Current Research Project

• Advanced Ion Channel Modeling and Computational Tools with Application to Voltage-Dependent Anion Channel and Mitochondrial Model Development.
  This project is supported by National Science Foundation (Award ID DMS-2153376, 7/15/2022 to 6/30/2025, $600,000). Prof. Dexuan Xie is working on this collaborative research project with Prof. Ranjan Dash at Medical College of Wisconsin. The major goals of this collaborative project are to develop a nonlocal dielectric continuum ion channel model and its effective finite element solver (algorithms and a software package) for computing ion channel kinetics and ion transports across membrane via a 3D cryptographic molecular structure of ion channel protein, and then apply this advanced ion channel model to the development of a novel integrated mitochondrial computational model to reflect the effects of ion sizes, nonlocal dielectric properties, and the atomic charges and molecular geometry of a voltage-dependent anion channel (VDAC) on the study of mitochondrial function/dysfunction under normal and pathological conditions.

• Advanced Nonlocal Dielectric Continuum Ion Channel Models and their Fast Finite Element Solvers.
  This project is supported by Simons Foundation (Award ID 711776). The major goals of this project are to develop a dielectric continuum ion channel model for computing ion channel electrostatics and simulating ions/metabolites transport across membrane.

Previous Research Projects

Prof. Dexuan Xie have being worked on the following four projects since 2002:

• Advances in Nonlocal Dielectric Modeling and Free Energy Calculation for Protein in Ionic Solvent.
  In this collaborative research project with Prof. L. Ridgway Scott at the University of Chicago, under the support of NSF grants, we studied nonlocal electrostatic continuum solvent modeling and related fast numerical solvers with applications to ion channel study, solvation free energy calculation, protein simulation, and rational drug design problems. One goal of the project is to understand the role of dielectric models in predicting the mechanism of ion channels (mainly sodium and calcium channels).
  Prediction of electrostatics of a protein in an ionic solvent is a fundamental task in the fields of mathematical biology, biochemistry, biophysics, biomedical science, and bioengineering. The main objective of PI Xie’s last NSF grant (DMS-1226259) was to extend the study of nonlocal dielectric continuum modeling of protein electrostatics which he had started in his prior NSF grant (DMS-0921004; 9/1/2009-8/31/2012). One important outcome was extending his prior nonlocal study results from ions in the water solvent to a protein in an ionic solvent.
  The results were presented at more than 20 professional conferences and workshops and reported in 20 peer-reviewed scientific publications. Two interactive web servers and five program packages were reported.
• Efficient Simulation of Protein-Membrane Interactions by Implicit Solvent Algorithms.
  This project was supported by the National Science Foundation (DMS-0241236, $520,479, 02/03/2003-4/10/2007). The co-PI was Dr. Peter Butko, Professor of Biochemistry at the University of Southern Mississippi. This project aims to develop a new computational model for studying protein conformation changes upon membrane interactions. Its objectives are to (1) develop a robust and efficient parallel iterative algorithm for solving the Poisson-Boltzmann equation; (2) define a new biomolecular potential-energy function through a large reduction of the number of conformation-freedom variables for a family of particular proteins; (3) develop a new sparse matrix compress scheme for programming an efficient application-tailored preconditioner in an optimal order of memory locations; (4) develop a parallel iterative algorithm for constrained molecular dynamics simulations; and (5) train undergraduate and graduate researchers for the post-genomic era. Specifically, the new algorithms and model will be applied to studying the molecular mechanism of membrane damage induced by the protein toxin Cyt1A upon membrane interactions. The theoretical results will also be compared to laboratory data produced by biochemical and biophysical methods such as fluorescence spectroscopy, surface tensiometry, and electron microscopy. Synthesis of the computational and experimental data may bring new insights into membrane permeabilization and damage by proteins that do not transverse the lipid bilayer.
• MSM Multiscale Modeling of the Heart in Cardiovascular.
  This project was supported by the National Institute of Biomedical Imaging and Bioengineering. The PI was Prof. Daniel A. Beard, the Biotechnology and Bioengineering Center at the Medical College of Wisconsin. Other co-PI included Dr. Nicolas Smith, the Bioengineering Institute at the University of Auckland, New Zealand.
• Visualization of structure-activity relationships of chemical databases.
  This project was supported by a research award from the Graduate School Research Committee of UWM.
• Electrostatic analysis of Cytochrome c by implicit solvent approach.
  The co-PI was Dr. Benjamin A. Feinberg, Professor of Chemistry at UWM.