论文标题
扩散限制反应速率及其后果的浓度依赖性
Concentration dependence of diffusion-limited reaction rates and its consequences
论文作者
论文摘要
扩散受限的关联反应本质上是普遍存在的。它们对于生物反应尤为重要，在生物反应中，反应速率通常取决于分子在二维表面（例如细胞膜）上的扩散转运。在二维表面上扩散的特征性可能导致非平凡的反应动力学，例如两个分子之间的浓度依赖性相关率。但是，传统上，生物分子缔合反应的动力学是使用质量作用定律建模的，该定律假定反应速率是独立的浓度常数。在本文中，使用多尺度分子模拟，我们研究了扩散限制的缔合反应在2D表面上的浓度依赖性。特别是，我们量化了短额对相互作用对反应速率浓度依赖性的影响，并在经验定律中编纂。在化学动力学模型中使用该定律，我们发现简单化学系统的稳态行为通过浓度依赖性速率的存在进行了巨大修饰。特别是，我们发现它会导致二聚反应中固有噪声的抑制，并破坏Lotka-Volterra Predator-Prey系统中稳健的振荡。实际上，我们看到后者从健壮到微调行为的过渡。此外，我们表明，由于固有的噪声，在随机捕食者系统中自然出现了浓度依赖性反应速率。我们评论这些结果的后果，并讨论它们在复杂化学和生物系统的建模中的影响。特别是，我们评论了大众行动定律的有效性范围，这是这些系统的所有理论建模中的主食。
Diffusion-limited association reactions are ubiquitous in nature. They are particularly important for biological reactions, where the reaction rates are often determined by the diffusive transport of the molecules on two-dimensional surfaces, such as the cell membrane. The peculiarities of diffusion on two-dimensional surfaces may lead to nontrivial reaction kinetics, such as concentration dependent rate of association between two molecules. However, traditionally, the kinetics of biomolecular association reactions has been modeled using the law of mass action, which assumes that the rate of reaction is a concentration independent constant. In this paper, using multiscale molecular simulation, we investigate the concentration dependence of diffusion-limited association reactions on 2D surfaces. In particular, we quantify the influence of short-ranged pair interactions on the concentration dependence of the reaction rates and codify it in an empirical law. Using this law in a chemical kinetic model, we find that the the steady state behaviors of simple chemical systems are drastically modified by the presence of concentration dependent rates. In particular, we find that it leads to suppression of intrinsic noise in dimerization reaction and destabilizes robust oscillation in Lotka-Volterra predator-prey systems. In fact, we see a transition from robust to fine-tuned behavior in the latter. In addition, we show that concentration dependent reaction rates arise naturally in stochastic predator-prey systems due to intrinsic noise. We comment on the consequences of these results and discuss their implications in the modeling of complex chemical and biological systems. In particular, we comment on the range of validity of the law of mass action, which is a staple in all theoretical modeling of these systems.
