Biomedical subjects

Ron O Dror

Publications and source records attributed to Ron O Dror.

5 recordsLinked to original sources

PubMed2006

The midpoint method for parallelization of particle simulations.

The evaluation of interactions between nearby particles constitutes the majority of the computational workload involved in classical molecular dynamics (MD) simulations. In this paper, we introduce a new method for the parallelization of range-limited particle interactions that proves particularly suitable to MD applications. Because it applies not only to pairwise interactions but also to interactions involving three or more particles, the method can be used for evaluation of both nonbonded and bonded forces in a MD simulation. It requires less interprocessor data transfer than traditional spatial decomposition methods at all but the lowest levels of parallelism. It gains an additional practical advantage in certain commonly used interprocessor communication networks by distributing the communication burden more evenly across network links and by decreasing the associated latency. When used to parallelize MD, it further reduces communication requirements by allowing the computations associated with short-range nonbonded interactions, long-range electrostatics, bonded interactions, and particle migration to use much of the same communicated data. We also introduce certain variants of this method that can significantly improve the balance of computational load across processors.

Algorithms↗

PubMed2005

Gaussian split Ewald: A fast Ewald mesh method for molecular simulation.

Gaussian split Ewald (GSE) is a versatile Ewald mesh method that is fast and accurate when used with both real-space and k-space Poisson solvers. While real-space methods are known to be asymptotically superior to k-space methods in terms of both computational cost and parallelization efficiency, k-space methods such as smooth particle-mesh Ewald (SPME) have thus far remained dominant because they have been more efficient than existing real-space methods for simulations of typical systems in the size range of current practical interest. Real-space GSE, however, is approximately a factor of 2 faster than previously described real-space Ewald methods for the level of force accuracy typically required in biomolecular simulations, and is competitive with leading k-space methods even for systems of moderate size. Alternatively, GSE may be combined with a k-space Poisson solver, providing a conveniently tunable k-space method that performs comparably to SPME. The GSE method follows naturally from a uniform framework that we introduce to concisely describe the differences between existing Ewald mesh methods.

Journal Article↗

PubMed2004

Statistical characterization of real-world illumination.

Although studies of vision and graphics often assume simple illumination models, real-world illumination is highly complex, with reflected light incident on a surface from almost every direction. One can capture the illumination from every direction at one point photographically using a spherical illumination map. This work illustrates, through analysis of photographically acquired, high dynamic range illumination maps, that real-world illumination possesses a high degree of statistical regularity. The marginal and joint wavelet coefficient distributions and harmonic spectra of illumination maps resemble those documented in the natural image statistics literature. However, illumination maps differ from typical photographs in that illumination maps are statistically nonstationary and may contain localized light sources that dominate their power spectra. Our work provides a foundation for statistical models of real-world illumination, thereby facilitating the understanding of human material perception, the design of robust computer vision systems, and the rendering of realistic computer graphics imagery.

Contrast Sensitivity↗

PubMed2003

Bayesian estimation of transcript levels using a general model of array measurement noise.

Gene arrays demonstrate a promising ability to characterize expression levels across the entire genome but suffer from significant levels of measurement noise. We present a rigorous new approach to estimate transcript levels and ratios from one or more gene array experiments, given a model of measurement noise and available prior information. The Bayesian estimation of array measurements (BEAM) technique provides a principled method to identify changes in expression level, combine repeated measurements, or deal with negative expression level measurements. BEAM is more flexible than existing techniques, because it does not assume a specific functional form for noise and prior models. Instead, it relies on computational techniques that apply to a broad range of models. We use Affymetrix yeast chip data to illustrate the process of developing accurate noise and prior models from existing experimental data. The resulting noise model includes novel features such as heavy-tailed additive noise and a gene-specific bias term. We also verify that the resulting noise and prior models fit data from an Affymetrix human chip set.

Bayes Theorem↗

PubMed2003

Real-world illumination and the perception of surface reflectance properties.

Under typical viewing conditions, we find it easy to distinguish between different materials, such as metal, plastic, and paper. Recognizing materials from their surface reflectance properties (such as lightness and gloss) is a nontrivial accomplishment because of confounding effects of illumination. However, if subjects have tacit knowledge of the statistics of illumination encountered in the real world, then it is possible to reject unlikely image interpretations, and thus to estimate surface reflectance even when the precise illumination is unknown. A surface reflectance matching task was used to measure the accuracy of human surface reflectance estimation. The results of the matching task demonstrate that subjects can match surface reflectance properties reliably and accurately in the absence of context, as long as the illumination is realistic. Matching performance declines when the illumination statistics are not representative of the real world. Together these findings suggest that subjects do use stored assumptions about the statistics of real-world illumination to estimate surface reflectance. Systematic manipulations of pixel and wavelet properties of illuminations reveal that the visual system's assumptions about illumination are of intermediate complexity (e.g., presence of edges and bright light sources), rather than of high complexity (e.g., presence of recognizable objects in the environment).

Contrast Sensitivity↗