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INVASION PERCOLATION: A computational algorithm FOR COMPLEX PHENOMENA

COMPUTING IN SCIENCE & ENGINEERING 2010年第2期12卷 84-93页

作者： Ebrahimi, Fatemeh Univ Birjand Birjand Iran

Developing efficient computational algorithms for studying complex phenomena has been a long-standing problem in physics and engineering. One such algorithm, invasion percolation, has found wide applications.

关键词： Statistical physics algorithm theory complex phenomena computational algorithm invasion percolation invasion percolation large-scale systems percolation percolation

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Simulation of vibro-impact gear model considering the lubricant influence with a new computational algorithm

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JOURNAL OF THE BRAZILIAN SOCIETY OF MECHANICAL SCIENCES AND ENGINEERING 2018年第3期40卷 1-14页

作者： Liu, Fuhao Zhang, Liang Jiang, Hanjun Yu, Xuehua Yancheng Inst Technol Coll Automobile Engn Yancheng 224051 Jiangsu Peoples R China Shanghai Jiao Tong Univ Dept Engn Mech Shanghai 200240 Peoples R China

In this paper, a vibro-impact gear model incorporating the influences of the lubricant and backlash is formulated. Then, a new computational algorithm validated in comparison with the "stiff'' solvers, by defining a transition area and adopting the double-changed time step, is proposed to identify the influences of the lubricant on the dynamic system. The results obtained in this paper indicate that the proposed numerical algorithm not only guarantees the precision of solutions, but also reduces the calculation speed of the whole system. The lubricant can potentially reduce the vibrations in the gear system, and the boundaries for double-sided impacts, single-sided impact and no impact are mainly dependent on the fluctuating driving torque and the stiffness of the lubricant. These results could provide a good source of information on the utilization of vibro-impact modeling and simulation for the study of spur gears dynamic performance, and quantification of the factors such as gear backlash, input power or torque fluctuations, lubrication, rattle, etc. In addition, the proposed numerical method could be used as a basic program of vibro-impact in Matlab environment.

关键词： Gear system computational algorithm Nonlinear vibration Gear backlash

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A computational algorithm for Calculating Fracture Index of Core Runs

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ROCK MECHANICS AND ROCK ENGINEERING 2023年第9期56卷 6905-6918页

作者： Wong, Louis Ngai Yuen Liu, Zihan Tse, Keith Ki Chun Cheung, Sai Hung Yu, Lequan Univ Hong Kong Dept Earth Sci Hong Kong Peoples R China Univ Hong Kong Dept Civil Engn Hong Kong Peoples R China Univ Hong Kong Dept Stat & Actuarial Sci Hong Kong Peoples R China

Fracture Index (FI), which represents the count of fractures over an arbitrary length of core with similar intensity of fracturing, provides insight into the fracture state of rock masses. Manual interpretation of core is not only time-consuming but also prone to human error. To address these challenges, this study develops a computational algorithm that automatically calculates the FI of core runs based on fracture spacing data. The variance of fracture spacing values is selected as the key evaluating indicator. The algorithm automatically groups fractures appearing in core imagery based on uniformity of fracture spacing. Upon counting the number of fractures in each group over a certain length of core run obtained from the optimal grouping scheme, the algorithm outputs the FIs automatically. The algorithm's performance has been effectively demonstrated on synthetic data and three real-life core datasets. algorithm results show good agreement with those produced by logging geologists and listed in standard human-generated reports. The occasional discrepancies are attributed to the inherent subjective nature associated with the manual logging.

