News
RECENT NEWS:
2023
June 7: Pratyush has been appointed as the inaugural endowed Millard and Lee Alexander Professor in Chemical Physics (effective July 1, 2023) at the University of Maryland. We are extremely grateful to Distinguished University Emeritus Professor Millard Alexander and his wife Lee Alexander for their generosity and support.
June 2: Pratyush has been promoted to Full Professor (effective July 1, 2023) at the University of Maryland, after 1 year as an Associate Professor.
Apr 17: Pratyush has been awarded the Board of Visitors Creative Educator Award from University of Maryland, College of Computer, Mathematical and Natural Sciences.
Mar 1: Pratyush has been appointed as an Associate Editor at the Journal of Chemical Theory and Computation, published by the American Chemical Society.
Feb 28: Pratyush has been appointed to the Scientific Advisory Board of Schrodinger, Inc. See announcement.
Feb 28-Mar 3: Maria Cameron (UMD Math) and Pratyush co-organized Brin Mathematics Research Centre Workshop on "Rare Events: Analysis, Numerics, and Applications".
Jan 25: Pratyush was recognized as the Joseph O. Hirschfelder Distinguished Visitor by the University of Wisconsin-Madison.
2022
Dec 1: Our manuscript "Path sampling of recurrent neural networks by incorporating known physics" has been featured as an Editors' Highlight at Nature Communications.
Oct 10: We welcome new PhD students Suemin Lee and Vanessa Meraz for joining our group for PhDs in biophysics and chemical physics respectively.
Sep 15: We are grateful to NSF-ACCESS for awarding us around 6 million hours of high-performance computing time.
May 27: We are grateful to the NCI-UMD partnership for funding two of our seed grant proposals in collaboration with NCI labs to develop / use methods to model Tcell-antigen interactions and disover druggable human RNAs.
May 20: Molecular Dynamics simulations with help of machine learning explain how hard-to-detect drug resistance for leukemia medication is caused by a new dissociation pathway where the drug leaves three times faster. Our paper on this has been just published in Angewandte Chemie and highlighted as a Hot Paper. See associated press release from the university.
May 17: Pratyush has been promoted to Associate Professor with tenure (effective July 1, 2022) at the University of Maryland in the Department of Chemistry and Biochemistry, after 5 years as an Assistant Professor.
April 13: Pratyush has won the Dean's Award for Excellence in Teaching at College of Computer, Mathematical and Natural Sciences, University of Maryland. This college-level award is nominated by students and is given to one faculty every year in the entire College.
March 30: Congratulations to Dr. Yihang Wang, the first PhD graduate from the group! Dr. Wang, with his degree in Biophysics, is headed as a Chicago Center for Theoretical Chemistry Research Fellow at the University of Chicago.
March 28: Congratulations to our graduate students Luke Evans and Zachary Smith for both winning the Ann Wylie Dissertation Fellowships from the University of Maryland graduate school.
February 15: Pratyush has been named a 2022 Sloan Research Fellow in Chemistry. See press release from the university.
January 7: Congratulations to our graduate students Luke Evans (Applied Math) and Dedi Wang for both of them receiving the Graduate School’s Outstanding Research Assistant Award for AY 2021-22. The award conveys the honor of being named among the top 2% of campus Graduate Assistants in a given year.
2021
December 15-18: Pratyush together with colleagues co-organized international workshop "Recent Advances in Modelling Rare Events (RARE)", supported by the Indo-US Science and Technology Forum (IUSSTF).
September 17: We are grateful to the National Institutes of Health (NIH) for supporting our research activities through a 5-year $1,868,775 MIRA R35 award. See press release from the University.
September 15: We have been awarded 3.1 million CPU+GPU hours on XSEDE-PSC-Bridges2 as renewal of our existing grant.
July 16: Pratyush Tiwary has joined the Editorial Board of Protein: Structure, Function and Bioinformatics
May 24: The American Chemical Society (ACS) has awarded Pratyush Tiwary with the ACS OpenEye Outstanding Junior Faculty Award for Fall 2021. We are grateful for this honor!
March 29: Congratulations to our graduate students Yihang Wang and Luke Evans for winning the Ann Wylie Dissertation Fellowship and Summer Research Fellowship respectively from the University of Maryland graduate school.
March 12: Congratulations to our undergrad researcher Pavan Ravindra for winning the Churchill Scholarship! See press release from the University.
March 10: Our manuscript titled "Confronting pitfalls of AI-augmented molecular dynamics using statistical physics" has been selected as Editors' choice at the Journal of Chemical Physics.
February 8: We are grateful to the National Science Foundation (NSF) for supporting our research and outreach activities through a 5-year $650,000 CAREER award! See press release from the University.
January 26: Our group's work using AI to simulate and enhance molecular motions using XSEDE-Allocated supercomputers has been featured in this "science success story" by NSF-XSEDE.
January 26: Our manuscript "Learning Molecular Dynamics with Simple Language Model built upon Long Short-Term Memory Neural Network" has been featured as an Editors' Highlight at Nature Communications. See the associated press release from the University.
