John A. Board

Conference Proceedings - Annual Reliability and Maintainability Symposium · March 29, 2017 Software vulnerability analysis plays a critical role in the prevention and mitigation of software security attacks, and vulnerability classification constitutes a key part of this analysis. This paper proposes a new approach for software vulnerability cla ... Full text Cite

Integrated sensing and information processing theme-based redesign of the undergraduate electrical and computer engineering curriculum at Duke University

Journal Article Advances in Engineering Education · 2010 The field of electrical and computer engineering has evolved significantly in the past two decades. This evolution has broadened the field of ECE, and subfields have seen deep penetration into very specialized areas. Remarkable devices and systems arising ... Cite

Integrating sensing and information processing in an electrical and computer engineering undergraduate curriculum

Conference Proceedings - Frontiers in Education Conference, FIE · December 1, 2009 The Department of Electrical and Computer Engineering Duke University has completed a full-scale redesign of its undergraduate program based on the theme of Integrated Sensing and Information Processing. This theme provides a coherent, overarching framewor ... Full text Cite

Redesign of the core curriculum at Duke University

Conference ASEE Annual Conference and Exposition, Conference Proceedings · December 1, 2006 Cite

Redesign of the core curriculum at Duke University

Conference ASEE Annual Conference and Exposition, Conference Proceedings · January 1, 2006 Cite

Efficient charge assignment and back interpolation in multigrid methods for molecular dynamics.

Journal Article Journal of computational chemistry · July 2005 The assignment of atomic charges to a regular computational grid and the interpolation of forces from the grid back to the original atomic positions are crucial steps in a multigrid approach to the calculation of molecular forces. For purposes of grid assi ... Full text Cite

Theme-based redesign of the duke university ECE curriculum: The first steps

Conference ASEE Annual Conference and Exposition, Conference Proceedings · 2005 Undergraduates in Electrical and Computer Engineering (ECE) at Duke University have benefited from the combination of curricular flexibility and rigorous coursework. The current curriculum is further limited in that the core courses do not offer a vertical ... Cite

Large-scale modeling of cardiac electrophysiology

Journal Article Computers in Cardiology · December 1, 2002 Simulation of wavefront propagation in the whole heart requires significant computational resources. The growth of cluster computing has made it possible to simulate very large scale problems in a lab environment. In this work, we present computational res ... Cite

An electromagnetic simulation environment

Journal Article Proceedings of SPIE-The International Society for Optical Engineering · January 1, 2001 We present a general purpose simulator that includes electromagnetic scattering tools for buried targets and standard signal processing functionality. Additional modules for genetic or gradient optimization, parallel processing, and multi-aspect target det ... Full text Cite

Automated membrane model creation

Journal Article Computers in Cardiology · December 1, 2000 We present an extension to CardioWave, our modular simulation system for the Bidomain Equations, which allows new membrane modules to be added by parsing a simple text file of equations, eliminating the need for the user to write source code. CardioWave ca ... Cite

Efficient particle-mesh Ewald based approach to fixed and induced dipolar interactions

Journal Article Journal of Chemical Physics · December 1, 2000 A particle-mesh based method for performing the Ewald summation of large systems of point charges and fixed or induced point dipoles was introduced. The method took advantage of the smooth differentiability of B-splines to perform gradients in real space d ... Full text Cite

Modular simulation of cardiac dynamics on distributed memory parallel computers

Journal Article Annals of Biomedical Engineering · December 1, 2000 A modular system for simulating wavefront conduction in the heart on parallel computers has beeb developed. With this system, the user selects the set of modules that most closely represents the simulation of interest and the simulator executable is built ... Cite

Computer simulations of cardiac electrophysiology

Journal Article SC'00 Proceedings of the 2000 ACM/IEEE conference on Supercomputing · November 1, 2000 CardioWave is a modular system for simulating wavefront conduction in the heart. These simulations may be used to investigate the factors that generate and sustain life-threatening arrhythmias such as ventricular fibrillation. The user selects a set of mod ... Link to item Cite

Modular simulation of cardiac dynamics on distributed memory parallel computers

Journal Article Annals of Biomedical Engineering · 2000 A modular system for simulating wavefront conduction in the heart on parallel computers has beeb developed. With this system, the user selects the set of modules that most closely represents the simulation of interest and the simulator executable is built ... Cite

