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Computational Biophysics
and Materials Science Group
-Department of Materials Science and Engineering


My long-term research goal is to explore molecular mechanisms of cellular systems and materials as well as to develop new computational tools in order to understand fundamental physical principles behind biological and materials phenomena.

  1. Bio-Nano Interactions
  2. Protein-Lipid Interactions
  3. Physics in Energy-Storage Materials and Interfaces

Bio-Nano Interactions

As the rapid development of nanomaterials and their emerging biomedical and biological applications such as drug/gene delivery and nanosensing, the interaction between nanomaterials and biological entities plays an increasingly important role in nanoscience. In particular, bio-nano interactions could interfere functions of proteins, lipids, etc., and even damage the structural integrity of cells. Thus, the cytotoxicity of nanomaterials has caused serious concerns over the safety and sustainability of nanotechnology. On the other hand, the toxicity of nanomaterials can also be utilized in antibacterial and antifouling applications. We perform MD simulations to study the interaction between nanoparticles/nanotubes/nanosheets and lipid membranes/proteins/DNA/organelles, providing insights into physics in bio-nano systems.

We have studied the interaction between 2D nanomaterials (nanosheets) and lipid membranes recently. Hydrophobic nanosheets could extract lipids and then insert into lipid membranes, which is very important for the cytotoxicity of nanosheets. Interestingly, we found that the lipid extraction behavior depends on the phase state of lipids that can be changed by temperature, lipid components, etc. In addition, the insertion of nanosheets into lipid membranes could lead to the ordering of lipids, which may perturb the function of transmembrane proteins.

References


Protein-Lipid Interactions

Peripheral membrane proteins and transmembrane proteins could influence the physical state and functions of lipids, and vice versa. Utilizing molecular dynamics (MD) simulations and other computational analyses, we aim to explore the relationship or coupling between proteins and lipids, including the membrane remodeling by BAR (Bin-Amphiphysin-Rvs) family proteins, the reversible gating of protein channels stimulated by the lateral pressure of lipid membranes, etc.

The BAR (Bin-Amphiphysin-Rvs) domain undergoes dimerization to produce a curved protein structure, which superimposes onto membrane through electrostatic interactions to sense and impart membrane curvature. In some cases, a BAR domain also possesses an amphipathic helix that inserts into the membrane to induce curvature. ACAP1 (Arfgap with Coil coil, Ankyrin repeat, and PH domain protein 1) contains a BAR domain. Here, we show that this BAR domain can neither bind membrane nor impart curvature, but instead requires a neighboring PH (Pleckstrin Homology) domain to achieve these functions. Specific residues within the PH domain are responsible for both membrane binding and curvature generation. The BAR domain adjacent to the PH domain instead interacts with the BAR domains of neighboring ACAP1 proteins to enable clustering at the membrane. Thus, we have uncovered the molecular basis for an unexpected and unconventional collaboration between PH and BAR domains in membrane bending.

References


Physics in Energy-Storage Materials and Interfaces

Combining DFT calculations and MD simulations, we explore physics in energy-storage materials such as Li-ion batteries, Na-ion betteries, and supercapacitors. With DFT calculations, we evaluate the energy-storage properties of nanomaterials (especially 2D materials), and predict novel electrode materials. MD simulations are implemented to explore the structural characteristics and physical behaviors of ions and electrolytes on the interface between electrodes and electrolytes.

We have studied the storage of Na-ion on MXene-family electrodes, and concluded that large charge transfer and small lattice mismatch are beneficial to the storage of Na-ions. We investigated the structure of ionic liquid electrolytes in electric double layers of supercapacitors, and clarified the charge-driven ordering transition and the role of electrolyte structures.

References