Theoretical Biology Forum最新文献_第7页

Master equation and relative species abundance distribution for Lotka-Volterra models of interacting ecological communities. 相互作用生态群落Lotka-Volterra模型的主方程和相对物种丰度分布。

IF 1.5 4区生物学

Theoretical Biology Forum Pub Date : 2016-01-01 DOI: 10.19272/201611402003

Armando Bazzani, Claudia Sala, Enrico Giampieri, Gastone Castellani

{"title":"Master equation and relative species abundance distribution for Lotka-Volterra models of interacting ecological communities.","authors":"Armando Bazzani, Claudia Sala, Enrico Giampieri, Gastone Castellani","doi":"10.19272/201611402003","DOIUrl":"https://doi.org/10.19272/201611402003","url":null,"abstract":"DESCRIPTION\u0000Understanding the factors that control the dynamics of interacting species is a fundamental problem in ecology. The nature of the interactions among different species is usually not completely understood, but it is assumed that the species interaction plays an important role in the ecosystem properties as predicted by the niches models for an ecosystem. However, recent studies point out as the neutral hypothesis proposed by Hubbell of non-interacting species with an external source from the surrounding environment, allows to explain the relative species abundance distribution when the ecosystem has reached a stationary situation. In this paper we use the concept of fitness landscape to introduce a random dynamical model that describes the evolution of different communities near a stationary situation. The average dynamics can be associated to a system of Lotka-Volterra equations with mutualistic interactions. Then we derive a Master equation that satisfies the detailed balance condition of thermodynamical equilibria and allows to analytically compute the relative species abundance distribution near the stationary state as a multinomial negative distribution. These results suggest a possible approach to a synthetic theory that joins the niche theories and the Hubbell's neutral theory for RSA distribution.","PeriodicalId":54453,"journal":{"name":"Theoretical Biology Forum","volume":null,"pages":null},"PeriodicalIF":1.5,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35890339","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

Cherry-picking functionally relevant substates from long md trajectories using a stratified sampling approach. 使用分层抽样方法从长md轨迹中挑选功能相关的子状态。

IF 1.5 4区生物学

Theoretical Biology Forum Pub Date : 2016-01-01 DOI: 10.19272/201611402004

Balasubramanian Chandramouli, Giordano Mancini

{"title":"Cherry-picking functionally relevant substates from long md trajectories using a stratified sampling approach.","authors":"Balasubramanian Chandramouli, Giordano Mancini","doi":"10.19272/201611402004","DOIUrl":"https://doi.org/10.19272/201611402004","url":null,"abstract":"Description: Classical Molecular Dynamics (MD) simulations can provide insights at the nanoscopic scale into protein dynamics. Currently, simulations of large proteins and complexes can be routinely carried out in the ns-μs time regime. Clustering of MD trajectories is often performed to identify selective conformations and to compare simulation and experimental data coming from different sources on closely related systems. However, clustering techniques are usually applied without a careful validation of results and benchmark studies involving the application of different algorithms to MD data often deal with relatively small peptides instead of average or large proteins; finally clustering is often applied as a means to analyze refined data and also as a way to simplify further analysis of trajectories. Herein, we propose a strategy to classify MD data while carefully benchmarking the performance of clustering algorithms and internal validation criteria for such methods. We demonstrate the method on two showcase systems with different features, and compare the classification of trajectories in real and PCA space. We posit that the prototype procedure adopted here could be highly fruitful in clustering large trajectories of multiple systems or that resulting especially from enhanced sampling techniques like replica exchange simulations.","PeriodicalId":54453,"journal":{"name":"Theoretical Biology Forum","volume":null,"pages":null},"PeriodicalIF":1.5,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35890340","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Order is present at every level but is not total. 秩序存在于每一个层面，但不是全部。

IF 1.5 4区生物学

Theoretical Biology Forum Pub Date : 2016-01-01 DOI: 10.19272/201611402007

Antonio Lima-de-Faria

引用次数: 0

L'etat, c'est moi. Fifty years of history and philosophy of evolutionary biology. 好了，好了。五十年的进化生物学的历史和哲学。

IF 1.5 4区生物学

Theoretical Biology Forum Pub Date : 2016-01-01 DOI: 10.19272/201611402008

Michael Ruse

引用次数: 1

Two dynamical models for cholera. 霍乱的两个动力学模型。

IF 1.5 4区生物学

Theoretical Biology Forum Pub Date : 2016-01-01 DOI: 10.19272/201611402010

Masomeh Taherian, Megerdich Toomanian, Mohammadreza Molaei

引用次数: 1

Cancer is the chaotic search for adaptation to previously unknown environments. 癌症是对未知环境的无序适应。

IF 1.5 4区生物学

Theoretical Biology Forum Pub Date : 2016-01-01 DOI: 10.19272/201611402011

Mesut Tez, Selda Tez

引用次数: 3

THE ESTABLISHMENT OF PREZYGOTIC REPRODUCTIVE ISOLATION IN SOME SIMPLE MODELS. 建立了一些简单的前合子生殖分离模型。

