Onufriev Lab

Research

We work at the interface of computer science, physics, biology, and chemistry; the research is a collective effort of our group members who have background in one or more of these fields. Most students who graduate from the group become proficient in cutting edge computing. Our funding comes from the NIH and the NSF.

Current work

Active Research Areas

Better Modeling Accuracy: novel models of water

All biological matter is surrounded by water, but modeling the effects of water accurately and efficiently remains a significant challenge, which we address at various levels. Our most recent efforts combine the power of machine learning with reliability of physics to deliver better models of water. Water -- the simplest most complex molecule -- still holds a number of mysteries, which better water models can help solve.

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Better Medicines, Faster: helping drug discovery efforts through molecular modeling and simulations

Atomistic simulations of biomolecules enable modern drug design efforts; these require fast and accurate algorithms. We harness the power of computer science, including machine learning, to develop better ways to model biomolecules and develop new therapeutics.

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3D organization of the genome: the basic principles.

The goal is to understand, through a combination of computation and experiment, the structure-function connections in the genome, which is organized in a complex manner within the cell. Our most recent interests in this direction focus on ageing and cancer. Shown is an artist's vision of the genome organization complexity. Image credit: Eric Standley, VT.

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Mathematical Entomology

Discovering simple mathematical patterns in complex behavior of insects.

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Research archive

Selected Earlier Research

DNA compaction and deformation

DNA compaction plays vital role in key cellular processes such as cell differentiation, DNA replication, repair, and transcription. We aim to uncover the fundamental principles that control the DNA compaction.

Nucleic acid condensation induced by ions

Our goal was to develop a quantitative, atomic-level understanding of how multivalent ions, including biologically relevant polyamines, mediate attractive forces between nucleic acid molecules (DNA, RNA) that lead to various nucleic acid condensation phenomena observed in experiments.

Protein Folding

One of the largest challenges in modern science is working out how proteins curl up into their complex shapes...

Functional dynamics of biomolecules

Biological function of many biomolecules, such as proteins or DNA, is intricately related to their dynamical properties. Can we understand these relationships using computational methods?

Theory of Cooperative Ligand Binding

Binding of ligands to macromolecules is one of the most important reactions in biology...

Proton-pumping mechanism of Bacteriorhodopsin

Bacteriorhodopsin is the smallest autonomous light-harvesting system...

Insights into the RNAi mechanism

Can we use bioinformatics to help us understand how small fragments of RNA interact with the messenger RNA?