Lab

Luo Lab in Biophysical Chemistry

About the lab

Our research interests are in the general area of computational structural biology and biophysical chemistry. We are particularly interested in computational analysis of solvation-mediated biomolecular energetics and dynamics. Our efforts cover both polar and nonpolar interactions, whose accurate modeling is crucial in the studies of molecular recognition and its applications to drug design and discovery. In addition, we are developing new biomolecular mechanics force fields with reduced or coarse-grained representation for efficiency and explicit representation of electronic polarization for accuracy. Together with our collaborators, we are also investigating a wide range of interesting problems of biomedical importance.

Featured projects (5)

Project
Elucidate the molecular mechanism of allosteric regulation in molecular recognition based on explicit-solvent molecular dynamics simulation and MMPBSA post analysis.
Project
Develop a set of computational models and tools to facilitate a concerted analysis of structural properties of disordered proteins using MD simulations and NMR measurements.
Project
To provide functions to support membrane proteins with/without channels in protein-ligand binding affinity calculations with MMPBSA methods.
Project
Porting linear and nonlinear FDPB methods to Nvidia CUDA platforms.
Project
The goal of this project is to develop a new electrostatic/polarizable model, termed the polarizable Gaussian Multipole model, and to port it to GPU for high performance MD simulations of biomolecules.

Featured research (7)

Molecular modeling at the atomic level has been applied in a wide range of biological systems. The widely adopted additive force fields typically use fixed atom-centered partial charges to model electrostatic interactions. However, the additive force fields cannot accurately model polarization effects, leading to unrealistic simulations in polarization-sensitive processes. Numerous efforts have been invested in developing induced dipole-based polarizable force fields. Whether additive atomic charge models or polarizable induced dipole models are used, proper parameterization of the electrostatic term plays a key role in the force field developments. In this work, we present a Python program called PyRESP for performing atomic multipole parameterizations by reproducing ab initio electrostatic potential (ESP) around molecules. PyRESP provides parameterization schemes for several electrostatic models, including the RESP model with atomic charges for the additive force fields and the RESP-ind and RESP-perm models with additional induced and permanent dipole moments for the polarizable force fields. PyRESP is a flexible and user-friendly program that can accommodate various needs during force field parameterizations for molecular modeling of any organic molecules.

Lab head

Ray Luo

Members (7)

Ruxi Qi
  • University of California, Irvine
Haixin Wei
  • University of California, Irvine
Shiji Zhao
  • University of California, Irvine
Vy Thuy Duong
  • University of California, Irvine
Lisha Zeng
  • Carnegie Mellon University
Tianyin Qiu
  • University of California, Irvine
Yongxian Wu
  • University of California, Irvine
D'Artagnan Greene
D'Artagnan Greene
  • Not confirmed yet
Zekai Zhao
Zekai Zhao
  • Not confirmed yet
Shiji Zhao
Shiji Zhao
  • Not confirmed yet
Tim Qiu
Tim Qiu
  • Not confirmed yet
Fanglue Ni
Fanglue Ni
  • Not confirmed yet

Alumni (20)

Li Xiao
  • University of California, Irvine
Hai-Feng Chen
  • Shanghai Jiao Tong University
Lijiang Yang
  • Peking University
Wesley M. Botello-Smith
Wesley M. Botello-Smith