There is, I think, something ethereal about i —the square root of minus one. I remember first hearing about it at school. It seemed an odd beast at that time—an intruder hovering on the edge of reality.

Usually familiarity dulls this sense of the bizarre, but in the case of i it was the reverse: over the years the sense of its surreal nature intensified. It seemed that it was impossible to write mathematics that described the real world in …

I and i

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.

An N⋅log(N) method for evaluating electrostatic energies and forces of large periodic systems is presented. The method is based on interpolation of the reciprocal space Ewald sums and evaluation of the resulting convolutions using fast Fourier transforms. Timings and accuracies are presented for three large crystalline ionic systems.

Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems

The previously developed particle mesh Ewald method is reformulated in terms of efficient B‐spline interpolation of the structure factors This reformulation allows a natural extension of the method to potentials of the form 1/rp with p≥1 Furthermore, efficient calculation of the virial tensor follows Use of B‐splines in place of Lagrange interpolation leads to analytic gradients as well as a significant improvement in the accuracy We demonstrate that arbitrary accuracy can be achieved, independent of system size N, at a cost that scales as N log(N) For biomolecular systems with many thousands of atoms this method permits the use of Ewald summation at a computational cost comparable to that of a simple truncation method of 10 A or less

A smooth particle mesh Ewald method

A mathematical tool for exploring the dynamics of biological networks (Proceedings of the National Academy of Sciences of the United States of America (2007) 104, 49, (19169-19174) DOI: 10.1073/pnas.0709955104)

In this paper, we consider acoustic or electromagnetic scattering in two dimensions from an infinite three-layer medium with thousands of wavelength-size dielectric particles embedded in the middle layer. Such geometries are typical of microstructured composite materials, and the evaluation of the scattered field requires a suitable fast solver for either a single configuration or for a sequence of configurations as part of a design or optimization process. We have developed an algorithm for problems of this type by combining the Sommerfeld integral representation, high order integral equation discretization, the fast multipole method and classical multiple scattering theory. The efficiency of the solver is illustrated with several numerical experiments.

A fast solver for multi-particle scattering in a layered medium

We introduce a numerical method for the solution of the time-dependent Schrodinger equation with a smooth potential, based on its reformulation as a Volterra integral equation. We present versions of the method both for periodic boundary conditions, and for free space problems with compactly supported initial data and potential. A spatially uniform electric field may be included, making the solver applicable to simulations of light-matter interaction. 
The primary computational challenge in using the Volterra formulation is the application of a space-time history dependent integral operator. This may be accomplished by projecting the solution onto a set of Fourier modes, and updating their coefficients from one time step to the next by a simple recurrence. In the periodic case, the modes are those of the usual Fourier series, and the fast Fourier transform (FFT) is used to alternate between physical and frequency domain grids. In the free space case, the oscillatory behavior of the spectral Green's function leads us to use a set of complex-frequency Fourier modes obtained by discretizing a contour deformation of the inverse Fourier transform, and we develop a corresponding fast transform based on the FFT. 
Our approach is related to pseudo-spectral methods, but applied to an integral rather than the usual differential formulation. This has several advantages: it avoids the need for artificial boundary conditions, admits simple, inexpensive high-order implicit time marching schemes, and naturally includes time-dependent potentials. We present examples in one and two dimensions showing spectral accuracy in space and eighth-order accuracy in time for both periodic and free space problems.

A high-order integral equation-based solver for the time-dependent Schrodinger equation

In this paper, we present a fast multipole method (FMM) for the half-space Green's function in a homogeneous elastic half-space subject to zero normal stress, for which an explicit solution was given by Mindlin (Physics 7, 195---202 1936). The image structure of this Green's function is unbounded, so that standard outgoing representations are not easily available. We introduce two such representations here, one involving an expansion in plane waves and one involving a modified multipole expansion. Both play a role in the FMM implementation.

A fast multipole method for the evaluation of elastostatic fields in a half-space with zero normal stress

Systems, methods and computer-accessible mediums for determining a specific absorption rate (SAR) of a radio frequency (RF) radiation on an object(s) can be provided, which can, for example hardware arrangement configured to receive thermal information for a portion(s) of the at least one object, and determine the SAR based on the thermal information.

System, method and computer-accessible medium for determining specific absorption rate obtained based on magnetic resonance imaging and temperature property measurements

Leslie Greengard

Papers

A mathematical tool for exploring the dynamics of biological networks (Proceedings of the National Academy of Sciences of the United States of America (2007) 104, 49, (19169-19174) DOI: 10.1073/pnas.0709955104)

A fast solver for multi-particle scattering in a layered medium

A high-order integral equation-based solver for the time-dependent Schrodinger equation

A fast multipole method for the evaluation of elastostatic fields in a half-space with zero normal stress

System, method and computer-accessible medium for determining specific absorption rate obtained based on magnetic resonance imaging and temperature property measurements