Read by QxMD icon Read


Thomas Kovac, Tom Haber, Frank Van Reeth, Niel Hens
BACKGROUND: Over the last years, substantial effort has been put into enhancing our arsenal in fighting epidemics from both technological and theoretical perspectives with scientists from different fields teaming up for rapid assessment of potentially urgent situations. This paper focusses on the computational aspects of infectious disease models and applies commonly available graphics processing units (GPUs) for the simulation of these models. However, fully utilizing the resources of both CPUs and GPUs requires a carefully balanced heterogeneous approach...
March 16, 2018: BMC Bioinformatics
Daniel J Mermelstein, Charles Lin, Gard Nelson, Rachael Kretsch, J Andrew McCammon, Ross C Walker
Alchemical free energy (AFE) calculations based on molecular dynamics (MD) simulations are key tools in both improving our understanding of a wide variety of biological processes and accelerating the design and optimization of therapeutics for numerous diseases. Computing power and theory have, however, long been insufficient to enable AFE calculations to be routinely applied in early stage drug discovery. One of the major difficulties in performing AFE calculations is the length of time required for calculations to converge to an ensemble average...
March 12, 2018: Journal of Computational Chemistry
Wing-Kin Tam, Yang Zhi
BACKGROUND: Large-scale neural recordings provide detailed information on neuronal activities and can help elicit the underlying neural mechanisms of the brain. However, the computational burden is also formidable when we try to process the huge data stream generated by such recordings. NEW METHOD: In this study, we report the development of Neural Parallel Engine (NPE), a toolbox for massively parallel neural signal processing on graphical processing units (GPUs)...
March 9, 2018: Journal of Neuroscience Methods
M Radek, J-G Tenberge, S Hilke, G Wilde, M Peterlechner
Electron microscopy images are interference patterns and can generally not be interpreted in a straight forward manner. Typically, time consuming numerical simulations have to be employed to separate specimen features from imaging artifacts. Directly comparing numerical predictions to experimental results, realistic simulation box sizes and varying imaging parameters are needed. In this work, we introduce an accelerated multislice algorithm, named STEMcl, that is capable of simulating series of large super cells typical for defective and amorphous systems, in addition to parameter series using the massive parallelization accessible in today's commercial PC-hardware, e...
February 16, 2018: Ultramicroscopy
Adam Wang, Alexander Maslowski, Philippe Messmer, Mathias Lehmann, Adam Strzelecki, Elaine Yu, Pascal Paysan, Marcus Brehm, Peter Munro, Josh Star-Lack, Dieter Seghers
PURPOSE: To correct for scatter in kV cone-beam CT (CBCT) projection data on a clinical system using a new tool, Acuros® CTS, that estimates scatter images rapidly and accurately by deterministically solving the linear Boltzmann transport equation. METHODS: Phantom and patient CBCT scans were acquired on TrueBeam® radiotherapy machines. A first-pass reconstruction was used to create water and bone density maps of the imaged object, which was updated to include a more accurate representation of the patient couch...
March 6, 2018: Medical Physics
Alexander Maslowski, Adam Wang, Mingshan Sun, Todd Wareing, Ian Davis, Josh Star-Lack
PURPOSE: To describe Acuros® CTS, a new software tool for rapidly and accurately estimating scatter in x-ray projection images by deterministically solving the linear Boltzmann transport equation (LBTE). METHODS: The LBTE describes the behavior of particles as they interact with an object across spatial, energy, and directional (propagation) domains. Acuros CTS deterministically solves the LBTE by modeling photon transport associated with an x-ray projection in three main steps: 1) Ray tracing photons from the x-ray source into the object where they experience their first scattering event and form scattering sources...
March 6, 2018: Medical Physics
Michał L Chodkiewicz, Szymon Migacz, Witold Rudnicki, Anna Makal, Jarosław A Kalinowski, Nigel W Moriarty, Ralf W Grosse-Kunstleve, Pavel V Afonine, Paul D Adams, Paulina Maria Dominiak
It has been recently established that the accuracy of structural parameters from X-ray refinement of crystal structures can be improved by using a bank of aspherical pseudoatoms instead of the classical spherical model of atomic form factors. This comes, however, at the cost of increased complexity of the underlying calculations. In order to facilitate the adoption of this more advanced electron density model by the broader community of crystallographers, a new software implementation called DiSCaMB , 'densities in structural chemistry and molecular biology', has been developed...
