Forward Evolution Research Articles

The Painlevé paradox in contact mechanics

The 120-year old so-called Painleve paradox involves the loss of determinism in models of planar rigid bodies in point contact with a rigid surface, subject to Coulomb-like dry friction. The phenomenon occurs due to coupling between normal and rotational degrees-of-freedom such that the effective normal force becomes attractive rather than repulsive. Despite a rich literature, the forward evolution problem remains unsolved other than in certain restricted cases in 2D with single contact points. Various practical consequences of the theory are revisited, including models for robotic manipulators, and the strange behaviour of chalk when pushed rather than dragged across a blackboard. Reviewing recent theory, a general formulation is proposed, including a Poisson or energetic impact law. The general problem in 2D with a single point of contact is discussed and cases or inconsistency or indeterminacy enumerated. Strategies to resolve the paradox via contact regularisation are discussed from a dynamical systems point of view. By passing to the infinite stiffness limit and allowing impact without collision, inconsistent and indeterminate cases are shown to be resolvable for all open sets of conditions. However, two unavoidable ambiguities that can be reached in finite time are discussed in detail, so called dynamic jam and reverse chatter. A partial review is given of 2D cases with two points of contact showing how a greater complexity of inconsistency and indeterminacy can arise. Extension to fully three-dimensional analysis is briefly considered and shown to lead to further possible singularities. In conclusion, the ubiquity of the Painleve paradox is highlighted and open problems are discussed.

A pivot mutation impedes reverse evolution across an adaptive landscape for drug resistance in Plasmodium vivax.

BackgroundThe study of reverse evolution from resistant to susceptible phenotypes can reveal constraints on biological evolution, a topic for which evolutionary theory has relatively few general principles. The public health catastrophe of antimicrobial resistance in malaria has brought these constraints on evolution into a practical realm, with one proposed solution: withdrawing anti-malarial medication use in high resistance settings, built on the assumption that reverse evolution occurs readily enough that populations of pathogens may revert to their susceptible states. While past studies have suggested limits to reverse evolution, there have been few attempts to properly dissect its mechanistic constraints.MethodsGrowth rates were determined from empirical data on the growth and resistance from a set of combinatorially complete set of mutants of a resistance protein (dihydrofolate reductase) in Plasmodium vivax, to construct reverse evolution trajectories. The fitness effects of individual mutations were calculated as a function of drug environment, revealing the magnitude of epistatic interactions between mutations and genetic backgrounds. Evolution across the landscape was simulated in two settings: starting from the population fixed for the quadruple mutant, and from a polymorphic population evenly distributed between double mutants.ResultsA single mutation of large effect (S117N) serves as a pivot point for evolution to high resistance regions of the landscape. Through epistatic interactions with other mutations, this pivot creates an epistatic ratchet against reverse evolution towards the wild type ancestor, even in environments where the wild type is the most fit of all genotypes. This pivot mutation underlies the directional bias in evolution across the landscape, where evolution towards the ancestor is precluded across all examined drug concentrations from various starting points in the landscape.ConclusionsThe presence of pivot mutations can dictate dynamics of evolution across adaptive landscape through epistatic interactions within a protein, leaving a population trapped on local fitness peaks in an adaptive landscape, unable to locate ancestral genotypes. This irreversibility suggests that the structure of an adaptive landscape for a resistance protein should be understood before considering resistance management strategies. This proposed mechanism for constraints on reverse evolution corroborates evidence from the field indicating that phenotypic reversal often occurs via compensatory mutation at sites independent of those associated with the forward evolution of resistance. Because of this, molecular methods that identify resistance patterns via single SNPs in resistance-associated markers might be missing signals for resistance and compensatory mutation throughout the genome. In these settings, whole genome sequencing efforts should be used to identify resistance patterns, and will likely reveal a more complicated genomic signature for resistance and susceptibility, especially in settings where anti-malarial medications have been used intermittently. Lastly, the findings suggest that, given their role in dictating the dynamics of evolution across the landscape, pivot mutations might serve as future targets for therapy.Electronic supplementary materialThe online version of this article (doi:10.1186/s12936-016-1090-3) contains supplementary material, which is available to authorized users.

