Combating Infection through Atomic-Scale Modeling of Unique Bacterial System



Biological Significances:  

Combating infection has become increasingly difficult because bacteria are acquiring resistance at an incredible pace, and current approaches to antibiotic development are producing diminishing returns.


Project Summary:

Predicting the rate of nonfacilitated permeation of solutes across lipid bilayers is important to drug design, toxicology, and signaling. Molecular Dynamics (MD) simulations provide a means for generating novel structural data and elucidating a system's evolution between structurally characterized states. We use umbrella sampling, replica exchange umbrella sampling, adaptive biasing force, and multiple-walker adaptive biasing force to calculatie of the transmembrane potential mean force. Our project contributes to computer-aided antibiotic development through the consideration of lipid membrane bilayer. 


Key Outcomes:

  • Lee CT, Comer J, Herndon C, Leung N, Pavlova A, Swift RV, Tung C, Rowley CN, Amaro RE, Chipot C, Wang Y, Gumbart JC. Simulation-Based Approaches for Determining Membrane Permeability of Small Compounds. J Chem Inf Model. 2016;56(4):721-33. doi: 10.1021/acs.jcim.6b00022.