On polymorphic logical gates in sub-excitable chemical medium

In a sub-excitable light-sensitive Belousov-Zhabotinsky chemical medium an asymmetric disturbance causes the formation of localized traveling wave-fragments. Under the right conditions these wave-fragment can conserve their shape and velocity vectors for extended time periods. The size and life span of a fragment depend on the illumination level of the medium. When two or more wave-fragments collide they annihilate or merge into a new wave-fragment. In computer simulations based on the Oregonator model we demonstrate that the outcomes of inter-fragment collisions can be controlled by varying the illumination level applied to the medium. We interpret these wave-fragments as values of Boolean variables and design collision-based polymorphic logical gates. The gate implements operation XNOR for low illumination, and it acts as NOR gate for high illumination. As a NOR gate is a universal gate then we are able to demonstrate that a simulated light sensitive BZ medium exhibits computational universality

Beyond Gross-Pitaevskii equation for 1D gas: Quasiparticles and solitons

Describing properties of a strongly interacting quantum many-body system poses a serious challenge both for theory and experiment. In this work, we study excitations of one-dimensional repulsive Bose gas for arbitrary interaction strength using a hydrodynamic approach. We use linearization to study particle (type-I) excitations and numerical minimization to study hole (type-II) excitations. We observe a good agreement between our approach and exact solutions of the Lieb-Liniger model for the particle modes and discrepancies for the hole modes. Therefore, the hydrodynamical equations find to be useful for long-wave structures like phonons and of a limited range of applicability for short-wave ones like narrow solitons. We discuss potential further applications of the method.Comment: 27 pages, 11 figures. Submission to SciPos

Maximum likelihood models and algorithms for gene tree evolution with duplications and losses

<p>Abstract</p> <p>Background</p> <p>The abundance of new genomic data provides the opportunity to map the location of gene duplication and loss events on a species phylogeny. The first methods for mapping gene duplications and losses were based on a parsimony criterion, finding the mapping that minimizes the number of duplication and loss events. Probabilistic modeling of gene duplication and loss is relatively new and has largely focused on birth-death processes.</p> <p>Results</p> <p>We introduce a new maximum likelihood model that estimates the speciation and gene duplication and loss events in a gene tree within a species tree with branch lengths. We also provide an, in practice, efficient algorithm that computes optimal evolutionary scenarios for this model. We implemented the algorithm in the program DrML and verified its performance with empirical and simulated data.</p> <p>Conclusions</p> <p>In test data sets, DrML finds optimal gene duplication and loss scenarios within minutes, even when the gene trees contain sequences from several hundred species. In many cases, these optimal scenarios differ from the lca-mapping that results from a parsimony gene tree reconciliation. Thus, DrML provides a new, practical statistical framework on which to study gene duplication.</p

The great time series classification bake off: a review and experimental evaluation of recent algorithmic advances

In the last five years there have been a large number of new time series classification algorithms proposed in the literature. These algorithms have been evaluated on subsets of the 47 data sets in the University of California, Riverside time series classification archive. The archive has recently been expanded to 85 data sets, over half of which have been donated by researchers at the University of East Anglia. Aspects of previous evaluations have made comparisons between algorithms difficult. For example, several different programming languages have been used, experiments involved a single train/test split and some used normalised data whilst others did not. The relaunch of the archive provides a timely opportunity to thoroughly evaluate algorithms on a larger number of datasets. We have implemented 18 recently proposed algorithms in a common Java framework and compared them against two standard benchmark classifiers (and each other) by performing 100 resampling experiments on each of the 85 datasets. We use these results to test several hypotheses relating to whether the algorithms are significantly more accurate than the benchmarks and each other. Our results indicate that only 9 of these algorithms are significantly more accurate than both benchmarks and that one classifier, the Collective of Transformation Ensembles, is significantly more accurate than all of the others. All of our experiments and results are reproducible: we release all of our code, results and experimental details and we hope these experiments form the basis for more rigorous testing of new algorithms in the future