IF 1.5 4区生物学

Theoretical Biology Forum Pub Date : 2015-01-01

Franco Spirito

{"title":"THE ESTABLISHMENT OF PREZYGOTIC REPRODUCTIVE ISOLATION IN SOME SIMPLE MODELS.","authors":"Franco Spirito","doi":"","DOIUrl":"","url":null,"abstract":"The probability of fixation of a mutant that causes assortative mating according to the 'mass action model' has been studied. A gene of this kind represents one of the simplest hypothetical mechanisms of prezygotic isolation. Computer analysis by Monte Carlo simulations revealed that the fixation of the mutant is very unlikely unless the population is very small in size and/or the degree of partial assortative mating is very low. The introduction into the biological model of pleiotropic effects of the gene on fitness (viability) can facilitate the process of fixation (even to a very large extent in the case of strong selection in favor of the mutant allele). The most interesting situation, from the point of view of a possible role of the mutant in triggering a process of allopatric speciation, occurs when the effect of assortative mating on gene frequency prevails over the effect of differential viability. In these cases, the probability of fixation of the mutant and the consequent establishment of partial prezygotic isolation shows a pattern similar to that described in literature for the simple case of postzygotic isolating mechanism constituted by a Mendelian factor (gene locus or chromosomal variant) with negative heterosis and selective advantage of the 'new' homozygote over the ancestral homozygote.","PeriodicalId":54453,"journal":{"name":"Theoretical Biology Forum","volume":null,"pages":null},"PeriodicalIF":1.5,"publicationDate":"2015-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34538794","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Interleukins (ILs), a fascinating family of cytokines. Part II: ILs from IL-20 to IL-38. 白细胞介素(il)，一个令人着迷的细胞因子家族。第二部分:IL-20到IL-38。

IF 1.5 4区生物学

Theoretical Biology Forum Pub Date : 2015-01-01

Pieranna Fietta, Elvira Costa, Giovanni Delsante

{"title":"Interleukins (ILs), a fascinating family of cytokines. Part II: ILs from IL-20 to IL-38.","authors":"Pieranna Fietta, Elvira Costa, Giovanni Delsante","doi":"","DOIUrl":"","url":null,"abstract":"Every nucleated cell can produce and respond to cytokines, extracellular proteic/glycoproteic mediators that constitute a complex, interconnected, and flexible signaling network, addressed to modulate cell behavior and homeostasis through the interaction with high-affinity surface receptors. These messenger molecules, whose main characteristics are potency, pleiotropism, and redundancy, primarily act in autocrine, paracrine, and juxtacrine way, but can also display systemic activity in endocrine-like modality. They are generally classified according to their cellular sources, three-dimensional structure, or biological functions. Among cytokines, interleukins (ILs) represent a fascinating and multifunctional group of immunomodulators that primarily mediate the leukocyte cross-talk (hence the name), and mainly regulate the immune cell proliferation, differentiation, growth, survival, activation, and functions. Up to 38 ILs have been so far identified, numbered according to the order of discovery, and grouped in different subsets, based on distinguishing structural/functional features. Due to their crucial role in regulating inflammation and immune response, ILs are known to be involved in the pathogenesis of human inflammatory/autoimmune diseases. Therefore, they have increasingly attracted great interest as effective or promising therapeutic targets. The biology and functions of the hitherto identified human ILs are reviewed and discussed: herein, ILs from IL-20 to IL-38 are presented.","PeriodicalId":54453,"journal":{"name":"Theoretical Biology Forum","volume":null,"pages":null},"PeriodicalIF":1.5,"publicationDate":"2015-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34384161","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

INTERACTION PATTERN OF FULLERENES (C20-C180) AND CARBON NANOTUBES WITH DIFFERENT FORMS OF DNA: A COMPUTATIONAL BIOLOGY APPROACH. 富勒烯(c20-c180)和碳纳米管与不同形式dna的相互作用模式:计算生物学方法。

IF 1.5 4区生物学

Theoretical Biology Forum Pub Date : 2015-01-01

Sumbul Firdaus, Anupam Dhasmana, Shafiul Haque, Snober S Mir, Roshan Jahan, Tasneem Bano, Vandana Srivastava, Saif Khan, Mohtashim Lohani

{"title":"INTERACTION PATTERN OF FULLERENES (C20-C180) AND CARBON NANOTUBES WITH DIFFERENT FORMS OF DNA: A COMPUTATIONAL BIOLOGY APPROACH.","authors":"Sumbul Firdaus, Anupam Dhasmana, Shafiul Haque, Snober S Mir, Roshan Jahan, Tasneem Bano, Vandana Srivastava, Saif Khan, Mohtashim Lohani","doi":"","DOIUrl":"","url":null,"abstract":"Recently, the venues of exposure to nanoparticles have increased significantly owing to their increased deliberate production. In this study the interaction of fullerenes with DNA was analyzed along with various factors affecting this interaction like mol. wt. of fullerenes (C20 to C180), the form of DNA i.e., A, B and Z, and sequences of DNA, and was compared with the DNA binding of CNTs. Increase in the molecular weight of the fullerene showed increase in the binding score with A & B-form of DNA, but no regular affect was seen on binding with Z-form of DNA. Although the binding of all fullerenes was best with A form. While CNTs bind with all forms of DNA, but best scores were with B form, which were comparable with those of fullerene C80 and C84 with A form. The interaction of both fullerenes and CNTs were not affected by the sequence of DNA. The number of interacting base pairs increased from 1 base-pair to 4, as the molecular size of fullerene increases in all A & B-and Z form of DNA. Whereas CNTs interact with 5 bases in A and B form, and 3 bases in Z form. The groove where binding occurs depended on the form of DNA. Smaller (< C48) fullerenes bind in minor groove of B-DNA, and larger fullerenes bind in major groove. While in A form of DNA, fullerenes of all sizes bind in major groove. The binding was random and not size dependent in Z form of DNA. Whereas, CNTs bind to major groove of DNA in a parallel fashion in A and B form of DNA, and in minor groove attached perpendicularly in Z form.","PeriodicalId":54453,"journal":{"name":"Theoretical Biology Forum","volume":null,"pages":null},"PeriodicalIF":1.5,"publicationDate":"2015-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34384162","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

THE CONCEPT OF PLANT LIFE: THE DAWN. 植物生命的概念:黎明。

IF 1.5 4区生物学

Theoretical Biology Forum Pub Date : 2015-01-01

Sergio Pennazio

引用次数: 0