Modeling of kinetic processes in biological systems

生物系统动力学过程建模

• 批准号: 10255221
• 负责人: Alexander Berezhkovskii
• 金额: $ 25.74万
• 依托单位: CENTER FOR INFORMATION TECHNOLOGY
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10255221
• 关键词: Affect; Alpha Particles; Complex; Crowding; Data; Dependence; Diffuse; Entropy; Environment; Equilibrium; Goals; Height; Individual; Kinetics; Molecular Motors; Periodicity; Process; Shapes; System; Time; Touch sensation; Transport Process; Walking; biological systems; experimental study; high dimensionality; kinetic model; particle; single molecule; theories; two-dimensional

Dependence of the mean transition path time on the height of the entropy barrier Transition path of a particle diffusing between points a and b is the final segment of the particle trajectory when it leaves point a and goes to point b without touching point a and vice versa. We studied the mean transition path time in entropy potentials focusing on its dependence of the entropy barrier height. We found that this dependence is highly non-trivial changing from monotonic decrease with the barrier height in high-dimensional spaces to monotonic increase in two dimensions. Dynamics of systems, like molecular motors, that randomly jump between states with different velocities and diffusivities At long times, stochastic dynamics of systems mentioned in the title can be characterized by two parameters: effective drift velocity and diffusivity. We developed a theory that explains how these effective parameters are related to the drift velocities and diffusivities in individual states and the rates of inter-state transitions. Random walk in crowded environment We developed a theory of cyclic random walk in crowded environment and demonstrated that crowding affects main features of the random walk in the absence of crowding. We explained how one can observe the discovered effects in single-molecule experiments. Forward-backward symmetry of the transition path time Conventional consideration of the transition path time assumes conservation of diffusing particles. Because of the detailed balance, the distribution of the transition path possesses the forward-backward symmetry. We generalized the conventional consideration to the case where diffusing particles can be trapped and proved that the detailed balance is fulfilled in the presence of a distributed sink of an arbitrary shape. This allowed us to show that the forward-backward symmetry of the distribution of the transition path time is conserved even in the presence of trapping.

平均跃迁路径时间对熵垒高度的依赖性 粒子在点a和B之间扩散的过渡路径是粒子离开点a并到达点B而不接触点a时的粒子轨迹的最后一段，反之亦然。我们研究了熵势中的平均跃迁路径时间，着重研究了平均跃迁路径时间与熵垒高度的关系。我们发现，这种依赖性是非常不平凡的变化，从单调减少的势垒高度在高维空间的单调增加的两个维度。 系统的动力学，如分子马达，以不同的速度和扩散率在状态之间随机跳跃 在很长一段时间，随机动力学的系统中提到的标题可以用两个参数：有效漂移速度和扩散率。我们开发了一个理论，解释这些有效的参数是如何相关的漂移速度和扩散率在个别国家和国家间的过渡率。 拥挤环境中的随机游动 我们提出了拥挤环境中的循环随机游动理论，并证明了在没有拥挤的情况下，拥挤会影响随机游动的主要特征。我们解释了如何在单分子实验中观察到所发现的效应。 跃迁路径时间的前后对称性 过渡路径时间的传统考虑假设扩散粒子守恒。由于细节的平衡，跃迁路径的分布具有前后对称性。我们推广了传统的考虑扩散粒子可以被捕获的情况下，并证明了详细的平衡是满足的存在下，一个任意形状的分布式水槽。这使我们能够表明，向前向后对称的过渡路径时间的分布是保守的，即使在存在的陷阱。