Thermodynamic principles and implementations of quantum machines

The efficiency of cyclic heat engines is limited by the Carnot bound. This bound follows from the second law of thermodynamics and is attained by engines that operate between two thermal baths under the reversibility condition whereby the total entropy does not increase. By contrast, the efficiency of engines powered by quantum non-thermal baths has been claimed to surpass the thermodynamic Carnot bound. The key to understanding the performance of such engines is a proper division of the energy supplied by the bath to the system into heat and work, depending on the associated change in the system entropy and ergotropy. Due to their hybrid character, the efficiency bound for quantum engines powered by a non-thermal bath does not solely follow from the laws of thermodynamics. Hence, the thermodynamic Carnot bound is inapplicable to such hybrid engines. Yet, they do not violate the principles of thermodynamics. An alternative means of boosting machine performance is the concept of heat-to-work conversion catalysis by quantum non-linear (squeezed) pumping of the piston mode. This enhancement is due to the increased ability of the squeezed piston to store ergotropy. Since the catalyzed machine is fueled by thermal baths, it adheres to the Carnot bound. We conclude by arguing that it is not quantumness per se that improves the machine performance, but rather the properties of the baths, the working fluid and the piston that boost the ergotropy and minimize the wasted heat in both the input and the output.Comment: As a chapter of: F. Binder, L. A. Correa, C. Gogolin, J. Anders, and G. Adesso (eds.), "Thermodynamics in the quantum regime - Recent Progress and Outlook", (Springer International Publishing

Reconciliation Revisited: Handling Multiple Optima when Reconciling with Duplication, Transfer, and Loss

Phylogenetic tree reconciliation is a powerful approach for inferring evolutionary events like gene duplication, horizontal gene transfer, and gene loss, which are fundamental to our understanding of molecular evolution. While duplication–loss (DL) reconciliation leads to a unique maximum-parsimony solution, duplication-transfer-loss (DTL) reconciliation yields a multitude of optimal solutions, making it difficult to infer the true evolutionary history of the gene family. This problem is further exacerbated by the fact that different event cost assignments yield different sets of optimal reconciliations. Here, we present an effective, efficient, and scalable method for dealing with these fundamental problems in DTL reconciliation. Our approach works by sampling the space of optimal reconciliations uniformly at random and aggregating the results. We show that even gene trees with only a few dozen genes often have millions of optimal reconciliations and present an algorithm to efficiently sample the space of optimal reconciliations uniformly at random in O(mn[superscript 2]) time per sample, where m and n denote the number of genes and species, respectively. We use these samples to understand how different optimal reconciliations vary in their node mappings and event assignments and to investigate the impact of varying event costs. We apply our method to a biological dataset of approximately 4700 gene trees from 100 taxa and observe that 93% of event assignments and 73% of mappings remain consistent across different multiple optima. Our analysis represents the first systematic investigation of the space of optimal DTL reconciliations and has many important implications for the study of gene family evolution.National Science Foundation (U.S.) (CAREER Award 0644282)National Institutes of Health (U.S.) (Grant RC2 HG005639)National Science Foundation (U.S.). Assembling the Tree of Life (Program) (Grant 0936234

Beyond representing orthology relations by trees

Reconstructing the evolutionary past of a family of genes is an important aspect of many genomic studies. To help with this, simple relations on a set of sequences called orthology relations may be employed. In addition to being interesting from a practical point of view they are also attractive from a theoretical perspective in that e.\,g.\,a characterization is known for when such a relation is representable by a certain type of phylogenetic tree. For an orthology relation inferred from real biological data it is however generally too much to hope for that it satisfies that characterization. Rather than trying to correct the data in some way or another which has its own drawbacks, as an alternative, we propose to represent an orthology relation $\delta$ in terms of a structure more general than a phylogenetic tree called a phylogenetic network. To compute such a network in the form of a level-1 representation for $\delta$, we formalize an orthology relation in terms of the novel concept of a symbolic 3- dissimilarity which is motivated by the biological concept of a ``cluster of orthologous groups'', or COG for short. For such maps which assign symbols rather that real values to elements, we introduce the novel {\sc Network-Popping} algorithm which has several attractive properties. In addition, we characterize an orthology relation $\delta$ on some set $X$ that has a level-1 representation in terms of eight natural properties for $\delta$ as well as in terms of level-1 representations of orthology relations on certain subsets of $X$