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Phase Diagram of Collective Motion of Bacterial Cells in a Shallow Circular Pool 浅圆形池中细菌细胞集体运动的相图
Pub Date : 2015-10-02 DOI: 10.7566/JPSJ.84.124001
J. Wakita, Shota Tsukamoto, K. Yamamoto, M. Katori, Yasuyuki Yamada
The collective motion of bacterial cells in a shallow circular pool is systematically studied using the bacterial species $Bacillus$ $subtilis$. The ratio of cell length to pool diameter (i.e., the reduced cell length) ranges from 0.06 to 0.43 in our experiments. Bacterial cells in a circular pool show various types of collective motion depending on the cell density in the pool and the reduced cell length. The motion is classified into six types, which we call random motion, turbulent motion, one-way rotational motion, two-way rotational motion, random oscillatory motion, and ordered oscillatory motion. Two critical values of reduced cell lengths are evaluated, at which drastic changes in collective motion are induced. A phase diagram is proposed in which the six phases are arranged.
利用枯草芽孢杆菌这一菌种,系统地研究了浅圆形池中细菌细胞的集体运动。在我们的实验中,细胞长度与池直径的比值(即减少的细胞长度)在0.06到0.43之间。细菌细胞在圆形池中表现出不同类型的集体运动,这取决于池中的细胞密度和减少的细胞长度。运动分为六种类型,我们称之为随机运动、湍流运动、单向旋转运动、双向旋转运动、随机振荡运动和有序振荡运动。减少细胞长度的两个临界值被评估,在集体运动的剧烈变化被诱导。提出了六相排列的相图。
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引用次数: 5
The avian tectorial membrane: Why is it tapered? 鸟类的被膜:为什么是锥形的?
Pub Date : 2015-09-30 DOI: 10.1063/1.4939396
K. Iwasa, A. Ricci
While the mammalian- and the avian inner ears have well defined tonotopic organizations as well as hair cells specialized for motile and sensing roles, the structural organization of the avian ear is different from its mammalian cochlear counterpart. Presumably this difference stems from the difference in the way motile hair cells function. Short hair cells, whose role is considered analogous to mammalian outer hair cells, presumably depends on their hair bundles, and not motility of their cell body, in providing the motile elements of the cochlear amplifier. This report focuses on the role of the avian tectorial membrane, specifically by addressing the question, “Why is the avian tectorial membrane tapered from the neural to the abneural direction?”
虽然哺乳动物和鸟类的内耳具有明确的同种组织以及专门用于运动和传感作用的毛细胞,但鸟类耳朵的结构组织与哺乳动物耳蜗的结构组织不同。据推测,这种差异源于运动毛细胞功能的不同。短毛细胞的作用被认为类似于哺乳动物的外毛细胞,在为耳蜗放大器提供运动元件时,可能依赖于它们的毛束,而不是它们细胞体的运动性。这篇报告的重点是鸟类被膜的作用,特别是通过解决这个问题,“为什么鸟类的被膜从神经方向逐渐变细到非神经方向?”
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引用次数: 1
Towards a robust algorithm to determine topological domains from colocalization data 从共定位数据中确定拓扑域的鲁棒算法
Pub Date : 2015-09-05 DOI: 10.3934/biophy.2015.4.503
A. P. Moscalets, L. Nazarov, M. Tamm
One of the most important tasks in understanding the complex spatial organization of the genome consists in extracting information about this spatial organization, the function and structure of chromatin topological domains from existing experimental data, in particular, from genome colocalization (Hi-C) matrices. Here we present an algorithm allowing to reveal the underlying hierarchical domain structure of a polymer conformation from analyzing the modularity of colocalization matrices. We also test this algorithm on several model polymer structures: equilibrium globules, random fractal globules and regular fractal (Peano) conformations. We define what we call a spectrum of cluster borders, and show that these spectra behave strikingly di erently for equilibrium and fractal conformations, allowing us to suggest an additional criterion to identify fractal polymer conformations.
