Abstract: Computerized systems and methods are used to create a model of interaction energies between a group of bodies, such as molecules or atoms in solution. A computer simulation of the molecular interactions of bodies in solution is performed by first creating a coordinate system that defines a position of each body in a two dimensional or a three-dimensional space. The system then divides the coordinate system into subsections called bins. Bins may be of different sizes. The number and size of bins varies depending on the number of bodies and each body's calculated position in the coordinate system. The number of bins is optimized, selected so that a maximum number of bins contain only one body. This means there is also a corresponding minimum number of bins that contain either multiple bodies or no bodies. The systems and methods select a radius at which, at a certain distance from a selected molecule, the effect of other molecules on the selected molecule approximates zero.

Abstract: A method and system are disclosed for simulating the behavior of atomic and molecular scale systems. The method makes use of two (or more) embedded or mixed molecular systems, or collections of particles, that interact with each other through a mediated process, allowing the effects of the forces from one collection of particles to act on the particles in the other. The system includes a series of modules, two of which contain the simulation techniques to be used on the collections particles, one of which is to mediate between the collections, for example one module may be used to evaluate positional and/or energetic information, and one may be included to wrap around the entire molecular system to drive all of the events. The method generates representations of the molecular system that allow the user to gain an understanding of the system being simulated.

Abstract: Computerized systems and methods are used to create a model of interaction energies between a group of bodies, such as molecules or atoms in solution. A computer simulation of the molecular interactions of bodies in solution is performed by first creating a coordinate system that defines a position of each body in a two dimensional or a three-dimensional space. The system then divides the coordinate system into subsections called bins. Bins may be of different sizes. The number and size of bins varies depending on the number of bodies and each body's calculated position in the coordinate system. The number of bins is optimized, selected so that a maximum number of bins contain only one body. This means there is also a corresponding minimum number of bins that contain either multiple bodies or no bodies. The systems and methods select a radius at which, at a certain distance from a selected molecule, the effect of other molecules on the selected molecule approximates zero.