Forward Evolution Research Articles

GENERIC QUANTUM MARKOV SEMIGROUPS, CYCLE DECOMPOSITION AND DEVIATION FROM EQUILIBRIUM

A generic quantum Markov semigroup [Formula: see text] of a d-level quantum open system with a faithful normal invariant state ρ admits a dual semigroup [Formula: see text] with respect to the scalar product induced by ρ. We show that the difference of the generators [Formula: see text] can be written as the sum of a derivation 2i[H, ⋅] and a weighted difference of automorphisms [Formula: see text] where [Formula: see text] is a family of cycles on the d levels of the system, wc are positive weights and [Formula: see text] are unitaries. This formula allows us to represent the deviation from equilibrium (in a "small" time interval) as the superposition of cycles of the system where the difference between the forward and backward evolution is written as the difference of a reversible evolution and its time reversal. Moreover, it generalises cycle decomposition of Markov jump processes. We also find a similar formula with partial isometries instead of unitaries.

Minimally invasive surgery for Ricci flow singularities

In this paper, we construct smooth forward Ricci flow evolutions of singular initial metrics resulting from rotationally symmetric neckpinches on 𝒮n + 1, without performing an intervening surgery. In the restrictive context of rotational symmetry, this construction gives evidence in favor of Perelman's hope for a “canonically defined Ricci flow through singularities”.

QoS‐aware and compromise‐resilient key management scheme for heterogeneous wireless Internet of Things

AbstractThe Internet of Things (IOT) is envisioned as a natural evolution of the Internet, promising to enable ubiquitous connections for pervasive objects. The evolutionary merging of heterogeneous wireless networks is inevitable for smooth migration to IOT; for example, in a typical application of IOT—smart homes—there exist sensor–radio frequency identification (RFID) hybrid networks. The communication security between sensor (or RFID tags) and home control center is critical, whereas an appropriate key management scheme is a prerequisite for communication security. In this paper, we propose a compromise resilient key management scheme including key agreement schemes and key evolution policies to tackle existing remarkable asymmetry with respect to computation resources of hybrid networks. In particular, a forward and backward secure key evolution policy with formal proof is proposed. We also propose a quality of service (QoS)‐aware enhancement method by measuring several metrics such as data assurance priority, attacking risk, and remaining power percentage. Security parameter negotiation and a tuning method are proposed, based on reactive measurement in real time. Our proposed scheme is built on abstract cryptographic primitives such as trapdoor permutation, pseudorandom function, pseudorandom number generator, one‐way function and hash function so as to retain flexibility for concrete options. Security and performance for proposed key agreement schemes and key evolution policies are compared in detail. Three QoS‐aware security strategies are proposed: performance first, security second (PFSS); security first, performance second (SFPS); and performance security made balanced (PSMB). Measurement‐based negotiation of security parameters is also proposed in terms of algorithm prototype. Copyright © 2011 John Wiley & Sons, Ltd.

Communication: Comment on the effective temporal and spectral resolution of impulsive stimulated Raman signals

A compact correlation-function expression for time-resolved stimulated Raman signals, generated by combining a spectrally narrow (picosecond) with a broad (femtosecond) pulse, is derived using a closed time path loop diagrammatic technique that represents forward and backward time evolution of the vibrational wave function. We show that even though the external spectral and temporal parameters of the pulses may be independently controlled, the effective temporal and spectral resolution of the experiment may not exceed the fundamental bandwidth limitation.

In Silico Evolution of Early Metabolism

We developed a simulation tool for investigating the evolution of early metabolism, allowing us to speculate on the formation of metabolic pathways from catalyzed chemical reactions and on the development of their characteristic properties. Our model consists of a protocellular entity with a simple RNA-based genetic system and an evolving metabolism of catalytically active ribozymes that manipulate a rich underlying chemistry. Ensuring an almost open-ended and fairly realistic simulation is crucial for understanding the first steps in metabolic evolution. We show here how our simulation tool can be helpful in arguing for or against hypotheses on the evolution of metabolic pathways. We demonstrate that seemingly mutually exclusive hypotheses may well be compatible when we take into account that different processes dominate different phases in the evolution of a metabolic system. Our results suggest that forward evolution shapes metabolic network in the very early steps of evolution. In later and more complex stages, enzyme recruitment supersedes forward evolution, keeping a core set of pathways from the early phase.

