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PubMed2005

Final Aperture Superposition Technique applied to fast calculation of electron output factors and depth dose curves.

The Final Aperture Superposition Technique (FAST) is described and applied to accurate, near instantaneous calculation of the relative output factor (ROF) and central axis percentage depth dose curve (PDD) for clinical electron beams used in radiotherapy. FAST is based on precalculation of dose at select points for the two extreme situations of a fully open final aperture and a final aperture with no opening (fully shielded). This technique is different than conventional superposition of dose deposition kernels: The precalculated dose is differential in position of the electron or photon at the downstream surface of the insert. The calculation for a particular aperture (x-ray jaws or MLC, insert in electron applicator) is done with superposition of the precalculated dose data, using the open field data over the open part of the aperture and the fully shielded data over the remainder. The calculation takes explicit account of all interactions in the shielded region of the aperture except the collimator effect: Particles that pass from the open part into the shielded part, or visa versa. For the clinical demonstration, FAST was compared to full Monte Carlo simulation of 10 x 10, 2.5 x 2.5, and 2 x 8 cm2 inserts. Dose was calculated to 0.5% precision in 0.4 x 0.4 x 0.2 cm3 voxels, spaced at 0.2 cm depth intervals along the central axis, using detailed Monte Carlo simulation of the treatment head of a commercial linear accelerator for six different electron beams with energies of 6-21 MeV. Each simulation took several hours on a personal computer with a 1.7 Mhz processor. The calculation for the individual inserts, done with superposition, was completed in under a second on the same PC. Since simulations for the pre calculation are only performed once, higher precision and resolution can be obtained without increasing the calculation time for individual inserts. Fully shielded contributions were largest for small fields and high beam energy, at the surface, reaching a maximum of 5.6% at 21 MeV. Contributions from the collimator effect were largest for the large field size, high beam energy, and shallow depths, reaching a maximum of 4.7% at 21 MeV. Both shielding contributions and the collimator effect need to be taken into account to achieve an accuracy of 2%. FAST takes explicit account of the shielding contributions. With the collimator effect set to that of the largest field in the FAST calculation, the difference in dose on the central axis (product of ROF and PDD) between FAST and full simulation was generally under 2%. The maximum difference of 2.5% exceeded the statistical precision of the calculation by four standard deviations. This occurred at 18 MeV for the 2.5 x 2.5 cm2 field. The differences are due to the method used to account for the collimator effect.

Algorithms↗
PubMed2002

Spatial coherence analysis applied to aberration correction using a two-dimensional array system.

Complex degree of coherence functions are computed using synthetic and measured ultrasound data to demonstrate noteworthy aspects of coherence analysis in the context of aberration correction. Coherence functions calculated from synthetic data illustrate the importance of proper normalization of the constituent cross-correlation integrals when weak elements and receiver directivity are significant factors. The synthetic data also show that a spike can occur at the zero-lag position of the coherence function when the signal-to-noise ratio is reduced by element directivity near the edges of a large aperture. The latter observation is confirmed by experimental data acquired through tissue-mimicking distributed aberration phantoms using a low f-number two-dimensional array system. The coherence of data acquired at neighboring elements is not changed by time-shift compensation of transmit and receive focusing, but time-shift compensation does improve the coherence of echoes measured over larger separations. The resulting increase in coherence widths evaluated at levels between 0.2 and 0.5 is correlated with narrower -10 dB and -20 dB effective widths in focuses visualized using single-transmit images. Iterative focus compensation methods may benefit from aberration estimation algorithms that take advantage of these longer-range correlations in random-scattering waveforms.

Artifacts↗
PubMed2004

Measuring of viscoelastic properties of homogeneous soft solid using transient elastography: an inverse problem approach.

