A parallel FDTD algorithm using the MPI library

Guiffaut, Christophe; Mahdjoubi, Kouroch

doi:10.1109/74.924608

Cited by 195 publications

(86 citation statements)

References 12 publications

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“…FDTD is now the start-of-the-art method for solving Maxwell's equations for complex geometries. [24][25][26][27][28][29][30][31][32][33][34][35][36][37] Being a direct time and space solution, FDTD offers the user a unique insight into all types of problems in photonics. Furthermore, FDTD can also be used to obtain the frequency solution by exploiting Fourier transforms, thus enabling a full range of useful quantities such as the complex Poynting vector and the transmission/reflection of light, in addition to fields around particles to be calculated.…”

Section: Finite-difference Time-domain Calculationsmentioning

confidence: 99%

Enhanced Förster Resonance Energy Transfer on Single Metal Particle. 2. Dependence on Donor−Acceptor Separation Distance, Particle Size, and Distance from Metal Surface

et al. 2007

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We studied the effect of metal particles on Förster resonance energy transfer (FRET) between nearby donor-acceptor pairs. The studies included the effect of donor-acceptor distance, silver particle size, and distance from the metal surface. The metal particles were synthesized with average diameters of 15, 40, and 80 nm, respectively. A Cy5-labeled oligonucleotide was chemically bound to a single silver particle with a distance of 2 or 10 nm from the surface of metal core. A Cy5.5-labeled complementary oligonucleotide was bound to the particle-conjugated oligonucleotide by hybridization. The spacer length between donor-acceptor was adjusted by the number of base pairs. FRET between the donor-acceptor pair was investigated by dual-channel single-molecule fluorescence detection. Both the emission intensities and lifetimes indicated that FRET was enhanced efficiently by the metal particles. The results showed an increase of apparent energy transfer distance with the size of silver particle and distance from the metal core. Simulations by finite-difference time-domain (FDTD) calculations were used to compare with the experimental results. The local fields at the location of the donor-acceptor pair appeared to correlate with the FRET efficiency. These results will aid in the design of metal particles for using FRET to determine biomolecule proximity at distances beyond the usual Förster distance.

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Section: Finite-difference Time-domain Calculationsmentioning

confidence: 99%

Enhanced Förster Resonance Energy Transfer on Single Metal Particle. 2. Dependence on Donor−Acceptor Separation Distance, Particle Size, and Distance from Metal Surface

et al. 2007

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“…[22][23][24][25][26][27][28][29][30][31][32][33][34] Since FDTD is a direct time and space solution, it offers the user a unique insight into all types of problems in electromagnetics and photonics. Furthermore, FDTD can also be used to obtain the frequency solution by exploiting Fourier transforms; thus, a full range of useful quantities in addition to fields around particles can be calculated, such as the complex Poynting vector and the transmission/reflection of light.…”

Section: Fdtd Calculationsmentioning

confidence: 99%

“…In the FDTD technique, Maxwell's curl equations are discretized by using finite-difference approximations in both time and space that are easy to program and are accurate. [22][23][24][25][26][27][28][29][30][31][32][33][34] To achieve high accuracy for realizing the spatial derivatives involved, the algorithm positions the components of the electric and magnetic field about a unit cell of the lattice that constitutes the FDTD computational domain. Each individual cube in the grid is called the Yee cell as it was first designed elegantly by Yee.…”

Section: Fdtd Calculationsmentioning

confidence: 99%

Single-Molecule Studies on Fluorescently Labeled Silver Particles: Effects of Particle Size

et al. 2007

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We studied the dependence of single-molecule fluorescence on the size of nearby metal particles. The silver particles were synthesized with average diameters of metal cores being 5, 20, 50, 70, and 100 nm, respectively. A single-stranded oligonucleotide was chemically bound to a single silver particle and a Cy5-labeled complementary single-stranded oligonucleotide was hybridized with the particle-bound oligonucleotide. The space between the fluorophore and metal core was separated by a rigid hybridized DNA duplex of 8 nm length. The single fluorescence images and intensity traces were recorded by scanning confocal microscopy. The single fluorophore-labeled 50 nm silver particles displayed the most enhanced intensity, a factor of 17-fold increase relative to the free fluorophores in the absence of metal. Numerical simulations by the finite-difference time-domain (FDTD) method and results from Mie theory were used to compare with the experimental results. The 50 nm silver particles were also labeled by multiple fluorophores. The fluorescence intensity of multiple fluorophore-labeled metal particles increases dramatically with the loading number and reached 400-fold relative to the free single fluorophore when the loading number of fluorophore per metal particle was 50. The fluorophore also displayed better photostability when binding on the metal particle. These results can aid us to develop novel nanoscale fluorophores for clinical diagnostics and bioassay.

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“…Mainly, we try to extend traditional parallelization techniques [4], [5], [6], to allow better results. It is paramount to redesign tiling [7] to take advantage of the memory behavior, since in the past, tiling techniques were heavily optimized to handle hardware-managed on-chip cache memories.…”

Section: Introductionmentioning

confidence: 99%

Mapping the FDTD Application to Many-Core Chip Architectures

Orozco

Gao

2009

2009 International Conference on Parallel Processing

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Abstract-This paper reports a study of mapping the Finite Difference Time Domain (FDTD) application to the IBM Cyclops-64 (C64) many-core chip architecture [1]. C64 is chosen for this study as it represents the current trend in computer architecture to develop a class of many-core architectures with distinct features e.g. software manageable on-chip memory hierarchy (vs. a hardware-managed data cache), high on-chip bandwidth, fine grain multithreading and synchronization, among others.Major results of our study include: 1. A good mapping of FDTD can effectively exploit the on-chip parallelism of C64-like architectures and show good performance and scalability.2. Such performance improvement is derived by employing a number of code optimization techniques such as time skewing and split tiling that judiciously exploit the architecture features described in (1).3. High performance requires maximum reuse of on-chip memory, which is obtained by tiling with non conventional tile shapes.4. Such code optimization techniques we used in (2) and tiling such as the one used in (3) should be implementable within a reasonable compilation framework, opening a new set of possibilities for compiler optimizations.

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A parallel FDTD algorithm using the MPI library

Cited by 195 publications

References 12 publications

Enhanced Förster Resonance Energy Transfer on Single Metal Particle. 2. Dependence on Donor−Acceptor Separation Distance, Particle Size, and Distance from Metal Surface

Enhanced Förster Resonance Energy Transfer on Single Metal Particle. 2. Dependence on Donor−Acceptor Separation Distance, Particle Size, and Distance from Metal Surface

Single-Molecule Studies on Fluorescently Labeled Silver Particles: Effects of Particle Size

Mapping the FDTD Application to Many-Core Chip Architectures

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