20 papers · ranked by Valyu relevance
Temitayo Adefemi
—Parallelization has become a cornerstone of modern computing, influencing everything from high-performance supercomputers to everyday mobile devices. This paper presents a comprehensive guide on the fundamentals of parallelization that every computer scientist should know, beginning with a historical perspective that…
Dhananjay Saikumar
Direct gravitational simulations of n-body systems have a time complexity O(n 2 ), which gets computationally expensive as the number of bodies increases. Distributing this workload to multiple cores significantly speeds up the computation and is the fundamental principle behind parallel computing. This project…
Jesper Larsson Träff
These lecture notes are designed to accompany an imaginary, virtual, undergraduate, one or two semester course on fundamentals of Parallel Computing as well as to serve as background and reference for graduate courses on High-Performance Computing, parallel algorithms and shared-memory multiprocessor programming. They…
Patrick Mukala
| Article Info | ABSTRACT | | --- | --- | | | A myriad of applications ranging from engineering and scientific | | | simulations, image and signal processing as well as high-sensitive data | | | retrieval demand high processing power reaching up to teraflops for their | | | efficient execution. While a standard serial…
Rajendra Purohit, K. R. Chowdhary, Sunıl Dutt Purohıt
—Arrival of multicore systems has enforced a new scenario in computing, the parallel and distributed algorithms are fast replacing the older sequential algorithms, with many challenges of these techniques. The distributed algorithms provide distributed processing using distributed file systems and processing units…
Predrag Brođanac, Josip Novak, Ivica Boljat
Today, almost every computer has at least one multicore processor. To remain in stride with hardware developments, numerous university faculties oriented towards computer science have introduced parallel programming as an integral part of their courses. The question is, given the availability of parallel architectures…
Ahmed Hadi Ali AL-Jumaili, Ravie Chandren Muniyandi, Mohammad Kamrul Hasan, Johnny Koh Siaw Paw + 2 more
Traditional parallel computing for power management systems has prime challenges such as execution time, computational complexity, and efficiency like process time and delays in power system condition monitoring, particularly consumer power consumption, weather data, and power generation for detecting and predicting…
Sikao Guo, Nenad Korolija, Kent Milfeld, Adip Jhaveri + 3 more
Particle-based reaction-diffusion models offer a high-resolution alternative to the continuum reaction-diffusion approach, capturing the discrete and volume-excluding nature of molecules undergoing stochastic dynamics. These methods are thus uniquely capable of simulating explicit self-assembly of particles into…
Zeyu Xia, Canqun Yang, Chenchen Peng, Yifei Guo + 3 more
'Tao Tang' 'Yingbo Cui'] Background The advent of Single Molecule Real-Time (SMRT) sequencing has overcome many limitations of second-generation sequencing, such as limited read lengths, PCR amplification biases. However, longer reads increase data volume exponentially and high error rates make many existing alignment…
Wilfried Agbeto, Camille Coti, Vladimir Reinharz
Advances in graph algorithmics have allowed in-depth study of many natural objects from molecular biology or chemistry to social networks. Particularly in molecular biology and cheminformatics, understanding complex structures by identifying conserved sub-structures is a key milestone towards the artificial design of…
Sirilak Ketchaya, Apisit Rattanatranurak
Quicksort is an important algorithm that uses the divide and conquer concept, and it can be run to solve any problem. The performance of the algorithm can be improved by implementing this algorithm in parallel. In this paper, the parallel sorting algorithm named the Multi-Deque Partition Dual-Deque Merge Sorting…
Ashish Chapagain, Dima Abuoliem, In Ho Cho, Tongbiao Wang
Multifunctional nanosurfaces receive growing attention due to their versatile properties. Capillary force lithography (CFL) has emerged as a simple and economical method for fabricating these surfaces. In recent works, the authors proposed to leverage the evolution strategies (ES) to modify nanosurface characteristics…
Peiyu Zong, Wenpeng Deng, Jian Liu, Jue Ruan
The rapid advancements in sequencing length necessitate the adoption of increasingly efficient sequence alignment algorithms. The Needleman-Wunsch method introduces the foundational dynamic programming (DP) matrix calculation for global alignment, which evaluates the overall alignment of sequences. However, this method…
Junichiro Makino, Toshikazu Ebisuzaki, Ryutaro Himeno, Yoshihide Hayashizaki
Rapidly increasing amount of short read data generated by NGSs (new-generation sequencers) calls for the development of fast and accurate read alignment programs. The programs based on hash table (BLAST) and Burrows-Wheeler transform (bwa-mem) are used, and the latter is known to give superior performance. We here…
Authors not listed
Protein conformational landscapes contain the functionally relevant information useful for understanding biological processes. Mapping out conformational landscapes provides valuable insights into protein behaviors and biological phenomena, and has relevance to therapeutic design. While experimental structural biology…
Christoph Stelz, Lukas Hübner, Alexandros Stamatakis
Phylogenetic trees describe the evolutionary history among biological species based on their genomic data. Maximum Likelihood (ML) based phylogenetic inference tools search for the tree and evolutionary model that best explain the observed genomic data. Given the independence of likelihood score calculations between…
Authors not listed
Computing electrostatic interactions remains the bottleneck of molecular dynamics (MD) simulations despite more than a century of effort in developing methods to accelerate the calculation. Previously we have developed the Spherical Grid and Treecode (SGT) and Gauss-Legendre-Spherical-t (GLST) algorithms for…
Authors not listed
The era of exascale computing presents both exciting opportunities and unique challenges for quantum mechanical simulations. While the transition from petaflops to exascale computing has been marked by a steady increase in computational power, the shift towards heterogeneous architectures, particularly the dominant…
Madushanka Manathunga, Hasan Metin Aktulga, Andreas W. Goetz, Kenneth M. Merz + 1 more
We have ported and optimized the GPU accelerated QUICK and AMBER based ab initio QM/MM implementation on AMD GPUs. This encompasses the entire Fock matrix build and force calculation in QUICK including one-electron integrals, two-electron repulsion integrals, exchange-correlation quadrature, and linear algebra…
Oliver Lee, Malte Gather, Eli Zysman-Colman
We describe a new tool for the efficient management of computational chemistry. Digichem is a program that automates and simplifies nearly the entire computational pipeline, including large-scale batch submission of calculations, analysis and results parsing, the generation of 3D density plots and 2D graphs of…