Welcome to Clemson Computational Biophysics Lab

We are a theoretical/computational biophysics group in the Department of Physics and Astronomy at Clemson UniversityCollege of Science. We apply concepts and methods in Physics, especially Statistical Mechanics and Thermodynamics, to study biological systems, and hopefully learn new physics emerging from the complex biological systems. The major theme throughout our research is to integrate dynamics into the study of structure-function relationship of biomolecules and molecular complexes. We believe that uncovering the interrelationship between structure, dynamics, and function of biomolecules can help better understand biology, and accelerate biomedical research in a cost-effective manner.

Our present research focus is multiscale modeling of biomolecules and molecular complexes. Experimental characterization of biological systems is often hindered by the limited ability to cover a wide range of time and length scales, associated with many biological processes. Multiscale molding, which innovatively combines atomic and coarse-grained simulations, provides a unique opportunity to bridge the gaps of time and length scales between experimental observation and underlying molecular systems. We apply the multiscale modeling approach to study structure, dynamics, and function of large biomolecules, formation of molecular complexes, and also interaction between nanomaterials and biological systems.

We are always interested in enthusiastic colleagues to join our lab.

Inhibition of islet amyloid polypeptide aggregation in type-II diabetes

Accumulating evidence suggests that the aggregation of islet amyloid polypeptide (IAPP, a.k.a. amylin) is associated with β-cell death in type 2 diabetes (T2D). IAPP is co-secreted with insulin by pancreatic beta-cells, and also works together with insulin to control the serum glucose level. In vitro studies suggest that IAPP is one of the most amyloidogenic …

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Protein Design and Protein Engineering

The ability to accurately manipulate a protein’s structure, dynamics and function, and eventually to create de novo proteins with specific functions is the holy grail of modern biology. The success in protein design & engineering requires the accurate knowledge of inter-residue interactions, protein folding, protein-ligand and protein-protein recognitions, and also the molecular mechanism of catalysis. …

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Post-translational modifications

The structural and energetic determinants of TPST enzyme specificity Many PTM enzymes have strong sequence preferences in the targeted substrate proteins/peptides while others do not. What are the molecular mechanism of such drastic differences in PTM enzyme specificities? It is expected that the binding affinity between substrate and enzyme plays an important role in defining …

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Molecular Recognition

A major challenge in modeling molecular recognition is the conformational flexibility. The structures of the receptors in the bound and un-bound states are often different, known as the induced-fit problem. In these cases, a rigid docking approach will fail to achieve accurate predictions. Existing flexible methods for modeling molecular recognition or docking often adopt the …

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Modeling RNA 3D structure using experimental constraints

RNA structure determination is one of the major challenges in structural biology. Many RNAs are not amenable to high-resolution structure characterization by either x-ray or NMR methods because of their conformational flexibility or large size. Recently, novel computational methods to determine RNA structures have begun to emerge, but have often been limited to small RNAs …

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Protein folding, misfolding and aggregation

Most proteins fold into specific three-dimensional structures, which determine their functions. The folding process can be described by the free energy landscape as in a first order phase transition. The native state features the lowest free energy and correspond to the most stable and most populated species in physiological conditions. However, due to either environmental …

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Interactions between nanomaterials and biomolecules at the Nano-Bio interface

Recent advances in Nanotechnology allow sophisticated synthesis of nanomaterials with well-defined composition, aspect ratio, size, surface chemistry and functionalization. Biomedical applications of engineered nanomaterials or nanomedine include imaging, sensing, targeting, drug and gene delivery, and therapeutics in diagnosis, prognosis, and treatment of human diseases. Upon entering biological media such as the bloodstream, a nanoparticle forms …

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Mitigation of amyloid aggregation and toxicity

Amyloid aggregation is associated with an increasing list of degenerative diseases such as Alzheimer’s disease, Parkinson’s disease, and type-2 diabetes. The hallmark common to all amyloid diseases is the deposition of beta-sheet rich fibrils formed of by misfolding and aggregation of otherwise soluble proteins and peptides. Mounting experiments suggest that soluble oligomers instead of mature …

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