A two-dimensional modified Lévy-walk model for the DNA sequences

2006 ◽  
Vol 369 (2) ◽  
pp. 688-698 ◽  
Author(s):  
Yuan-Yen Tai ◽  
Ping-Cheng Li ◽  
Hsen-Che Tseng
Keyword(s):  
Dna Sequences ◽  
Two Dimensional ◽  
Lévy Walk ◽  
Levy Walk

Noisy Lévy walk analog of two-dimensional DNA walks for chromosomes of S. cerevisiae

1998 ◽  
Vol 58 (1) ◽  
pp. 914-918 ◽  
Author(s):  
Guillermo Abramson ◽  
Pablo A. Alemany ◽  
Hilda A. Cerdeira
Keyword(s):  
Two Dimensional ◽  
Lévy Walk ◽  
Levy Walk

Multi-Fractal Analysis for Feature Extraction from DNA Sequences

2012 ◽  
pp. 100-118
Author(s):  
Witold Kinsner ◽  
Hong Zhang
Keyword(s):  
Feature Extraction ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Window Size ◽  
Signal Spectrum ◽  
Coding Region ◽  
Lévy Walk ◽  
Fractal Measures ◽  
Levy Walk ◽  
Biological Functionality

This paper presents estimations of multi-scale (multi-fractal) measures for feature extraction from deoxyribonucleic acid (DNA) sequences, and demonstrates the intriguing possibility of identifying biological functionality using information contained within the DNA sequence. We have developed a technique that seeks patterns or correlations in the DNA sequence at a higher level than the local base-pair structure. The technique has three main steps: (i) transforms the DNA sequence symbols into a modified Lévy walk, (ii) transforms the Lévy walk into a signal spectrum, and (iii) breaks the spectrum into sub-spectra and treats each of these as an attractor from which the multi-fractal dimension spectrum is estimated. An optimal minimum window size and volume element size are found for estimation of the multi-fractal measures. Experimental results show that DNA is multi-fractal, and that the multi-fractality changes depending upon the location (coding or non-coding region) in the sequence.

Multi-Fractal Analysis for Feature Extraction from DNA Sequences

2010 ◽  
Vol 2 (2) ◽  
pp. 1-18 ◽  
Author(s):  
Witold Kinsner ◽  
Hong Zhang
Keyword(s):  
Feature Extraction ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Window Size ◽  
Signal Spectrum ◽  
Coding Region ◽  
Lévy Walk ◽  
Fractal Measures ◽  
Levy Walk ◽  
Biological Functionality

This paper presents estimations of multi-scale (multi-fractal) measures for feature extraction from deoxyribonucleic acid (DNA) sequences, and demonstrates the intriguing possibility of identifying biological functionality using information contained within the DNA sequence. We have developed a technique that seeks patterns or correlations in the DNA sequence at a higher level than the local base-pair structure. The technique has three main steps: (i) transforms the DNA sequence symbols into a modified Lévy walk, (ii) transforms the Lévy walk into a signal spectrum, and (iii) breaks the spectrum into sub-spectra and treats each of these as an attractor from which the multi-fractal dimension spectrum is estimated. An optimal minimum window size and volume element size are found for estimation of the multi-fractal measures. Experimental results show that DNA is multi-fractal, and that the multi-fractality changes depending upon the location (coding or non-coding region) in the sequence.

scholarly journals Intermittent inverse-square Lévy walks are optimal for finding targets of all sizes

2021 ◽  
Vol 7 (15) ◽  
pp. eabe8211
Author(s):  
Brieuc Guinard ◽  
Amos Korman
Keyword(s):  
Random Walk ◽  
Mathematical Proof ◽  
Higher Dimensions ◽  
Two Dimensional ◽  
Power Law Distribution ◽  
Arbitrary Size ◽  
Lévy Walk ◽  
Lévy Walks ◽  
Levy Walk ◽  
Biological Organisms

Lévy walks are random walk processes whose step lengths follow a long-tailed power-law distribution. Because of their abundance as movement patterns of biological organisms, substantial theoretical efforts have been devoted to identifying the foraging circumstances that would make such patterns advantageous. However, despite extensive research, there is currently no mathematical proof indicating that Lévy walks are, in any manner, preferable strategies in higher dimensions than one. Here, we prove that in finite two-dimensional terrains, the inverse-square Lévy walk strategy is extremely efficient at finding sparse targets of arbitrary size and shape. Moreover, this holds even under the weak model of intermittent detection. Conversely, any other intermittent Lévy walk fails to efficiently find either large targets or small ones. Our results shed new light on the Lévy foraging hypothesis and are thus expected to affect future experiments on animals performing Lévy walks.

