Biomolecular electrostatics, confinement, and dynamics

我的建议致力于从理论上理解生物界面(类脂膜)附近或限制下的一些相互关联的生物分子现象，如下所述。 (I)“抗菌肽细胞选择性的物理模型”。众所周知，抗菌肽可以选择性地破坏微生物膜。我们的工作旨在开发一个粗粒度的预测模型，用于描述它们在不同条件下(例如，不同的盐浓度和不同的膜电荷密度)的膜破坏活性。 (Ii)“封闭圆柱形约束下的聚合物”。我们的重点将集中在研究封闭圆柱孔中具有非平凡链拓扑(例如，环和支链)和“可调”链间相互作用的链的分离行为。我们将阐明控制链相容和分离动力学的各种因素，如受限空间的形状和链间交叉点。 (Iii)“在纳米孔中操纵单一生物聚合物”。这项工作将与Pi的合作者关于微通道内染色体扩展和压缩的实验工作并行进行。以聚合物模型(具有非线性拓扑结构)为模型染色体，我们将研究这种受限链在初始压缩和释放时的时间演化以及链的弹性响应。 (Iv)“类脂膜的静电整形”。这项工作将致力于研究脂膜的静电重塑，特别是镁离子和阳离子多肽的作用。我们将主要致力于建立一个简单的静电结合模型来描述它们的竞争结合及其对侧向堆积和膜稳定性的影响。

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.