学习复杂多尺度系统的有效动力学 | 网络科学论文速递14篇-集智俱乐部

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核心速递



  • 学习复杂多尺度系统的有效动力学;

  • 非线性激光模型中的同宿困惑与混沌
  • 一种自主运动控制的突触学习方法;
  • 基于双相似变换耦合团簇理论的分子基态离散时间动力学;
  • 水平随机力驱动的可倒摆法: 永不下落轨迹和超对称性的统计;
  • 具有反馈电流的自旋电子储存器记忆函数的周期结构;
  • 应用于传染病新型冠状病毒肺炎流行病的 PECAIQR 模型;
  • 计算复制数字的 matlab 代码及其在新型冠状病毒肺炎疫情爆发中的应用;
  • 新型冠状病毒肺炎行为惯性对纽约城市交通重新开放策略的影响;
  • 民族宽容能抑制自我强化的学校隔离吗? 一个基于 Agent 的理论模型;
  • 从形式到信息: 分析不同空间文化中的建筑环境;
  • 病毒在建成环境中传播的详细模拟;
  • 利用量子光探测和跟踪细菌;
  • 水在主客互动中的作用;
  • 纳米孔捕获棒状分子: 定义“取向捕获半径;
  • 活性聚合物和细丝的物理学;


学习复杂多尺度系统的有效动力学


原文标题:

Learning the Effective Dynamics of Complex Multiscale Systems

地址:

http://arxiv.org/abs/2006.13431

作者:

Pantelis R. Vlachas,Georgios Arampatzis,Caroline Uhler,Petros Koumoutsakos


Abstract:Simulations of complex multiscale systems are essential for science and technology ranging from weather forecasting to aircraft design. The predictive capabilities of simulations hinges on their capacity to capture the governing system dynamics. Large scale simulations, resolving all spatiotemporal scales, provide invaluable insight at a high computational cost. In turn, simulations using reduced order models are affordable but their veracity hinges often on linearisation and/or heuristics. Here we present a novel systematic framework to extract and forecast accurately the effective dynamics (LED) of complex systems with multiple spatio-temporal scales. The framework fuses advanced machine learning algorithms with equation-free approaches. It deploys autoencoders to obtain a mapping between fine and coarse grained representations of the system and learns to forecast the latent space dynamics using recurrent neural networks. We compare the LED framework with existing approaches on a number of benchmark problems and demonstrate reduction in computational efforts by several orders of magnitude without sacrificing the accuracy of the system.

摘要:复杂多尺度系统的模拟对从天气预报到飞机设计的科学和技术至关重要。模拟的预测能力取决于它们捕捉管理系统动态的能力。大规模模拟,解决所有的时空尺度,提供了宝贵的洞察力在高计算成本。反过来,使用降阶模型的模拟是可承受的,但其准确性往往取决于线性化和 / 或启发式。本文提出了一个新的系统框架,用于精确提取和预测具有多时空尺度的复杂系统的有效动力学(LED)。该框架融合了先进的机器学习算法与方程自由的方法。它利用自动编码器获得系统的细粒度表示和粗粒度表示之间的映射,并利用递归神经网络学习预测潜在的空间动态。我们比较了 LED 框架和现有方法在一些基准问题上的优缺点,证明了在不牺牲系统精确性的前提下,通过几个数量级的努力减少了计算量。




非线性激光模型中的同宿困惑与混沌


原文标题:

Homoclinic puzzles and chaos in a nonlinear laser model

地址:

http://arxiv.org/abs/2006.13812

作者:

K. Pusuluri,H. G. E. Meijer,A. L. Shilnikov


Abstract:We present a case study elaborating on the multiplicity and self-similarity of homoclinic and heteroclinic bifurcation structures in the 2D and 3D parameter spaces of a nonlinear laser model with a Lorenz-like chaotic attractor. In a symbiotic approach combining the traditional parameter continuation methods using MatCont and a newly developed technique called the Deterministic Chaos Prospector (DCP) utilizing symbolic dynamics on fast parallel computing hardware with graphics processing units (GPUs), we exhibit how specific codimension-two bifurcations originate and pattern regions of chaotic and simple dynamics in this classical model. We show detailed computational reconstructions of key bifurcation structures such as Bykov T-point spirals and inclination flips in 2D parameter space, as well as the spatial organization and 3D embedding of bifurcation surfaces, parametric saddles, and isolated closed curves (isolas).