Two main questions are at the center of this paper. The first one concerns the choice of a rheological model in the frequency range of transient elastography, sonoelasticity or NMR elastography for soft solids (20-1000 Hz). Transient elastography experiments based on plane shear waves that propagate in an Agar-gelatin phantom or in bovine muscles enable one to quantify their viscoelastic properties. The comparison of these experimental results to the prediction of the two simplest rheological models indicate clearly that Voigt's model is the better. The second question studied in the paper deals with the feasibility of quantitative viscosity mapping using inverse problem algorithm. In the ideal situation where plane shear waves propagate in a sample, a simple inverse problem based on the Helmholtz equation correctly retrieves both elasticity and viscosity. In a more realistic situation with nonplane shear waves, this simple approach fails. Nevertheless, it is shown that quantitative viscosity mapping is still possible if one uses an appropriate inverse problem that fully takes into account diffraction in solids.

Algorithms↗
PubMed2005

Simulation of ultrasound propagation through bovine cancellous bone using elastic and Biot's finite-difference time-domain methods.

The propagation of ultrasonic pulse waves in bovine cancellous bone has been numerically analyzed in two dimensions by using two finite-difference time-domain (FDTD) methods: the commonly used elastic FDTD method and an FDTD method extended with Biot's theory for a porous elastic solid saturated with viscous fluid. Both FDTD results were compared with the results of previous experiments by Hosokawa and Otani [J. Acoust. Soc. Am. 101, 558-562 (1997)], in which the Biot's fast and slow longitudinal waves were clearly identified. It was difficult to analyze both the fast and slow waves with the elastic FDTD method because of the inadequate 2D model of cancellous bone. On the other hand, in Biot's FDTD results that consider the pore fluid motion relative to the solid frame, both waves could be clearly observed. The experimental and simulated values of the speeds of these waves were in good agreement. Using the modified Biot's FDTD equations containing the possible attenuations for the fast wave other than the viscous loss due to the pore fluid motion, the amplitude ratio of the slow wave to the fast wave largely increased with the porosity, which also agrees with the experimental results.

Animals↗
PubMed2006

Efficient array beam forming by spatial filtering for ultrasound B-mode imaging.

This paper proposes an efficient array beam-forming method using spatial matched filtering (SMF) for ultrasonic imaging. In the proposed method, ultrasonic waves are transmitted from an array subaperture with fixed transmit focus as in conventional array imaging. At receive, radio frequency echo signals from each receive channel are passed through a spatial matched filter that is constructed based on the system transmit-receive spatial impulse response. The filtered echo signals are then summed without time delays. The filter concentrates and spatially registers the echo energy from each element so that the pulse-echo impulse response of the summed output is focused with acceptably low side lobes. Analytical beam pattern analysis and simulation results using a linear array show that this spatial filtering method can improve lateral resolution and contrast-to-noise ratio as compared with conventional dynamic receive focusing (DRF) methods. Experimental results with a linear array are consistent but point out the need to address additional practical issues. Spatial filtering is equivalent to synthetic aperture methods that dynamically focus on both transmit and receive throughout the field of view. In one common example of phase aberrations, the SMF method was degraded to a degree comparable to conventional DRF methods.

Computer Simulation↗
PubMed2006

A fast near-field method for calculations of time-harmonic and transient pressures produced by triangular pistons.

Analytical expressions are demonstrated for fast calculations of time-harmonic and transient near-field pressures generated by triangular pistons. These fast expressions remove singularities from the impulse response, thereby reducing the computation time and the peak numerical error with a general formula that describes the near-field pressure produced by any triangular piston geometry. The time-domain expressions are further accelerated by a time-space decomposition approach that analytically separates the spatial and temporal components of the numerically computed transient pressure. Applied to a Hanning-weighted input pulse, time-space decomposition converts each spatio-temporal integral into six spatial integral evaluations at each field point. Time-harmonic and transient calculations are evaluated for an equilateral triangle with sides equal to four wavelengths, and the resulting errors are compared to pressures obtained with exact and approximate implementations of the impulse response method. The results show that the fast near-field method achieves smaller maximum errors and is consistently faster than the impulse response and methods that approximate the impulse response.

Acoustics↗
PubMed1998

Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution.

