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Life at the edge: complexity and criticality in biological function 边缘的生命:生物功能的复杂性和临界性
Pub Date : 2018-10-28 DOI: 10.5506/APhysPolB.49.1955
D. Chialvo
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.
为什么生命是复杂的,最重要的是,自然界中过多的复杂性的起源是什么?这是一个基本的科学问题,用已故的佩尔•巴克(Per Bak)的话来说,“迫切需要回答,但却很少有人问”。在这些讲座中,我们回顾了最近在几个尺度上的尝试,从批判现象的角度来理解复杂生物学问题的起源。为了说明这种方法,讨论了三个案例,即大规模的脑动力学,蛋白质自发波动的特征和细胞线粒体网络的生理复杂性。
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引用次数: 15
Quantum Patterns of Genome Size Variation in Angiosperms 被子植物基因组大小变异的量子模式
Pub Date : 2018-07-16 DOI: 10.2174/1574893615999200420071919
L. Luo, Lirong Zhang
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.
从基因组进化算子H的特征值方程出发,研究被子植物的核DNA量。通过物理模拟引入算子H,将其定义为基因组大小N的函数及其与大小的导数。由方程的解成功地推导出了近缘被子植物种间DNA大小分布的不连续性及其协同性。结果与芦荟、克拉克兰、烟叶、石竹属、葱属等已有实验数据吻合较好。这可能表明被子植物基因组的进化限制本质上是量子起源的。
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引用次数: 1
Telling apart Felidae and Ursidae from the distribution of nucleotides in mitochondrial DNA. 从线粒体DNA中核苷酸的分布来区分狐科和熊科。
Pub Date : 2018-02-07 DOI: 10.1142/S0217984918500574
Andrij Rovenchak
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.
线粒体DNA中核苷酸序列的秩-频率分布以类似于语言学方法的方式定义,频率最高的核碱基作为空白。对于这样的序列,计算熵和平均长度。这些参数被证明可以区分猫科和熊科的物种。从纯粹的数值来看,我们能够特别地看到大熊猫是熊,而考拉不是。用一个简单的概率模型解释了观测到的参数之间的线性关系。采用基于玻色分布的非加性泛化方法分析核苷酸序列的频谱。在这种情况下,家庭的分离并不是很明显。然而,与熊科相比,Felidae的分布平均尾巴更长。
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引用次数: 4
Symmetry and Minimum Principle at the Basis of the Genetic Code 遗传密码基础上的对称和最小原则
Pub Date : 2017-04-04 DOI: 10.1142/9789813227880_0019
A. Sciarrino, P.Sorba
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.
对称概念在物理学中的重要性是公认的:它是否也适用于遗传密码?本着这种精神,几年前有人提出了一个基于连续对称的遗传密码模型,名为“晶体基模型”。本文回顾了该模型的一些最初的应用以及它最近的发展。事实上,在对我们的数学模型进行了有动机的介绍之后,我们通过将其应用于密码子使用概率的和规则的阐述和验证,以及建立氨基酸的物理化学性质之间的关系和一些预测,来说明其针对性。然后,在这种情况下定义核苷酸和密码子的“生物自旋”结构,一对密码子-反密码子之间的相互作用可以简单地用(生物)自旋-自旋势来表示。这种方法将构成论文的第二部分,其中,施加最小能量原理,遗传密码的进化分析可以与普遍接受的方案很好地一致进行。对这种相互作用模型的更精确的研究提供了关于密码子偏差的信息,与数据一致。
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引用次数: 0
Biochemical mechanism of resistance in some Brassica genotypes against Lipaphis erysimi (Kaltenbach) (Homoptera: Aphididae) 部分芸苔属基因型对褐蚜(Lipaphis erysimi)抗性的生化机制(同翅目:蚜科)
Pub Date : 2017-03-23 DOI: 10.5958/J.2229-4473.26.2.103
Sarwan Kumar, M. Sangha
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.
在2006-07和2007-08两个作物季,研究了油菜不同基因型对田间和网房条件下蚜虫侵染的反应,以及各种生化成分与蚜虫侵染的关系。各基因型中,褐沙菌在油菜品种褐沙菌(brown sarson cv)上的居群显著高。BSH 1和B. rapa var. yellow sarson cv。无保护组的YST 151分别为53.7和52.3只蚜虫/株。但以苜蓿(Eruca sativa cv)最低。t27(4.7只/株)次之;dlsc2(20.9只蚜虫/株)产量损失最小,分别为5.79%和10.59%。幼苗死亡率的变化趋势几乎相同,在BSH 1和YST 151中最高,而t27在两个研究年份中均未观察到幼苗死亡率。各种生化成分分析表明,硫代葡萄糖苷类、总酚类和邻二羟基酚类与蚜虫侵害呈反比关系。这些生化成分在t27和dlsc2中含量较高,导致这些基因型的蚜虫侵染率较低。
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引用次数: 12
Measuring Light Pollution with Fisheye Lens Imagery from A Moving Boat, A Proof of Concept 用移动船上的鱼眼镜头图像测量光污染,概念验证
Pub Date : 2017-03-22 DOI: 10.26607/IJSL.V19I1.62
A. Jechow, Z. Koll'ath, A. Lerner, A. Hanel, N. Shashar, Franz Holker, C. Kyba
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.