理解基因组复杂的空间组织的最重要任务之一是从现有的实验数据中提取有关这种空间组织的信息,染色质拓扑结构域的功能和结构,特别是从基因组共定位(Hi-C)矩阵中提取信息。在这里,我们提出了一种算法,允许通过分析共定位矩阵的模块化来揭示聚合物构象的底层层次结构。我们还测试了几种模型聚合物结构:平衡球,随机分形球和规则分形(Peano)构象。我们定义了我们所谓的簇边界光谱,并表明这些光谱在平衡和分形构象中表现出惊人的不同,这使我们能够提出一个额外的标准来识别分形聚合物构象。
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引用次数: 4
Resonant alignment of microswimmer trajectories in oscillatory shear flows 振荡剪切流中微游泳者轨迹的共振排列
Pub Date : 2015-07-26 DOI: 10.1103/PhysRevFluids.1.051201
A. Hope, O. A. Croze, W. Poon, M. Bees, M. Haw
Oscillatory flows are commonly experienced by swimming microorganisms in the environment, industrial applications and rheological investigations. We experimentally characterise the response of the alga {it Dunaliella salina} to oscillatory shear flows, and report the surprising discovery that algal swimming trajectories orient perpendicular to the flow-shear plane. The ordering has the characteristics of a resonance in the driving parameter space. The behaviour is qualitatively reproduced by a simple model and simulations accounting for helical swimming, providing the mechanism for ordering and criteria for the resonant amplitude and frequency. The implications of this work for active oscillatory rheology and industrial algal processing are discussed.
在环境、工业应用和流变学研究中,游动的微生物通常会经历振荡流动。我们通过实验表征了海藻对振荡剪切流的响应,并报告了藻类游泳轨迹垂直于流动剪切面的惊人发现。该排序在驱动参数空间中具有共振特性。通过一个简单的模型和计算螺旋游动的模拟,定性地再现了这种行为,提供了排序机制和共振振幅和频率的准则。讨论了本工作对主动振荡流变学和工业藻类加工的影响。
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引用次数: 9
Statistical physics of neural systems with non-additive dendritic coupling 具有非加性树突耦合的神经系统的统计物理
Pub Date : 2015-07-14 DOI: 10.1103/PhysRevX.4.011053
David Breuer, M. Timme, Raoul-Martin Memmesheimer
How neurons process their inputs crucially determines the dynamics of biological and artificial neural networks. In such neural and neural-like systems, synaptic input is typically considered to be merely transmitted linearly or sublinearly by the dendritic compartments. Yet, single-neuron experiments report pronounced supralinear dendritic summation of sufficiently synchronous and spatially close-by inputs. Here, we provide a statistical physics approach to study the impact of such non-additive dendritic processing on single neuron responses and the performance of associative memory tasks in artificial neural networks. First, we compute the effect of random input to a neuron incorporating nonlinear dendrites. This approach is independent of the details of the neuronal dynamics. Second, we use those results to study the impact of dendritic nonlinearities on the network dynamics in a paradigmatic model for associative memory, both numerically and analytically. We find that dendritic nonlinearities maintain network convergence and increase the robustness of memory performance against noise. Interestingly, an intermediate number of dendritic branches is optimal for memory functionality.
神经元如何处理它们的输入至关重要地决定了生物和人工神经网络的动态。在这样的神经和类神经系统中,突触输入通常被认为仅仅是由树突隔室线性或亚线性传递的。然而,单神经元实验报告了明显的超线性树突和足够同步和空间相近的输入。在这里,我们提供了一种统计物理方法来研究这种非加性树突处理对人工神经网络中单个神经元反应和联想记忆任务性能的影响。首先,我们计算随机输入对包含非线性树突的神经元的影响。这种方法与神经元动力学的细节无关。其次,我们使用这些结果来研究树突非线性对联想记忆的范式模型中网络动力学的影响,包括数值和分析。我们发现树状非线性保持了网络的收敛性,并增加了记忆性能对噪声的鲁棒性。有趣的是,中等数量的树突分支对于记忆功能来说是最佳的。
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引用次数: 15
Green thermoelectrics: Observation and analysis of plant thermoelectric response 绿色热电:植物热电响应的观察与分析
Pub Date : 2015-02-12 DOI: 10.1051/bioconf/20160603006
C. Goupil, H. Ouerdane, Eric Herbert, Arnold Kamsing, Y. Apertet, François Bouteau, Stefano Mancuso, Rodrigo Patino, Rodrigo Patino, Philippe Lecoeur
Plants are sensitive to thermal and electrical effects; yet the coupling of both, known as thermoelectricity, and its quantitative measurement in vegetal systems never were reported. We recorded the thermoelectric response of bean sprouts under various thermal conditions and stress. The obtained experimental data unambiguously demonstrate that a temperature difference between the roots and the leaves of a bean sprout induces a thermoelectric voltage between these two points. Basing our analysis of the data on the force-flux formalism of linear response theory, we found that the strength of the vegetal equivalent to the thermoelectric coupling is one order of magnitude larger than that in the best thermoelectric materials. Experimental data also show the importance of the thermal stress variation rate in the plant's electrophysiological response. Therefore, thermoelectric effects are sufficiently important to partake in the complex and intertwined processes of energy and matter transport within plants.