摘要:本文给出了一个具有类 lorenz 混沌吸引子的非线性激光模型的二维和三维参数空间中同宿结构和异宿分岔结构的多重性和自相似性的个例研究。利用 MatCont 的传统参数延拓方法和一种新发展的利用带图形处理单元的快速并行计算硬件的确定性混沌预测技术(DCP)相结合的共生方法,我们展示了这个经典模型中特定余维数-2分叉的产生和混沌及简单动力学的模式区域。给出了二维参数空间中 Bykov t 点螺旋线和倾斜翻转线等关键分岔结构的详细计算重构,以及分岔曲面、参数鞍点和孤立闭曲线的空间组织和三维嵌入。



一种自主运动控制的突触学习方法


原文标题:

An approach to synaptic learning for autonomous motor control

地址:

http://arxiv.org/abs/2006.13471

作者:

Sergio Verduzco-Flores,William Dorrell,Erik DeSchutter


Abstract:In the realm of motor control, artificial agents cannot match the performance of their biological counterparts. We thus explore a neural control architecture that is both biologically plausible, and capable of fully autonomous learning. The architecture consists of feedback controllers that learn to achieve a desired state by selecting the errors that should drive them. This selection happens through a family of differential Hebbian learning rules that, through interaction with the environment, can learn to control systems where the error responds monotonically to the control signal. We next show that in a more general case, neural reinforcement learning can be coupled with a feedback controller to reduce errors that arise non-monotonically from the control signal. The use of feedback control reduces the complexity of the reinforcement learning problem, because only a desired value must be learned, with the controller handling the details of how it is reached. This makes the function to be learned simpler, potentially allowing to learn more complex actions. We discuss how this approach could be extended to hierarchical architectures.

摘要:在运动控制领域,人工制剂的性能无法与生物制剂相比。因此,我们探索了一个神经控制架构,既是生物学上可信的,并能够完全自主学习。该体系结构由反馈控制器组成,这些反馈控制器通过选择驱动它们的错误来学习达到所需的状态。这种选择通过一系列微分赫布学习规则发生,通过与环境的互动,可以学会控制系统的错误单调响应的控制信号。我们接下来展示的是,在更一般的情况下,神经元 / 强化学习可以与反馈控制器耦合,以减少与控制信号非单调产生的误差。反馈控制的使用降低了强化学习问题的复杂性,因为只有一个期望值必须学习,控制器处理如何达到它的细节。这使得学习函数变得更简单,潜在地允许学习更复杂的动作。我们将讨论如何将这种方法扩展到层次结构。



基于双相似变换耦合团簇理论

的分子基态离散时间动力学


原文标题:

Discrete-Time Dynamics of Molecular Ground State with a Double Similarity Transformed Coupled Cluster Theory

地址:

http://arxiv.org/abs/2006.13691

作者:

Valay Agarawal,Anish Chakraborty,Rahul Maitra


Abstract:The discrete-time propagation of a double similarity transformed Coupled Cluster theory with input perturbation is studied. The coupled iterative scheme to solve the ground state Schr{"o}dinger equation is cast as a multivariate logistic map, the solutions show the universal Feigenbaum dynamics. Using recurrence analysis, it is shown that the dynamics is dictated by a small subgroup of cluster operators, mostly those involving chemically active orbitals, whereas all other cluster operators with smaller amplitudes are enslaved.

摘要:研究了具有输入扰动的双相似变换耦合簇理论的离散传播问题。将求解基态薛定谔方程的耦合迭代格式转化为多元 logistic 映射,得到了通用的 Feigenbaum 动力学解。利用递归分析,我们发现这种动力学是由一小部分集群算子决定的,大多数集群算子涉及化学活性轨道,而所有其他振幅较小的集群算子都受到束缚。



水平随机力驱动的可倒摆法: 

永不下落轨迹和超对称性的统计


原文标题:

Inverted pendulum driven by a horizontal random force: statistics of the never-falling trajectory and supersymmetry

地址:

http://arxiv.org/abs/2006.13819

作者:

