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10th International Conference on Information, Intelligence, Systems and Applications (IISA)

作者： Giannakis, Konstantinos Papalitsas, Christos Theocharopoulou, Georgia Fanarioti, Sofia Andronikos, Theodore Ionian Univ Dept Informat Corfu Greece

ISBN: (纸本)9781728149592

Data related to biology are characterized by large volume and requirements for enormous computational power. biological sequences, either of proteins or DNA/RNA segments, can be large and usually need massive computations in order to discover relations and study particular properties Aligning sequences is of great importance for various practical reasons. Multiple sequence alignment studies the problem of aligning several strings resulting in a complete alignment, a problem for which several different approaches exist. In this work, a novel heuristic method to progressively solve this problem is proposed using elements of quantum-inspired optimization. The proposed algorithm is described in detail and evaluated through simulations against other aligning methods. The experimental results seem promising for providing a good initial alignment, especially for the case of large sets of sequences.

关键词： multiple sequence alignment optimization quantum-inspired TSP bio-inspired bio-computing bioinformatics

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Observation of Autonomous Behavioral Selection in Physarum Plasmodium

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LOGICA UNIVERSALIS 2022年第4期16卷 643-653页

作者： Shirakawa, Tomohiro Sato, Hiroshi Ishimaru, Kazuki Nagaoka Niigata Japan Yokosuka Japan

The plasmodium of Physarum polycephalum is a unicellular and multinuclear giant amoeba with computational abilities. The plasmodium has been widely used as a model organism in the field of bio-computing;however, its ability to perform computation related to its biological nature itself in the essential sense has not yet been fully realized. Therefore, in this study, we focused on the phenomenon in which a plasmodium trapped in a closed space surrounded by repellent substances escapes from the field by changing its own behavior rules. We demonstrated that this phenomenon is bio-computationally important in that it may enable the implementation of biological characteristics in computing.

关键词： Physarum plasmodium bio-computing Behavior biological autonomy

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End-to-End Optimized Pipeline for Prediction of Protein Folding Kinetics 22

End-to-End Optimized Pipeline for Prediction of Protein Fold...

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22nd IEEE International Conference on Machine Learning and Applications, ICMLA 2023

作者： Vijay Arvind, R. Haribharathi, S. Brindha, R. Srm Institute of Science and Technology Faculty of Engineering and Technology Department of Computing Technologies Tamil Nadu 603 203 India

ISBN: (纸本)9798350345346

Protein folding is the intricate process by which a linear sequence of amino acids self-assembles into a unique three-dimensional structure. Protein folding kinetics is the study of pathways and time-dependent mechanisms a protein undergoes when it folds. Understanding protein kinetics is essential as a protein needs to fold correctly for it to perform its biological functions optimally, and a misfolded protein can sometimes be contorted into shapes that are not ideal for a cellular environment giving rise to many degenerative, neuro-degenerative disorders and amyloid diseases. Monitoring at-risk individuals and de-tecting protein discrepancies in a protein's folding kinetics at the early stages could majorly result in public health benefits, as preventive measures can be taken. This research proposes an efficient pipeline for predicting protein folding kinetics with high accuracy and low memory footprint. The deployed machine learning (ML) model outperformed the state-of-the-art ML models by 4.8% in terms of accuracy while consuming 327x lesser memory and being 7.3% faster. © 2023 IEEE.

关键词： bio-computing Logarithmic folding rate loT Machine learning algorithms

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The Charme of the Discrete Error - When Mathematical Socialism Becomes Art

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JOURNAL OF CELLULAR AUTOMATA 2021年第1-2期16卷 153-171页

作者： Roth, Tim Otto Imachinat Projects Oppenau Germany Imachinat Projects Cologne Germany

Automata theoreticians have occasionally suggested a certain affinity to arts and music. For Tommaso Toffoli and Norman Margulies performing cellular automata recalls the enactment of a music instrument: "A cellular automata machine is a universal synthesizer. Like an organ, it has keys and stops by which the resources of the instrument can be called into action. combined, and reconfigured. Its color screen is a window through which one can watch the universe that is being 'played'." [Toffoli & Margulies 1987, p. 5]. More a methodological commonality you can find in John von Neumann's heuristic plea promoting an "unmathematical process of experimentation with physical problems" - an approach lot of artists feel familiar with [Neumann 1966, p. 35]. But if you look back into art and music history you can observe that cellular automata are rarely used for artistic purposes.

