scholarly journals Single Stranded dna Translocation Through a Fluctuating Nanopore

2003 ◽  
Vol 790 ◽  
Author(s):  
O. Flomenbom ◽  
J. Klafter
Keyword(s):  
First Passage Time ◽  
Passage Time ◽  
Dna Translocation ◽  
First Passage ◽  
Single Stranded Dna ◽  
System Parameters ◽  
The Mean ◽  
Probability Density Function Pdf ◽  
Passage Times

ABSTRACTWe investigate the translocation of a single stranded DNA (ssDNA) through a pore, which fluctuates between two conformations, by using coupled master equations (ME). The probability density function (PDF) of the first passage times (FPT) of the translocation process is calculated, displaying a triple, double or mono-peaked behavior, depending on the system parameters. An analytical expression for the mean first passage time (MFPT) of the translocation process is derived, and provides an extensive characterization of the translocation process.

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 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>

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>

First-passage behavior of under-damped asymmetric bistable system driven by Lévy noise

2020 ◽  
Vol 34 (31) ◽  
pp. 2050348
Author(s):  
Xiuxian Yu ◽  
Yongfeng Guo ◽  
Xiaojuan Lou ◽  
Qiang Dong
Keyword(s):  
First Passage Time ◽  
Passage Time ◽  
Bistable System ◽  
Lévy Noise ◽  
Mean First Passage Time ◽  
First Passage ◽  
System Parameters ◽  
Text Response ◽  
The Mean ◽  
Levy Noise

In this paper, the first-passage behavior of under-damped asymmetric bistable system driven by Lévy noise is studied. The two aspects considered are the mean first-passage time (MFPT) and the distribution of first-passage time in two opposite directions. To begin with, using the Janicki–Weron algorithm to generate Lévy noise, the system driven by Lévy noise is simulated through the fourth-order Runge–Kutta algorithm. Then the first-passage time of [Formula: see text] response tracks is calculated, and the MFPT and the distribution of first-passage time are obtained. Finally, the influence of Lévy noise and system parameters on MFPT and the distribution of first-passage time are analyzed. Moreover, the noise enhanced stability (NES) effect is found.

Spectral Theory for Skip-Free Markov Chains

1989 ◽  
Vol 3 (1) ◽  
pp. 77-88 ◽  
Author(s):  
Joseph Abate ◽  
Ward Whitt
Keyword(s):  
Markov Chains ◽  
Spectral Theory ◽  
First Passage Time ◽  
Passage Time ◽  
First Passage Times ◽  
Simple Relationship ◽  
First Passage ◽  
Birth And Death Processes ◽  
The Laplace Transform ◽  
Passage Times

The distribution of upward first passage times in skip-free Markov chains can be expressed solely in terms of the eigenvalues in the spectral representation, without performing a separate calculation to determine the eigenvectors. We provide insight into this result and skip-free Markov chains more generally by showing that part of the spectral theory developed for birth-and-death processes extends to skip-free chains. We show that the eigenvalues and eigenvectors of skip-free chains can be characterized in terms of recursively defined polynomials. Moreover, the Laplace transform of the upward first passage time from 0 to n is the reciprocal of the nth polynomial. This simple relationship holds because the Laplace transforms of the first passage times satisfy the same recursion as the polynomials except for a normalization.

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.

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.

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