Search results for "Computation"

The evolutionary history of the Arabidopsis arenosa complex: diverse tetraploids mask the Western Carpathian center of species and genetic diversity.

2012

The Arabidopsis arenosa complex is closely related to the model plant Arabidopsis thaliana. Species and subspecies in the complex are mainly biennial, predominantly outcrossing, herbaceous, and with a distribution range covering most parts of latitudes and the eastern reaches of Europe. In this study we present the first comprehensive evolutionary history of the A. arenosa species complex, covering its natural range, by using chromosome counts, nuclear AFLP data, and a maternally inherited marker from the chloroplast genome [trnL intron (trnL) and trnL/F intergenic spacer (trnL/F-IGS) of tRNA(Leu) and tRNA(Phe), respectively]. We unravel the broad-scale cytogeographic and phylogeographic pa…

Spectral moments of the edge adjacency matrix in molecular graphs. 3. Molecules containing cycles

1998

A substructural approach to quantitative structure−property relationships based on the spectral moments of the edge adjacency matrix is extended to molecules containing cycles. Spectral moments are expressed as linear combinations of structural fragments of any kind of nonweighted graphs. The boiling points of a series of 80 cycloalkanes was well-described by the present approach. The predictive power of the model was proved by using a test set of another 26 compounds. An equation that expresses the contribution of the different fragments of the molecules to the boiling point was obtained.

Hydration/elimination reactions of trapped protonated fluoroalkyl triazines

2007

Isolated glyoxylic acid-water 1:1 complexes in low temperature argon matrices

2015

Abstract The 1:1 hydrogen bonded complexes between glyoxylic acid (GA) and water are studied in low temperature argon matrices. Four different complex structures were found in deposited matrices. The lowest energy conformer (T1) of GA was found to form complex, where the water molecule was attached to the opposite side of the intramolecular hydrogen bond in the molecule (T1B). Interestingly, this complex was estimated to be +8.0 kJ mol −1 higher in energy than the most stable structure (T1A), where the water is inserted into the internal hydrogen bond, and also found in solid argon but in smaller abundance. For the second-lowest energy conformer of GA (T2), the two lowest-energy complex str…

Interaction in Spoken Word Recognition Models: Feedback Helps

2018

Human perception, cognition, and action requires fast integration of bottom-up signals with top-down knowledge and context. A key theoretical perspective in cognitive science is the interactive activation hypothesis: forward and backward flow in bidirectionally connected neural networks allows humans and other biological systems to approximate optimal integration of bottom-up and top-down information under real-world constraints. An alternative view is that online feedback is neither necessary nor helpful; purely feed forward alternatives can be constructed for any feedback system, and online feedback could not improve processing and would preclude veridical perception. In the domain of spo…

Reconstruction of Low Energy Neutrino Events with GPUs at IceCube

2020

IceCube is a cubic kilometer neutrino observatory located at the South Pole that produces massive amounts of data by measuring individual Cherenkov photons from neutrino interaction events in the energy range from few GeV to several PeV. The actual reconstruction of neutrino events in the GeV range is computationally challenging due to the scarcity of data produced by single events. This can lead to run times of several weeks for the state-of-the-art reconstruction method – Pegleg – on CPUs for typical workloads of many ten-thousand events. We propose a GPU version of Pegleg that probes the likelihood space with several hypotheses in parallel while adapting the amount of parallel sampled hy…

The Dynamical Kernel Scheduler - Part 1

2015

Emerging processor architectures such as GPUs and Intel MICs provide a huge performance potential for high performance computing. However developing software using these hardware accelerators introduces additional challenges for the developer such as exposing additional parallelism, dealing with different hardware designs and using multiple development frameworks in order to use devices from different vendors. The Dynamic Kernel Scheduler (DKS) is being developed in order to provide a software layer between host application and different hardware accelerators. DKS handles the communication between the host and device, schedules task execution, and provides a library of built-in algorithms. …

Optimization of Reactive Force Field Simulation: Refactor, Parallelization, and Vectorization for Interactions

2022

Molecular dynamics (MD) simulations are playing an increasingly important role in many areas ranging from chemical materials to biological molecules. With the continuing development of MD models, the potentials are getting larger and more complex. In this article, we focus on the reactive force field (ReaxFF) potential from LAMMPS to optimize the computation of interactions. We present our efforts on refactoring for neighbor list building, bond order computation, as well as valence angles and torsion angles computation. After redesigning these kernels, we develop a vectorized implementation for non-bonded interactions, which is nearly $100 \times$ 100 × faster than the management processing…

Reducing complexity in H.264/AVC motion estimation by using a GPU

2011

H.264/AVC applies a complex mode decision technique that has high computational complexity in order to reduce the temporal redundancies of video sequences. Several algorithms have been proposed in the literature in recent years with the aim of accelerating this part of the encoding process. Recently, with the emergence of many-core processors or accelerators, a new approach can be adopted for reducing the complexity of the H.264/AVC encoding algorithm. This paper focuses on reducing the inter prediction complexity adopted in H.264/AVC and proposes a GPU-based implementation using CUDA. Experimental results show that the proposed approach reduces the complexity by as much as 99% (100x of spe…

Finding near-perfect parameters for hardware and code optimizations with automatic multi-objective design space explorations

2012

Summary In the design process of computer systems or processor architectures, typically many different parameters are exposed to configure, tune, and optimize every component of a system. For evaluations and before production, it is desirable to know the best setting for all parameters. Processing speed is no longer the only objective that needs to be optimized; power consumption, area, and so on have become very important. Thus, the best configurations have to be found in respect to multiple objectives. In this article, we use a multi-objective design space exploration tool called Framework for Automatic Design Space Exploration (FADSE) to automatically find near-optimal configurations in …