Minimizing memory as an objective for coarse-graining
Minimizing memory as an objective for coarse-graining
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DOI：
10.1063/1.4793313
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发表时间：
2013-03-07
影响因子：
4.4
通讯作者：
Dinner, Aaron R.
中科院分区：
文献类型：
--
作者：
Guttenberg, Nicholas;Dama, James F.;Dinner, Aaron R.
粗粒化分子模型是在自由度上积分以获得简化表示的过程。这个过程通常涉及两个独立但相关的步骤，选择组成简化系统的坐标并对它们的相互作用进行建模。坐标选择和建模过程都提出了挑战。在这里，我们专注于前者。通常，人们寻求在快自由度上积分并保留慢自由度。未能分离时间刻度会导致内存。有了这个动机，我们引入了一个启发式的内存措施，并表明它可以用来比较竞争的坐标选择一个给定的建模过程。我们数值探索的效用，这种启发式的三个系统的复杂性不断增加。第一个例子是一个四粒子线性模型，它是精确可解的。第二个例子是一个16粒子非线性模型;这个系统具有分子力场的特征相互作用，但仍然足够简单，允许详尽的数值处理。第三个例子是蛋白质的原子分辨率表示，这类模型最常被相关的粗粒度方法处理;我们专门研究肌动蛋白单体。在所有三种情况下，我们发现，启发式建议坐标选择，是物理直观，反映分子结构。因此，记忆启发式可以作为专家知识的客观编码，并指导模型中需要进一步关注的站点。(C)2013年美国物理学会。[http：//dx.doi.org/10.1063/1.4793313]
Coarse-graining a molecular model is the process of integrating over degrees of freedom to obtain a reduced representation. This process typically involves two separate but related steps, selection of the coordinates comprising the reduced system and modeling their interactions. Both the coordinate selection and the modeling procedure present challenges. Here, we focus on the former. Typically, one seeks to integrate over the fast degrees of freedom and retain the slow degrees of freedom. Failure to separate timescales results in memory. With this motivation, we introduce a heuristic measure of memory and show that it can be used to compare competing coordinate selections for a given modeling procedure. We numerically explore the utility of this heuristic for three systems of increasing complexity. The first example is a four-particle linear model, which is exactly solvable. The second example is a sixteen-particle nonlinear model; this system has interactions that are characteristic of molecular force fields but is still sufficiently simple to permit exhaustive numerical treatment. The third example is an atomic-resolution representation of a protein, the class of models most often treated by relevant coarse-graining approaches; we specifically study an actin monomer. In all three cases, we find that the heuristic suggests coordinate selections that are physically intuitive and reflect molecular structure. The memory heuristic can thus serve as an objective codification of expert knowledge and a guide to sites within a model that requires further attention. (C) 2013 American Institute of Physics. [http://dx.doi.org/10.1063/1.4793313]