关键词： Cellular automata self-organization bio-computing pixelsex mathematical socialism art & science organ carpet robustness India anthropology Iannis Xenakis Andreas Deutsch Hiroaki Kitano John von Neumann Stephen Wolfram Paul Klee

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Magnetotaxis of the Physarum Plasmodium and Construction of a Magnetically Controlled Physarum Logic Gate

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INTERNATIONAL JOURNAL OF UNCONVENTIONAL computing 2020年第4期15卷 245-258页

作者： Shirakawa, Tomohiro Sato, Hiroshi Muro, Michinori Konagano, Ryusuke Ohno, Ryota Inoue, Keita Natl Def Acad Japan Sch Elect & Comp Engn Dept Comp Sci 1-10-20 Hashirimizu Yokosuka Kanagawa 2398686 Japan

The plasmodium of Physarum polycephalum is a unicellular multinucleate giant amoeba. The plasmodium exhibits many types of taxes and uses these movements to adapt to its environment. In our previous study, we revealed that the plasmodium also exhibits magnetotaxis. In this study, we further investigated factors related to this magnetotaxis for use as a controlling factor in bio-computing and proposed a hypothesis on magnetotactic response of the plasmodium. Additionally, as a demonstration of magnetically controlled bio-computing, we constructed a magnetically controlled Physarum logic gate.

关键词： bio-computing amoeba-based computing Physarum plasmodium magnetotaxis logic gate magnetic control

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Diversity in the Chemotactic Behavior of Physarum Plasmodium Induced by Bi-modal Stimuli

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INTERNATIONAL JOURNAL OF UNCONVENTIONAL computing 2020年第4期15卷 275-285页

作者： Shirakawa, Tomohiro Gunji, Yukio-Pegio Sato, Hiroshi Tsubakino, Hiroto Natl Def Acad Japan Sch Elect & Comp Engn Dept Comp Sci 1-10-20 Hashirimizu Yokosuka Kanagawa 2398686 Japan Waseda Univ Sch Fundamental Sci & Technol Dept Intermedia Art & Sci Shinjuku Ku 3-4-1 Ohkubo Tokyo 1698555 Japan

The plasmodium of the true slime mold Physarum polycephalum is a unicellular, multinuclear giant amoeba that is attracting much attention in the field of bio-computing as a living computing substrate. To observe how the plasmodium of Physarum polycephalum responds to a contradictory situation, in which there is no single optimal solution, we applied bi-modal stimuli, consisting of a mixture of an attractant and a repellent, to plasmodia. The plasmodia showed diverse responses that could not be explained by a simple model of the stimulus-response system. We constructed a simulation model of the behavior that replicated the behavioral diversity with a simple combination of molecular apparatuses. In summary, we demonstrated the diversity of the behaviors of the plasmodium and how these behaviors may arise.

关键词： bio-computing amoeba-based computing physarum plasmodium chemotaxis behavior decision making

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A NEW APPROACH TO GENERATE MULTI S-BOXES BASED ON RNA computing

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INTERNATIONAL JOURNAL OF INNOVATIVE computing INFORMATION AND CONTROL 2020年第1期16卷 331-348页

作者： Farhan, Alaa Kadhim Ali, Rasha Subhi Yassein, Hassan Rashed Al-Saidi, Nadia Mohammed Ghanim Abdul-Majeed, Ghassan Hameed Univ Technol Baghdad Comp Sci Dept Al Sinaa St Baghdad 10066 Bagdad Iraq Univ Technol Baghdad Dept Appl Sci Al Sinaa St Baghdad 10066 Bagdad Iraq AL Nisour Univ Coll Dept Comp Tech Engn Al Harthiya Al Nisour Sq Baghdad 10092 Iraq Univ Al Qadisiyah Coll Educ Dept Math Ad Diwaniyah 58001 Al Qadisiyah Iraq Univ Baghdad Coll Engn Baghdad 10071 Iraq

Many scientists have tried to design new security methods in the domains of cryptography and steganography that are inspired by biological techniques, such as Deoxyribose Nucleic Acid (DNA), Ribonucleic Acid (RNA), Messenger RNA (mRNA), and other bio-molecular methods. Encryption techniques are typically applied to preserving the confidentiality of data, and this work aims to increase the protection of data through modern cryptographic methods. Based on DNA computing, our approach increases confusion through the design of multiple S-boxes. First, a new mRNA-based S-box generates different S-boxes for each user, and a secret key recursively creates these S-boxes until obtaining the required number of S-boxes. This proposed design passes S-box test criteria effectively, including invertibility, balance, completeness, avalanche, and strict avalanche. When changing only one bit in the key used to generate the S-boxes, the results show the newly constructed S-box changes with approximately 99% differences from the original. With comparisons between our technique to other searches, we found it converges to an optimal solution faster in abstracted steps. This new method can be leveraged in block cipher algorithms, such as AES, DES, and Ghost.

