arXiv: Other Quantitative Biology最新文献

{"title":"Life at the edge: complexity and criticality in biological function","authors":"D. Chialvo","doi":"10.5506/APhysPolB.49.1955","DOIUrl":"https://doi.org/10.5506/APhysPolB.49.1955","url":null,"abstract":"Why life is complex and --most importantly-- what is the origin of the over abundance of complexity in nature? This is a fundamental scientific question which, paraphrasing the late Per Bak, \"is screaming to be answered but seldom is even being asked\". In these lectures we review recent attempts across several scales to understand the origins of complex biological problems from the perspective of critical phenomena. To illustrate the approach three cases are discussed, namely the large scale brain dynamics, the characterisation of spontaneous fluctuations of proteins and the physiological complexity of the cell mitochondria network.","PeriodicalId":8460,"journal":{"name":"arXiv: Other Quantitative Biology","volume":"2009 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78666263","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Quantum Patterns of Genome Size Variation in Angiosperms","authors":"L. Luo, Lirong Zhang","doi":"10.2174/1574893615999200420071919","DOIUrl":"https://doi.org/10.2174/1574893615999200420071919","url":null,"abstract":"The nuclear DNA amount in angiosperms is studied from the eigen-value equation of the genome evolution operator H. The operator H is introduced by physical simulation and it is defined as a function of the genome size N and the derivative with respective to the size. The discontinuity of DNA size distribution and its synergetic occurrence in related angiosperms species are successfully deduced from the solution of the equation. The results agree well with the existing experimental data of Aloe, Clarkia, Nicotiana, Lathyrus, Allium and other genera. It may indicate that the evolutionary constrains on angiosperm genome are essentially of quantum origin.","PeriodicalId":8460,"journal":{"name":"arXiv: Other Quantitative Biology","volume":"2 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75995648","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Telling apart Felidae and Ursidae from the distribution of nucleotides in mitochondrial DNA.","authors":"Andrij Rovenchak","doi":"10.1142/S0217984918500574","DOIUrl":"https://doi.org/10.1142/S0217984918500574","url":null,"abstract":"Rank--frequency distributions of nucleotide sequences in mitochondrial DNA are defined in a way analogous to the linguistic approach, with the highest-frequent nucleobase serving as a whitespace. For such sequences, entropy and mean length are calculated. These parameters are shown to discriminate the species of the Felidae (cats) and Ursidae (bears) families. From purely numerical values we are able to see in particular that giant pandas are bears while koalas are not. The observed linear relation between the parameters is explained using a simple probabilistic model. The approach based on the nonadditive generalization of the Bose-distribution is used to analyze the frequency spectra of the nucleotide sequences. In this case, the separation of families is not very sharp. Nevertheless, the distributions for Felidae have on average longer tails comparing to Ursidae.","PeriodicalId":8460,"journal":{"name":"arXiv: Other Quantitative Biology","volume":"14 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76689042","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Symmetry and Minimum Principle at the Basis of the Genetic Code","authors":"A. Sciarrino, P.Sorba","doi":"10.1142/9789813227880_0019","DOIUrl":"https://doi.org/10.1142/9789813227880_0019","url":null,"abstract":"The importance of the notion of symmetry in physics is well established: could it also be the case for the genetic code? In this spirit, a model for the Genetic Code based on continuous symmetries and entitled the \"Crystal Basis Model\" has been proposed a few years ago. The present paper is a review of the model, of some of its first applications as well as of its recent developments. Indeed, after a motivated presentation of our mathematical model, we illustrate its pertinence by applying it for the elaboration and verification of sum rules for codon usage probabilities, as well as for establishing relations and some predictions between physical-chemical properties of amino-acids. Then, defining in this context a \"bio-spin\" structure for the nucleotides and codons, the interaction between a couple of codon-anticodon can simply be represented by a (bio) spin-spin potential. This approach will constitute the second part of the paper where, imposing the minimum energy principle, an analysis of the evolution of the genetic code can be performed with good agreement with the generally accepted scheme. A more precise study of this interaction model provides informations on codon