Forward–backward semiclassical and quantum trajectory methods for time correlation functions

Forward-backward trajectory formulations of time correlation functions are reviewed. Combination of the forward and reverse time evolution operators within the time-dependent semiclassical approximation minimizes phase cancellation, giving rise to an efficient methodology for simulating the dynamics of low-temperature fluids. A quantum mechanical version of the forward-backward formulation, based on the hydrodynamic formulation of time-dependent quantum mechanics, is also available but is practical only for small systems.

News Analytics for Energy Futures

We investigate how crude oil futures markets respond to positive and negative sentiment in news, as measured by the Thomson Reuters News Analytics. We measure the impact of the news sentiment on daily futures returns and on the fundamental factors of the forward curve evolution, such as the forward curve’s level and the slope. We define positive and negative news events as those days when the aggregated daily sentiment is in the top 10% quantiles of the corresponding sentiment distribution. We then relate these events to abnormal futures returns and to significant changes in the forward curve’s level and slope. We find that, for all maturities, positive resp. negative news events are accompanied by long periods of higher resp. lower than normal returns. These abnormal returns are observed already prior to the significant news events, suggesting that news are correlated with price momentum. Furthermore, after a negative news event occurs, returns continue decreasing at least for the subsequent 20 days. This is especially pronounced for nearby maturities, whose returns decrease by more than 3% on average. After a positive news event, returns increase on average by 2-3%. These effects are both statistically and economically significant. We also show a great asymmetry in the market’s behavior: although positive and negative events are both 10% of days, the negative events are accompanied by much greater losses than the gains surrounding positive events. We analyze the complex effect of news on the slope of the forward curve, and show that negative news increase the slope both in backwardation and contango markets. This means that contango deepens and backwardation flattens following a negative news event. Positive news have the opposite, albeit smaller, effect on the forward curve’s slope. Generally, the reaction to news is significantly more pronounced in contango than in backwardation market. The results of the analysis lay foundation for profitable trading strategies, based on taking a long/short position in oil futures of a fixed maturity immediately after a significant positive/negative news event. However, we expect such strategies to be quite risky. The analysis of news effects on the entire forward curve can be used to construct profitable (but much less risky) calendar spread trading strategies.

Influence of genetic architecture on contemporary local evolution in the soapberry bug,Jadera haematoloma:artificial selection on beak length

Little is known about the influence of genetic architecture on local adaptation. We investigated the genetic architecture of the rapid contemporary evolution of mouthparts, the flight polymorphism and life history traits in the soapberry bug Jadera haematoloma (Hemiptera) using laboratory selection. The mouthparts of these seed-feeding bugs have adapted in 40-50 years by decreasing in length following novel natural selection induced by a host switch to the seeds of an introduced tree with smaller fruits than those of the native host vine. Laboratory selection on beak length in both an ancestral population feeding on the native host and a derived population feeding on the introduced host reveals genetic variance allowing a rapid response (heritabilities of 0.51-0.87) to selection for either longer or shorter beaks. This selection resulted in reverse evolution by restoring long beaks in the derived population and forward evolution by re-creating short beaks in the ancestral bugs. There were strong genetic correlations (0.68-0.84) in both populations between beak lengths and the frequency of flight morphs, with short beaks associated with short wings. The results reveal a genetically interrelated set of adaptive multivariate traits including both beak length and flight morph. This suite of traits reflects host plant patchiness and seeding phenology. Weaker evidence suggests that egg mass and early egg production may be elements of the same suite. Reversible or forward evolution thus may occur in a broad set of genetically correlated multivariate traits undergoing rapid contemporary adaptation to altered local environments.