February 1, 2018: Journal of Applied Crystallography
Benedict Diederich, Rolf Wartmann, Harald Schadwinkel, Rainer Heintzmann
Cellphones equipped with high-quality cameras and powerful CPUs as well as GPUs are widespread. This opens new prospects to use such existing computational and imaging resources to perform medical diagnosis in developing countries at a very low cost. Many relevant samples, like biological cells or waterborn parasites, are almost fully transparent. As they do not exhibit absorption, but alter the light's phase only, they are almost invisible in brightfield microscopy. Expensive equipment and procedures for microscopic contrasting or sample staining often are not available...
2018: PloS One
Byunghan Lee, Hyeyoung Min, Sungroh Yoon
Motivation: Metagenomic sequencing has become a crucial tool for obtaining a gene catalogue of operational taxonomic units (OTUs) in a microbial community. A typical metagenomic sequencing produces a large amount of data (often in the order of terabytes or more), and computational tools are indispensable for efficient processing. In particular, error correction in metagenomics is crucial for accurate and robust genetic cataloging of microbial communities. However, many existing error-correction tools take a prohibitively long time and often bottleneck the whole analysis pipeline...
February 20, 2018: Bioinformatics
Leiming Yu, Fanny Nina-Paravecino, David Kaeli, Qianqian Fang
We present a highly scalable Monte Carlo (MC) three-dimensional photon transport simulation platform designed for heterogeneous computing systems. Through the development of a massively parallel MC algorithm using the Open Computing Language framework, this research extends our existing graphics processing unit (GPU)-accelerated MC technique to a highly scalable vendor-independent heterogeneous computing environment, achieving significantly improved performance and software portability. A number of parallel computing techniques are investigated to achieve portable performance over a wide range of computing hardware...
January 2018: Journal of Biomedical Optics
Hirochika Sato, Takashi Kakue, Yasuyuki Ichihashi, Yutaka Endo, Koki Wakunami, Ryutaro Oi, Kenji Yamamoto, Hirotaka Nakayama, Tomoyoshi Shimobaba, Tomoyoshi Ito
Although electro-holography can reconstruct three-dimensional (3D) motion pictures, its computational cost is too heavy to allow for real-time reconstruction of 3D motion pictures. This study explores accelerating colour hologram generation using light-ray information on a ray-sampling (RS) plane with a graphics processing unit (GPU) to realise a real-time holographic display system. We refer to an image corresponding to light-ray information as an RS image. Colour holograms were generated from three RS images with resolutions of 2,048 × 2,048; 3,072 × 3,072 and 4,096 × 4,096 pixels...
January 24, 2018: Scientific Reports
Timothy J Giese, Darrin M York
There has been a resurgence of interest in free energy methods motivated by the performance enhancements offered by molecular dynamics (MD) software written for specialized hardware, such as graphics processing units (GPUs). In this work, we exploit the properties of a parameter-interpolated thermodynamic integration (PI-TI) method to connect states by their molecular mechanical (MM) parameter values. This pathway is shown to be better behaved for Mg$^{2+}\rightarrow$Ca$^{2+}$ transformations than traditional linear alchemical pathways (with and without soft-core potentials)...
January 22, 2018: Journal of Chemical Theory and Computation
Robert M Parrish, Keiran C Thompson, Todd J Martínez
Symmetry-adapted perturbation theory (SAPT) is a valuable method for analyzing intermolecular interactions. The functional group SAPT partition (F-SAPT) has been introduced to provide additional insight into the origins of noncovalent interactions. Until now, SAPT analysis has been too costly for large ligand-protein complexes where it could provide key insights for chemical modifications that might improve ligand binding. In this paper, we present a large-scale implementation of F-SAPT which is especially efficient when one of the interacting monomers is significantly larger than the other, as is usually the case for drug-protein interactions...