Relaxations of Approximate Linear Programs for the Real Option Management of Commodity Storage

The real option management of commodity conversion assets gives rise to intractable Markov decision processes (MDPs), in part because of the use of high-dimensional models of commodity forward curve evolution, as commonly done in practice. Focusing on commodity storage, we identify a deficiency of approximate linear programming (ALP), which we address by developing a novel approach to derive relaxations of approximate linear programs. We apply our approach to obtain a class of tractable ALP relaxations, also subsuming an existing method. We provide theoretical support for the use of these ALP relaxations rather than their associated approximate linear programs. Applied to existing natural gas storage instances, our ALP relaxations significantly outperform their corresponding approximate linear programs. Our best ALP relaxation is both near optimal and competitive with, albeit slower than, state-of-the-art methods for computing heuristic policies and lower bounds on the value of commodity storage, but is more directly applicable for dual (upper) bound estimation than these methods. Our approach is potentially relevant for the approximate solution of MDPs that arise in the real option management of other commodity conversion assets, as well as the valuation of real and financial options that depend on forward curve dynamics. This paper was accepted by Dimitris Bertsimas, optimization.

THE DYNAMICAL STATE AND LONG-TERM STABILITY OF HIP 102589

The dynamical state (component masses and kinematic parameters) of the triple star HIP 102589 is redetermined by fitting the simple double two-body model and the accurate three-body model, respectively, to observational data including those accumulated since the last orbit determination in 1992. Though the precision-weighted sum of squared residuals calculated from our results with both models are significantly smaller than the previous ones, only the result with the three-body model is statistically acceptable according to the goodness-of-fit test. The forward and backward long-term dynamical evolutions are numerically explored on the timescale of an estimated age of the components. It is found that the three-body system remains integrated and its hierarchical configuration keeps unchanged since the formation of the components, despite the fact that the instantaneous double two-body orbits vary significantly. This implies that the triple star may not be formed by a three-body encounter. Also, the possibility that the most massive component is itself a tightly bounded binary is discussed based on the redetermined mass and a stellar empirical mass–luminosity relation.

An analysis of the evolving comoving number density of galaxies in hydrodynamical simulations

The cumulative comoving number-density of galaxies as a function of stellar mass or central velocity dispersion is commonly used to link galaxy populations across different epochs. By assuming that galaxies preserve their number-density in time, one can infer the evolution of their properties, such as masses, sizes, and morphologies. However, this assumption does not hold in the presence of galaxy mergers or when rank ordering is broken owing to variable stellar growth rates. We present an analysis of the evolving comoving number density of galaxy populations found in the Illustris cosmological hydrodynamical simulation focused on the redshift range $0\leq z \leq 3$. Our primary results are as follows: 1) The inferred average stellar mass evolution obtained via a constant comoving number density assumption is systematically biased compared to the merger tree results at the factor of $\sim$2(4) level when tracking galaxies from redshift $z=0$ out to redshift $z=2(3)$; 2) The median number density evolution for galaxy populations tracked forward in time is shallower than for galaxy populations tracked backward in time; 3) A similar evolution in the median number density of tracked galaxy populations is found regardless of whether number density is assigned via stellar mass, stellar velocity dispersion, or dark matter halo mass; 4) Explicit tracking reveals a large diversity in galaxies' assembly histories that cannot be captured by constant number-density analyses; 5) The significant scatter in galaxy linking methods is only marginally reduced by considering a number of additional physical and observable galaxy properties as realized in our simulation. We provide fits for the forward and backward median evolution in stellar mass and number density and discuss implications of our analysis for interpreting multi-epoch galaxy property observations.

