Biomolecular electrostatics, confinement, and dynamics

我的建议是致力于理论上了解一些相互关联的生物分子现象附近的生物界面（脂膜）或限制，如下所述。 (i)"抗菌肽细胞选择性的物理模型。“已知抗菌肽可以选择性地破坏微生物膜。 我们在这里的努力旨在开发一种粗粒度的预测模型，用于描述它们在各种条件下的膜破坏活性（例如，不同的盐浓度和不同的膜电荷密度）。 (ii)"封闭圆柱形约束下的聚合物。"我们的重点将是研究具有非平凡链拓扑结构的链的分离行为（例如，环和支链）和"可调"链间相互作用，限制在封闭的圆柱形孔中。我们将阐明各种因素，如有限空间的形状和链间交叉控制链的可折叠性和分离动力学。 (iii)"纳米孔中的单一生物聚合物操作。“这项工作将与PI的合作者在微通道内染色体扩增和压缩的实验工作并行进行。使用一个聚合物模型（非线性拓扑结构）作为模型染色体，我们将调查这样一个有限的链最初压缩和释放的时间演化以及链的弹性响应。 (iv)"脂质膜的静电重塑。“这项工作将致力于研究脂质膜的静电重塑，特别是通过Mg 2+和阳离子肽。 我们将主要集中在发展一个简单的静电结合模型来描述它们的竞争性结合及其对膜的侧向填充和稳定性的影响。

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.