January 18, 2018: Journal of Chemical Theory and Computation
Rui Liu, Lin Fu, Bruno De Man, Hengyong Yu
Projection and backprojection operations are essential in a variety of image reconstruction and physical correction algorithms in CT. The distance-driven (DD) projection and backprojection are widely used for their highly sequential memory access pattern and low arithmetic cost. However, a typical DD implementation has an inner loop that adjusts the calculation depending on the relative position between voxel and detector cell boundaries. The irregularity of the branch behavior makes it inefficient to be implemented on massively parallel computing devices such as graphics processing units (GPUs)...
December 2017: IEEE Transactions on Computational Imaging
T Rydén, J Heydorn Lagerlöf, J Hemmingsson, I Marin, J Svensson, M Båth, P Gjertsson, P Bernhardt
BACKGROUND: Full Monte Carlo (MC)-based SPECT reconstructions have a strong potential for correcting for image degrading factors, but the reconstruction times are long. The objective of this study was to develop a highly parallel Monte Carlo code for fast, ordered subset expectation maximum (OSEM) reconstructions of SPECT/CT images. The MC code was written in the Compute Unified Device Architecture language for a computer with four graphics processing units (GPUs) (GeForce GTX Titan X, Nvidia, USA)...
January 4, 2018: EJNMMI Physics
Dmitri Matenine, Geoffroi Côté, Julia Mascolo-Fortin, Yves Goussard, Philippe Després
PURPOSE: Iterative reconstruction algorithms in computed tomography (CT) require a fast method for computing the intersection distances between the trajectories of photons and the object, also called ray tracing or system matrix computation. This work focused on the thin-ray model is aimed at comparing different system matrix handling strategies using graphical processing units (GPUs). METHODS: In this work, the system matrix is modeled by thin rays intersecting a regular grid of box-shaped voxels, known to be an accurate representation of the forward projection operator in CT...
February 2018: Medical Physics
Daniel Probst, Jean-Louis Reymond
Motivation: During the past decade, big data has become a major tool in scientific endeavors. While statistical methods and algorithms are well-suited for analyzing and summarizing enormous amounts of data, the results do not allow for a visual inspection of the entire data. Current scientific software, including R packages and Python libraries such as ggplot2, matplotlib, and, do not support interactive visualizations of datasets exceeding 100,000 data points on the web. Other solutions enable the web-based visualization of big data only through data reduction or statistical representations...
November 24, 2017: Bioinformatics
Aaron Hagan, Amit Sawant, Michael Folkerts, Arezoo Modiri
We report on the design, implementation and characterization of a multi-graphic processing unit (GPU) computational platform for higher-order optimization in radiotherapy treatment planning. In collaboration with a commercial vendor (Varian Medical Systems, Palo Alto, CA), a research prototype GPU-enabled Eclipse (V13.6) workstation was configured. The hardware consisted of dual 8-core Xeon processors, 256 GB RAM and four NVIDIA Tesla K80 general purpose GPUs. We demonstrate the utility of this platform for large radiotherapy optimization problems through the development and characterization of a parallelized particle swarm optimization (PSO) four dimensional (4D) intensity modulated radiation therapy (IMRT) technique...
January 16, 2018: Physics in Medicine and Biology
Philippe Després, Xun Jia
Tomographic image reconstruction is a computationally demanding task, even more so when advanced models are used to describe a more complete and accurate picture of the image formation process. Such advanced modeling and reconstruction algorithms can lead to better images, often with less dose, but at the price of long calculation times that are hardly compatible with clinical workflows. Fortunately, reconstruction tasks can often be executed advantageously on Graphics Processing Units (GPUs), which are exploited as massively parallel computational engines...
October 2017: Physica Medica: PM
Alan Pryor, Colin Ophus, Jianwei Miao
Simulation of atomic-resolution image formation in scanning transmission electron microscopy can require significant computation times using traditional methods. A recently developed method, termed plane-wave reciprocal-space interpolated scattering matrix (PRISM), demonstrates potential for significant acceleration of such simulations with negligible loss of accuracy. Here, we present a software package called Prismatic for parallelized simulation of image formation in scanning transmission electron microscopy (STEM) using both the PRISM and multislice methods...
2017: Advanced Structural and Chemical Imaging
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"