The fast multipole algorithm

Journal Article Computing in Science and Engineering · January 1, 2000 Accurate computation of the mutual interactions of N particles through electrostatic or gravitational forces has impeded progress in many areas of simulation science. The fast multipole algorithm provides an efficient scheme for reducing computational comp ... Full text Cite

The development and integration of a distributed 3D FFT for a cluster of workstations

Conference Proceedings of 4th Annual Linux Showcase and Conference 2000, ALS 2000 · January 1, 2000 In this paper, the authors discuss the steps taken in the formulation of a parallel 3D FFT with good scalability on a cluster of fast workstations connected via commo dity 100 Mb/s ethernet. The motivation for this work is to improve the p erformance and s ... Cite

Algorithmic Challenges in Computational Molecular Biophysics

Journal Article Journal of Computational Physics · May 1, 1999 A perspective of biomolecular simulations today is given, with illustrative applications and an emphasis on algorithmic challenges, as reflected by the work of a multidisciplinary team of investigators from five institutions. Included are overviews and rec ... Full text Cite

Algorithmic challenges in computational molecular biophysics

Journal Article J. Comput. Phys. (USA) · 1999 A perspective of biomolecular simulations today is given, with illustrative applications and an emphasis on algorithmic challenges, as reflected by the work of a multidisciplinary team of investigators from five institutions. Included are overviews and rec ... Full text Link to item Cite

The implicit pipeline method

Journal Article Proceedings of the 1st Merged International Parallel Processing Symposium and Symposium on Parallel and Distributed Processing, IPPS/SPDP 1998 · January 1, 1998 We present a novel scheme for the solution of linear differential equation systems on parallel computers. The Implicit Pipeline (ImP) method uses an implicit time-integration scheme coupled with an iterative linear solver to solve the resulting differentia ... Full text Cite

Introduction to “A Fast Algorithm for Particle Simulations”

Journal Article Journal of Computational Physics · August 1997 Full text Cite

Ewald summation techniques in perspective: A survey

Journal Article Computer Physics Communications · January 1, 1996 The simulation of large macromolecular systems has been and remains a challenging problem. There is a general presumption that simulations carried in periodic boundary conditions (PBC) are often the most appropriate to suppress boundary effects. To this en ... Full text Cite

A multipole-based algorithm for efficient calculation of forces and potentials in macroscopic periodic assemblies of particles

Journal Article Journal of Computational Physics · January 1, 1996 A new and efficient algorithm based on multipole techniques is presented which calculates the electrostatic forces and potentials in macroscopic periodic assemblies of particles. The fast multipole algorithm (FMA) can be used to compute forces with in the ... Full text Cite

Fast fourier transform accelerated fast multipole algorithm

Journal Article SIAM Journal on Scientific Computing · January 1, 1996 This paper describes an O(p2 log2(p)N) implementation of the fast multipole algorithm (FMA) for N-body simulations. This method of computing the FMA is faster than the original, which is O(p4N), where p is the number of terms retained in the truncated mult ... Full text Cite

The geometric solution of Laplace's equation

Journal Article Journal of Computational Physics · January 1, 1996 A new numerical method for the rapid solution of Laplace's equation in exterior domains and in interior domains with complicated boundaries is presented. The method is based on a formula first stated by J. J. Thomson and later refined by the authors. The m ... Full text Cite

Portable distributed implementation of the parallel multipole tree algorithm

Journal Article IEEE International Symposium on High Performance Distributed Computing, Proceedings · December 1, 1995 Several variants of parallel multipole-based algorithms have been implemented to further research in fields such as computational chemistry and astrophysics. We present a distributed parallel implementation of a multipole-based algorithm that is portable t ... Cite

Pollution control caching

Journal Article Proceedings - IEEE International Conference on Computer Design: VLSI in Computers and Processors · December 1, 1995 Two novel cache architectures called Pollution Control Caching (PCC) and PCC plus Victim Buffering are presented. Trace driven simulation is used to obtain miss ratio statistics, and analytical models of the expected clock cycles per instruction (E[CPI]) a ... Cite

Scalable implementations of multipole-accelerated algorithms for molecular dynamics

Journal Article Proceedings of the Scalable High-Performance Computing Conference · December 1, 1994 We consider efficient, scalable solutions to the long-range force computation problem in molecular dynamics (MD) simulation. Straightforward implementation of a solver for the time-consuming Coulomb force yields O(N2) runtime for N atoms in a system; this ... Cite

Modeling Biomolecules: Larger Scales, Longer Durations

Journal Article IEEE Computational Science and Engineering · January 1, 1994 Full text Cite

Generalized formula for the first derivative of the electric-field intensity.

