, Melissa Romanus, Pradeep Kumar Mantha, Yaakoub El Khamra, Thomas C. Bishop, Shantenu Jha
    DOI: https://doi.org/10.1145/2484762.2484819

2012

  • Pilot-MapReduce
    Authors: Pradeep Kumar Mantha, Andre Luckow, Shantenu Jha
    DOI: https://doi.org/10.1145/2287016.2287020

  • Distributed Application Runtime Environment (DARE): A Standards-based Middleware Framework for Science-Gateways
    Authors: Sharath Maddineni, Joohyun Kim, Yaakoub El-Khamra, Shantenu Jha
    DOI: https://doi.org/10.1007/s10723-012-9244-1

  • Conformational Heterogeneity of the SAM-I Riboswitch Transcriptional ON State: A Chaperone-Like Role for S-Adenosyl Methionine
    Authors: Wei Huang, Joohyun Kim, Shantenu Jha, Fareed Aboul-ela
    DOI: https://doi.org/10.1016/j.jmb.2012.02.019

  • Corrigendum to “Conformational Heterogeneity of the SAM-I Riboswitch Transcriptional ON State: A Chaperone-Like Role for S-Adenosyl Methionine” [J. Mol. Biol. 418 (2012) 331–349]
    Authors: Wei Huang, Joohyun Kim, Shantenu Jha, Fareed Aboul-ela
    DOI: https://doi.org/10.1016/j.jmb.2012.05.002

  • Pilot abstractions for compute, data, and network
    Authors: Mark Santcroos, Silvia Delgado Olabarriaga, Daniel S. Katz, Shantenu Jha
    DOI: https://doi.org/10.1109/escience.2012.6404459

  • Understanding mapreduce-based next-generation sequencing alignment on distributed cyberinfrastructure
    Authors: Pradeep Kumar Mantha, Nayong Kim, Andre Luckow, Joohyun Kim, Shantenu Jha
    DOI: https://doi.org/10.1145/2483954.2483957

  • Quantized Water Access to the HIV-1 Protease Active Site as a Proposed Mechanism for Cooperative Mutations in Drug Affinity
    Authors: Benjamin A. Hall, David W. Wright, Shantenu Jha, Peter V. Coveney
    DOI: https://doi.org/10.1021/bi300432u

  • Running many molecular dynamics simulations on many supercomputers
    Authors: Rajib Mukherjee, Abhinav Thota, Hideki Fujioka, Thomas C. Bishop, Shantenu Jha
    DOI: https://doi.org/10.1145/2335755.2335787

  • Towards a common model for pilot-jobs
    Authors: Andre Luckow, Mark Santcroos, Ole Weidner, Andre Merzky, Sharath Maddineni, Shantenu Jha
    DOI: https://doi.org/10.1145/2287076.2287094

  • P∗: A model of pilot-abstractions
    Authors: Andre Luckow, Mark Santcroos, Andre Merzky, Ole Weidner, Pradeep Mantha, Shantenu Jha
    DOI: https://doi.org/10.1109/escience.2012.6404423

  • Distributed computing practice for large‐scale science and engineering applications
    Authors: Shantenu Jha, Murray Cole, Daniel S. Katz, Manish Parashar, Omer Rana, Jon Weissman
    DOI: https://doi.org/10.1002/cpe.2897

  • Multi-species Fluid Flow Simulations Using a Hybrid Computational Fluid Dynamics - Molecular Dynamics Approach
    Authors: Nayong Kim, Soon-Heum Ko, Shantenu Jha, Brian Novak, Dorel Moldovan, Dimitris Nikitopoulos
    DOI: https://doi.org/10.2514/6.2012-3157

  • FutureGrid education
    Authors: Jerome E. Mitchell, Judy Qiu, Massimo Canonio, Shantenu Jha, Linda Hayden, Barbara Ann O'Leary, Renato Figueiredo, Geoffrey Fox
    DOI: https://doi.org/10.1145/2335755.2335859

  • The anatomy of successful ECSS projects
    Authors: Melissa Romanus, Pradeep Kumar Mantha, Matt McKenzie, Thomas C. Bishop, Emilio Gallichio, Andre Merzky, Yaakoub El Khamra, Shantenu Jha
    DOI: https://doi.org/10.1145/2335755.2335843

2011

  • Building gateways for life-science applications using the dynamic application runtime environment (DARE) framework
    Authors: Joohyun Kim, Sharath Maddineni, Shantenu Jha
    DOI: https://doi.org/10.1145/2016741.2016782

  • Efficient large-scale replica-exchange simulations on production infrastructure
    Authors: Abhinav Thota, André Luckow, Shantenu Jha
    DOI: https://doi.org/10.1098/rsta.2011.0151