Experimental evolution reveals natural selection on standing genetic variation

Evolution depends on genetic variation generated by mutation or recombination from standing genetic variation. In sexual organisms, little is known about the molecular population genetics of adaptation and reverse evolution. We carry out 50 generations of experimental reverse evolution in populations of Drosophila melanogaster, previously differentiated by forward evolution, and follow changes in the frequency of SNPs in both arms of the third chromosome. We characterize the effects of sampling finite population sizes and natural selection at the genotype level. We demonstrate that selection has occurred at several loci and further that there is no general loss or gain of allele diversity. We also observe that despite the complete convergence to ancestral levels of adaptation, allele frequencies only show partial return.

The Quantum Speed up as Advanced Cognition of the Solution

Solving a problem requires a problem solving step (deriving, from the formulation of the problem, the solution algorithm) and a computation step (running the algorithm). The latter step is generally oblivious of the former. We unify the two steps into a single physical interaction: a many body interaction in an idealized classical framework, a measurement interaction in the quantum framework. The many body interaction is a useful conceptual reference. The coordinates of the moving parts of a perfect machine are submitted to a relation representing problem-solution interdependence. Moving an “input” part nondeterministically produces a solution through a many body interaction. The kinematics and the statistics of this problem solving mechanism apply to quantum computation—once the physical representation is extended to the oracle that produces the problem. Configuration space is replaced by phase space. The relation between the coordinates of the machine parts now applies to a set of variables representing the populations of the qubits of a quantum register during reduction. The many body interaction is replaced by the measurement interaction, which changes the population variables from the values before to the values after measurement (and the forward evolution into the backward evolution, the same unitary transformation but ending with the state after measurement). Quantum computation is reduction on the solution of the problem under the problem-solution interdependence relation. The speed up is explained by a simple consideration of time-symmetry, it is the gain of information about the solution due to backdating, to before running the algorithm, a time-symmetric part of the reduction on the solution. This advanced cognition of the solution reduces the solution space to be explored by the algorithm. The quantum algorithm takes the time taken by a classical algorithm that knows in advance 50% of the information acquired by reading the solution (i.e. by measuring the content of the computer register at the end of the quantum algorithm). From another standpoint, the notion that a computation process is condensed into a single physical interaction explains the fact that we perceive many things at the same time in the introspective “present” (the instant of the interaction in the classical case, the time interval spanned by backdated reduction in the quantum case).

Rapid whole-genome mutational profiling using next-generation sequencing technologies

Forward genetic mutational studies, adaptive evolution, and phenotypic screening are powerful tools for creating new variant organisms with desirable traits. However, mutations generated in the process cannot be easily identified with traditional genetic tools. We show that new high-throughput, massively parallel sequencing technologies can completely and accurately characterize a mutant genome relative to a previously sequenced parental (reference) strain. We studied a mutant strain of Pichia stipitis, a yeast capable of converting xylose to ethanol. This unusually efficient mutant strain was developed through repeated rounds of chemical mutagenesis, strain selection, transformation, and genetic manipulation over a period of seven years. We resequenced this strain on three different sequencing platforms. Surprisingly, we found fewer than a dozen mutations in open reading frames. All three sequencing technologies were able to identify each single nucleotide mutation given at least 10-15-fold nominal sequence coverage. Our results show that detecting mutations in evolved and engineered organisms is rapid and cost-effective at the whole-genome level using new sequencing technologies. Identification of specific mutations in strains with altered phenotypes will add insight into specific gene functions and guide further metabolic engineering efforts.

The scalar field kernel in cosmological spaces

We construct the quantum-mechanical evolution operator in the functional Schrödinger picture—the kernel—for a scalar field in spatially homogeneous FLRW spacetimes when the field is (a) free and (b) coupled to a spacetime-dependent source term. The essential element in the construction is the causal propagator, linked to the commutator of two Heisenberg picture scalar fields. We show that the kernels can be expressed solely in terms of the causal propagator and derivatives of the causal propagator. Furthermore, we show that our kernel reveals the standard light cone structure in FLRW spacetimes. We finally apply the result to Minkowski spacetime, to de Sitter spacetime and calculate the forward time evolution of the vacuum in a general FLRW spacetime.