关键词： computational algorithm Fracture Index Joint spacing Core run

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Whole genome analysis of CRISPR Cas9 sgRNA off-target homologies via an efficient computational algorithm

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BMC GENOMICS 2017年第Sup9期18卷 31-38页

作者： Zhou, Hong Zhou, Michael Li, Daisy Manthey, Joseph Lioutikova, Ekaterina Wang, Hong Zeng, Xiao Univ St Joseph Dept Math Sci 1678 Asylum Ave Hartford CT 06117 USA Hall High Sch 975 N Main St Hartford CT 06117 USA Rutgers State Univ Ernest Mario Sch Pharm Dept Biol Chem Susan L Cullman Lab Canc Res 164 Frelinghuysen Rd Piscataway NJ 08854 USA Rutgers State Univ Ernest Mario Sch Pharm Ctr Canc Prevent Res 164 Frelinghuysen Rd Piscataway NJ 08854 USA PBSG LLC POB 771 Braddock Heights MD 21714 USA

Background: The beauty and power of the genome editing mechanism, CRISPR Cas9 endonuclease system, lies in the fact that it is RNA-programmable such that Cas9 can be guided to any genomic loci complementary to a 20-nt RNA, single guide RNA (sgRNA), to cleave double stranded DNA, allowing the introduction of wanted mutations. Unfortunately, it has been reported repeatedly that the sgRNA can also guide Cas9 to off-target sites where the DNA sequence is homologous to sgRNA. Results: Using human genome and Streptococcus pyogenes Cas9 (SpCas9) as an example, this article mathematically analyzed the probabilities of off-target homologies of sgRNAs and discovered that for large genome size such as human genome, potential off-target homologies are inevitable for sgRNA selection. A highly efficient computationl algorithm was developed for whole genome sgRNA design and off-target homology searches. By means of a dynamically constructed sequence-indexed database and a simplified sequence alignment method, this algorithm achieves very high efficiency while guaranteeing the identification of all existing potential off-target homologies. Via this algorithm, 1,876,775 sgRNAs were designed for the 19,153 human mRNA genes and only two sgRNAs were found to be free of off-target homology. Conclusions: By means of the novel and efficient sgRNA homology search algorithm introduced in this article, genome wide sgRNA design and off-target analysis were conducted and the results confirmed the mathematical analysis that for a sgRNA sequence, it is almost impossible to escape potential off-target homologies. Future innovations on the CRISPR Cas9 gene editing technology need to focus on how to eliminate the Cas9 off-target activity.

关键词： sgRNA Off-target homology Crispr Cas9 computational algorithm Genome wide

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Applications of computational algorithm tools to identify functional SNPs in cytokine genes

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CYTOKINE 2006年第1-2期35卷 62-66页

作者： Shen, Jie Deininger, Prescott L. Zhao, Hua Tulane Univ Tulane Canc Ctr New Orleans LA 70118 USA Tulane Univ Dept Epidemiol Sch Publ Hlth & Trop Med New Orleans LA 70118 USA Roswell Pk Canc Inst Dept Epidemiol Div Canc Prevent & Populat Sci Buffalo NY 14263 USA

Understanding the functions of single nucleotide polymorphisms (SNPs) can greatly help to understand the genetics of the human phenotype variation and especially the genetic basis of human complex diseases. However, how to identify functional SNPs from a pool containing both functional and neutral SNPs is challenging. In this study, we analyzed the genetic variations that can alter the expression and function of a group of cytokine proteins using computational tools. As a result, we extracted 4552 SNPs from 45 cytokine proteins from SNPper database. Of particular interest, 828 SNPs were in the 5'UTR region, 961 SNPs were in the 3' UTR region, and 85 SNPs were non-synonymous SNPs (nsSNPs), which cause amino acid change. Evolutionary conservation analysis using the SIFT tool suggested that 8 nsSNPs may disrupt the protein function. Protein structure analysis using the PolyPhen tool suggested that 5 nsSNPs might alter protein structure. Binding motif analysis using the UTResource tool suggested that 27 SNPs in 5' or 3'UTR might change protein expression levels. Our study demonstrates the presence of naturally occurring genetic variations in the cytokine proteins that may affect their expressions and functions with possible roles in complex human disease, such as immune diseases. (c) 2006 Elsevier Ltd. All rights reserved.