Three-Dimensional Structure of Cloned T3 Connector Protein at 1.6nm Resolution

1990 ◽  
Vol 48 (1) ◽  
pp. 282-283
Author(s):  
José L. Carrascosa ◽  
José M. Valpuesta ◽  
Hisao Fujisawa
Keyword(s):  
Dna Sequences ◽  
Expression Vector ◽  
Three Dimensional ◽  
Deae Cellulose ◽  
Dna Packaging ◽  
Dimensional Structure ◽  
Two Dimensional ◽  
Freezing And Thawing ◽  
Three Dimensional Structure ◽  
Dimensional Reconstruction

The head to tail connector of bacteriophages plays a fundamental role in the assembly of viral heads and DNA packaging. In spite of the absence of sequence homology, the structure of connectors from different viruses (T4, Ø29, T3, P22, etc) share common morphological features, that are most clearly revealed in their three-dimensional structure. We have studied the three-dimensional reconstruction of the connector protein from phage T3 (gp 8) from tilted view of two dimensional crystals obtained from this protein after cloning and purification.DNA sequences including gene 8 from phage T3 were cloned, into Bam Hl-Eco Rl sites down stream of lambda promotor PL, in the expression vector pNT45 under the control of cI857. E R204 (pNT89) cells were incubated at 42°C for 2h, harvested and resuspended in 20 mM Tris HC1 (pH 7.4), 7mM 2 mercaptoethanol, ImM EDTA. The cells were lysed by freezing and thawing in the presence of lysozyme (lmg/ml) and ligthly sonicated. The low speed supernatant was precipitated by ammonium sulfate (60% saturated) and dissolved in the original buffer to be subjected to gel nitration through Sepharose 6B, followed by phosphocellulose colum (Pll) and DEAE cellulose colum (DE52). Purified gp8 appeared at 0.3M NaCl and formed crystals when its concentration increased above 1.5 mg/ml.

Diffusion

2018 ◽  
Author(s):  
Ginestra Bianconi
Keyword(s):  
Random Walks ◽  
Spectral Properties ◽  
Diffusion Constant ◽  
Network Structures ◽  
Multilayer Networks ◽  
Multilayer Network ◽  
Lévy Walk ◽  
Number Of Layers ◽  
Levy Walk ◽  
Speed Up

This chapter addresses diffusion, random walks and congestion in multilayer networks. Here it is revealed that diffusion on a multilayer network can be significantly speed up with respect to diffusion taking place on its single layers taken in isolation, and that sometimes it is possible also to observe super-diffusion. Diffusion is here characterized on multilayer network structures by studying the spectral properties of the supra-Laplacian and the dependence on the diffusion constant among different layers. Random walks and its variations including the Lévy Walk are shown to reflect the improved navigability of multilayer networks with more layers. These results are here compared with the results of traffic on multilayer networks that, on the contrary, point out that increasing the number of layers could be detrimental and could lead to congestion.

scholarly journals Amoebic Foraging Model of Metastatic Cancer Cells

Symmetry ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 1140
Author(s):  
Daiki Andoh ◽  
Yukio-Pegio Gunji
Keyword(s):  
Bayesian Inference ◽  
Cancer Cells ◽  
Metastatic Cancer ◽  
Gait Patterns ◽  
Lévy Walk ◽  
Levy Walk ◽  
Unicellular Organisms ◽  
Living Organisms ◽  
Walk Algorithm ◽  
Metastatic Cancer Cells

The Lévy walk is a pattern that is often seen in the movement of living organisms; it has both ballistic and random features and is a behavior that has been recognized in various animals and unicellular organisms, such as amoebae, in recent years. We proposed an amoeba locomotion model that implements Bayesian and inverse Bayesian inference as a Lévy walk algorithm that balances exploration and exploitation, and through a comparison with general random walks, we confirmed its effectiveness. While Bayesian inference is expressed only by P(h) = P(h|d), we introduce inverse Bayesian inference expressed as P(d|h) = P(d) in a symmetry fashion. That symmetry contributes to balancing contracting and expanding the probability space. Additionally, the conditions of various environments were set, and experimental results were obtained that corresponded to changes in gait patterns with respect to changes in the conditions of actual metastatic cancer cells.

scholarly journals Langevin dynamics for a Lévy walk with memory

2019 ◽  
Vol 99 (1) ◽  
Author(s):  
Yao Chen ◽  
Xudong Wang ◽  
Weihua Deng
Keyword(s):  
Langevin Dynamics ◽  
Lévy Walk ◽  
Levy Walk ◽  
With Memory
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