A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
Filters
Special Purpose Parallel Computer for Modelling Supramolecular Systems based on the Dynamic Lattice Liquid Model
2010
Computational Methods in Science and Technology
Preserved Fulltext
We propose constructing a parallel computing system which realizes the 3D architecture and the cooperative dynamics based on the dynamic lattice liquid (DLL) model. ...
Hierarchical, structural and dynamic complexities of such systems require new methodological developments. ...
The authors thank Dr.Witold Zatorski for electronic circuits preparation. ...
doi:10.12921/cmst.2010.16.02.147-153
fatcat:qo2s7kkwezfxvef7l75jysswwa
Cellular Automaton Simulation of Polymers
1991
Materials Research Society Symposium Proceedings
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
A highly efficient, two-space algorithm is devised and tested on both Cellular Automata Machines (CAMs) and serial computers. ...
Preliminary results on the static and dynamic properties of polymers in two dimensions are reported. ...
In the CA twospace polymer model on a CAM the time scales as M ! t m /(PV p /V) and on connection machine or hypercube as M ! t m /P. ...
doi:10.1557/proc-248-483
fatcat:56jtf66swrem3ohdaycnlel2zu
Incorporating metadata in HIV transmission network reconstruction: A machine learning feasibility assessment
2021
PLoS Computational Biology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
Support vector machine demonstrated one order of magnitude improvement in accuracy of assigning the sequences to the correct cluster compared to dummy uniform random classifier. ...
We use machine learning algorithms to learn the non-linear correlation patterns between patient metadata and transmissions between HIV-positive cases. ...
Acknowledgments We would like thank the PIRC team and UCSD Red Cap team for their in providing data and technical support in duration of this project. ...
doi:10.1371/journal.pcbi.1009336
pmid:34550966
pmcid:PMC8457453
fatcat:ud5tezoakrfnfbudf5qm3asmui
The Mechanisms for Preferential Attachment of Nanoparticles in Liquid Determined Using Liquid Cell Electron Microscopy, Machine Learning, and Molecular Dynamics
2016
Microscopy and Microanalysis
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
Here we employ liquid cell scanning transmission electron microscopy (STEM), machine learning-based image analysis [4], and steered molecular dynamics (SMD) simulations to demonstrate that the experimentally ...
The use of advanced machine learning-based image analysis algorithms [3] to interpret dynamic liquid cell electron microscopy in situ movies promises to provide insights into complex nanoparticle growth ...
Here we employ liquid cell scanning transmission electron microscopy (STEM), machine learning-based image analysis [4] , and steered molecular dynamics (SMD) simulations to demonstrate that the experimentally ...
doi:10.1017/s1431927616004918
fatcat:a4ae2b4mk5hpjlngcaqku5qsz4
Parallel atomistic simulations
2000
Computer Physics Communications
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
However, systolic loop methods are designed for multi-processor machines with limited inter connectivity and have faded from the scene for use with molecular dynamics [96] [97] [98] [99] [100] [101] 4 ...
Two other similar algorithms appear in the literature, both for single instruction multiple data (SJMD) architectures, one for the Connection Machine CM-200 [74] and another for a MasPar NIP-2 [75] ...
doi:10.1016/s0010-4655(00)00050-3
fatcat:kj2ce3cjzvgf5khzk4t3qqyz7m
Molecular dynamics simulation on a network of workstations using a machine-independent parallel programming language
1991
Proceedings. Symposium on Computer Applications in Medical Care
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
This paper develops a straightforward but effective algorithm for molecular dynamics simulations using the machine-independent parallel programming language, Linda. ...
This algorithm offers a portable cost-effective alternative for molecular dynamics simulations. ...
Acknowledgements This research was funded in part by NIH grants T15 LM07056 and RO1 LM05044 from the National Library of Medicine. ...
pmid:1807634
pmcid:PMC2247565
fatcat:abpixqi6rzbmvi77zrokudkpji
A high performance, low complexity algorithm for compile-time task scheduling in heterogeneous systems
2005
Parallel Computing
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2005; you can also visit the original URL.
The file type is application/pdf.
The analysis and experiments have shown that HCPFD outperforms on average all other higher complexity algorithms. ...
In this paper we present a simple scheduling algorithm based on list-scheduling and task-duplication on a bounded number of heterogeneous machines called Heterogeneous Critical Parents with Fast Duplicator ...
Molecular Dynamic Code), HCPFD outperformed the other algorithms in terms of performance and complexity. ...
doi:10.1016/j.parco.2005.04.002
fatcat:yx6mefq3pbaqfbf5cevbappwui
Hyper-systolic parallel computing
1998
IEEE Transactions on Parallel and Distributed Systems
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
A new class of parallel algorithms is introduced that can achieve a complexity of O(n 1 In molecular dynamics applications with long range forces, e. g., exact state-of-the-art calculations are restricted ...
rôle in molecular dynamics with short range forces [8] . 3 Here we assume that the numbers of processors, p, and array elements, n, are equal. ...