Emergence of the product of constant curvature spaces in loop quantum cosmology

The loop quantum dynamics of Kantowski–Sachs spacetime and the interior of higher genus black hole spacetimes with a cosmological constant has some peculiar features not shared by various other spacetimes in loop quantum cosmology. As in the other cases, though the quantum geometric effects resolve the physical singularity and result in a non-singular bounce, after the bounce a spacetime with small spacetime curvature does not emerge in either the subsequent backward or the forward evolution. Rather, in the asymptotic limit the spacetime manifold is a product of two constant curvature spaces. Interestingly, though the spacetime curvature of these asymptotic spacetimes is very high, their effective metric is a solution to Einstein’s field equations. Analysis of the components of the Ricci tensor shows that after the singularity resolution, the Kantowski–Sachs spacetime leads to an effective metric which can be interpreted as the ‘charged’ Nariai, while the higher genus black hole interior can similarly be interpreted as an anti Bertotti–Robinson spacetime with a cosmological constant. These spacetimes are ‘charged’ in the sense that the energy–momentum tensor that satisfies Einstein’s field equations is formally the same as the one for the uniform electromagnetic field, albeit it has a purely quantum geometric origin. The asymptotic spacetimes also have an emergent cosmological constant which is different in magnitude, and sometimes even its sign, from the cosmological constant in the Kantowski–Sachs and the interior of higher genus black hole metrics. With a fine tuning of the latter cosmological constant, we show that ‘uncharged’ Nariai, and anti Bertotti–Robinson spacetimes with a vanishing emergent cosmological constant can also be obtained.

Simulation of forward and backward waves evolution of few-cycle pulses propagating in an optical waveguide with dispersion and cubic nonlinearity of electronic and electronic-vibration nature

Numerical method for calculation of forward and backward waves of intense few-cycle laser pulses propagating in an optical waveguide with dispersion and cubic nonlinearity of electronic and electronic-vibration nature is described. Simulations made with the implemented algorithm show that accounting for Raman nonlinearity does not lead to qualitative changes in behavior of the backward wave. Speaking about quantitative changes, the increase of efficiency of energy transfer from the forward wave to the backward wave is observed. Presented method can be also used to simulate interaction of counterpropagating pulses.

Projecting High-Dimensional Parametric Uncertainties for Improved State Estimation Error Confidence

The navigation of vehicles oftentimes involves the use of key environment and vehicle parameters in the forward evolution of the state estimate and its associated uncertainty. Given the objective of achieving precision navigation, it is critical that the full effect of the parameters, including their uncertainties, is taken into account in the estimation process. When the parameter set is of high dimension, the computational complexity involved in projecting the parametric uncertainties into state uncertainties can make the navigation solution intractable for onboard computation. A method is presented that projects the uncertainties in the parameters through an equivalent process-noise structure leading to real-time computations supporting precision navigation. Having first shown that the procedure works for linear systems, the method is applied to generating a process-noise-like term that accounts for the uncertainty present in the spherical harmonics coefficients of a high-order gravitational acceleration model. Simulation studies are performed to show that the method can be applied to the conversion of the uncertainty in spherical harmonics gravity coefficients, which can be of dimension 10,000 and higher, to a process-noise representation that accurately predicts the position and velocity uncertainties for spacecraft navigation.

Entropy Production for Quantum Markov Semigroups

An invariant state of a quantum Markov semigroup is an equilibrium state if it satisfies a quantum detailed balance condition. In this paper, we introduce a notion of entropy production for faithful normal invariant states of a quantum Markov semigroup on B(h) as a numerical index measuring "how much far" they are from equilibrium. The entropy production is defined as the derivative of the relative entropy of the one-step forward and backward evolution in analogy with the classical probabilistic concept. We prove an explicit trace formula expressing the entropy production in terms of the completely positive part of the generator of a norm continuous quantum Markov semigroup showing that it turns out to be zero if and only if a standard quantum detailed balance condition holds.

Scaling-up NLP Pipelines to Process Large Corpora of Clinical Notes.

This article is part of the Focus Theme of Methods of Information in Medicine on "Big Data and Analytics in Healthcare". This paper describes the scale-up efforts at the VA Salt Lake City Health Care System to address processing large corpora of clinical notes through a natural language processing (NLP) pipeline. The use case described is a current project focused on detecting the presence of an indwelling urinary catheter in hospitalized patients and subsequent catheter-associated urinary tract infections. An NLP algorithm using v3NLP was developed to detect the presence of an indwelling urinary catheter in hospitalized patients. The algorithm was tested on a small corpus of notes on patients for whom the presence or absence of a catheter was already known (reference standard). In planning for a scale-up, we estimated that the original algorithm would have taken 2.4 days to run on a larger corpus of notes for this project (550,000 notes), and 27 days for a corpus of 6 million records representative of a national sample of notes. We approached scaling-up NLP pipelines through three techniques: pipeline replication via multi-threading, intra-annotator threading for tasks that can be further decomposed, and remote annotator services which enable annotator scale-out. The scale-up resulted in reducing the average time to process a record from 206 milliseconds to 17 milliseconds or a 12- fold increase in performance when applied to a corpus of 550,000 notes. Purposely simplistic in nature, these scale-up efforts are the straight forward evolution from small scale NLP processing to larger scale extraction without incurring associated complexities that are inherited by the use of the underlying UIMA framework. These efforts represent generalizable and widely applicable techniques that will aid other computationally complex NLP pipelines that are of need to be scaled out for processing and analyzing big data.