Nikolai A. Stepanov,Mikhail A. Skvortsov


Abstract:We study stochastic dynamics of an inverted pendulum subject to a random force in the horizontal direction (Whitney's problem). Considered on the entire time axis, the problem admits a unique solution that always remains in the upper half plane. We formulate the problem of statistical description of this never-falling trajectory and solve it by a field-theoretical technique assuming a white-noise driving. In our approach based on the supersymmetric formalism of Parisi and Sourlas, statistic properties of the never-falling trajectory are expressed in terms of the zero mode of the corresponding transfer-matrix Hamiltonian. The emerging mathematical structure is similar to that of the Fokker-Planck equation, which however is written for the ``square root'' of the probability distribution function. Our results for the statistics of the non-falling trajectory are in perfect agreement with direct numerical simulations of the stochastic pendulum equation. In the limit of strong driving (no gravitation), we obtain an exact analytical solution for the instantaneous joint probability distribution function of the pendulum's angle and its velocity.

摘要:我们研究了可倒摆法在水平方向上受到随机力的随机动力学(惠特尼问题)。从整个时间轴来看,这个问题有一个唯一的解,它总是停留在上半平面上。我们提出了这种永不下落轨迹的统计描述问题,并用场论技术解决了白噪声驱动下的永不下落轨迹。本文基于 Parisi 和 Sourlas 的超对称形式,用相应的传递矩阵哈密顿量的零模表示永不下降轨迹的统计性质。新出现的数学结构类似于福克-普朗克方程,但是它是为概率分布函数的“平方根”而写的。我们的非下落轨迹统计结果与随机摆方程的直接数值模拟结果完全一致。在强力驱动(无引力)的极限下,我们得到了摆角和摆速的瞬时联合分布函数的精确解析解。



具有反馈电流的自旋电子

储存器记忆函数的周期结构


原文标题:

Periodic structure of memory function in spintronics reservoir with feedback current

地址:

http://arxiv.org/abs/2006.13404

作者:

Terufumi Yamaguchi,Nozomi Akashi,Sumito Tsunegi,Hitoshi Kubota,Kohei Nakajima,Tomohiro Taniguchi


Abstract:The role of the feedback effect on physical reservoir computing is studied theoretically by solving the vortex-core dynamics in a nanostructured ferromagnet. Although the spin-transfer torque due to the feedback current makes the vortex dynamics complex, it is clarified that the feedback effect does not always contribute to the enhancement of the memory function in a physical reservoir. The memory function, characterized by the correlation coefficient between the input data and the dynamical response of the vortex core, becomes large when the delay time of the feedback current is not an integral multiple of the pulse width. On the other hand, the memory function remains small when the delay time is an integral multiple of the pulse width. As a result, a periodic behavior for the short-term memory capacity is observed with respect to the delay time, the phenomenon of which can be attributed to correlations between the virtual neurons via the feedback current.

摘要:通过求解纳米结构铁磁体中的涡核动力学,从理论上研究了反馈效应对物理油藏计算的影响。虽然反馈电流引起的自旋转移扭矩使涡旋动力学复杂化,但是反馈效应并不总是有助于提高物理储层的记忆功能。当反馈电流的延迟时间不是脉冲宽度的整数倍时,记忆函数拥有属性输入数据和涡核动态响应之间的相关系数变大。另一方面,当延迟时间为脉冲宽度的整数倍时,记忆函数仍然很小。结果表明,短时记忆容量随延迟时间呈现周期性变化,这种现象可以归结为虚拟神经元之间通过反馈电流的相关性。



应用于传染病新型冠状病毒

肺炎流行病的 PECAIQR 模型


原文标题:

PECAIQR: A Model for Infectious Disease Applied to the Covid-19 Epidemic

地址:

http://arxiv.org/abs/2006.13693

作者:

