Our work highlighted by the Oak Ridge Leadership Computing Facility
Our work was included in the OLCF’s 2025 year in review.
Tag: supercomputing
NEW INCITE POJECT AWARDED FOR 2026
Our INCITE Award was competitively renewed for 2026 by the DOE Office of Science. Open to researchers from academia, government laboratories, and industry, the Innovative and Novel Computational Impact on Theory and Experiment (INCITE) program is the major means by which the scientific community gains access to the world’s fastest supercomputers. The program aims to accelerate […]
NEW PAPER IN NATURE COMMUNICATIONS
Congratulations to Tanmoy Paul, Chunli Yan and Grant Derdeyn-Blackwell who are co-authors on a just published paper in the journal Nature Communications entitled “Translocation mechanism of xeroderma pigmentosum group D protein on single-stranded DNA and genetic disease etiology”. We investigated the molecular basis of translocation by the xeroderma pigmentosum group D (XPD) helicase on single-stranded […]
OAK RIDGE NATIONAL LAB HIGHLIGHTS OUR WORK ON GLOBAL GENOME REPAIR
Oak Ridge National Lab highlights our work on the mechanisms of global genome nucleotide excision repair: “Summit Supercomputer Draws Molecular Blueprint for Repairing Damaged DNA”. Related articles: Yu, J., Yan, C., Paul, T. et al. Molecular architecture and functional dynamics of the pre-incision complex in nucleotide excision repair. Nat Commun 15, 8511 (2024). Yu, J., Yan, C., Dodd, T. et […]
NEW PAPER IN NATURE COMMUNICATIONS
Congratulations to Tanmoy Paul, Chunli Yan and Jina Yu who are co-authors on a just published paper in the journal Nature Communications. The paper is entitled “Molecular model of TFIIH recruitment to the transcription-coupled repair machinery“. Transcription-coupled repair is a vital nucleotide excision repair sub-pathway that removes DNA lesions from actively transcribed DNA strands. Binding of the […]
NEW PAPER IN NATURE COMMUNICATIONS
Congratulations to Jina Yu, Chunli Yan, Tanmoy Paul and Lucas Brewer who are co-authors on a just published paper in the journal Nature Communications. The paper is entitled “Molecular architecture and functional dynamics of the pre-incision complex in nucleotide excision repair.” The nucleotide excision repair (NER) pathway is vital for genome integrity. By synthesizing cryo-EM and XL-MS […]
NEW INCITE POJECT AWARDED FOR 2024
Our INCITE Award was competitively renewed for 2024 by the DOE Office of Science. The Innovative and Novel Computational Impact on Theory and Experiment (INCITE) program accelerates scientific discoveries and technological innovations by awarding, on a competitive basis, time on the world’s fastest supercomputers to researchers with large-scale, computationally intensive projects that address “grand challenges” in science and […]
NEW INCITE POJECT AWARDED FOR 2023
Our INCITE Award was competitively renewed for 2023 by the DOE Office of Science. The Innovative and Novel Computational Impact on Theory and Experiment (INCITE) program accelerates scientific discoveries and technological innovations by awarding, on a competitive basis, time on the world’s fastest supercomputers to researchers with large-scale, computationally intensive projects that address “grand challenges” in science and […]
OAK RIDGE NATIONAL LAB HIGHLIGHTS OUR WORK ON TRANSCRIPTION-COUPLED DNA REPAIR
Oak Ridge National Lab highlights our recent work on the mechanisms of transcription-coupled nucleotide excision repair: “Decoding the Role of CSB Protein in DNA Repair“. Below is a recent video recording on the same topic:
NEW INCITE POJECT AWARDED FOR 2022
Our INCITE Award was competitively renewed for 2022 by the DOE Office of Science. The Innovative and Novel Computational Impact on Theory and Experiment (INCITE) program accelerates scientific discoveries and technological innovations by awarding, on a competitive basis, time on the world’s fastest supercomputers to researchers with large-scale, computationally intensive projects that address “grand challenges” in science and […]
New INCITE Project Awarded for 2021
Our group received a new INCITE Award from the U.S. Department of Energy Office of Science. The Innovative and Novel Computational Impact on Theory and Experiment (INCITE) program accelerates scientific discoveries and technological innovations by awarding, on a competitive basis, time on the world’s fastest supercomputers to researchers with large-scale, computationally intensive projects that address “grand challenges” in science and […]
DEPARTMENT OF ENERGY ISSUES A PRESS RELEASE ABOUT OUR 2020 INCITE AWARD
Our group was among the 47 recipients of INCITE Awards from the U.S. Department of Energy’s Office of Science. The projects originate in national laboratories, academia, and industry, and encompass a remarkable range of scientific inquiry. Ours was among the projects in the areas of Biological Sciences/Biophysics. Here are the 2020 INCITE Announcement and the list of 2020 […]
NEW INCITE POJECT AWARDED FOR 2020
Our INCITE Award was competitively renewed for 2020 by the DOE Office of Science. The Innovative and Novel Computational Impact on Theory and Experiment (INCITE) program accelerates scientific discoveries and technological innovations by awarding, on a competitive basis, time on the world’s fastest supercomputers to researchers with large-scale, computationally intensive projects that address “grand challenges” in science and engineering. Our […]
OAK RIDGE NATIONAL LAB HIGHLIGHTS OUR RECENT WORK ON THE PIC
Oak Ridge National Lab highlights our recent work on the transcription preinitiation complex (PIC): “Summit Charts a Course to Uncover the Origins of Genetic Diseases”.
