THEORETICAL STUDIES ON THE DYNAMIC ASPECTS OF MACROMOLECULAR FUNCTION

孪生和双分子扩散影响反应理论 用于解释一氧化碳与血红素的再结合 在经过十年时间（1ps至10ps）测量的光解离之后， 10ms）。 结果表明， 初始双生相，不能用简单的动力学解释 方案，是反应物的扩散运动的反映。 分子动力学模拟已被用来获得动力学的 硬球液体中荧光猝灭的简单模型。 这些计算机生成的“实验”结果，我们然后用来测试 不可逆反应的Smoluchowski理论 考虑 许多粒子性质的问题，理论和 在宽范围的猝灭剂上， 浓度的 Smoluchowski理论已经被推广到治疗 二级可逆扩散影响的双分子反应。 它 结果表明，一个小的初始偏差的浓度，从他们的 平衡值以非指数方式衰减到零， 普通化学动力学的预测。 一种理论被发展出来， 部分地获得配体与细胞结合的时间依赖性速率， 被受体覆盖。 本文结果的一个特例 是用来找到一个解析表达式的电流在一个随机的 微盘电极阵列。 最后，一个新的布朗动力学 提出了一种模拟时间依赖的双分子速率的算法 涉及具有复杂几何形状的物质的反应系数， 通过任意势相互作用。

The theory of geminate and bimolecular diffusion influenced reactions was used to interpret the rebinding of carbon monoxide to protoheme following photodissociation measured over ten decades of time (1ps to 10ms). It was shown that the highly nonexponential behavior of the initial geminate phase, which cannot be explained using simple kinetic schemes, is a reflection of the diffusive motion of the reactants. Molecular dynamics simulations have been used to obtain the kinetics of a simple model of fluorescence quenching in a hard sphere liquid. These computer generated "experimental" results we then used to test the Smoluchowski theory of irreversible reactions. Considering the many particle nature of the problem, the agreement between theory and simulations was surprisingly good over a wide range of quencher concentrations. The Smoluchowski theory has been generalized to treat second order reversible diffusion-influenced bimolecular reactions. It was shown that a small initial deviation of the concentrations from their equilibrium values decays to zero nonexponentially in contrast to the prediction of ordinary chemical kinetics. A theory was developed to obtain the time dependent rate of binding of ligands to a cell partially covered by receptors. A special case of the result derived in this work was used to find an analytic expression for the current at a random array of microdisk electrodes. Finally, a new brownian dynamics algorithm was developed to simulate the time dependent bimolecular rate coefficient for reactions involving species with complex geometries that interact via an arbitrary potential.