Part of our numerical results has been achieved on the 1024-node connection machine CM5 of the Advanced Computing Laboaratory at Los Alamos National Laboratory, USA. ...
doi:10.1109/71.663861
fatcat:jshlqyog4barzmipc2lcpkwoau
Protein Structured Reservoir computing for Spike-based Pattern Recognition
[article]
2020
arXiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
Other Versions
We apply on a single readout layer various training methods in a supervised fashion to investigate whether the molecular structured Reservoir Computing (RC) system is capable to deal with machine learning ...
Following the trend, we explore an unconventional route of implementing a reservoir computing on a single protein molecule and introduce neuromorphic connectivity with a small-world networking property ...
VT-1 molecule, while their neuromorphic communication relies on the architecture based on both its hard molecular connectivity that is described by its chemical bonds and soft molecular connectivity described ...
arXiv:2008.03330v1
fatcat:fjzlh7ta65gvdpyr44xz7mik3a
A Priority-Based Task Scheduling Algorithm in Grid
2010
2010 3rd International Symposium on Parallel Architectures, Algorithms and Programming
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2013; you can also visit the original URL.
The file type is application/pdf.
Simulations are done on examples of DAG, and simulation results shown that the performance of P-TSA is better than other scheduling algorithms such as Min-min and Max-min. ...
Task scheduling algorithms are used to improve the grid performance by minimizing the scheduling length. A priority-based task scheduling algorithm (P-TSA) in grid is proposed in this paper. ...
The average of scheduling length of P-TSA based on DAG of molecular dynamics code is 73.3% of Max-min algorithm and 76.3% of Min-min algorithm, and the scheduling length can save 41.2% time at most. ...
doi:10.1109/paap.2010.24
dblp:conf/paap/SunZSJL10
fatcat:gfrdiacdv5hhlbdu3fk7shw35m
Exact Maximum Clique Algorithm for Different Graph Types Using Machine Learning
2021
Mathematics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2022; you can also visit the original URL.
The file type is application/pdf.
In this paper, improvements based on machine learning (ML) are added to a dynamic algorithm for finding the maximum clique in a protein graph, Maximum Clique Dynamic (MaxCliqueDyn; short: MCQD). ...
Such adaptability to graph types based on state-of-the-art machine learning is a novel approach that has not been used in most graph-theoretic algorithms. ...
A molecular docking graph is a graph whose nodes are docked molecular fragments and in which two nodes are connected if the docked fragments can be connected with linker atoms to reconstruct the original ...
doi:10.3390/math10010097
fatcat:sq476pdli5b4njy3zarvwfpuci
Overcoming Communication Latency Barriers in Massively Parallel Scientific Computation
2011
IEEE Micro
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2015; you can also visit the original URL.
The file type is application/pdf.
Acknowledgments We thank Ed Priest, Larry Nociolo, Chester Li, and Jon Peticolas for their work on high-speed analog circuits and signal integrity in Anton's communication channels; Stan Wang for design ...
This article describes the architectural and algorithmic approaches 7 that reduce the total communication time on Anton's critical path to less than 3 percent of that of the nextfastest molecular dynamics ...
Shaw Research, where he works on the development of new algorithms and machine architectures for high-speed biomolecular simulations and on the application of such simulations to basic scientific research ...
doi:10.1109/mm.2011.38
fatcat:n5hkj2k53jforilvu23bt2bbly
Molecular simulations: past, present, and future (a Topical Issue in EPJB)
2022
European Physical Journal B : Condensed Matter Physics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2022; you can also visit the original URL.
The file type is application/pdf.
Two of the corner stones of molecular simulations were introduced then, namely the Monte Carlo (MC) sampling technique [3] and the molecular dynamics (MD) method [4] . ...
That the two techniques appeared almost simultaneously at this ...
Acknowledgements The authors wish to express their gratefulness for the assistance offered by Sandrine Karpe, Christiane Winter-Todorov and Isabelle Auffret-Babak during the preparation and publication ...
doi:10.1140/epjb/s10051-021-00249-x
fatcat:nfavyrnn75egvoog57nyl6p45e
Parallel protein folding with STAPL
2005
Concurrency and Computation
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2006; you can also visit the original URL.
The file type is application/pdf.
These include lattice models [14], energy minimization [15,16], molecular dynamics [17-20], Monte Carlo methods [21,22], and genetic algorithms [23,24]. ...
Molecular dynamics and Monte Carlo methods PARALLEL PROTEIN FOLDING WITH STAPL STAPL STAPL is a framework for parallel C++ code [10] [11] [12] . ...
NAMD [35, 36] is a parallel molecular dynamics code designed for high-end parallel machines. ...
doi:10.1002/cpe.950
fatcat:is77asyxcjhgpb5aqlrlmor6da
Integrating Machine Learning with Physics-Based Modeling
[article]
2020
arXiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
Molecular dynamics and moment closure of kinetic equations are used as examples to illustrate the main issues discussed. ...
We end with a general discussion on where this integration will lead us to, and where the new frontier will be after machine learning is successfully integrated into scientific modeling. ...
Molecular modeling One of the most successful applications of machine learning to scientific modeling is in molecular dynamics. ...
arXiv:2006.02619v1
fatcat:dbaswddd7bdljjhl3can7tjzfm
« Previous
Showing results 1 — 15 out of 46,367 results