Multiple-scale stochastic processes: Decimation, averaging and beyond

被引:64
作者
Bo, Stefano [1 ,2 ]
Celani, Antonio [3 ]
机构
[1] KTH Royal Inst Technol, Nordita, Roslagstullsbacken 23, SE-10691 Stockholm, Sweden
[2] Stockholm Univ, Roslagstullsbacken 23, SE-10691 Stockholm, Sweden
[3] Abdus Salam Int Ctr Theoret Phys ICTP, Quantitat Life Sci, Str Costiera 11, I-34151 Trieste, Italy
来源
PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS | 2017年 / 670卷
关键词
Markov processes; Diffusive processes; Multiscale methods; Irreversibility; Stochastic functionals; CONFORMATIONAL SPREAD; FLUCTUATION; FITNESS; SELECTION; PROTEINS; SYSTEMS; IRREVERSIBILITY; THERMODYNAMICS; EXPRESSION; MECHANISM;
D O I
10.1016/j.physrep.2016.12.003
中图分类号
O4 [物理学];
学科分类号
0702 ;
摘要
The recent experimental progresses in handling microscopic systems have allowed to probe them at levels where fluctuations are prominent, calling for stochastic modeling in a large number of physical, chemical and biological phenomena. This has provided fruitful applications for established stochastic methods and motivated further developments. These systems often involve processes taking place on widely separated time scales. For an efficient modeling one usually focuses on the slower degrees of freedom and it is of great importance to accurately eliminate the fast variables in a controlled fashion, carefully accounting for their net effect on the slower dynamics. This procedure in general requires to perform two different operations: decimation and coarse-graining. We introduce the asymptotic methods that form the basis of this procedure and discuss their application to a series of physical, biological and chemical examples. We then turn our attention to functionals of the stochastic trajectories such as residence times, counting statistics, fluxes, entropy production, etc. which have been increasingly studied in recent years. For such functionals, the elimination of the fast degrees of freedom can present additional difficulties and naive procedures can lead to blatantly inconsistent results. Homogenization techniques for functionals are less covered in the literature and we will pedagogically present them here, as natural extensions of the ones employed for the trajectories. We will also discuss recent applications of these techniques to the thermodynamics of small systems and their interpretation in terms of information-theoretic concepts. (C) 2016 Elsevier B.V. All rights reserved.
引用
收藏
页码:1 / 59
页数:59
相关论文
共 109 条
[1]   Fluctuation-Preserving Coarse Graining for Biochemical Systems [J].
Altaner, Bernhard ;
Vollmer, Juergen .
PHYSICAL REVIEW LETTERS, 2012, 108 (21)
[2]  
[Anonymous], 1985, Stochastic methods
[3]  
[Anonymous], ARXIV150206406V2
[4]  
[Anonymous], ARXIV11064146
[5]  
[Anonymous], PRINCIPLES POPULATIO
[6]  
[Anonymous], 2002, Mathematical biology, Interdisciplinary applied mathematics
[7]  
[Anonymous], ARXIV160604354
[8]  
[Anonymous], 1932, ROLES MUTATION INBRE
[9]   Conformational Spread as a Mechanism for Cooperativity in the Bacterial Flagellar Switch [J].
Bai, Fan ;
Branch, Richard W. ;
Nicolau, Dan V., Jr. ;
Pilizota, Teuta ;
Steel, Bradley C. ;
Maini, Philip K. ;
Berry, Richard M. .
SCIENCE, 2010, 327 (5966) :685-689
[10]   The rotary motor of bacterial flagella [J].
Berg, HC .
ANNUAL REVIEW OF BIOCHEMISTRY, 2003, 72 :19-54