植物对热和电效应很敏感;然而,这两者的耦合,即热电,及其在植物系统中的定量测量从未被报道过。记录了豆芽在不同热条件和应力下的热电响应。得到的实验数据明确地表明,豆芽的根和叶之间的温差在这两点之间引起热电电压。根据线性响应理论的力-通量形式分析数据,我们发现植物等效热电耦合的强度比最好的热电材料的强度大一个数量级。实验数据还显示了热胁迫变化率在植物电生理反应中的重要性。因此,热电效应在植物体内复杂的能量和物质传输过程中起着非常重要的作用。
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引用次数: 0
Topological effects of charge transfer in telomere G-quadruplex: Mechanism on telomerase activation and inhibition 端粒g -四重体电荷转移的拓扑效应:端粒酶激活和抑制的机制
Pub Date : 2015-02-02 DOI: 10.1142/S021797921350001X
Xin Wang, Shiming Liang
We explore charge transfer in the telomere G-Quadruplex (TG4) DNA theoretically by the nonequilibrium Green's function method, and reveal the topological effect of charge transport in TG4 DNA. The consecutive TG4(CTG4) is semiconducting with 0.2 ~ 0.3eV energy gap. Charges transfers favorably in the consecutive TG4, but are trapped in the non-consecutive TG4 (NCTG4). The global conductance is inversely proportional to the local conductance for NCTG4. The topological structure transition from NCTG4 to CTG4 induces abruptly ~ 3nA charge current, which provide a microscopic clue to understand the telomerase activated or inhibited by TG4. Our findings reveal the fundamental property of charge transfer in TG4 and its relationship with the topological structure of TG4.
利用非平衡格林函数方法从理论上探讨了端粒g -四重体(TG4) DNA中的电荷转移,揭示了TG4 DNA中电荷转移的拓扑效应。连续的TG4(CTG4)具有半导体性质,能隙为0.2 ~ 0.3eV。电荷在连续TG4中传输有利,但在非连续TG4 (NCTG4)中被捕获。NCTG4的全局电导与局部电导成反比。从NCTG4到CTG4的拓扑结构转变引起了~ 3nA电荷电流的突变,这为了解TG4激活或抑制端粒酶提供了一个微观线索。我们的发现揭示了TG4中电荷转移的基本性质及其与TG4拓扑结构的关系。
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引用次数: 2
Computational Studies of Biomembrane Systems: Theoretical Considerations, Simulation Models, and Applications 生物膜系统的计算研究:理论考虑,模拟模型和应用
Pub Date : 2014-12-16 DOI: 10.1007/12_2013_258
M. Deserno, K. Kremer, H. Paulsen, C. Peter, F. Schmid
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引用次数: 22
Statistical Physics of Adaptation 适应统计物理
Pub Date : 2014-12-05 DOI: 10.1103/PhysRevX.6.021036
Nikolai Perunov, R. Marsland, Jeremy L. England
All living things exhibit adaptations that enable them to survive and reproduce in the natural environment that they inhabit. From a biological standpoint, it has long been understood that adaptation comes from natural selection, whereby maladapted individuals do not pass their traits effectively to future generations. However, we may also consider the phenomenon of adaptation from the standpoint of physics, and ask whether it is possible to delineate what the difference is in terms of physical properties between something that is well-adapted to its surrounding environment, and something that is not. In this work, we undertake to address this question from a theoretical standpoint. Building on past fundamental results in far-from-equilibrium statistical mechanics, we demonstrate a generalization of the Helmholtz free energy for the finite-time stochastic evolution of driven Newtonian matter. By analyzing this expression term by term, we are able to argue for a general tendency in driven many-particle systems towards self-organization into states formed through exceptionally reliable absorption and dissipation of work energy from the surrounding environment. Subsequently, we illustrate the mechanism of this general tendency towards physical adaptation by analyzing the process of random hopping in driven energy landscapes.