Richard Bao,August Chen,Jethin Gowda,Shiva Mudide


Abstract:The Covid-19 pandemic has made clear the need to improve modern multivariate time-series forecasting models. Current state of the art predictions of future daily deaths and, especially, hospital resource usage have confidence intervals that are unacceptably wide. Policy makers and hospitals require accurate forecasts to make informed decisions on passing legislation and allocating resources. We used US county-level data on daily deaths and population statistics to forecast future deaths. We extended the SIR epidemiological model to a novel model we call the PECAIQR model. It adds several new variables and parameters to the naive SIR model by taking into account the ramifications of the partial quarantining implemented in the US. We fitted data to the model parameters with numerical integration. Because of the fit degeneracy in parameter space and non-constant nature of the parameters, we developed several methods to optimize our fit, such as training on the data tail and training on specific policy regimes. We use cross-validation to tune our hyper parameters at the county level and generate a CDF for future daily deaths. For predictions made from training data up to May 25th, we consistently obtained an averaged pinball loss score of 0.096 on a 14 day forecast. We finally present examples of possible avenues for utility from our model. We generate longer-time horizon predictions over various 1-month windows in the past, forecast how many medical resources such as ventilators and ICU beds will be needed in counties, and evaluate the efficacy of our model in other countries.

摘要:新型冠状病毒肺炎流感大流行清楚地表明了改进现代多变量时间序列预测模型的必要性。目前最先进的预测未来每日死亡,特别是医院资源使用的置信区间是不可接受的宽。决策者和医院需要准确的预测,以便就通过立法和分配资源作出知情的决定。我们使用美国县级的每日死亡和人口统计数据来预测未来的死亡人数。我们将 SIR 流行病学模型推广到一个新的模型—— PECAIQR 模型。它通过考虑美国实施的部分隔离的后果,为原本的 SIR 模型增加了几个新的变量和参数。我们使用数值积分软件对模型参数进行了拟合。由于参数空间的拟合简并性和参数的非常数性质,我们发展了几种方法来优化我们的拟合,如数据尾的训练和具体的政策制度的训练。我们使用交叉验证来调整我们在县一级的超参数,并为未来每日死亡生成一个 CDF。对于5月25日之前的训练数据,我们一直在14天的预测中获得了0.096的平均分。最后,我们给出了从我们的模型中获得效用的可能途径的示例。我们对过去的各种1个月窗口进行了较长时间的预测,预测了各县将需要多少呼吸机和 ICU 床位等医疗资源,并对我们的模型在其他国家的效果进行了评估。



计算复制数字的 matlab 代码及其

在新型冠状病毒肺炎疫情爆发中的应用


原文标题:

A matlab code to compute reproduction numbers with applications to the Covid-19 outbreak

地址:

http://arxiv.org/abs/2006.13752

作者:

Paulo R. Zingano,Janaina P. Zingano,Alessandra M. Silva,Carolina P. Zingano


Abstract:We discuss the generation of various reproduction ratios or numbers that are very useful to monitor an ongoing epidemic like Covid-19 and examine the effects of intervention measures. A detailed SEIR algorithm is described for their computation, with applications given to the current Covid-19 outbreaks in a number of countries (Argentina, Brazil, France, Italy, Mexico, Spain, UK and USA). The corresponding matlab script, complete and ready to use, is provided for free downloading.

摘要:我们讨论了各种繁殖率或数字的产生,这些数字对于监测像新型冠状病毒肺炎这样的持续流行病非常有用,并且检验了干预措施的效果。一个详细的 SEIR 算法描述了他们的计算,并应用于当前在一些国家爆发的新型冠状病毒肺炎疫情(阿根廷,巴西,法国,意大利,墨西哥,西班牙,英国和美国)。相应的 matlab 脚本,完整和准备使用,提供免费下载。



新型冠状病毒肺炎行为惯性对

纽约城市交通重新开放策略的影响


原文标题:

Impact of COVID-19 Behavioral Inertia on Reopening Strategies for New York City Transit

地址:

http://arxiv.org/abs/2006.13368

作者:

Ding Wang,Brian Yueshuai He,Jingqin Gao,Joseph Y. J. Chow,Kaan Ozbay,Shri Iyer


Abstract:The COVID-19 pandemic has affected travel behaviors and transportation system operations, and cities are grappling with what policies can be effective for a phased reopening shaped by social distancing. A baseline model was previously developed and calibrated for pre-COVID conditions as MATSim-NYC. A new COVID model is calibrated that represents travel behavior during the COVID-19 pandemic by recalibrating the population agendas to include work-from-home and re-estimating the mode choice model for MATSim-NYC to fit observed traffic and transit ridership data. Assuming the change in behavior exhibits inertia during reopening, we analyze the increase in car traffic due to the phased reopen plan guided by the state government of New York. Four reopening phases and two reopening scenarios (with and without transit capacity restrictions) are analyzed. A Phase 4 reopening with 100% transit capacity may only see as much as 73% of pre-COVID ridership and an increase in the number of car trips by as much as 142% of pre-pandemic levels. Limiting transit capacity to 50% would decrease transit ridership further from 73% to 64% while increasing car trips to as much as 143% of pre-pandemic levels. While the increase appears small, the impact on consumer surplus is disproportionately large due to already increased traffic congestion. Many of the trips also get shifted to other modes like micromobility. The findings imply that a transit capacity restriction policy during reopening needs to be accompanied by (1) support for micromobility modes, particularly in non-Manhattan boroughs, and (2) congestion alleviation policies that focus on reducing traffic in Manhattan, such as cordon-based pricing.

摘要:新型冠状病毒肺炎流感大流行已经影响了旅游行为和交通系统的运作,各个城市正在努力解决什么样的政策才能有效地实现由社会距离塑造的分阶段重新开放。先前已经为前 covid 条件开发和校准了一个基线模型,即 MATSim-NYC。通过重新校准人口议程以包括在家工作和重新估计 MATSim-NYC 的模式选择模型以适应观测到的交通和运输客流数据,校准了一个新的 COVID 模型,该模型代表了新型冠状病毒肺炎流感大流行期间的旅行行为。假设在重新开放过程中行为的改变表现出惯性,我们分析了由于纽约州政府指导的分阶段重新开放计划导致的汽车交通量的增加。分析了四个重新开放阶段和两个重新开放情景(有和没有过境能力限制)。100% 运输能力的第4阶段重新开放可能只能看到 covid 前乘客人数多达73% ,汽车出行次数增加多达大流行前水平的142% 。将运输能力限制在50% 将进一步降低运输乘客数量,从73% 降至64% ,同时将汽车旅行增至大流行前水平的143% 。虽然增长看起来很小,但是由于第一交通堵塞的增长,对消费者剩余的影响不成比例的大。许多旅行也被转移到其他模式,比如微型机动车。研究结果意味着,在重新开放期间实行运输能力限制政策的同时,需要(1)支持微型机动模式,特别是在非曼哈顿行政区,(2)以减少曼哈顿交通为重点的缓解交通拥堵政策,例如基于警戒线的定价。



民族宽容能抑制

自我强化的学校隔离吗? 

一个基于 Agent 的理论模型


原文标题:

Can ethnic tolerance curb self-reinforcing school segregation? A theoretical Agent Based Model

地址:

http://arxiv.org/abs/2006.13531

作者:

Lucas Sage,Andreas Flache


Abstract:Schelling and Sakoda prominently proposed computational models suggesting that strong ethnic residential segregation can be the unintended outcome of a self-reinforcing dynamic driven by choices of individuals with rather tolerant ethnic preferences. There are only few attempts to apply this view to school choice, another important arena in which ethnic segregation occurs. In the current paper, we explore with an agent-based theoretical model similar to those proposed for residential segregation, how ethnic tolerance among parents can affect the level of school segregation. More specifically, we ask whether and under which conditions school segregation could be reduced if more parents hold tolerant ethnic preferences. We move beyond earlier models of school segregation in three ways. First, we model individual school choices using a random utility discrete choice approach. Second, we vary the pattern of ethnic segregation in the residential context of school choices systematically, comparing residential maps in which segregation is unrelated to parents' level of tolerance to residential maps reflecting their ethnic preferences. Thirdly, we introduce heterogeneity in tolerance levels among parents belonging to the same group. Our simulation experiments suggest that ethnic school segregation can be a very robust phenomenon, occurring even when about half of the population prefers mixed to segregated schools. However, we also identify a sweet spot in the parameter space in which a larger proportion of tolerant parents makes the biggest difference. This is the case when the preference for nearby schools weighs heavily in parents' utility function and the residential map is only moderately segregated. Further experiments are presented that unravel the underlying mechanisms.