  • Characterizing deep sequencing analytics using BFAST
    Authors: Joohyun Kim, Sharath Maddineni, Shantenu Jha
    DOI: https://doi.org/10.1145/1996023.1996027

  • Numerical Experiments of Solving Moderate-Velocity Flow Field Using a Hybrid CFD-MD Approach
    Authors: Soon-Heum Ko, Nayong Kim, Shantenu Jha
    DOI: https://doi.org/10.1115/ajk2011-01021

  • Understanding application-level interoperability: Scaling-out MapReduce over high-performance grids and clouds
    Authors: Saurabh Sehgal, Miklos Erdelyi, Andre Merzky, Shantenu Jha
    DOI: https://doi.org/10.1016/j.future.2010.11.001

  • Exploring the Use of Hybrid HPC-Grids/Clouds Infrastructure for Science and Engineering
    Authors: Hyunjoo Kim, Yaakoub El-Khamra, Shantenu Jha, Manish Parashar
    DOI: https://doi.org/10.1201/b11149-29

  • Application-Level Interoperability Across Grids and Clouds
    Authors: Shantenu Jha, Andre Luckow, Andre Merzky, Miklos Erdely, Saurabh Sehgal
    DOI: https://doi.org/10.1007/978-0-85729-049-6_9

  • Energy landscape analysis for regulatory RNA finding using scalable distributed cyberinfrastructure
    Authors: Joohyun Kim, Wei Huang, Sharath Maddineni, Fareed Aboul‐ela, Shantenu Jha
    DOI: https://doi.org/10.1002/cpe.1796

  • Understanding Scientific Applications for Cloud Environments
    Authors: Shantenu Jha, Daniel S. Katz, Andre Luckow, Andre Merzky, Katerina Stamou
    DOI: https://doi.org/10.1002/9780470940105.ch13

  • Autonomic Management of Application Workflows on Hybrid Computing Infrastructure
    Authors: Hyunjoo Kim, Yaakoub el-Khamra, Ivan Rodero, Shantenu Jha, Manish Parashar
    DOI: https://doi.org/10.1155/2011/940242

  • Using the TeraGrid to teach scientific computing
    Authors: Frank Löffler, Gabrielle Allen, Werner Benger, Andrei Hutanu, Shantenu Jha, Erik Schnetter
    DOI: https://doi.org/10.1145/2016741.2016800

  • A practical and comprehensive graduate course preparing students for research involving scientific computing
    Authors: Gabrielle Allen, Werner Benger, Andrei Hutanu, Shantenu Jha, Frank Löffler, Erik Schnetter
    DOI: https://doi.org/10.1016/j.procs.2011.04.210

  • Towards high-throughput, high-performance computational estimation of binding affinities for patient specific HIV-1 protease sequences
    Authors: Owain Kenway, David W. Wright, Helmut Heller, Andre Merzky, Gavin Pringle, Jules Wolfrat, Peter Coveney, Shantenu Jha
    DOI: https://doi.org/10.1145/2016741.2016746

2010

2009

2008

2007

  • Grid Interoperability at the Application Level Using SAGA
    Authors: Shantenu Jha, Hartmut Kaiser, Andre Merzky, Ole Weidner
    DOI: https://doi.org/10.1109/e-science.2007.39

  • Design and Implementation of Network Performance Aware Applications Using SAGA and Cactus
    Authors: Shantenu Jha, Hartmut Kaiser, Yaakoub El Khamra, Ole Weidner
    DOI: https://doi.org/10.1109/e-science.2007.28

  • Rapid, Accurate, and Precise Calculation of Relative Binding Affinities for the SH2 Domain Using a Computational Grid
    Authors: Philip W. Fowler, Sebastien Geroult, Shantenu Jha, Gabriel Waksman, Peter V. Coveney
    DOI: https://doi.org/10.1021/ct6003017

  • NEKTAR, SPICE and Vortonics: using federated grids for large scale scientific applications
    Authors: Bruce Boghosian, Peter Coveney, Suchuan Dong, Lucas Finn, Shantenu Jha, George Karniadakis, Nicholas Karonis
    DOI: https://doi.org/10.1007/s10586-007-0029-4

2006

2005

  • Grid-based steered thermodynamic integration accelerates the calculation of binding free energies
    Authors: Philip W Fowler, Shantenu Jha, Peter V Coveney
    DOI: https://doi.org/10.1098/rsta.2005.1625

  • Force field validation for nucleic acid simulations: Comparing energies and dynamics of a DNA dodecamer
    Authors: Shantenu Jha, Peter V. Coveney, Charles A. Laughton
    DOI: https://doi.org/10.1002/jcc.20300