Milestoning: An Efficient Approach for Atomically Detailed Simulations of Kinetics in Biophysics

2020 ◽  
Vol 49 (1) ◽  
pp. 69-85 ◽  
Author(s):  
Ron Elber
Keyword(s):  
Protein Translocation ◽  
First Passage Time ◽  
Passage Time ◽  
Phospholipid Membrane ◽  
Molecular Processes ◽  
Time Dynamics ◽  
Wide Range ◽  
Long Time ◽  
The Mean ◽  
Kinetics Of

Recent advances in theory and algorithms for atomically detailed simulations open the way to the study of the kinetics of a wide range of molecular processes in biophysics. The theories propose a shift from the traditionally very long molecular dynamic trajectories, which are exact but may not be efficient in the study of kinetics, to the use of a large number of short trajectories. The short trajectories exploit a mapping to a mesh in coarse space and allow for efficient calculations of kinetics and thermodynamics. In this review, I focus on one theory: Milestoning is a theory and an algorithm that offers a hierarchical calculation of properties of interest, such as the free energy profile and the mean first passage time. Approximations to the true long-time dynamics can be computed efficiently and assessed at different steps of the investigation. The theory is discussed and illustrated using two biophysical examples: ion permeation through a phospholipid membrane and protein translocation through a channel.

First passage time for the state of exact chemical equilibrium

1980 ◽  
Vol 45 (3) ◽  
pp. 777-782 ◽  
Author(s):  
Milan Šolc
Keyword(s):  
Chemical Equilibrium ◽  
First Passage Time ◽  
Passage Time ◽  
The State ◽  
Recurrence Time ◽  
First Passage ◽  
First Order ◽  
The Mean ◽  
Passage Times ◽  
Number Of Particles

The establishment of chemical equilibrium in a system with a reversible first order reaction is characterized in terms of the distribution of first passage times for the state of exact chemical equilibrium. The mean first passage time of this state is a linear function of the logarithm of the total number of particles in the system. The equilibrium fluctuations of composition in the system are characterized by the distribution of the recurrence times for the state of exact chemical equilibrium. The mean recurrence time is inversely proportional to the square root of the total number of particles in the system.

scholarly journals Mean first-passage time of a tumor cell growth system with time delay and colored cross-correlated noises excitation

2017 ◽  
Vol 37 (2) ◽  
pp. 191-198 ◽  
Author(s):  
Shenghong Li ◽  
Yong Huang
Keyword(s):  
Time Delay ◽  
Noise Intensity ◽  
First Passage Time ◽  
Passage Time ◽  
Mean First Passage Time ◽  
Tumor Cell Growth ◽  
First Passage ◽  
Growth System ◽  
The Mean ◽  
Correlated Noises

In this paper, the mean first-passage time of a delayed tumor cell growth system driven by colored cross-correlated noises is investigated. Based on the Novikov theorem and the method of probability density approximation, the stationary probability density function is obtained. Then applying the fastest descent method, the analytical expression of the mean first-passage time is derived. Finally, effects of different kinds of delays and noise parameters on the mean first-passage time are discussed thoroughly. The results show that the time delay included in the random force, additive noise intensity and multiplicative noise intensity play a positive role in the disappearance of tumor cells. However, the time delay included in the determined force and the correlation time lead to the increase of tumor cells.

scholarly journals Probing Protein Shelf Lives from Inverse Mean First Passage Times

2019 ◽  
Author(s):  
Vishal Singh ◽  
Parbati Biswas
Keyword(s):  
Protein Aggregation ◽  
Rate Constants ◽  
Survival Probability ◽  
First Passage Time ◽  
Passage Time ◽  
First Passage ◽  
First Order Kinetics ◽  
The Mean ◽  
Passage Times ◽  
Good Agreement

Protein aggregation is investigated theoretically via protein turnover, misfolding, aggregation and degradation. The Mean First Passage Time (MFPT) of aggregation is evaluated within the framework of Chemical Master Equation (CME) and pseudo first order kinetics with appropriate boundary conditions. The rate constants of aggregation of different proteins are calculated from the inverse MFPT, which show an excellent match with the experimentally reported rate constants and those extracted from the ThT/ThS fluorescence data. Protein aggregation is found to be practically independent of the number of contacts and the critical number of misfolded contacts. The age of appearance of aggregation-related diseases is obtained from the survival probability and the MFPT results, which matches with those reported in the literature. The calculated survival probability is in good agreement with the only available clinical data for Parkinson’s disease.<br>

Scaling of average receiving time on double-weighted polygon networks

2021 ◽  
Author(s):  
Xiaoyan Li ◽  
Yu Sun
Keyword(s):  
Iterative Method ◽  
Path Length ◽  
First Passage Time ◽  
Passage Time ◽  
Traffic Networks ◽  
Mean First Passage Time ◽  
First Passage ◽  
Specific Calculation ◽  
Calculation Process ◽  
The Mean

In this paper, we introduce a class of double-weighted polygon networks with two different meanings of weighted factors [Formula: see text] and [Formula: see text], which represent path-difficulty and path-length, respectively, based on actual traffic networks. Picking an arbitrary node from the hub nodes set as the trap node, and the double-weighted polygon networks are divided into [Formula: see text] blocks by combining with the iterative method. According to biased random walks, the calculation expression of average receiving time (ART) of any polygon networks is given by using the intermediate quantity the mean first-passage time (MFPT), which is applicable to any [Formula: see text] ([Formula: see text]) polygon networks. What is more, we display the specific calculation process and results of ART of the double-weighted quadrilateral networks, indicating that ART grows exponentially with respect to the networks order and the exponent is [Formula: see text] which grows with the product of [Formula: see text]. When [Formula: see text] increases, ART increases linearly ([Formula: see text]) or sublinearly ([Formula: see text]) with the size of networks, and the smaller value of [Formula: see text], the higher transportation efficiency.

Calculations of first passage time of delayed tree-like networks

2015 ◽  
Vol 29 (28) ◽  
pp. 1550200
Author(s):  
Shuai Wang ◽  
Weigang Sun ◽  
Song Zheng
Keyword(s):  
Random Walks ◽  
First Passage Time ◽  
Passage Time ◽  
The Novel ◽  
Mean First Passage Time ◽  
First Passage ◽  
Initial Node ◽  
Network Parameters ◽  
Self Similar ◽  
The Mean

In this paper, we study random walks in a family of delayed tree-like networks controlled by two network parameters, where an immobile trap is located at the initial node. The novel feature of this family of networks is that the existing nodes have a time delay to give birth to new nodes. By the self-similar network structure, we obtain exact solutions of three types of first passage time (FPT) measuring the efficiency of random walks, which includes the mean receiving time (MRT), mean sending time (MST) and mean first passage time (MFPT). The obtained results show that the MRT, MST and MFPT increase with the network parameters. We further show that the values of MRT, MST and MFPT are much shorter than the nondelayed counterpart, implying that the efficiency of random walks in delayed trees is much higher.

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