Our science is driven by curiosity of the world around us. We are guided by experimental and theoretical advances in various fields of science from physics and mathematics to biophysics. We are inherently collaborative and open-minded, and we treat each other with kindness, gratitude, and humility.
Our Quest, Research, and Principles
Our Quest
- To identify questions that are testable by experiments;
- To identify biological systems that are of fundamental significance and difficult to describe with established theoretical and computational approaches;
- To develop emerging theoretical and computational techniques applicable to problems of interest;
- To ascertain materials that facilitates innovations in battery technology.
Our Research
- Biophysics (computational). Development of structure-based (SMOG v2.4.2) models and OpenSMOG with aim to study via highly-optimized MD simulation packages, such as Gromacs and OpenMM, the large-scale conformational dynamics of the ribosome and other larger biomolecular systems in aqueous solution in the presence of ions.
- Chemical biology (computational). Development of computational methods in OpenMM environment to study conformational dynamics of glycosaminoglycans polysaccharides, haparan sulfates, and their synthetic analogs. Our tool-kit includes state-of-the-art molecular dynamics simulations (explicit and coarse-grained) with sampling techniques, statistical mechanics, quantum chemsitry, and deep-learning (AI) methods.
- Physical chemistry (theoretical). Development of renormalization group and holographic methods with aim to study dynamics of low temperature liquids.
- Materials chemistry (computational). To study charge behaviors in metal-organic frameworks (MOFs) with aim to understand whether these materials can serve as a promising solid-state medium for the transport of multivalent ions. Our tool-kit includes state-of-the-art statistical mechanics and quantum chemsitry methods.
Our Principles
Our science is driven by curiosity of the world around us. This is coupled with passion, long-term vision, guided by experimental and theoretical advances in various fields of science from physics and mathematics to biophysics. We are inherently collaborative, open-minded in the way we approach a problem, value scientists from any discipline, and treat each other with kindness, gratitude, and humility. Docet Omnia. “Not acquired truths, but the idea of freely-executed research” (Maurice Merleau-Ponty, College de France)
Funding
National Science Foundation (collaborative)
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Codes
We have developed all-atom structure-based model (SMOG) generalization of Manning counterion condensation theory to RNA and riboswitches that is explicit divalent (magnesium) but implicit monovalent ion. The C++ codes and files are available online.
All-atom stucture-based models, SMOG v2.4, and OpenSMOG (v 1.1.0) are both open souce and freely available at https:/smog-server.org/smog2. The OpenSMOG is a python library for molecular dynamics (MD) simulations of structure-based models that can be installed via pip or conda.