关键词： computational algorithm cytokine SNP

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An improved computational algorithm for finding the factorial

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MATHEMATICAL NOTES 2008年第5-6期83卷 783-789页

作者： Ladikov, A. V. Moscow State Univ Railway Engn MIIT Moscow Russia

In the present paper, we consider a method for improving the computational algorithm for finding the factorials of integers;this method linearly accelerates the computations. We also present several algorithms effecti... 详细信息

关键词： computational algorithm factorial algorithm complexity

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Social sharing and risk reduction - Exploring a computational algorithm for the psychology of windfall gains

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EVOLUTION AND HUMAN BEHAVIOR 2002年第1期23卷 11-33页

作者： Kameda, T Takezawa, M Tindale, RS Smith, CM Hokkaido Univ Dept Behav Sci Kita Ku Sapporo Hokkaido 0600810 Japan Max Planck Inst Human Dev D-14195 Berlin Germany Loyola Univ Dept Psychol Chicago IL 60626 USA Grand Valley State Univ Dept Psychol Allendale MI 49401 USA

Sharing important resources widely beyond direct kin group members is one of the core features characterizing human societies. Moreover, generalized exchange involving many community members (e.g., meat sharing in bands) seems to be a uniquely human practice. This paper explores a computational algorithm for the psychology of social sharing that may underlie such practices, based on the risk-reduction hypothesis in food sharing of Kaplan and Hill [Curr. Anthropol. 26 (1985) 223]. We predicted that, independent of the amount of effort actually invested, uncertainty involved in resource acquisition is a key factor that triggers the psychology of social sharing for both acquirers and nonacquirers of a resource. It was also predicted that the "windfall effect" is independent of individual preferences as to modem distributive ideologies. Four multisample/multimethod studies, using Japanese and American participants, and laboratory as well as vignette experiments, supported these predictions: although the identical fungible resource (money) was under consideration, different psychological processes were triggered, depending on the degree of uncertainty involved in the money acquisition. Implications of the windfall effect for egalitarianism in resource sharing, observed not only in hunter-gatherer bands but also in highly industrialized societies, are discussed. (C) 2002 Elsevier Science Inc. All rights reserved.

关键词： resource sharing risk reduction computational algorithm egalitarianism

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A computational algorithm for personalized medicine in schizophrenia

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SCHIZOPHRENIA RESEARCH 2018年 192卷 131-136页

作者： Lee, Beom S. McIntyre, Roger S. Gentle, James E. Park, Nan Sook Chiriboga, David A. Lee, Yena Singh, Sabrina McPherson, Marie A. Univ S Florida Louis Parte Florida Mental Hlth Inst Dept Mental Hlth Law & Policy Tampa FL 33612 USA Univ Toronto Dept Psychiat Toronto ON M5T 1R8 Canada George Mason Univ Dept Computat & Data Sci Fairfax VA 22030 USA Univ S Florida Sch Social Work Tampa FL 33612 USA Univ S Florida Louis Parte Florida Mental Hlth Inst Dept Child & Family Studies Tampa FL 33612 USA Univ Hlth Network Mood Disorders Psychopharmacol Unit Toronto ON M5T 2S8 Canada

Despite advances in sequencing candidate genes and whole genomes, no method has accurately predicted who will or will not benefit from a specific antipsychotic medication among patients with schizophrenia. We propose a computational algorithm that utilizes a person-centered approach that directly identifies individual patients who will respond to a specific antipsychotic medication. The algorithm was applied to the data obtained from the Clinical Anti psychotic Trials of Intervention Effectiveness (CATIE) study. The predictors were either (1) 13 single-nucleotide polymorphisms (SNPs) and 53 baseline variables or (2) 25 SNPs and the same 53 baseline variables, depending on the existing findings and data availability. The outcome variables were either (1) improvement in the Positive and Negative Syndrome Scale (PANSS) (Yes/No) or (2) completion of phase 1/1A (Yes/No). Each of those four predictor-outcome combinations was tried for each of the five antipsychotic medications (Per-phenazine, Olanzapine, Quetiapine, Risperidone, and Ziprasidone), leading to 20 prediction experiments. For 18 out of 20 experiments, all three performance measures were greater than 0.50 (sensitivity 0.51-0.79, specificity 0.52-0.79, accuracy 0.52-0.74). Notably, the model provided a promising prediction for Ziprasidone for the case involving completion of phase 1/1A (Yes/No) predicted by 13 SNPs and 53 baseline variables (sensitivity 0.75, specificity 0.74, accuracy 0.74). The proposed algorithm simultaneously used both genetic information and clinical profiles to predict individual patients' response to antipsychotic medications. As the method is not disease-specific but a general algorithm, it can be easily adopted in many other clinical practices for personalized medicine. (C) 2017 Elsevier B.V. All rights reserved.