Dualities in population genetics: A fresh look with new dualities

We apply our general method of duality, introduced in Giardinà et al. (2007), to models of population dynamics. The classical dualities between forward and ancestral processes can be viewed as a change of representation in the classical creation and annihilation operators, both for diffusions dual to coalescents of Kingman’s type, as well as for models with finite population size.Next, using SU(1,1) raising and lowering operators, we find new dualities between the Wright–Fisher diffusion with d types and the Moran model, both in presence and absence of mutations. These new dualities relates two forward evolutions. From our general scheme we also identify self-duality of the Moran model.

Large-scale thrusting at the northern Junggar Basin since Cretaceous and its implications for the rejuvenation of the Central Asian Orogenic Belt

The Wulungu Depression is the northernmost first-order tectonic unit in the Junggar Basin. It can be divided into three sub-units: the Hongyan step-fault zone, the Suosuoquan sag and the Wulungu south slope. The Cenozoic strata in the basin are intact and Mesozoic–Cenozoic deformation can be observed in the Wulungu step-fault zone, so this is an ideal place to study the Mesozoic–Cenozoic deformation. By integration of fault-related folding theories, regional geology and drilling data, the strata of the Cretaceous–Paleogene systems are divided into small layers which are selected as the subjects of this research. The combination of the developing unconformity with existing growth strata makes it conceivable that faults on the step-fault zone have experienced different degrees of reactivation of movement since the Cretaceous. Evolutionary analyses of the small layers using 2D-Move software showed certain differences in the reactivation of different segments of the Wulungu Depression such as the timing of reactivation of thrusting, for which the reactivity time of the eastern segment was late compared with those of the western and middle segments. In addition the resurrection strength was similarly slightly different, with the shortening rate being higher in the western segment than in the other segments. Moreover, the thrust fault mechanism is basement-involved combined with triangle shear fold, for which a forward evolution model was proposed.

Predictive Modeling of the Evolution of Fault Structure: 3-D Modeling and Coupled Geomechanical/Flow Simulation

Reconstruction of geological structures has the potential to provide additional insight into the effect of the depositional history on the current-day geomechanical and hydro-geologic state. Accurate modeling of the reconstruction process is, however, complex, necessitating advanced procedures for the prediction of fault formation and evolution within fully coupled geomechanical, fluid flow and temperature fields. In this paper, a 3-D computational approach is presented that is able to forward model complex structural evolution with multiple intersecting faults that exhibit large relative movement within a coupled geomechanical/flow environment. The approach adopts the Lagrangian method, complemented by robust and efficient automated adaptive meshing techniques, an elasto-plastic constitutive model based on critical state concepts, and global energy dissipation regularized by inclusion of fracture energy in the equations governing state variable evolution. The proposed model is validated by comparison of 2-D plane strain and 3-D thin-slice predictions of a bench-scale experiment, and then applied to two conceptual coupled geomechanical/fluid flow field-scale benchmarks.

On resolving singularities of piecewise-smooth discontinuous vector fields via small perturbations

A two-fold singularity is a point on a discontinuity surface of a piecewise-smooth vector field at which the vector field is tangent to the surface on both sides. Due to the double tangency, forward evolution from a two-fold is typically ambiguous. This is an especially serious issue for two-folds that are reached by the forward orbits of a non-zero measure set of initial points. However, arbitrarily small perturbations of the vector field can make forward evolution well-defined, and from an applied perspective, such perturbations may represent additional model features that enhance the realism of a piecewise-smooth mathematical model. Three physically motivated forms of perturbation: hysteresis, time-delay, and noise, are analysed individually. The purpose of this paper is to characterise the perturbed dynamics in the limit that the size of the perturbation tends to zero. This concept is applied to a two-fold in two dimensions. In each case the limit leads to a novel probabilistic notion of forward evolution from the two-fold.

