Sauerwine Ben, Widom Michael
Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA.
Phys Rev E Stat Nonlin Soft Matter Phys. 2011 Dec;84(6 Pt 1):061912. doi: 10.1103/PhysRevE.84.061912. Epub 2011 Dec 19.
Kinetic Monte Carlo on coarse-grained systems, such as nucleic acid secondary structure, is advantageous for being able to access behavior at long time scales, even minutes or hours. Transition rates between coarse-grained states depend upon intermediate barriers, which are not directly simulated. We propose an Arrhenius rate model and an intermediate energy model that incorporates the effects of the barrier between simulated states without enlarging the state space itself. Applying our Arrhenius rate model to DNA hairpin folding, we demonstrate improved agreement with experiment compared to the usual kinetic Monte Carlo model. Further improvement results from including rigidity of single-stranded stacking.
对粗粒度系统（如核酸二级结构）进行动力学蒙特卡罗模拟，其优势在于能够研究长时间尺度（甚至数分钟或数小时）下的行为。粗粒度状态之间的转变速率取决于中间势垒，而这些势垒并非直接模拟得到。我们提出了一个阿仑尼乌斯速率模型和一个中间能量模型，该模型在不扩大状态空间本身的情况下纳入了模拟状态之间势垒的影响。将我们的阿仑尼乌斯速率模型应用于DNA发夹折叠，结果表明与通常的动力学蒙特卡罗模型相比，与实验的吻合度有所提高。进一步的改进来自于纳入单链堆积的刚性。
