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Molecular Dynamics

water moleculesScience

Something in the Water Does Not Compute

Computational scientists at the Department of Energy’s Oak Ridge National Laboratory have published a study in the Journal of Chemical Theory and Computation that questions a long-accepted factor in simulating the molecular dynamics of water: the 2 femtosecond (one quadrillionth of a second) time step. The femtosecond is a timescale…
Coury Turczyn
May 6, 2024
cicada wing nanosurfaceScience

Advancing Nanoscience Through Largescale MD Simulations

Over the past decade, teams of engineers, chemists and biologists have analyzed the physical and chemical properties of cicada wings, hoping to unlock the secret of their ability to kill microbes on contact. If this function of nature can be replicated by science, it may lead to products with inherently…
Coury Turczyn
July 14, 2023
Rad26-RNA polymerase IIScience

Decoding the Role of CSB Protein in DNA Repair

Using the Summit supercomputer at the US Department of Energy’s (DOE’s) Oak Ridge National Laboratory (ORNL), a Georgia State University (GSU) research team has revealed the structural mechanism of the Cockayne Syndrome B (CSB) protein in transcription-coupled DNA repair. Led by GSU chemistry professor Ivaylo Ivanov, the team recently published…
Coury Turczyn
February 2, 2022
Science

Supercomputing for Swift Protein Modeling

Uncovering the molecular structures of proteins can help scientists elucidate biological functions of proteins and search for drug candidates for diseases. To better understand proteins, scientists can use imaging techniques to probe their molecular structures. However, many imaging techniques fall short of capturing details at the atomic level. That’s why…
Rachel McDowell
January 25, 2022
Science

Shape-Based Model Sheds Light on Simplified Protein Binding

Can something as simple as shape fully determine whether or not proteins will bind together? Scientists are commissioning supercomputers to find out. A team led by Sharon Glotzer, distinguished professor and department chair of chemical engineering at the University of Michigan (UM), used the 200-petaflop Summit supercomputer at the US…
Rachel McDowell
August 9, 2021
Science

Two Finalists Nominated for Gordon Bell Special Prize for COVID-19 Work on Summit

Every year at the International Conference for High Performance Computing, Networking, Storage and Analysis (SC), one deserving team is awarded the Association for Computing Machinery (ACM) Gordon Bell Prize to recognize an outstanding achievement in high-performance computing (HPC). Winners are chosen based on the demonstrated innovativeness of their algorithm development…
Rachel McDowell
November 18, 2020
ORNL Gordon Bell finalistsScience

Four Teams Using ORNL’s Summit Supercomputer Named Finalists in 2020 Gordon Bell Prize

Since 1987, the Association for Computing Machinery has awarded the annual Gordon Bell Prize to recognize outstanding achievements in high-performance computing (HPC). Presented each year at the International Conference for High-Performance Computing, Networking, Storage and Analysis (SC), the prizes not only reward innovative projects that employ HPC for applications in…
Coury Turczyn
November 10, 2020
Science

Machine Learning for Better Drug Design

When Harel Weinstein and his team at the Joan & Sanford I. Weill Medical College (Weill Cornell Medicine) of Cornell University set out to learn the molecular mechanisms of drugs, they weren’t expecting to train computers to analyze some of the most complex data in pharmacology. In fact, they really…
Rachel McDowell
February 21, 2020
configurational ensemble (a collection of 3D structures) of an intrinsically disordered proteinScience

Titan Supercomputer and Spallation Neutron Source Unite to Probe the Inner Workings of c-Src kinase

Proteins are the workhorses of our body’s cells, performing vital functions we can’t live without—everything from helping form antibodies to transporting nutrients to providing structure for the cells themselves. The individual role of each protein can be determined by studying its unique three-dimensional structure. However, one particular class of protein…
Coury Turczyn
October 3, 2019
Science

Summit Charts a Course to Uncover the Origins of Genetic Diseases

https://vimeo.com/336592112 A visualization of a new structure of the human PIC. The spheres correspond to the positions of patient-derived mutations color-coded by disease phenotype. Video credit: Ivaylo Ivanov, Georgia State University. Environmental conditions, lifestyle choices, chemical exposure, and foodborne and airborne pathogens are among the external factors that can cause…
Elizabeth Rosenthal
May 20, 2019
Science

Breaching the Biomass Problem

In a farewell nod to Titan, scheduled to be decommissioned in August 2019, we present a short series of features highlighting some of Titan’s impactful contributions to scientific research. https://vimeo.com/307039163 A visualization of a cellulose fiber (green) interacting with lignin (brown). Using supercomputers like the OLCF’s Cray XK7 Titan, ORNL…
Jonathan Hines
December 20, 2018
Science

A Problem with Polymer Theory

Researchers at the Center for Nanophase Materials Sciences, a US Department of Energy (DOE) Office of Science User Facility located at DOE’s Oak Ridge National Laboratory (ORNL), used high-performance computing to verify experiments that challenge a 40-year-old theory in soft-matter physics. The findings, published in ACS Macro Letters, add to…
Jonathan Hines
April 16, 2018