关键词： Personalized medicine computational algorithm Predictive modeling GWAS SNPs Pharmacogenomics

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The Dynamic Allan Variance II: A Fast computational algorithm

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IEEE TRANSACTIONS ON ULTRASONICS FERROELECTRICS AND FREQUENCY CONTROL 2010年第1期57卷 182-188页

作者： Galleani, Lorenzo Politecn Torino Dept Elect Turin Italy

The stability of an atomic clock can change with time due to several factors, such as temperature, humidity, radiations, aging, and sudden breakdowns. The dynamic Allan variance, or DAVAR, is a representation of the time-varying stability of an atomic clock, and it can be used to monitor the clock behavior. Unfortunately, the computational time of the DAVAR grows very quickly with the length of the analyzed time series. In this article, we present a fast algorithm for the computation of the DAVAR, and we also extend it to the case of missing data. Numerical simulations show that the fast algorithm dramatically reduces the computational time. The fast algorithm is useful when the analyzed time series is long, or when many clocks must be monitored, or when the computational power is low, as happens onboard satellites and space probes.

关键词： artificial satellites atomic clocks stability time series time-varying systems aging atomic clock stability clock behavior monitoring computational algorithm computational time dynamic Allan variance humidity numerical simulation radiation satellite space probe sudden breakdown temperature time-varying stability Atomic clocks Allan Variance time varying Space probes computational time Aging satellites time-varying systems artificial satellite numerical simulation Time series Radiation moistening

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Pro-Environmental Potential in Activity-Travel Routine of Individuals: A Data Driven computational algorithm 9th

Pro-Environmental Potential in Activity-Travel Routine of In...

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9th International Conference on Ambient Systems, Networks and Technologies (ANT) / 8th International Conference on Sustainable Energy Information Technology (SEIT)

作者： Ahmed, Shiraz Adnan, Muhammand Janssens, Davy Yasar, Ansar-ul-Haque Kumar, Prashant Shakshuki, Elhadi M. UHasselt Hasselt Univ Transportat Res Inst IMOB Agr Laan B-3590 Diepenbeek Belgium Univ Surrey Fac Engn & Phys Sci Global Ctr Clean Air Res GCARE Dept Civil & Environm Engn Guildford GU2 7XH Surrey England Acadia Univ Jodrey Sch Comp Sci Wolfville NS Canada

Informational interventions are considered important to bring positive changes in attitudes and perception about pro-environmental life styles among individuals. In relation to mobility aspects, it is vital to identify relatively easier changes that have potential to reduce negative impacts of mobility on environment and individual health. This paper provides a comprehensive methodological framework and developed a computation algorithm that helps identify such an easy changes in the travel behavior of an individual. The development of algorithm is based on a variety of different data sources such as activity-travel diaries and related constraint information, meteorological conditions, bicycle and public transport supply data. A variety of rules that are part of the computational algorithm are taken from the transport modelling literature, where constraints and factors were examined for various activity-travel decisions. Three major aspects of activity-travel behavior such as lesser car use, cold start of car engines and participation in non-mandatory outdoor activities are considered in assessing pro-environmental potential. The algorithm is applied to data collected, using citizens from Hasselt and their pro-environmental potential is determined, which has been found significant. (C) 2018 The Authors. Published by Elsevier B.V.

关键词： Pro-environmantal potential acitivity-travel behavior informational intervention computational algorithm

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