摘要:谢林和萨科达突出地提出了计算模型,表明强烈的种族居住隔离可能是一种自我强化的动态的意外结果,这种动态由具有相当宽容的种族偏好的个人的选择驱动。很少有人试图把这种观点应用到学校选择上,这是种族隔离发生的另一个重要领域。本文采用类似于居住隔离理论的基于主体的理论模型,探讨了家长间的族裔宽容对学校隔离水平的影响。更具体地说,我们想知道,如果更多的家长持有宽容的种族偏好,学校隔离是否可以减少,以及在何种条件下可以减少。我们在三个方面超越了早期的学校隔离模式。首先,我们使用随机效用离散选择方法对个体的学校选择进行建模。其次,我们系统地改变了学校选择居住环境中的种族隔离模式,比较了与父母容忍程度无关的居住地图和反映他们种族偏好的居住地图。第三,引入同一群体亲本间耐受水平的异质性。我们的模拟实验表明,种族学校隔离可能是一种非常强烈的现象,甚至在大约一半的人口喜欢混合学校而不喜欢隔离学校的时候也会发生。然而,我们也在参数空间中确定了一个最佳点,在这个点上,更大比例的宽容父母产生了最大的差异。这种情况下,对附近学校的偏好在家长的效用函数中占很大比重,而住宅地图只是适度隔离。进一步的实验揭示了潜在的机制。



从形式到信息: 

分析不同空间文化中的建筑环境


原文标题:

From form to information: Analysing built environments in different spatial cultures

地址:

http://arxiv.org/abs/2006.13897

作者:

Vinicius M. Netto,Edgardo Brigatti,Caio Cacholas


Abstract:Cities are different around the world, but does this fact bare any relation to culture? The idea that urban form embodies idiosyncrasies related to cultural identities captures the imagination of many in urban studies, but it is an assumption yet to be carefully examined. Approaching spatial configurations in the built environment as a proxy of urban culture, this paper searches for differences potentially consistent with specific regional cultures or cultures of planning in urban development. It does so focusing on the elementary components shaping cities: buildings and how they are aggregated in cellular complexes of built form. Exploring Shannon's work, we introduce an entropy measure to analyse the probability distribution of cellular arrangements in built form systems. We apply it to downtown areas of 45 cities from different regions of the world as a similarity measure to compare and cluster cities potentially consistent with specific spatial cultures. Findings suggest a classification scheme that sheds further light on what we call the "cultural hypothesis": the possibility that different cultures and regions find different ways of ordering space.

摘要:世界各地的城市是不同的,但是这个事实与文化有什么联系吗?城市形态体现了与文化认同相关的特质这一观点在城市研究中激发了许多人的想象力,但这只是一个有待仔细研究的假设。以城市文化为代表,探讨城市建成环境中的空间结构,寻找与城市发展中特定地域文化或规划文化潜在的一致性差异。它专注于塑造城市的基本组成部分: 建筑以及它们是如何聚集在建筑形式的细胞复合体中的。探索 Shannon 的工作,我们引入了熵测度来分析构建形式系统中细胞排列的概率分布。我们将其应用于世界不同地区的45个城市的市中心区域,作为一种相似性度量,来比较和聚集与特定空间文化潜在一致的城市。研究结果表明,一个分类方案进一步阐明了我们所说的“文化假说” : 不同的文化和地区找到不同的空间排序方式的可能性。



病毒在建成环境中传播的详细模拟


原文标题:

Detailed Simulation of Viral Propagation In The Built Environment

地址:

http://arxiv.org/abs/2006.13792

作者:

Rainald Löhner,Harbir Antil,Sergio Idelsohn,Eugenio Oñate


Abstract:A summary is given of the mechanical characteristics of virus contaminants and the transmission via droplets and aerosols. The ordinary and partial differential equations describing the physics of these processes with high fidelity are presented, as well as appropriate numerical schemes to solve them. Several examples taken from recent evaluations of the built environment are shown, as well as the optimal placement of sensors.