2020
December 22: Congratulations to our graduate student Zachary Smith for receiving the Graduate School’s Outstanding Research Assistant Award for AY 2020-21. The award conveys the honor of being named among the top 2% of campus Graduate Assistants in a given year.
December 21: Our manuscript "Confronting pitfalls of AI-augmented molecular dynamics using statistical physics" was just published in the Journal of Chemical Physics, where it was highlighted as a "Featured Article" as well as displayed on the cover of the issue.
August 26: We are grateful to Department of Energy - Basic Energy Sciences for supporting our research for 3 years through grant on "Modeling liquids, interfaces and nucleation with Local Molecular Field theory and Artificial Intelligence sampling methods".
August 25: Our manuscript "Discovering Protein Conformational Flexibility Through Artificial Intelligence Aided Molecular Dynamics" was just published in J. Phys. Chem. B special issue on machine learning.
August 24: Congratulations to rising 2nd year Biophysics PhD student Dedi Wang for passing his PhD qualifying exams.
Jun 10: Congratulations to our undergraduate researcher Pavan Ravindra for being named a 2020-21 Philip Merrill Presidential Scholar, with Pratyush being recognized as a faculty mentor.
Mar 27: Congratulations to our undergraduate researcher Pavan Ravindra for being named a 2020 Goldwater scholar in Chemistry! The scholarship — the most prestigious undergraduate scholarship given in the natural sciences, engineering and mathematics — is awarded annually to about 400 college sophomores and juniors nationwide. Pavan is a junior undergrad majoring in Biochemistry and Computer Science. While doing research with us, Pavan co-developed the method AMINO. See the feature article carried out by our college in this context.
Mar 22: Our manuscript "Understanding the role of predictive time delay and biased propagator in RAVE" has just been accepted for publication in J. Chem. Phys. special issue on "Machine Learning Meets Chemical Physics Here is the arXiv pre-print
Mar 13: We have been awarded 1.8 million CPU+GPU hours on XSEDE-PSC-Bridges as renewal of our existing grant.
Jan 7: Congratulations to our graduate student Yihang Wang for receiving the Graduate School’s Outstanding Research Assistant Award for AY 2019-20. The award conveys the honor of being named among the top 2% of campus Graduate Assistants in a given year.
2019
Nov 14: Our latest work "Automatic mutual information noise omission (AMINO): generating order parameters for molecular systems" has just been published in Mol. Sys. Des. Engg. as a part of their 2020 Emerging Investigators Collection. Undergraduate researcher Pavan Ravindra's first first-author paper, jointly shared with Zachary Smith.
Oct 16: Our work studying driving force-memory interplay in liquid droplet nucleation has just been published in Journal of Chemical Physics as a part of the JCP Emerging Investigators Special Collection.
Aug 9: Congratulations to rising 2nd year grad student Zachary Smith for being admitted to the University of Maryland’s COMBINE (Computation and Mathematics for Biological Networks) program as part of their Fall 2019 cohort of fellows; and (Aug 22) for passing his PhD qualifying exams with flying colors! Here's to your bright future.
Aug 8: Our latest work that uses Past-future Information Bottleneck to design a method for sampling biomolecular structure and dynamics through iterative rounds of progressively biased simulations and deep learning, has just been published in Nature Communications
Jul 1: We are grateful to American Chemical Society-Petroleum Research Fund (ACS-PRF) for awarding us with the Doctoral New Investigator (DNI) grant
Apr 12: New manuscript "Can One Trust Kinetic and Thermodynamic Observables from Biased Metadynamics Simulations: Detailed Quantitative Benchmarks on Millimolar Drug Fragment Dissociation" published in J. Phys. Chem. B
Feb 26: Our research was featured in a news article at the website of UMD's College of Computer, Mathematical and Natural Sciences (CMNS).
Feb 6: Congratulations to Sun-Ting Tsai, 2nd year PhD (Physics) student in our group for passing his qualifying exams with flying colors!
Jan 9: Our lab has been featured in "Future of Biochemistry" special issue, in a list of ~30 young scientists and their groups from around the world! Our lab is arguably the only "purely computational" lab featured in this list. Our work was also featured on the journal cover.
2018
Dec 28: New pre-print "Past-future information bottleneck framework for simultaneously sampling biomolecular reaction coordinate, thermodynamics and kinetics" now available at bioRxiv
Dec 14: Our invited perspective article "Kinetics of Ligand-Protein Dissociation from All-Atom Simulations: Are We There Yet?" has been accepted for publication in the Future of Biochemistry: The International Issue of Biochemistry
Dec 7: Our work "Towards Achieving Efficient and Accurate Ligand-Protein Unbinding with Deep Learning and Molecular Dynamics through RAVE" has been accepted for publication in the Journal of Chemical Theory and Computation!
Nov 30: Our work "Multi-dimensional spectral gap optimization of order parameters (SGOOP) through conditional probability factorization" has been accepted for publication in the Journal of Chemical Physics. Graduate student Zachary Smith's first publication ever!
Oct 29: We are very grateful to @Schrodinger (https://www.schrodinger.com/) for their generous support of the @tiwarylab at University of Maryland. We are very excited about our collaboration and look forward to testing and applying our methods in the real world!
