"Dividing and Conquering" and "Caching" in Molecular Modeling

A peer-reviewed article of this Preprint also exists.

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To divide and conquer, and to cache intermediate results have been long standing principles in development of algorithms. Not surprisingly, most important methodological advancements in more than half century of molecular modeling are various implementations of these two fundamental principles. In the mainstream classical computational molecular science, tremendous efforts have been invested on two lines of algorithm development. The first is coarse graining, which is to represent multiple basic particles in higher resolution modeling as a single larger and softer particle in lower resolution counterpart, with resulting force fields of partial transferability at the expense of some information loss. The second is enhanced sampling, which realizes \u201cdividing and conquering\u201d and\/or \u201ccaching\u201d in configurational space with focus either on reaction coordinates and collective variables as in metadynamics and related algorithms, or on the transition matrix and state discretization as in Markov state models. For this line of algorithms, spatial resolution is maintained but results are not transferable. Deep learning has been utilized to realize more efficient and accurate ways of \u201cdividing and conquering\u201d and \u201ccaching\u201d along these two lines of algorithmic research. We proposed and demonstrated the local free energy landscape approach, a new framework for classical computational molecular science. This framework is based on a third class of algorithm that facilitates molecular modeling through partially transferable in resolution \u201ccaching\u201d of distributions for local clusters of molecular degrees of freedom. Differences, connections and potential interactions among these three algorithmic directions are discussed, with the hope to stimulate development of more elegant, efficient and reliable formulations and algorithms for \u201cdividing and conquering\u201d and \u201ccaching\u201d in complex molecular systems.<\/jats:p>","DOI":"10.3390\/ijms22095053","type":"journal-article","created":{"date-parts":[[2021,5,11]],"date-time":"2021-05-11T06:14:05Z","timestamp":1620713645000},"page":"5053","source":"Crossref","is-referenced-by-count":3,"title":["\u201cDividing and Conquering\u201d and \u201cCaching\u201d in Molecular 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Impressive progress has been made in development of theories, algorithms and software packages. To divide and conquer, and to cache intermediate results have been long standing principles in development of algorithms. Not surprisingly, most important methodological advancements in more than half century of molecular modeling are various implementations of these two fundamental principles. In the mainstream classical computational molecular science, tremendous efforts have been invested on two lines of algorithm development. The first is coarse graining, which is to represent multiple basic particles in higher resolution modeling as a single larger and softer particle in lower resolution counterpart, with resulting force fields of partial transferability at the expense of some information loss. The second is enhanced sampling, which realizes \u201cdividing and conquering\u201d and\/or \u201ccaching\u201d in configurational space with focus either on reaction coordinates and collective variables as in metadynamics and related algorithms, or on the transition matrix and state discretization as in Markov state models. For this line of algorithms, spatial resolution is maintained but results are not transferable. Deep learning has been utilized to realize more efficient and accurate ways of \u201cdividing and conquering\u201d and \u201ccaching\u201d along these two lines of algorithmic research. We proposed and demonstrated the local free energy landscape approach, a new framework for classical computational molecular science. This framework is based on a third class of algorithm that facilitates molecular modeling through partially transferable in resolution \u201ccaching\u201d of distributions for local clusters of molecular degrees of freedom. Differences, connections and potential interactions among these three algorithmic directions are discussed, with the hope to stimulate development of more elegant, efficient and reliable formulations and algorithms for \u201cdividing and conquering\u201d and \u201ccaching\u201d in complex molecular systems.","DOI":"10.3390\/ijms22095053","type":"journal-article","created":{"date-parts":[[2021,5,11]],"date-time":"2021-05-11T06:14:05Z","timestamp":1620713645000},"page":"5053","source":"Crossref","is-referenced-by-count":3,"title":["\u201cDividing and Conquering\u201d and \u201cCaching\u201d in Molecular 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DOI: 10.3390/ijms22095053