在亚喀巴湾的一艘船上进行了近全天成像光度测量,以测量沿海环境下的夜空亮度。船没有抛锚,因此漂来荡去。相机安装在没有任何惯性/运动稳定的三脚架上。使用商用数码单反相机(DSLR)和鱼眼镜头,ISO设置为6400,曝光时间在0.5 s到5 s之间变化。我们发现,尽管运动的血管测量产生定量可比的结果除了饱和的影响。我们讨论了这种方法在海洋和淡水系统光污染制图中的潜力和局限性。这项工作代表了一个概念的证明,即用商用数码单反相机进行全天测光是一种可行的工具,可以确定生态环境中来自移动船只的光污染。
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引用次数: 35
CHROTRAN: A mathematical and computational model for in situ heavy metal remediation in heterogeneous aquifers 非均质含水层重金属原位修复的数学与计算模型
Pub Date : 2017-03-04 DOI: 10.5194/gmd-2017-51
S. Hansen, S. Pandey, S. Karra, V. Vesselinov
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.
地下水重金属污染是一个严重的环境问题,就地修复往往是唯一可行的处理办法。对于此类干预,相关生物地球化学过程的三维反应输运模型是非常宝贵的。为此,我们开发了一个模型,CHROTRAN,用于原位处理,其中包括五个物种的完整动力学:待修复的重金属,电子供体,生物质,无毒保守生物抑制剂和杀菌剂。模拟了通过供体-金属相互作用进行的直接非生物还原以及供体驱动的生物质生长和生物还原,以及供体吸附、生物污染和生物质死亡等关键过程。我们的软件实现处理异构流场,任意多的化学物质和改进剂注射点,并具有流动和反应输运之间的完全耦合。我们描述了安装和使用,并给出了两个示例模拟,展示了其独特的功能。一个模拟提出了一种非正统的方法来修复Cr(VI)污染。
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引用次数: 4
Stem Cell Networks 干细胞网络
Pub Date : 2016-07-11 DOI: 10.1007/978-1-4419-9863-7_1577
E. Werner
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引用次数: 1
The “Hard Problem” of Life 生活中的“难题”
Pub Date : 2016-06-23 DOI: 10.1017/9781316584200.002
S. Walker, P. Davies
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.
在科学中,很少有像生命和意识的本质这样令人困惑的开放性问题。目前,我们对这两方面都没有太多的科学研究。在意识的例子中,似乎很明显,某些方面最终会违背还原论的解释,最重要的是感质现象——粗略地说,我们作为观察者的主观经验。我们为什么会有诸如闻到咖啡的味道或天空的蓝色之类的感觉,这是先天的,远不是显而易见的。主观经验对于智力的进化并不是必需的(例如,我们可以成为哲学意义上的僵尸,从外部看,我们的内在并没有发生任何变化,但我们的功能却一样好)。即使我们最终成功地揭示了对大脑中每个神经元的连接和放电的完整的机械理解,它也可能无法告诉我们关于思想、感觉和体验事物的感觉。我们的现象体验是意识的唯一方面,即使在原则上,它们似乎也不能被简化为已知的物理原理。这使得查尔默斯把对我们主观体验的精确解释定义为“意识的难题”。相应的“容易的问题”(实际上不那么容易)与绘制各种经验的神经关联相关联。通过将注意力集中在主观经验问题上,查尔默斯强调了基于我们目前的理解,意识真正难以解释的方面。然而,这个问题绝不局限于哲学。查尔默斯提出的解决方案是,将主观意识视为一种不可约的、基本的心理属性,有自己的规律和原则。通过关注意识理论与我们的物质理论并立所需要的条件,可以期待取得进展,即使事实证明根本不需要一些新的东西。同样的道理也适用于生活。就生命而言,我们似乎更有可能把它理解为一种物理现象,而不是意识。
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引用次数: 13
The Complexity of Molecular Interactions and Bindings between Cyclic Peptide and Inhibit Polymerase A and B1 (PAC-PB1N) H1N1 环肽与抑制聚合酶A和B1 (PAC-PB1N) H1N1分子相互作用和结合的复杂性
Pub Date : 2015-10-27 DOI: 10.13140/RG.2.1.1439.6969
A. A. Parikesit, Harry Noviardi, D. Kerami, U. S. Tambunan
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.
甲型H1N1流感病毒对许多国家的公共卫生造成危害。因此,由于病毒的高突变率,现有的流感药物无法应对H1N1感染。在这方面,设计了新的阻断病毒的方法。聚合酶PAC-PB1N酶负责H1N1病毒的复制。因此,开发了新的抑制剂来抵御酶的功能。本研究选择环肽来抑制PAC-PB1N,因为环肽在达到药物靶点方面具有稳定性。因此,利用MOE 2008.10软件中的LigX工具,开发了阐明环肽与PAC-PB1N分子相互作用的计算方法。这些工具可以呈现交互中涉及的绑定。抑制剂中单个氨基酸与酶之间的相互作用也可以看到。因此,选择CKTTC和CKKTC的肽序列作为先导化合物。因此,环状肽作为H1N1候选药物的可行性可以通过分子相互作用的二维和三维建模来揭示。
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引用次数: 3
期刊
arXiv: Other Quantitative Biology
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