Journal Article Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics · May 1993 Full text Cite

Accelerated molecular dynamics simulation with the parallel fast multipole algorithm

Journal Article Chemical Physics Letters · October 2, 1992 We have implemented the fast multipole algorithm (FMA) of Greengard and Rokhlin and incorporated it into the molecular dynamics program MD of Windemuth and Schulten, allowing rapid computation of the non-bonded forces acting in dynamical protein systems wi ... Full text Cite

Mapping the adaptive fast multipole algorithm onto MIMD systems

Journal Article Unstructured Scientific Computation on Scalable Multiprocessors · 1992 The adaptive fast multipole algorithm (AFMA) is an algorithm developed by Greengard and Rohklin (Yale Univ., Dept. of Comp. Sci., Res. rep., RR 602, 1988) for evaluating potential fields in nonuniformly distributed particle systems (N-body problems). The A ... Cite

Grand challenges in biomedical computing.

Journal Article Critical reviews in biomedical engineering · January 1992 Advances in computing technology (both algorithms and hardware) over the next several years promise to make increasingly sophisticated computer modeling of biomedical phenomena a routine part of biomedical research. Improvements in both the absolute speed ... Cite

Light scattering by alkali halide melts: A computer simulation study

Journal Article The Journal of Chemical Physics · January 1, 1991 A model for the interaction-induced polarizability of halide ions in condensed phases has been developed from ab initio electronic structure calculations. This model is incorporated into computer simulations of molten LiF, LiCl, and NaCl and used to calcul ... Full text Cite

High performance implementations of the fast multipole algorithm

Journal Article American Society of Mechanical Engineers, Heat Transfer Division, (Publication) HTD · December 1, 1990 Implementations of a fast algorithm for the solution of the N body problem on two parallel computers are described. The recent fast multipole algorithm of Greengard and Rokhlin which solves the N body problem in order N time is implemented on two commercia ... Cite

The fast multipole algorithm on Transputer networks

Journal Article Transputer Research and Applications 3. NATUG-3. Proceedings of the Third North American Transputer Users Group · 1990 The authors describe an implementation of a fast algorithm for the solution of the N body problem on a Transputer network of P processors with a run time complexity that approaches O(N/P). The recent serial fast multipole algorithm of Greengard and Rokhlin ... Cite

Performance of parallel neural network simulations

Journal Article Transputer Research and Applications 2. NATUG-2 Proceedings of the North American Transputer Users Group · 1990 A general constraint satisfaction neural network simulator is implemented on two different parallel machines, the BBN Butterfly and the INMOS Transputer. The general constraint satisfaction algorithm is partitioned similarly for both implementations. The s ... Cite

Shell model molecular dynamics calculations of the Raman spectra of molten NaI

Journal Article Journal of Physics: Condensed Matter · December 1, 1989 The shell model used in lattice dynamics is applied to construct an interionic potential for use in molecular dynamics (MD) simulations of molten NaI. The ion shell-core displacements generated by the shell model potentials are used as an approximation to ... Full text Cite

Algorithms and architecture constraints for a class of real-time image processing problems

Journal Article Proc. SPIE - Int. Soc. Opt. Eng. (USA) · 1989 Many important problems in real-time image processing involve both high computational requirements and a complex and substantial data flow. The system designer must weigh the difficulty of partitioning the problem to fit onto commercial hardware versus the ... Cite

Light scattering by liquid and solid sodium chloride. A simulation study

Journal Article Journal of the Chemical Society, Faraday Transactions 2: Molecular and Chemical Physics · December 1, 1987 The development of a computationally tractable model for the fluctuating polarization responsible for the light scattering by a condensed ionic system is described, and its application to NaCl in particular is considered. The model is then employed in mole ... Full text Cite

General discussion

Journal Article Journal of the Chemical Society, Faraday Transactions 2: Molecular and Chemical Physics · January 1, 1987 Full text Cite

INTERACTIVE SIMULATION FACILITY FOR THE EVALUATION OF SHARED-RESOURCE ARCHITECTURES (PARALLEL ARCHITECTURE SIMULATOR - PARSIM).

Journal Article Proceedings - Design Automation Conference · January 1, 1983 Full text Cite