An implementation of classical molecular dynamics on parallel computers of increased efficiency has enabled a simulation of protein folding with explicit representation of water for 1 microsecond, about two orders of magnitude longer than the longest simulation of a protein in water reported to date. Starting with an unfolded state of villin headpiece subdomain, hydrophobic collapse and helix formation occur in an initial phase, followed by conformational readjustments. A marginally stable state, which has a lifetime of about 150 nanoseconds, a favorable solvation free energy, and shows significant resemblance to the native structure, is observed; two pathways to this state have been found.

Carrier Proteins↗
PubMed2004

Spectral analysis of calcium oscillations.

Calcium (Ca2+) oscillations are universal signals exploited by cells to regulate a vast number of cellular processes. Frequency and amplitude, the key features of oscillating waves, can yield information that can be decoded by intracellular processes. Analysis and quantification of Ca2+ oscillations are crucial for understanding the general concept of Ca2+ signaling. This protocol presents a method for performing spectral analysis of Ca2+ oscillations using MATLAB software.

Calcium↗
PubMed2004

Advanced fitness landscape analysis and the performance of memetic algorithms.

Memetic algorithms (MAs) have demonstrated very effective in combinatorial optimization. This paper offers explanations as to why this is so by investigating the performance of MAs in terms of efficiency and effectiveness. A special class of MAs is used to discuss efficiency and effectiveness for local search and evolutionary meta-search. It is shown that the efficiency of MAs can be increased drastically with the use of domain knowledge. However, effectiveness highly depends on the structure of the problem. As is well-known, identifying this structure is made easier with the notion of fitness landscapes: the local properties of the fitness landscape strongly influence the effectiveness of the local search while the global properties strongly influence the effectiveness of the evolutionary meta-search. This paper also introduces new techniques for analyzing the fitness landscapes of combinatorial problems; these techniques focus on the investigation of random walks in the fitness landscape starting at locally optimal solutions as well as on the escape from the basins of attractions of current local optima. It is shown for NK-landscapes and landscapes of the unconstrained binary quadratic programming problem (BQP) that a random walk to another local optimum can be used to explain the efficiency of recombination in comparison to mutation. Moreover, the paper shows that other aspects like the size of the basins of attractions of local optima are important for the efficiency of MAs and a local search escape analysis is proposed. These simple analysis techniques have several advantages over previously proposed statistical measures and provide valuable insight into the behaviour of MAs on different kinds of landscapes.

Algorithms↗
PubMed2004

Automatic generation of controllers for embodied legged organisms: a Pareto evolutionary multi-objective approach.

In this paper, we investigate the use of a self-adaptive Pareto evolutionary multi-objective optimization (EMO) approach for evolving the controllers of virtual embodied organisms. The objective of this paper is to demonstrate the trade-off between quality of solutions and computational cost. We show empirically that evolving controllers using the proposed algorithm incurs significantly less computational cost when compared to a self-adaptive weighted sum EMO algorithm, a self-adaptive single-objective evolutionary algorithm (EA) and a hand-tuned Pareto EMO algorithm. The main contribution of the self-adaptive Pareto EMO approach is its ability to produce sufficiently good controllers with different locomotion capabilities in a single run, thereby reducing the evolutionary computational cost and allowing the designer to explore the space of good solutions simultaneously. Our results also show that self-adaptation was found to be highly beneficial in reducing redundancy when compared against the other algorithms. Moreover, it was also shown that genetic diversity was being maintained naturally by virtue of the system's inherent multi-objectivity.

Algorithms↗
PubMed2004

Real-coded memetic algorithms with crossover hill-climbing.

This paper presents a real-coded memetic algorithm that applies a crossover hill-climbing to solutions produced by the genetic operators. On the one hand, the memetic algorithm provides global search (reliability) by means of the promotion of high levels of population diversity. On the other, the crossover hill-climbing exploits the self-adaptive capacity of real-parameter crossover operators with the aim of producing an effective local tuning on the solutions (accuracy). An important aspect of the memetic algorithm proposed is that it adaptively assigns different local search probabilities to individuals. It was observed that the algorithm adjusts the global/local search balance according to the particularities of each problem instance. Experimental results show that, for a wide range of problems, the method we propose here consistently outperforms other real-coded memetic algorithms which appeared in the literature.

Algorithms↗