摘要:综述了病毒污染物的力学特性及其通过液滴和气溶胶传播的机理。给出了描述这些过程物理过程的高保真常微分方程和偏微分方程,并给出了相应的数值解法。从最近的建筑环境评价的几个例子显示,以及传感器的最佳位置。



利用量子光探测和跟踪细菌


原文标题:

Detecting and tracking bacteria with quantum light

地址:

http://arxiv.org/abs/2006.13250

作者:

Gaetana Spedalieri,Lolita Piersimoni,Omar Laurino,Samuel L. Braunstein,Stefano Pirandola


Abstract:The field of quantum sensing aims at improving the detection and estimation of classical parameters that are encoded in physical systems by resorting to quantum sources of light and quantum detection strategies. The same approach can be used to improve the current classical measurements that are performed on biological systems. Here we consider the scenario of two bacteria (E. coli and Salmonella) growing in a Luria Bertani broth and monitored by classical spectrophotometers. Their concentration can be related to the optical transmissivity via the Beer-Lambert-Bouguer's law and their growth curves can be described by means of Gompertz functions. Starting from experimental data points, we extrapolate the growth curves of the two bacteria and we study the theoretical performance that would be achieved with a quantum setup. In particular, we discuss how the bacterial growth can in principle be tracked by irradiating the samples with orders of magnitude fewer photons, identifying the clear superiority of quantum light in the early stages of growth. We then show the superiority and the limits of quantum resources in two basic tasks: (i) the early detection of bacterial growth and (ii) the early discrimination between two bacteria species.

摘要:量子传感领域的目标是通过量子光源和量子检测策略来改进对物理系统中编码的经典参数的检测和估计。同样的方法也可以用来改进目前在生物系统上进行的经典测量。在这里,我们考虑这样一种情况: 两种细菌(大肠杆菌和沙门氏菌)生长在 Luria Bertani 肉汤中,并通过经典的分光光度计进行监测。它们的浓度可以通过 Beer-Lambert-Bouguer 定律与光透过率有关,它们的生长曲线可以用 Gompertz 函数来描述。从实验数据点出发,我们外推了这两种细菌的生长曲线,并研究了量子装置所能达到的理论性能。特别是,我们讨论了原则上如何通过用更少的光子照射样品来跟踪细菌的生长,确定了在生长的早期阶段量子光的明显优势。数量级。然后我们在两个基本任务中展示了量子资源的优越性和局限性: (i)细菌生长的早期检测和(ii)两种细菌的早期鉴别。



水在主客互动中的作用


原文标题:

The role of water in host-guest interaction

地址:

https://arxiv.org/abs/2006.13274

作者:

Valerio Rizzi,Luigi Bonati,Narjes Ansari,Michele Parrinello


Abstract:One of the main applications of atomistic computer simulations is the calculation of ligand binding energies. The accuracy of these calculations depends on the force field quality and on the thoroughness of configuration sampling. Sampling is an obstacle in modern simulations due to the frequent appearance of kinetic bottlenecks in the free energy landscape. Very often this difficulty is circumvented by enhanced sampling techniques. Typically, these techniques depend on the introduction of appropriate collective variables that are meant to capture the system's degrees of freedom. In ligand binding, water has long been known to play a key role, but its complex behaviour has proven difficult to fully capture. In this paper we combine machine learning with physical intuition to build a non-local and highly efficient water-describing collective variable. We use it to study a set of of host-guest systems from the SAMPL5 challenge. We obtain highly accurate binding energies and good agreement with experiments. The role of water during the binding process is then analysed in some detail.

摘要:原子计算机模拟的主要应用之一是配体结合能的计算。这些计算的准确性取决于力场的质量和构型采样的彻底性。由于动能瓶颈的频繁出现,采样是现代模拟中的一个障碍。通常情况下,这种困难是通过增强抽样技术来避免的。通常,这些技术依赖于引入适当的集合变量,这些集合变量旨在捕获系统的自由度。在配体结合中,水一直被认为起着关键作用,但是它的复杂行为已经被证明很难被完全捕获。本文将机器学习和物理直觉相结合,构造了一个非局部的、高效的水描述集合变量。我们使用它来研究一组来自于 SAMPL5挑战的主客系统。获得了高精度的结合能,与实验符合良好。然后详细分析了水在胶合过程中的作用。



纳米孔捕获棒状分子: 

定义“取向捕获半径


原文标题:

Capture of rod-like molecules by a nanopore: defining an "orientational capture radius"