城市复合生态及生态空间管理

PDF HTML阅读 XML下载 导出引用 引用提醒 城市复合生态及生态空间管理 DOI: 10.5846/stxb201312102920 作者: 作者单位: 中国科学院生态环境研究中心 城市与区域生态国家重点实验室,中国科学院生态环境研究中心 城市与区域生态国家重点实验室,中国科学院生态环境研究中心 城市与区域生态国家重点实验室,中国科学院生态环境研究中心 城市与区域生态国家重点实验室,中国科学院生态环境研究中心 城市与区域生态国家重点实验室 作者简介: 通讯作者: 中图分类号: 基金项目: 国家自然科学基金资助项目（71033005，71273254，71033005） Urban eco-complex and eco-space management Author: Affiliation: State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences,Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences,,, Fund Project: 摘要 | 图/表 | 访问统计 | 参考文献 | 相似文献 | 引证文献 | 资源附件 | 文章评论 摘要:城市是一类基于区域水-土-气-生-矿五类生态因子，生产-流通-消费-还原-调控五类生态过程，以及经济-政治-文化-社会-环境五类生态功能，在时间-空间-数量-结构-功序范畴耦合的复合生态系统。阐述了城市复合生态的整合机制、体制、结构、功能的内涵，提出以净化、绿化、活化、美化、进化型安全生态保障目标，生物链-矿物链-服务链-静脉链-智慧链五链合一的循环经济耦合构架，以及污染防治、清洁生产、产业生态、生态社区和生态文明五位一体的和谐社会建设模式为城市生态管理的3个支柱。城市生态管理是对城市涵养、调节、流通、供给和支持五类生态服务功能的调节、修复和建设而不只是保护城市生物。城市生态空间是指城市生态系统结构所占据的物理空间、其代谢所依赖的区域腹地空间，以及其功能所涉及的多维关系空间。通过天津、扬州、淮北、合肥等市复合生态规划与建设的案例，阐述了区域、市域、城域和社区/园区4尺度城市生态空间的管理方略。最后以延庆和北京主城关系的演变探讨了复合生态位势在城市生态管理中的应用。 Abstract:City is a kind of social-economic-natural complex ecosystem (SENCE), supported by 5 kinds of eco-factors (water, soil, fire, biome and minerals), 5 eco-processes (production, transportation, consumption, recycling and regulation), 5 kinds of function (economy, politics, culture, society and environment), and coupled in time, space, quantity, structure and function). This paper explained its integrative dynamics, cybernetics and systematics, three supporters of its development: eco-security (cleaning, greening, vitalizing, beautification and forward evolution), circular economy (coupling five chains of biological, mineral, service, recycling and wisdom), and harmonious society (with a integrative management model of pollution control, cleaner production, eco-industry, eco-polis and eco-civilization). Urban ecological management is rather a kind of regulation, restoration and creation process to enforce the urban ecological service of cultivation, regulation, circulation, supply and supporting than just nature conservation. Urban eco-space includes the physical space the city occupied, the hinterland ecosystem for city metabolism using, and the super eco niche for the city function. Through case studies of Tianjin, Yangzhou, Huaibei and Hefei, the paper has shown the approaches for urban eco-space planning and management. Finally, the application of integrative eco-niche and eco-potentials are discussed with a case of Yanqing County for its development relationship with its mother city of Beijing. 参考文献 相似文献 引证文献

Relaxations of Approximate Linear Programs for the Real Option Management of Commodity Storage

The real option management of commodity conversion assets gives rise to intractable Markov decision processes (MDPs), in part due to the use of high dimensional models of commodity forward curve evolution, as commonly done in practice. Focusing on commodity storage, we identify a deficiency of approximate linear programming, which we address by developing a novel approach to derive relaxations of approximate linear programs (ALPs). We apply our approach to obtain a class of tractable ALP relaxations, also subsuming an existing method. We provide theoretical support for the use of these ALP relaxations rather than their corresponding ALPs. Applied to existing natural gas storage instances, our ALP relaxations significantly outperform their corresponding ALPs. Our best ALP relaxation is both near optimal and competitive with, albeit slower than, state-of-the-art methods for computing heuristic policies and lower bounds on the value of commodity storage, but is more directly applicable for dual upper bound estimation than these methods. Our approach is potentially relevant for the approximate solution of MDPs that arise in the real option management of other commodity conversion assets, as well as the valuation of real and financial options that depend on forward curve dynamics.

