Cross-
Cutting
Research Area
Modeling life processes at the molecular and subcellular levels
Biological processes are conducted at multiple temporal and spatial scales and are tightly regulated by the cell. Computational Molecular Biophysics focuses on fundamental and modulated processes at the subcellular and cellular levels. Many of these processes rely on molecular machines that conduct mechanical work, transmit timely signals, transport material across boundaries of compartments and execute biochemical reactions. Our research is firmly rooted in Hamilton’s equations of motions and statistical mechanics. These fundamental physical laws underpin computer simulations based on novel algorithms and theories developed to understand, predict and manipulate these processes at the atomistic level. We then conduct these simulations and test the predictions with experimental groups.
Examples of current research areas:
The mechanism of drug–kinase interactions
Protein kinases participate in many signaling processes, and their malfunction may cause diseases like cancer. Since there are many different kinases, it is hard to design a drug molecule that is specific to a particular pathway while also avoiding side effects. We study the drug-kinase interaction to understand the specificity of drug molecules. A success story is the drug ‘Imatinib’ that binds preferably to Abl kinase.
Cell-Penetrating Peptides
Cell-Penetrating Peptides (CPP) are small molecules that efficiently cross membrane barriers into cells and between compartments. We model the permeation process and consider the natural and synthetic design of these permeation agents.
Protein sliding along DNA
To read, synthesize and repair, protein machines slide along DNA. We point out the critical role counter ions play in the sliding process.
The operation of the Anthrax toxin
The anthrax toxin is a protein complex. It consists of a channel that enables the translocation of a protein called the Lethal Factor (LF) to the cytosol. Once in the cytosol, the LF causes significant damage. We model the translocation of the LF and use our Milestoning theory to conduct the simulations.
Current partnerships include collaborations with the Department of Chemistry and Department of Neuroscience at UT’s College of Natural Sciences, and with external groups and experts from University of Missouri, University of Rome, Sapienza, and the Hebrew University of Jerusalem.
To learn more about projects and people in Computational Biology, explore the centers and groups with research activities in this cross-cutting research area.
News
Feb. 20, 2025
Keon Ho Kim, Peter O'Donnell, Jr. PostDoctoral Fellow, recieved a fellowship award, funding his research in mitral valve regurgitation treatment.
News
Dec. 9, 2024
Oden Institute faculty and researchers led three panels at UT's AI LIVE, a three-day showcase capping off the university's Year of AI initiative.
News
Dec. 8, 2024
The fifth annual Joint Center for Computational Oncology (JCCO) retreat highlighted advancements in digital twin technology, Researchers discussed challenges, while showcasing collaborative progress and future goals to integrate digital twins into clinical oncology.
News
Dec. 3, 2024
Thomas J.R. Hughes received an honorary doctorate from INSA Lyon on November 5, 2024, recognizing his research and collaborations with INSA’s LaMCoS Laboratory. A core faculty member at the Oden Institute, Hughes continues to advance engineering and medicine through innovative research and a forward-looking vision for integrating artificial intelligence with computational mechanics.
Profile
June 23, 2024
Read about the astrophysicist-turned-computational-biologist's journey as Professor and Presidential Advisor.
News
Feb. 26, 2024
Using a mathematical model researchers found that using Paxlovid prescribed for COVID has the potential to reduce hospitalizations, save lives, and reduce medical costs.
Feature
Jan. 11, 2024
Read about Tom Yankeelov's fruitful career at the Oden Institute and his mission to individualize cancer care through computational science.
News
Dec. 15, 2023
Across multiple domains of science, engineering, and medicine, excitement is growing about the potential of digital twins to transform scientific research, industrial practices, and many aspects of daily life.
This report identifies the foundational research and resources needed to support the development of digital twin technologies.
News
Dec. 5, 2023
Announcing the 2023-2024 MD Anderson, Oden Institue, and TACC Collaboration Grant Recipients.
Profile
Aug. 15, 2023
As he transitions into retirement, the computational biologist looks forward to continuing a research career in industry.
News
Aug. 3, 2023
Researchers discovered that adult trees in a Panamanian forest are three times more distant from other adults of the same species than what the proverbial ‘the apple doesn’t fall far from the tree’ would suggest, leading to a better understanding of forest biodiversity.
News
June 16, 2022
Feature
May 18, 2022
News
Sept. 22, 2021
Profile
April 27, 2021