In this chapter, we present several GPU algorithms for evaluating molecular orbitals on three-dimensional lattices, as is commonly used for molecular visualization. For each kernel, we describe necessary design trade-offs, applicability to various problem sizes, and performance on different generations of GPU hardware. Further, we demonstrate the appropriate and effective use of fast on-chip GP...

Increasingly, computational approaches are having a central role across many areas of research tackling the challenges of understanding the complexity of biological systems. A resource such as BLAST (Basic Local Alignment Search Tool) (1), which was published in this journal in 1990, has transformed sequence searching because of its speed and power in detect distant but biologically significant...

UNLABELLED fconv is a program intended for parsing and manipulating multiple aspects and properties of molecular data. Up to now, it has been developed and extensively tested for 3 years. It has become a very robust and comprehensive tool involved in a broad range of computational workflows that are currently applied in our drug design environment. Typical tasks are as follows: conversion and e...

An algorithm for rapid computation of Richards's smooth molecular surface is described. The entire surface is computed analytically, triangulated, and displayed at interactive rates. The faster speeds for our program have been achieved by algorithmic improvements, parallelizing the computations, and by taking advantage of the special geometrical properties of such surfaces. Our algorithm is eas...

We describe an adaptive method for achieving load balance in parallel computations simulating phenomena which are distributed over a spatially extended region, but are local in nature. We have tested the method on standard short-ranged parallel molecular dynamics calculations. The performance gain we observe confirms the value of the method for this type of calculation. We discuss possible gene...

Biomolecular Computation (BMC) is computation done at the molecular scale, using biotechnology techniques. This paper discusses the underlying biotechnology that BMC may utilize, and surveys a number of distinct paradigms for doing BMC. We also identify a number of key future experimental milestones for the eld of BMC.

The pioneering work of Adleman (1994) demonstrated that DNA molecules in test tubes can be manipulated to perform a certain type of mathematical computation. This has stimulated a theoretical interest in the possibility of constructing DNA-based molecular computers. To gauge the practicality of realizing such microscopic computers, it was thought necessary to learn as much as possible from the ...

Biochemists often wish to compute surface areas of proteins. A variety of algorithms have been developed for this task, but they are designed for traditional single-processor architectures. The current trend in computer hardware is towards increasingly parallel architectures for which these algorithms are not well suited. We describe a parallel, stochastic algorithm for molecular surface area c...

We present a multiscale model for numerical simulation of dynamics of crystalline solids. The method couples nonlinear elastodynamics as the continuum description and molecular dynamics as another component at the atomic scale. The governing equations on the macroscale are solved by the discontinuous Galerkin method, which is built up with an appropriate local curl-free space to produce a coher...