bias, consistent with data.","PeriodicalId":8460,"journal":{"name":"arXiv: Other Quantitative Biology","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2017-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88902817","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Biochemical mechanism of resistance in some Brassica genotypes against Lipaphis erysimi (Kaltenbach) (Homoptera: Aphididae)","authors":"Sarwan Kumar, M. Sangha","doi":"10.5958/J.2229-4473.26.2.103","DOIUrl":"https://doi.org/10.5958/J.2229-4473.26.2.103","url":null,"abstract":"Two years study was carried out during 2006-07 and 2007-08 crop seasons to study the response of different genotypes of oilseeds Brassica to Lipaphis erysimi (Kaltenbach) infestation both under field and screen house conditions and to find out the relationship of various biochemical constituents to aphid infestation. Among the various genotypes, the population of L. erysimi was significantly high on Brassica rapa variety brown sarson cv. BSH 1 and B. rapa var. yellow sarson cv. YST 151 in unprotected set i.e. 53.7 and 52.3 aphids/ plant, respectively. However, it was the lowest on Eruca sativa cv. T 27 (4.7 aphids/plant) followed by B. carinata cv. DLSC 2 (20.9 aphids/ plant) which suffered the least yield loss i.e. 5.79 and 10.59 per cent, respectively. Almost similar trend was observed in seedling mortality, which was the maximum in BSH 1 and YST 151, while no seedling mortality was observed in the case of T 27 during both the years of study. Analysis of various biochemical constituents revealed that glucosinolates, total phenols and ortho-dihydroxy phenols had inverse relationship with the aphid infestation. Higher amount of these biochemical constituents in T 27 and DLSC 2 was responsible for lower aphid infestation on these genotypes.","PeriodicalId":8460,"journal":{"name":"arXiv: Other Quantitative Biology","volume":"17 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2017-03-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85161173","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Measuring Light Pollution with Fisheye Lens Imagery from A Moving Boat, A Proof of Concept","authors":"A. Jechow, Z. Koll'ath, A. Lerner, A. Hanel, N. Shashar, Franz Holker, C. Kyba","doi":"10.26607/IJSL.V19I1.62","DOIUrl":"https://doi.org/10.26607/IJSL.V19I1.62","url":null,"abstract":"Near all-sky imaging photometry was performed from a boat on the Gulf of Aqaba to measure the night sky brightness in a coastal environment. The boat was not anchored, and therefore drifted and rocked. The camera was mounted on a tripod without any inertia/motion stabilization. A commercial digital single lens reflex (DSLR) camera and fisheye lens were used with ISO setting of 6400, with the exposure time varied between 0.5 s and 5 s. We find that despite movement of the vessel the measurements produce quantitatively comparable results apart from saturation effects. We discuss the potential and limitations of this method for mapping light pollution in marine and freshwater systems. This work represents the proof of concept that all-sky photometry with a commercial DSLR camera is a viable tool to determine light pollution in an ecological context from a moving boat.","PeriodicalId":8460,"journal":{"name":"arXiv: Other Quantitative Biology","volume":"184 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2017-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80534547","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"CHROTRAN: A mathematical and computational model for in situ heavy metal remediation in heterogeneous aquifers","authors":"S. Hansen, S. Pandey, S. Karra, V. Vesselinov","doi":"10.5194/gmd-2017-51","DOIUrl":"https://doi.org/10.5194/gmd-2017-51","url":null,"abstract":"Groundwater contamination by heavy metals is a critical environmental problem for which in situ remediation is frequently the only viable treatment option. For such interventions, a three-dimensional reactive transport model of relevant biogeochemical processes is invaluable. To this end, we developed a model, CHROTRAN, for in situ treatment, which includes full dynamics for five species: a heavy metal to be remediated, an electron donor, biomass, a nontoxic conservative bio-inhibitor, and a biocide. Direct abiotic reduction by donor-metal interaction as well as donor-driven biomass growth and bio-reduction are modeled, along with crucial processes such as donor sorption, bio-fouling and biomass death. Our software implementation handles heterogeneous flow fields, arbitrarily many chemical species and amendment injection points, and features full coupling between flow and reactive transport. We describe installation and usage and present two example simulations demonstrating its unique capabilities. One simulation suggests an unorthodox approach to remediation of Cr(VI) contamination.","PeriodicalId":8460,"journal":{"name":"arXiv: Other Quantitative Biology","volume":"9 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2017-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90520957","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Stem Cell Networks","authors":"E. Werner","doi":"10.1007/978-1-4419-9863-7_1577","DOIUrl":"https://doi.org/10.1007/978-1-4419-9863-7_1577","url":null,"abstract":"","PeriodicalId":8460,"journal":{"name":"arXiv: Other Quantitative Biology","volume":"40 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89287760","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The “Hard Problem” of Life","authors":"S. Walker, P. Davies","doi":"10.1017/9781316584200.002","DOIUrl":"https://doi.org/10.1017/9781316584200.002","url":null,"abstract":"There are few open problems in science as perplexing as the nature of life and consciousness. At present, we do not have many scientific windows into either. In the case of consciousness, it seems evident that certain aspects will ultimately defy reductionist explanation, the most important being the phenomenon of qualia – roughly speaking, our subjective experience as observers. It is a priori far from obvious why we should have experiences such as the sensation of the smell of coffee or the blueness of the sky. Subjective experience isn't necessary for the evolution of intelligence (we could, for example, be zombies in the philosophical sense and appear to function just as well from the outside with nothing going on inside ). Even if we do succeed in eventually uncovering a complete mechanistic understanding of the wiring and firing of every neuron in the brain, it might tell us nothing about thoughts, feelings, and what it is like to experience something. Our phenomenal experiences are the only aspect of consciousness that appears as though they cannot, even in principle , be reduced to known physical principles. This led Chalmers to identify pinpointing an explanation for our subjective experience as the “hard problem of consciousness.” The corresponding “easy problems” (in practice not so easy) are associated with mapping the neural correlates of various experiences. By focusing attention on the problem of subjective experience, Chalmers highlighted the truly inexplicable aspect of consciousness, based on our current understanding. The issue, however, is by no means confined to philosophy. Chalmers’ proposed resolution is to regard subjective consciousness as an irreducible, fundamental property of mind, with its own laws and principles. Progress can be expected to be made by focusing on what would be required for a theory of consciousness to stand alongside our theories for matter, even if it turns out that something fundamentally new is not necessary. The same may be true for life. With the case of life, it seems as though we have a better chance of understanding it as a physical phenomenon than we do with consciousness.","PeriodicalId":8460,"journal":{"name":"arXiv: Other Quantitative Biology","volume":"30 1","pages":"19-37"},"PeriodicalIF":0.0,"publicationDate":"2016-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87484080","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Complexity of Molecular Interactions and Bindings between Cyclic Peptide and Inhibit Polymerase A and B1 (PAC-PB1N) H1N1","authors":"A. A. Parikesit, Harry Noviardi, D. Kerami, U. S. Tambunan","doi":"10.13140/RG.2.1.1439.6969","DOIUrl":"https://doi.org/10.13140/RG.2.1.1439.6969","url":null,"abstract":"The influenza/H1N1 virus has caused hazard in the public health of many countries. Hence, existing influenza drugs could not cope with H1N1 infection due to the high mutation rate of the virus. In this respect, new method to block the virus was devised. The polymerase PAC-PB1N enzyme is responsible for the replication of H1N1 virus. Thus, novel inhibitors were developed to ward off the functionality of the enzyme. In this research, cyclic peptides has been chosen to inhibit PAC-PB1N due to its proven stability in reaching the drug target. Thus, computational method for elucidating the molecular interaction between cyclic peptides and PAC-PB1N has been developed by using the LigX tools from MOE 2008.10 software. The tools could render the bindings that involved in the interactions. The interactions between individual amino acid in the inhibitor and enzyme could be seen as well. Thus, the peptide sequences of CKTTC and CKKTC were chosen as the lead compounds. In this end, the feasibility of cyclic peptides to act as drug candidate for H1N1 could be exposed by the 2d and 3d modeling of the molecular interactions.","PeriodicalId":8460,"journal":{"name":"arXiv: Other Quantitative Biology","volume":"18 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2015-10-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85455652","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}