论文标题
超级扩散,坚固的能源景观和过渡网络
Ultrametric Diffusion, Rugged Energy Landscapes and Transition Networks
论文作者
论文摘要
在本文中,我们介绍了超法网络,这些网络是使用主方程构建的标准马尔可夫状态模型的P-ADIC连续类似物。 P-ADIC过渡网络(或超级网络)是一个复杂系统的模型,该系统由分层能量景观,能量景观上的马尔可夫过程和主方程组成。我们专注于网络,其中两个不同盆地之间的过渡速率是恒定函数,并且每个盆地内部的跳跃过程都由P-ADIC径向函数控制。我们为此类网络附加的主方程式明确解决了Cauchy问题。该问题的解决方案是对给定初始浓度的网络响应。如果附加到网络的马尔可夫进程是保守的,则网络的长期响应由马尔可夫链控制。如果该过程不保守,则网络具有吸收状态。我们定义了一个吸收时间,这取决于初始浓度,如果这段时间是有限的,则网络在有限的时间内达到了吸收状态。我们在网络的响应中确定负责将网络带到吸收状态的术语,我们称它们为快速过渡模式。快速过渡模式的存在是能量格局是超级(分层)的假设的结果,并且在我们的最大程度上,无法使用马尔可夫状态模型的标准方法获得该结果。如今,人们普遍认为,蛋白质本地状态是可以从任何其他状态迅速到达的动力学枢纽。快速过渡模式的存在表明,超级网络上的某些状态可作为动力学枢纽。
In this article we introduce the ultrametric networks which are p-adic continuous analogues of the standard Markov state models constructed using master equations. A p-adic transition network (or an ultrametric network) is a model of a complex system consisting of a hierarchical energy landscape, a Markov process on the energy landscape, and a master equation. We focus on networks where the transition rates between two different basins are constant functions, and the jumping process inside of each basin is controlled by a p-adic radial function. We solve explicitly the Cauchy problem for the master equation attached to this type of networks. The solution of this problem is the network response to a given initial concentration. If the Markov process attached to the network is conservative, the long term response of the network is controlled by a Markov chain. If the process is not conservative the network has absorbing states. We define an absorbing time, which depends on the initial concentration, if this time is finite the network reaches an absorbing state in a finite time. We identify in the response of the network the terms responsible for bringing the network to an absorbing state, we call them the fast transition modes. The existence of the fast transition modes is a consequence of the assumption that the energy landscape is ultrametric (hierarchical), and to the best of our understanding this result cannot be obtained using standard methods of Markov state models. Nowadays, it is widely accepted that protein native states are kinetic hubs that can be reached quickly from any other state. The existence of fast transition modes implies that certain states on an ultrametric network work as kinetic hubs.