Sequence-level population simulations over large genomic regions.

Simulation is an invaluable tool for investigating the effects of various population genetics modeling assumptions on resulting patterns of genetic diversity, and for assessing the performance of statistical techniques, for example those designed to detect and measure the genomic effects of selection. It is also used to investigate the effectiveness of various design options for genetic association studies. Backward-in-time simulation methods are computationally efficient and have become widely used since their introduction in the 1980s. The forward-in-time approach has substantial advantages in terms of accuracy and modeling flexibility, but at greater computational cost. We have developed flexible and efficient simulation software and a rescaling technique to aid computational efficiency that together allow the simulation of sequence-level data over large genomic regions in entire diploid populations under various scenarios for demography, mutation, selection, and recombination, the latter including hotspots and gene conversion. Our forward evolution of genomic regions (FREGENE) software is freely available from www.ebi.ac.uk/projects/BARGEN together with an ancillary program to generate phenotype labels, either binary or quantitative. In this article we discuss limitations of coalescent-based simulation, introduce the rescaling technique that makes large-scale forward-in-time simulation feasible, and demonstrate the utility of various features of FREGENE, many not previously available.

On Wright–Fisher diffusion and its relatives

We present a series of elementary stochastic models arising from population genetics.Various mathematical aspects are investigated at the intuitive level. Special emphasis is puton the diffusion method. The focus is on the Wright–Fisher diffusion model and itsvariations, describing the forward evolution of one colony undergoing random sampling,possibly under the additional forces arising from mutation and selection with or withoutdominance. Some aspects of their dual coalescents obtained while running the diffusionprocess backward in time are also investigated.

Ethical and social issues in nanobiotechnologies

Nanobiotechnologies represent a rapidly growing field of interest. Several European conferences during the past year have highlighted the wide‐ranging potential of applying techniques at the molecular and atomic levels to understand and transform biosystems, and of using biological principles and materials to create new devices at the nanoscale. This convergence of disciplines holds great promise in medicine for improved diagnostics, less invasive monitoring devices and more targeted therapies, and also has potential for agricultural and environmental applications. However, relatively little has been written about the ethical and social implications of this emerging research area. This article seeks to examine some of these questions, and is based on a report produced by the ethical, legal and social advisory (ELSA) board of the Nano2Life European Network of Excellence in Nanobiotechnology (Bruce, 2006). Nano2Life is funded by the European Commission (EC) under the Sixth Framework Programme. It brings together European research groups from 12 countries to collaborate in specific multidisciplinary projects, which combine the life sciences with microtechnologies and nanotechnologies, materials science, physics and chemistry. The aim is to develop new research tools and applications for medical diagnosis and therapy, and for monitoring food safety and environmental health. Seeking to learn from the major controversy in Europe over genetically modified (GM) foods, Nano2Life established—as an integral part of the network—an advisory board to evaluate possible ethical, legal and social implications. Its role is to advise on particular research projects, to educate participating scientists, and to produce a broad overview of the ethical and social issues (Bruce, 2006), which are summarized in this article. The reflections presented here are insights from board members and some participating scientists, and draw on an initial literature survey (Jomann, 2006). A main aim is to make researchers in both academia and industry aware of the broad ethical …

Predictive modelling of structure evolution in sandbox experiments

In this paper a computational approach is presented that is able to forward model complex structural evolution with multiple intersecting faults that exhibit large relative movement. The approach adopts the Lagrangian method, complemented by robust and efficient automated adaptive meshing techniques, a 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 efficacy of the approach is benchmarked by forward simulation of two extensional analogue experiments that exhibit the development of a roll-over anticline with a series of superimposed crestal collapse graben systems. These sandbox experiments are excellent benchmarks for computational models, as both intersecting localisations with different rates of slip and large relative movement on localisations must be represented, while other complex phenomena associated with structural evolution over geological timeframes are not present.