关键词： Multi S-box RNA bio-computing DNA map rules

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Construction of DNA-based logic gates on nanostructured microelectrodes

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Nuclear Science and Techniques 2017年第3期28卷 68-73页

作者： Tao Wei Min Li Yue-Yue Zhang Ali Aldalbahi Li-Hua Wang Xiao-Lei Zuo Yun Zhao Key Laboratory of Bio-Resources and Eco-Environment Ministry of Education College of Life Sciences Sichuan University Division of Physical Biology and Bioimaging Center Shanghai Synchrotron Radiation Facility CAS Key Laboratory of Interfacial Physics and Technology Shanghai Institute of Applied Physics Chinese Academy of Sciences Chemistry Department King Saud University

Electrochemical logical operations utilizing biological molecules(protein or DNA), which can be used in disease diagnostics and bio-computing, have attracted great research interest. However, the existing logic operations, being realized on macroscopic electrode, are not suitable for implantable logic devices. Here, we demonstrate DNA-based logic gates with electrochemical signal as output combined with gold flower microelectrodes. The designed logic gates are of fast response, enzyme-free, and micrometer scale. They perform well in either pure solution or complex matrices, such as fetal bovine serum,suggesting great potential for in vivo applications.

关键词： Logic gates Microelectrode bio-computing Electrochemical Nanostructured electrode

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Reconfigurable Hardware Accelerator for Profile Hidden Markov Models

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ARABIAN JOURNAL FOR SCIENCE AND ENGINEERING 2016年第8期41卷 3267-3277页

作者： Ibrahim, Atef Elsimary, Hamed Aljumah, Abdullah Gebali, Fayez Prince Sattam Bin Abdulaziz Univ Alkharj Saudi Arabia Elect Res Inst Cairo Egypt Univ Victoria Victoria BC Canada

We propose a processor array accelerator for profile hidden Markov models of the Viterbi algorithm. The proposed processor array has the advantage that it can be modified to enable hardware reuse rather than replicating processing elements of the processor array on a cluster of FPGAs. Also, it has the advantage of reducing the area overhead of the FPGA compared to the previously published conventional processor arrays. This allows for increasing the number of processing elements and the system throughput. The proposed processor array and the previously reported conventional one are coded using the VHDL language and implemented using the FPGA technology. The implementation results showed that the proposed design achieves 1.31x to 1.75xspeedup and saves area ranging from 24.4 to 34.0% over the conventional design for profile HMM query lengths ranging from 38 to 2295.

关键词： High-performance computing Parallel processing Processor arrays bio-computing Protein sequence alignment Reconfigurable computing Profile hidden Markov model

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Run-length encoding graphic rules, biochemically editable designs and steganographical numeric data embedment for DNA-based cryptographical coding system

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Communicative and Integrative biology 2013年第2期6卷 e23478页

作者： Kawano, Tomonori Faculty and Graduate School of Environmental Engineering The University of Kitakyushu Kitakyushu Japan University of Florence LINV Kitakyushu Research Center (LINV at Kitakyushu) Kitakyushu Japan International Plant Neurobiology Laboratory University of Florence Sesto Fiorentino Italy LEM Université Paris Diderot-Paris 7 Institut de Biologie des Plantes Orsay cedex France

There have been a wide variety of approaches for handling the pieces of DNA as the "unplugged" tools for digital information storage and processing, including a series of studies applied to the security-related area, such as DNA-based digital barcodes, water marks and cryptography. In the present article, novel designs of artificial genes as the media for storing the digitally compressed data for images are proposed for bio-computing purpose while natural genes principally encode for proteins. Furthermore, the proposed system allows cryptographical application of DNA through biochemically editable designs with capacity for steganographical numeric data embedment. As a model case of image-coding DNA technique application, numerically and biochemically combined protocols are employed for ciphering the given "passwords" and/or secret numbers using DNA sequences. The "passwords" of interest were decomposed into single letters and translated into the font image coded on the separate DNA chains with both the coding regions in which the images are encoded based on the novel run-length encoding rule, and the noncoding regions designed for biochemical editing and the remodeling processes revealing the hidden orientation of letters composing the original "passwords." The latter processes require the molecular biological tools for digestion and ligation of the fragmented DNA molecules targeting at the polymerase chain reaction-engineered termini of the ***, additional protocols for steganographical overwriting of the numeric data of interests over the image-coding DNA are also discussed.

关键词： Artificial gene for imaging Artificial genes bio-computing DNA Encryption Informatics RLE Run-length encoding Steganography

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