所有生物都表现出适应能力,使它们能够在它们所居住的自然环境中生存和繁殖。从生物学的角度来看,长期以来人们一直认为适应来自自然选择,因此不适应的个体不能将其特征有效地传给后代。然而,我们也可以从物理学的角度来考虑适应现象,并问是否有可能描绘出很好地适应周围环境的事物与不适应周围环境的事物在物理性质上的区别。在这项工作中,我们承诺从理论的角度来解决这个问题。在过去的非平衡统计力学的基本结果的基础上,我们展示了驱动牛顿物质的有限时间随机演化的亥姆霍兹自由能的推广。通过逐项分析这个表达式,我们能够论证在被驱动的多粒子系统中有一种普遍趋势,即通过从周围环境中异常可靠地吸收和耗散功而形成自组织状态。随后,我们通过分析驱动能量景观中随机跳跃的过程来说明这种普遍倾向于物理适应的机制。
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引用次数: 103
New oil modified acrylic polymer for pH sensitive drug release: Experimental results and statistical analysis 用于pH敏感药物释放的新型油改性丙烯酸聚合物:实验结果与统计分析
Pub Date : 2014-12-05 DOI: 10.24297/jns.v3i1.5013
N. Panja, A. Chattopadhyay
We report results of an experimental study, complemented by detailed statistical analysis of the experimental data, on the development of a more effective control method of drug delivery using a pH sensitive acrylic polymer. New copolymers based on acrylic acid and fatty acid are constructed from dodecyl castor oil and a tercopolymer based on methyl methacrylate, acrylic acid and acryl amide were prepared using this new approach. Water swelling characteristics of fatty acid, acrylic acid copolymer and tercopolymer respectively in acid and alkali solutions have been studied by a step-change method. The antibiotic drug cephalosporin and paracetamol have also been incorporated into the polymer blend through dissolution with the release of the antibiotic drug being evaluated in bacterial stain media and buffer solution. Our results show that the rate of release of paracetamol getss affected by the pH factor and also by the nature of polymer blend. Our experimental data have later been statistically analyzed to quantify the precise nature of polymer decay rates on the pH density of the relevant polymer solvents. The time evolution of the polymer decay rates indicate a marked transition from a linear to a strictly non-linear regime depending on the whether the chosen sample is a general copolymer (linear) or a tercopolymer (non-linear). Non-linear data extrapolation techniques have been used to make probabilistic predictions about the variation in weight percentages of retained polymers at all future times, thereby quantifying the degree of efficacy of the new method of drug delivery.
我们报告了一项实验研究的结果,并辅以对实验数据的详细统计分析,研究了一种使用pH敏感丙烯酸聚合物的更有效的药物递送控制方法。以十二烷基蓖麻油为原料,制备了以丙烯酸和脂肪酸为共聚物,并以甲基丙烯酸甲酯、丙烯酸和丙烯酰胺为共聚物。采用步变法研究了脂肪酸、丙烯酸共聚物和三共聚物在酸、碱溶液中的溶胀特性。抗生素药物头孢菌素和扑热息痛也通过溶解加入到聚合物混合物中,抗生素药物的释放在细菌染色介质和缓冲溶液中进行评估。结果表明,对乙酰氨基酚的释放速度受pH和聚合物共混物性质的影响。我们的实验数据后来进行了统计分析,以量化聚合物衰减率对相关聚合物溶剂pH密度的精确性质。聚合物衰变速率的时间演化表明,根据所选样品是一般共聚物(线性)还是三共聚物(非线性),从线性到严格非线性的显著转变。非线性数据外推技术已被用于对未来所有时间内保留聚合物重量百分比的变化进行概率预测,从而量化新药物递送方法的有效性程度。
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引用次数: 0
期刊
arXiv: Biological Physics
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