Theory of Diffusion-Influenced Reaction Networks.
Theory of Diffusion-Influenced Reaction Networks.
复制标题
DOI：
10.1021/acs.jpcb.8b07250
复制
发表时间：
2018-12-13
期刊：
影响因子：
--
通讯作者：
Szabo A
中科院分区：
文献类型：
--
作者：
Gopich IV;Szabo A
A formalism is developed to describe how diffusion alters the kinetics of coupled reversible association-dissociation reactions in the presence of conformational changes that can modify the reactivity. The major difficulty in constructing a general theory is that, even to lowest order, diffusion can change the structure of the rate equations of chemical kinetics by introducing new reaction channels (i.e., modifies the kinetic scheme). Therefore, the right formalism must be found that allows the influence of diffusion to be described in a concise and elegant way for networks of arbitrary complexity. Our key result is a set of non-Markovian rate equations involving stoichiometric matrices and net reaction rates (fluxes), in which these rates are coupled by a time-dependent pair association flux matrix, whose elements have a simple physical interpretation. Specifically, each element is the probability density that an isolated pair of reactants irreversibly associates at time t via one reaction channel on condition that it started out with the dissociation products of another (or the same) channel. In the Markovian limit, the coupling of the chemical rates is described by committors (or splitting/capture probabilities). The committor is the probability that an isolated pair of reactants formed by dissociation at one site will irreversibly associate at another rather than diffuse apart. We illustrate the use of our formalism by considering three reversible reaction schemes: (1) binding to a single site, (2) binding to two inequivalent sites, and (3) binding to a site whose reactivity fluctuates. In the first example, we recover the results published earlier, while in the second one we show that a new reaction channel appears, which directly connects the two bound states. The third example is particularly interesting because all species become coupled and an exchange-type bimolecular reaction appears. In the Markovian limit, some of the diffusion-modified rate constants that describe new transitions become negative, indicating that memory effects cannot be ignored even in an approximate description.
登录
查看更多内容
DOI：
10.1021/jp508375q
发表时间：
2015-07-23
期刊：
The journal of physical chemistry. B
影响因子：
--
作者：
Hummer G;Szabo A
通讯作者：
Szabo A
影响因子：
2.3
作者：
BERG, OG
通讯作者：
BERG, OG
影响因子：
4.4
作者：
Berezhkovskii, Alexander;Szabo, Attila
通讯作者：
Szabo, Attila
影响因子：
4.4
作者：
Dagdug, Leonardo;Vazquez, Marco-Vinicio;Zitserman, Vladimir Yu.
通讯作者：
Zitserman, Vladimir Yu.
DOI：
10.1073/pnas.1319943110
发表时间：
2013-12-03
影响因子：
11.1
作者：
Gopich, Irina V.;Szabo, Attila
通讯作者：
Szabo, Attila