NEW PAPER IN NATURE STRUCTURAL & MOLECULAR BIOLOGY
Congratulation to Chunli Yan and Tom Dodd who published a new paper in the journal Nature Structural & Molecular Biology on the molecular architecture and functional dynamics of the transcription preinitiation complex (PIC). Yan, C.; Dodd, T.; Tainer, J.A.; He, Y.; Tsutakawa, S.E.; & Ivanov, I.* Transcription preinitiation complex structure and dynamics provide insight into genetic diseases Nature Structural […]
Department of Energy issues a press release about the 2019 INCITE Awards
Our group was among the 62 recipients of INCITE Awards from the U.S. Department of Energy’s Office of Science. The projects originate in national laboratories, academia, and industry, and encompass a remarkable range of scientific inquiry. Ours was among 8 projects in the areas of Biological Sciences/Biophysics awarded nationwide. Here are the 2019INCITEAnnouncement and the […]
New INCITE Award provides access to the Oak Ridge Leadership Computing Facility
Ivaylo received a new INCITE Award from the DOE Office of Science. The Innovative and Novel Computational Impact on Theory and Experiment (INCITE) program accelerates scientific discoveries and technological innovations by awarding, on a competitive basis, time on the world’s fastest supercomputers to researchers with large-scale, computationally intensive projects that address “grand challenges” in science […]
Our thymine DNA glycosylase story highlighted by SDSC
Our project on the base extrusion mechanism of thymine DNA glycosylase (TDG) was highlighted by the San Diego Supercomputer Center. How an Enzyme Repairs DNA via a “Pinch-Push-Pull” Mechanism
Bernard Scott selected for the XSEDE Scholars Program
Congratulations to Bernard Scott who has won a fellowship from the XSEDE Scholars Program. The XSEDE Scholars Program (XSP) is a selective year-long program for U.S. students from underrepresented groups in the computing sciences who receive opportunities to learn more about high performance computing and XSEDE resources. XSEDE, the Extreme Science and Engineering Discovery Environment, is the most […]
Supercomputers Simulate the Molecular Machines that Replicate and Repair DNA
Scientists use Jaguar to model replisome components to understand their role in health and disease. Source: Supercomputers Simulate the Molecular Machines that Replicate and Repair DNA
Group given access to Anton machine at NRBSC
Our proposal for computational time on the special purpose Anton machine at the National Resource for Biomedical Supercomputing (NRBSC) in Pittsburgh is approved.
New NERSC Initiative for Scientific Exploration (NISE) Award
Ivaylo Ivanov receives NERSC Initiative for Scientific Exploration (NISE) Award.
New XSEDE Award
Ivaylo Ivanov receives a XSEDE award of computational time at the NICS to futher our research efforts on base excision repair. Our proposal entitled “Exploring the Chemical Landscape for Base Excision DNA Repair” was approved to receive 2,500,000 CPU hours under allocation CHE110042.
Supercomputing 2010 Highlight
Our work on PCNA highlighted by the NCCS at Supercomputing 2010 Conference in New Orleans.
Supercomputers Simulate the Molecular Machines that Replicate and Repair DNA
Scientists use Jaguar to model replisome components to understand their role in health and disease. Source: Supercomputers Simulate the Molecular Machines that Replicate and Repair DNA
INCITE AWARD
Our renewal proposal through the DOE INCITE initiative was awarded 4,000,000 CPU hours at the leadership computing facility at ORNL. We are gratified that the award exceeded our original request by 400,000 units For more details about the award refer to the new DOE Office of Science.
INCITE Proposal
A renewal proposal for computational resources through the DOE INCITE initiative has been submitted (07/01/2009). In 2009 our research project entitled “Interplay of AAA+ molecular machines, DNA repair enzymes and sliding clamps at the replication fork: A multiscale approach to modeling replisome assembly and function” was competitively chosen to receive 2,600,000 CPU hours of supercomputing […]
Integrative Biomolecular Modeling 