Oct 13: Physics grad student Freddy Cisneros from has won the best oral presentation award in Physics & Astronomy category at the annual SACNAS conference in San Antonio, Texas for his work on using machine learning to study rare events in condensed matter systems. The Presentation awards recognize the next generation of scientists and STEM leaders for exemplary science. Congratulations Freddy!
Sep 18: We have been awarded 1.7 million and 1.8 million CPU+GPU hours respectively on XSEDE-PSC-Bridges and MARCC-Blue Crab supercomputers respectively.
Sep 5: Suhas Gotla, 1st year PhD student in Biochemistry joins our group for lab rotation. Welcome Suhas!
Aug 22: Congratulations to Yihang Wang for passing his PhD qualifying exams!
July 22-27: Sun-Ting Tsai, 1st year PhD student in our group presented a poster on his research at the Gordon Research Conference on Water and Aqueous Solutions. Pratyush gave an invited talk at the same conference.
July 19: Adam Kells, PhD student at King's College London is visiting us this summer on a research internship. Welcome to the group Adam!
June 25: Netsanet Woldegerima has been selected to give a talk on her research on DNA-transcription factor interactions at the UM School of Medicine 2018 Mid-summer research retreat
June 23: Yihang Wang gave a talk on his research using predictive AI for enhanced sampling at the annual "Physics of Living Systems" conference at Rice University
June 10: Zachary Smith, 1st year PhD student in Biophysics joins our group for lab rotation. Welcome Zachary!
June 4: We have been funded! Our lab has won a seed grant from NCI-UMD Partnership for Integrative Cancer Research. Together with collaborators at NCI, we will be using our Stat Mech and Deep Learning based molecular simulations to investigate DNA-protein interactions in the context of latent-to-lytic transformations of Epstein-Barr virus, a virus associated with many killer diseases.
May 4: Our new manuscript "Reweighted autonecoded variational Bayes for enhanced sampling (RAVE)", which is an iterative deep learning- molecular dynamics scheme to enhance sampling of molecular systems, is published in the Journal of Chemical Physics special issue on enhanced sampling.
May 2: Freddy Cisneros, 1st year graduate student in Physics joins our group for Master's Thesis research
April 19: 3 students will be joining us for summer research: (i) Danielle Sidelnikov is a sophomore towards double major in Neurobiology & Physiology and History. (ii) Netsanet Woldegerima is a 1st year Medicine student at the University of Maryland, School of Medicine, and a winner of the competitive UM Scholars Program. (iii) Kliment Ziko is an incoming 1st year graduate student in Chemistry. Welcome to all three young scientists!
April 19: 3 students will be joining us for summer research: (i) Danielle Sidelnikov is a sophomore towards double major in Neurobiology & Physiology and History. (ii) Netsanet Woldegerima is a 1st year Medicine student at the University of Maryland, School of Medicine, and a winner of the competitive UM Scholars Program. (iii) Kliment Ziko is an incoming 1st year graduate student in Chemistry. Welcome to all three young scientists!
February 28: The paper "Predicting reaction coordinates in energy landscapes with diffusion anisotropy" by Tiwary and Berne has been selected as a 2017 Editor's choice paper at the Journal of Chemical Physics
February 19: We have received a start-up grant comprising GPU/CPU hours to use RAVE on the national supercomputing resource Bridges maintained by XSEDE
February 16: Pratyush gave an invited talk at the National Cancer Institute-University of Maryland Annual Symposium
2017
December 7-10: Chris Jarzynski (Maryland), K Srihari (Kanpur), Nisanth Nair (Kanpur) and Pratyush organized a 3-day international conference on Recent Advances in Modeling Rare Events (RARE) in Agra, India. With 84 participants drawing from over 10 countries, the conference was a huge success.
November 22: Pratyush has won the Research and Scholarship Award (RASA) from the Graduate School at the University of Maryland. The objective of the RASA is to support faculty research, scholarship and creative activity, while enhancing graduate student mentoring
November 18: Evan Yamaguchi, freshman student in Physics will be joining the lab in spring semester to learn and perform cutting-edge simulations in Biophysics!
November 9: Our work detailing the dissociation dynamics of biotin-streptavidin is accepted for publication in the Journal of Physical Chemistry B! First publication from Tiwary group!
September 8: Sun-Ting Tsai, 1st year grad student, joins us for his PhD in Physics. Welcome to the group, Sun-Ting!
September 6: Pablo Bravo Collado, undergraduate student in Biophysics, visiting from Pontificia Universidad Católica de Chile has joined us for the fall semester of 2017. Welcome to the group, Pablo!
August 31: Yihang Wang, 1st year PhD student in the UMD Biophysics Program, joins us for lab rotation this fall. Welcome to the group, Yihang!
August 18: We are grateful to Schrödinger for giving our group access to their suite of software. Their support will go a long way in helping the group perform cutting edge biomolecular research.
August 1: João Marcelo Ribeiro (Ph.D. (Chemistry), Florida International University) has joined the group as a postdoctoral research associate starting August 2017. Welcome João!