Structure of the Bacterial Cell Envelope and Interactions with Antimicrobials: Insights from Molecular Dynamics Simulations.

Bacteria have evolved over 3 billion years, shaping our intrinsic and symbiotic coexistence with these single-celled organisms. With rising populations of drug-resistant strains, the search for novel antimicrobials is an ongoing area of research. Advances in high-performance computing platforms have led to a variety of molecular dynamics simulation strategies to study the interactions of antimicrobial molecules with different compartments of the bacterial cell envelope of both Gram-positive and Gram-negative species.

Trajectory-Extending Kinetic Monte Carlo Simulations to Evaluate Pure and Gas Mixture Diffusivities through a Dense Polymeric Membrane.

With renewed interest in CO separations, carbon molecular sieving (CMS) membrane performance evaluation requires diffusion coefficients as inputs to have a reliable estimate of the permeability. An optimal material is desired to have both high selectivity and permeability. Gases diffusing through dense CMS and polymeric membranes experience extended subdiffusive regimes, which hinders reliable extraction of diffusion coefficients from mean squared displacement data.

Selective Photonic Gasification of Strained Oxygen Clusters on Graphene for Tuning Pore Size in the Å Regime.

Controlling the size of single-digit pores, such as those in graphene, with an Å resolution has been challenging due to the limited understanding of pore evolution at the atomic scale. The controlled oxidation of graphene has led to Å-scale pores; however, obtaining a fine control over pore evolution from the pore precursor (i.e.

Cholesterol catalyzes unfolding in membrane-inserted motifs of the pore forming protein cytolysin A.

Plasma membrane-induced protein folding and conformational transitions play a central role in cellular homeostasis. Several transmembrane proteins are folded in the complex lipid milieu to acquire a specific structure and function. Bacterial pore forming toxins (PFTs) are proteins expressed by a large class of pathogenic bacteria that exploit the plasma membrane environment to efficiently undergo secondary structure changes, oligomerize, and form transmembrane pores.

Martini-3 Coarse-Grained Models for the Bacterial Lipopolysaccharide Outer Membrane of .

The outer lipopolysaccharide (LPS) membrane of Gram-negative bacteria forms the main barrier for transport of antimicrobial molecules into the bacterial cell. In this study we develop coarse-grained models for the outer membrane of in the Martini-3 framework. The coarse-grained model force field was parametrized and validated using all-atom simulations of symmetric membranes of lipid A and rough LPS as well as a complete asymmetric membrane of LPS with the O-antigen.