地址:

http://arxiv.org/abs/2006.13338

作者:

Le Qiao,Gary W. Slater


Abstract:Both the translational diffusion coefficientD and the electrophoretic mobility μ of a short rod-like molecule (such as dsDNA) that is being pulled towards a nanopore by an electric field should depend on its orientation. Since a charged rod-like molecule tends to orient in the presence of an inhomogeneous electric field, D and μ will change as the molecule approaches the nanopore, and this will impact the capture process. We present a simplified study of this problem using theoretical arguments and Langevin Dynamics simulations. In particular, we introduce a new textit{orientational capture radius} which we compare to the capture radius for the equivalent point-like particle, and we discuss the different physical regimes of orientation during capture and the impact of initial orientations on the capture time.

摘要:两者的平动扩散系数D 还有电泳涂层μ 一个短棒状分子(比如 dsDNA)被电场拉向纳米孔,这应该取决于它的方向。由于带电的棒状分子在非均匀电场中倾向于定向,D 及μ 会随着分子接近纳米孔而改变,这会影响捕获过程。我们提出了一个简化的研究,这个问题使用理论论证和朗之万动力学模拟。特别地,我们引入了一种新的方向捕获半径,并与等效点状粒子的捕获半径进行了比较,讨论了捕获过程中取向的不同物理状态以及初始取向对捕获时间的影响。



活性聚合物和细丝的物理学


原文标题:

The physics of active polymers and filaments

地址:

http://arxiv.org/abs/2006.13509

作者:

Roland G. Winkler,Gerhard Gompper


Abstract:Active matter agents consume internal energy or extract energy from the environment for locomotion and force generation. Already rather generic models, such as ensembles of active Brownian particles, exhibit phenomena, which are absent at equilibrium, in particular motility-induced phase separation and collective motion. Further intriguing nonequilibrium effects emerge in assemblies of bound active agents as in linear polymers or filaments. The interplay of activity and conformational degrees of freedom gives rise to novel structural and dynamical features of individual polymers as well as in interacting ensembles. Such out-of-equilibrium polymers are an integral part of living matter, ranging from biological cells with filaments propelled by motor proteins in the cytoskeleton, and RNA/DNA in the transcription process, to long swarming bacteria and worms such as Proteus mirabilis and Caenorhabditis elegans, respectively. Even artificial active polymers have been synthesized. The emergent properties of active polymers or filaments depend on the coupling of the active process to their conformational degrees of freedom, aspects which are addressed in this article. The theoretical models for tangentially and isotropically self-propelled or active-bath driven polymers are presented, both in presence and absence of hydrodynamic interactions. The consequences for their conformational and dynamical properties are examined, emphasizing the strong influence of the coupling between activity and hydrodynamic interactions. Particular features of emerging phenomena, induced by steric and hydrodynamic interactions, are highlighted. Various important, yet theoretically unexplored, aspects are featured and future challenges are discussed.

摘要:活性物质介质消耗内能或从环境中提取能量,用于运动和产生力。已经相当普遍的模型,如活跃的布朗粒子的集合,展示了在平衡状态下不存在的现象,特别是运动诱导的相分离和集体运动。进一步有趣的非平衡效应出现在结合活性剂的组合中,如线性聚合物或丝状体。活性和构象自由度的相互作用导致了单个聚合物以及相互作用的整体具有新颖的结构和动力学特征。这种失去平衡的聚合物是生物体不可分割的一部分,从细胞骨架中由运动蛋白推动的细丝状生物细胞,到转录过程中的 rna / dna,再到长的群集细菌和蠕虫,分别是奇异变形杆菌和秀丽隐桿线虫。甚至人工合成了活性聚合物。活性聚合物或纤维的突现性质取决于活性过程与其构象自由度的耦合,本文对这些方面进行了讨论。提出了有无流体动力学相互作用的切向和等流速自推进或主动浴驱动聚合物的理论模型。考察了它们的构象和动力学性质的结果,强调了活动和流体动力学相互作用之间耦合的强烈影响。突出了由空间相互作用和流体动力学相互作用引起的新现象的特点。各种重要的,但理论上尚未探讨,方面的特点和未来的挑战进行了讨论。


来源:集智斑图
编辑:王建萍


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