Exact solution of qubit decoherence models by a transfer matrix method

We present a method for the solution of the behavior of an ensemble of qubits in a random time-dependent external field. The forward evolution in time is governed by a transfer matrix. The elements of this matrix determine the various decoherence times. The method provides an exact solution in cases where the noise is piecewise constant in time. We show that it applies, for example, to a realistic model of decoherence of electron spins in semiconductors. Results are obtained for the nonperturbative regimes of the models, and we see a transition from weak relaxation to overdamped behavior as a function of noise anisotropy.

Interaction of an external impurity with the surface intrinsic mode in a Heisenberg chain

In this paper we have demonstrated the existence of surface intrinsic localized modes in one-dimensional classical spin systems. These modes have frequencies above the top of the magnon band and are more localized than the corresponding modes that were found in the lattice dynamics. By numerical methods we have studied the forward evolution in time. These entities are stable in time for many time steps. Also, we consider the interaction of these surface excitations with an external dipolar field. We have first considered the case in which the external dipole is parallel to the spins of the bulk. According to the distance of the impurity from the surface we find that at a particular distance a new surface mode appears, that we have called a mixed mode because it is formed by a localized state at the surface plus a plane wave. At large distances the dipole traps the surface mode, while at small distances the external impurity potential is so strong that all the spins are forced to be aligned in the $z$ direction. For the case in which the external magnetic dipole is antiparallel to the bulk spins there are no mixed modes and the external impurity is so strong that the surface modes are trapped at large distances, and the bulk modes are trapped at very short distances.

Teilhard de Chardin’s Engagement with the Relationship between Science and Theology in Light of Discussions about Environmental Ethics

Pierre Teilhard de Chardin was among the most outstanding palaeontologists of the twentieth century. He was also a Jesuit whose task was to bring to the Church the novelty of the modern world. This novelty was evolution, the irreversible change in time characterized by a movement toward complexity and consciousness. Teilhard de Chardin proposed a research programme that would provide evidence for this increasing complexity in the animal evolution of canalizations and parallelisms. The most important of these was the move toward cerebralisation observed in various phyla. In order to investigate the mechanisms, he proposed biology as the science of the complexity of life, and geobiology as the science of the evolving biosphere. Teilhard de Chardin developed a synthesis with theology where humankind carried forward evolution with convergence towards the Omega point, the moment of the parousia of Christ. This eschatological perspective was strictly related to the survival of Earth, which itself allowed the emergence of humanity. At this point the preservation of the biosphere acquires all of its ethical value as it is the means to reach the eschatological task of the parousia of Christ. Finally, the relationship between the biosphere and the noosphere is suggested by the concept of symbiosis. In this way, the model of Teilhard de Chardin is a model of continuing exchange between science and theology with a reciprocal enrichment providing, among the many aspects, a new vision of the relationships between humankind and the biosphere.

Stochasticity, decoherence and an arrow of time from the discretization of time?

Certain intriguing consequences of the discreteness of time on the time evolution of dynamical systems are discussed. In the discrete-time classical mechanics proposed here, there is an arrow of time that follows from the fact that the replacement of the time derivative by the backward difference operator alone can preserve the non-negativity of the phase space density. It is seen that, even for free particles, all the degrees of freedom are correlated in principle. The forward evolution of functions of phase space variables by a finite number of time steps, in this discrete-time mechanics, depends on the entire continuous-time history in the interval [0, ∞]. In this sense, discrete time evolution is nonlocal in time from a continuous-time point of view. A corresponding quantum mechanical treatment is possible via the density matrix approach. The interference between nondegenerate quantum mechanical states decays exponentially. This decoherence is present, in principle, for all systems; however, it is of practical importance only in macroscopic systems, or in processes involving large energy changes.