A cellular automaton model for the study of DNA sequence evolution

Sirakoulis, Georgios Ch.; Karafyllidis, Ioannis; Mizas, Ch.; Mardiris, Vassilios A.; Thanailakis, A.; Tsalides, Ph.

doi:10.1016/s0010-4825(03)00017-9

Cited by 41 publications

(16 citation statements)

References 12 publications

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“…Advanced computer modelling techniques (often referred to as in silico models), is an expression used to mean "performed on computer or via computer simulation" [38]. The expression in silico "appears" for the first time in 1989 in the workshop "Cellular Automata: Theory and Applications" in Los Alamos, New Mexico [39,40]. The experimental tribological devices for the simulation of hip and knee prostheses have been improved over the years in order to make them able to reproduce tribological wear tests in kinematic and dynamic conditions very close to the real ones [30][31][32][33].…”

Section: Toward the In Silico Wear Testmentioning

confidence: 99%

A Perspective on Biotribology in Arthroplasty: From In Vitro toward the Accurate In Silico Wear Prediction

Affatato

Ruggiero

2020

Applied Sciences

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Nowadays hip arthroplasty is recognized as one of the most successful orthopedic surgical procedures, even if it involves challenges to overcome, such that lately, younger and more active patients are in need of total arthroplasty. Wear is still one of the main issues affecting joint prostheses endurance, and often causes loosening accompanied by implant failures. Actual in vitro wear tests executed by mechanical simulators have a long duration, are very expensive, and do not take into account all the possible daily activities of the patients; thus, the challenge to obtain a complete in silico tribological and dynamical model of (bio) tribo-systems could give the possibility to overcome the actual testing procedures and could contribute as a tool for a more accurate tribological design of human prostheses. This prospective paper is intended to underline actual research trends toward the challenge of having accurate numerical algorithms to be used both in preclinical testing and in the optimizations of the prostheses design. With this aim we depicted the possible in silico approach in artificial joints’ wear assessment over time, accounting for contact mechanics, numerical stress–strain analysis, musculoskeletal multibody, and synovial lubrication modelling (boundary/mixed, hydrodynamic, and elastohydrodynamic).

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Section: Toward the In Silico Wear Testmentioning

confidence: 99%

A Perspective on Biotribology in Arthroplasty: From In Vitro toward the Accurate In Silico Wear Prediction

Affatato

Ruggiero

2020

Applied Sciences

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“…The idea of employing CA to the central dogma of molecular biology is not new and many attempts were made to model the central dogma in terms of structure, function, and evolution. CA models were used in modeling DNA sequences [11], evolution [12], mutation prediction [13], and gene networks [14].…”

Section: Related Workmentioning

confidence: 99%

Computational Modeling of Proteins based on Cellular Automata

Madain¹,

Dalhoum²,

Sleit³

2016

ijacsa

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Abstract-The literature of building computational and mathematical models of proteins is rich and diverse, since its practical applications are of a vital importance in the development of many fields. Modeling proteins is not a straightforward process and in some modeling strategies, it requires to combine concepts from different fields including physics, chemistry, thermodynamics, and computer science. The focus here will be on models that are based on the concept of cellular automata and equivalent systems. Cellular automata are discrete computational models that are capable of universal computation, in other words, they are capable of doing any computation that a normal computer can do. What is special about cellular automata is its ability to produce complex and chaotic global behavior from local interactions. The paper discusses the effort done so far by the researchers community in this direction and proposes a computational model of protein folding that is based on 3D cellular automata. Unlike common models, the proposed model maintains the basic properties of cellular automata and keeps a realistic view of proteins operations. As in any cellular automata model, the dimension, neighborhood, boundary, and rules were specified. In addition, a discussion is given to clarify why these parameters are in place and what possible alternatives can be used in the protein folding context.

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“…Sirakoulis et al [167] designed a cellular automata model for DNA structure, function and evolution. In their model, DNA was treated as a one-dimensional cellular automaton with four states per cell.…”

Section: Protein Sequence Evolution Modelmentioning

confidence: 99%

Cellular Automata and Its Applications in Protein Bioinformatics

Xiao¹,

Wang²,

Chou

2011

CPPS

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With the explosion of protein sequences generated in the postgenomic era, it is highly desirable to develop high-throughput tools for rapidly and reliably identifying various attributes of uncharacterized proteins based on their sequence information alone. The knowledge thus obtained can help us timely utilize these newly found protein sequences for both basic research and drug discovery. Many bioinformatics tools have been developed by means of machine learning methods. This review is focused on the applications of a new kind of science (cellular automata) in protein bioinformatics. A cellular automaton (CA) is an open, flexible and discrete dynamic model that holds enormous potentials in modeling complex systems, in spite of the simplicity of the model itself. Researchers, scientists and practitioners from different fields have utilized cellular automata for visualizing protein sequences, investigating their evolution processes, and predicting their various attributes. Owing to its impressive power, intuitiveness and relative simplicity, the CA approach has great potential for use as a tool for bioinformatics.

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A cellular automaton model for the study of DNA sequence evolution

Cited by 41 publications

References 12 publications

A Perspective on Biotribology in Arthroplasty: From In Vitro toward the Accurate In Silico Wear Prediction

A Perspective on Biotribology in Arthroplasty: From In Vitro toward the Accurate In Silico Wear Prediction

Computational Modeling of Proteins based on Cellular Automata

Cellular Automata and Its Applications in Protein Bioinformatics

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