Biomolecular electrostatics, confinement, and dynamics

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My proposal is devoted to theoretical understanding of a few interrelated biomolecular phenomena near a biological interface (a lipid membrane) or under confinement, as outlined below. (i) "A physical model for the cell selectivity of antimicrobial peptides." Antimicrobial peptides are known to selectively rupture microbial membranes. Our effort here is aimed at developing a coarse-grained, predictive model for describing their membrane disrupting activity under various conditions (e.g., different salt concentrations and varying membrane charge densities). (ii) "Polymers under closed cylindrical confinement." Our focus will be on studying the segregational behavior of chains with nontrivial chain topology (e.g., ring and branched) and "tunable" interchain interactions, confined in a closed cylindrical pore. We will clarify various factors that control chain miscibility and segregation dynamics such as the shape of the confined space and interchain crossings. (iii) "Single biopolymer manipulation in a nano pore." This work will be carried out in parallel with the experimental effort of PI's collaborator on chromosome expansion and compression inside micro-channels. Using a polymer model (with nonlinear topology) as a model chromosome, we will investigate the time evolution of such a confined chain initially compressed and released as well the elastic response of the chain. (iv) "Electrostatic reshaping of a lipid membrane." This effort will be devoted to studying the electrostatic reshaping of a lipid membrane, especially by Mg2+ and cationic peptides. We will mainly focus on developing a simple electrostatic binding model for describing their competitive binding and its effect on the lateral packing and stability of the membrane.