منابع مشابه
An explicit-solvent conformation search method using open software
Computer modeling is a popular tool to identify the most-probable conformers of a molecule. Although the solvent can have a large effect on the stability of a conformation, many popular conformational search methods are only capable of describing molecules in the gas phase or with an implicit solvent model. We have developed a work-flow for performing a conformation search on explicitly-solvate...
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We present a new hybrid explicit/implicit solvent method for dynamics simulations of macromolecular systems. The method models explicitly the hydration of the solute by either a layer or sphere of water molecules, and the generalized Born (GB) theory is used to treat the bulk continuum solvent outside the explicit simulation volume. To reduce the computational cost, we implemented a multigrid m...
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Software defined network is a new computer network architecture who separates controller and data layer in network devices such as switches and routers. By the emerge of software defined networks, a class of location problems, called controller placement problem, has attracted much more research attention. The task in the problem is to simultaneously find optimal number and location of controll...
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Purpose YADE–OPEN DEM is an open source software based on the Discrete Element Method which uses object oriented programming techniques. The paper describes the software architecture. Design/methodology/approach The DEM chosen uses position, orientation, velocity and angular velocity as independent variables of simulated particles which are subject to explicit leapfrog time–integration scheme (...
متن کاملConformation of a flexible chain in explicit solvent: exact solvation potentials for short Lennard-Jones chains.
The average conformation of a flexible chain molecule in solution is coupled to the local solvent structure. In a dense solvent, local chain structure often mirrors the pure solvent structure, whereas, in a dilute solvent, the chain can strongly perturb the solvent structure which, in turn, can lead to either chain expansion or compression. Here we use Monte Carlo (MC) simulation to study such ...
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ژورنال
عنوان ژورنال: PeerJ
سال: 2016
ISSN: 2167-8359
DOI: 10.7717/peerj.2088