https://www.sandia.gov/~sjplimp/papers/jcompphys95.pdf

Fast parallel algorithms for short-range molecular dynamics

Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

6.2.2. Definition of Effective Properties 3064 6.3. Response Properties to Magnetic Fields 3066 6.3.1. Nuclear Shielding 3066 6.3.2. Indirect Spin−Spin Coupling 3067 6.3.3. EPR Parameters 3068 6.4. Properties of Chiral Systems 3069 6.4.1. Electronic Circular Dichroism (ECD) 3069 6.4.2. Optical Rotation (OR) 3069 6.4.3. VCD and VROA 3070 7. Continuum and Discrete Models 3071 7.1. Continuum Methods within MD and MC Simulations 3072

/pdf/quantum-mechanical-continuum-solvation-models-3edv963g14.pdf

Quantum mechanical continuum solvation models.

Evaluation of the electrostatic properties of biomolecules has become a standard practice in molecular biophysics. Foremost among the models used to elucidate the electrostatic potential is the Poisson-Boltzmann equation; however, existing methods for solving this equation have limited the scope of accurate electrostatic calculations to relatively small biomolecular systems. Here we present the application of numerical methods to enable the trivially parallel solution of the Poisson-Boltzmann equation for supramolecular structures that are orders of magnitude larger in size. As a demonstration of this methodology, electrostatic potentials have been calculated for large microtubule and ribosome structures. The results point to the likely role of electrostatics in a variety of activities of these structures.

/pdf/electrostatics-of-nanosystems-application-to-microtubules-j1w88z2zlk.pdf

Electrostatics of nanosystems: Application to microtubules and the ribosome

BIOE 402. Medical Technology Assessment. 2 or 3 hours. Bioentrepreneur course. Assessment of medical technology in the context of commercialization. Objectives, competition, market share, funding, pricing, manufacturing, growth, and intellectual property; many issues unique to biomedical products. Course Information: 2 undergraduate hours. 3 graduate hours. Prerequisite(s): Junior standing or above and consent of the instructor.

“Bioinformatics” 특집을 내면서

Preface(2nd ed.).- Preface(1st ed.).- Basic Concepts.- Sobolev Spaces.- Variational Formulation of Elliptic Boundary Value Problems.- The Construction of a Finite Element of Space.- Polynomial Approximation Theory in Sobolev Spaces.- n-Dimensional Variational Problems.- Finite Element Multigrid Methods.- Additive Schwarz Preconditioners.- Max-norm Estimates.- Adaptive Meshes.- Variational Crimes.- Applications to Planar Elasticity.- Mixed Methods.- Iterative Techniques for Mixed Methods.- Applications of Operator-Interpolation Theory.- References.- Index.

The Mathematical Theory of Finite Element Methods

In this paper, we propose a modified Lagrange type interpolation operator to approximate functions in Sobolev spaces by continuous piecewise polynomials. In order to define interpolators for "rough" functions and to preserve piecewise polynomial boundary conditions, the approximated functions are averaged appropriately either on dor (d 1)-simplices to generate nodal values for the interpolation operator. This combination of averaging and interpolation is shown to be a projection, and optimal error estimates are proved for the projection error.

/pdf/finite-element-interpolation-of-nonsmooth-functions-3qh4jiqsfn.pdf

Finite element interpolation of nonsmooth functions satisfying boundary conditions

Electrostatics and diffusion of molecules in solution: simulations with the University of Houston Brownian dynamics program

It is shown that the Ritz projection onto spaces of piecewise linear finite elements is bounded in the Sobolev space, Wl, for 2 - p < oc. This implies that for functions in wf n W2 the error in approximation behaves like 0(h) in Wp, for 2 ? p < oo, and like 0(h2) in Lp, for 2 - p < oo. In all these cases the additional logarithmic factor previously included in error estimates for linear finite elements does not occur.

/pdf/some-optimal-error-estimates-for-piecewise-linear-finite-31vx1tc03s.pdf

L. Ridgway Scott

Papers

The Mathematical Theory of Finite Element Methods

Finite element interpolation of nonsmooth functions satisfying boundary conditions

Electrostatics and diffusion of molecules in solution: simulations with the University of Houston Brownian dynamics program

Some Optimal Error Estimates for Piecewise Linear Finite Element Approximations

The Finite Element Method for Elliptic Problems.