METALLICITY-DEPENDENT GALACTIC ISOTOPIC DECOMPOSITION FOR NUCLEOSYNTHESIS

All stellar evolution models for nucleosynthesis require an initial isotopic abundance set to use as a starting point. Generally, our knowledge of isotopic abundances of stars is fairly incomplete except for the Solar System. We present a first model for a complete average isotopic decomposition as a function of metallicity. Our model is based on the underlying nuclear astrophysics processes, and is fitted to observational data, rather than traditional forward galactic chemical evolution modeling which integrates stellar yields beginning from big bang nucleosynthesis. We first decompose the isotopic solar abundance pattern into contributions from astrophysical sources. Each contribution is then assumed to scale as a function of metallicity. The resulting total isotopic abundances are summed into elemental abundances and fitted to available halo and disk stellar data to constrain the model's free parameter values. This procedure allows us to use available elemental observational data to reconstruct and constrain both the much needed complete isotopic evolution that is not accessible to current observations, and the underlying astrophysical processes. Our model finds a best fit for Type Ia contributing \simeq 0.7 to the solar Fe abundance, and and Type Ia onset occurring at [Fe/H]\simeq -1.2.

A simulation framework for evolution on uneven terrains for synchronous drive robot

This paper presents a simulation framework for evolution on uneven terrains for a wheeled mobile robot (WMR) such as a synchronous drive robot. The framework lends itself as a tool capable of solving various problems, such as forward kinematic-based evolution, inverse kinematic-based evolution, path planning and trajectory tracking. This framework becomes particularly useful when we understand that the evolution problem (and hence, the various associated problems based on evolution) is particularly challenging on uneven terrain. Specifically, it is entailed to bring in the contact constraints posed by the interaction of the wheel and the ground as well as the holonomic constraints as the problem is formulated in a Differential Algebraic Equation setting. The problem becomes all the more crucial as vehicles moving on uneven terrain are becoming the order of the day. Nonetheless, there has not been much literature that deals in length the various aspects that go into the framework. This paper elaborates on the various aspects of the framework, presents simulation results on uneven terrain, where the vehicle evolves without slipping, and also presents substantial quantitative analysis in regard to wheel slippage. The main contributions of this paper are the motion planning using forward kinematic framework and a new formulation of inverse kinematics for wheeled robots on uneven terrains.

Compact Embeddings for Spaces of Forward Rate Curves

The goal of this paper is to prove a compact embedding result for spaces of forward rate curves. As a consequence of this result, we show that any forward rate evolution can be approximated by a sequence of finite dimensional processes in the larger state space.

Incomplete Phase Space Reconstruction Method Based on Subspace Adaptive Evolution Approximation

The chaotic time series can be expanded to the multidimensional space by phase space reconstruction, in order to reconstruct the dynamic characteristics of the original system. It is difficult to obtain complete phase space for chaotic time series, as a result of the inconsistency of phase space reconstruction. This paper presents an idea of subspace approximation. The chaotic time series prediction based on the phase space reconstruction can be considered as the subspace approximation problem in different neighborhood at different time. The common static neural network approximation is suitable for a trained neighborhood, but it cannot ensure its generalization performance in other untrained neighborhood. The subspace approximation of neural network based on the nonlinear extended Kalman filtering (EKF) is a dynamic evolution approximation from one neighborhood to another. Therefore, in view of incomplete phase space, due to the chaos phase space reconstruction, we put forward subspace adaptive evolution approximation method based on nonlinear Kalman filtering. This method is verified by multiple sets of wind speed prediction experiments in Wulong city, and the results demonstrate that it possesses higher chaotic prediction accuracy.