"In this paper we have considered a spherical envelope model (so-called squirmer) to investigate energetics in cilia dynamics and locomotion. Allowing only tangential but time-periodic deformations, we have used an optimization method based on a variational approach to derive computationally the stroke leading to the largest swimming efficiency. The optimal stroke was shown to display weak Lagrangian asymmetry, but strong Eulerian asymmetry, indicative of symmetry-breaking at the whole-organism level, but not at the level of individual cilia.…"

"Linux package managers have to deal with dependencies and conflicts of packages required to be installed by the user. As an NP-complete problem, this is a hard task to solve. In this context, several approaches have been pursued. Apt-pbo is a package manager based on the apt project that encodes the dependency solving problem as a pseudo-Boolean optimization (PBO) problem. This paper compares different PBO solvers and their effectiveness on solving the dependency solving problem."

"The problem the pattern attempts to solve: identify the URLs in an arbitrary string of text, where by “arbitrary” let’s agree we mean something unstructured such as an email message or a tweet."

"We have embarked on a research program designed to develop universal models that can recreate empiri- cally observed phenomena in dynamic complex networks. We have shown that, using a suitable reinforced random walk on a “long-term” underlay network, one is able to produce instantaneous networks which reproduce qualitatively characteristic features of real world dynamic networks. This includes, in particular, the construc- tion of scale-free sub-networks of a scale-free “underlay” network, whose local hubs substantially differ from sub- network to sub-network and from those of the underlay.…"

"…For cyclic games with two players and three strategies, we show that the resulting deterministic dynamics crucially depends on the initial condition in a non–trivial way."

"The transition of the flow in a duct of square cross-section is studied. Like in the similar case of the pipe flow, the motion is linearly stable for all Reynolds numbers; this flow is thus a good candidate to investigate the 'bypass' path to turbulence. Initially the so-called 'linear optimal perturbation problem' is formulated and solved, yielding optimal disturbances in the form of longitudinal vortices. Such optimals, however, fail to elicit a significant response from the system in the nonlinear regime. Thus, streamwise-inhomogeneous, sub-optimal disturbances are focussed upon; nonlinear quadratic interactions are immediately evoked by such initial perturbations and an unstable streamwise-homogeneous large amplitude mode rapidly emerges. The subsequent evolution of the flow, at a value of the Reynolds number at the edge between fully developed turbulence and relaminarization, shows the alternance of patterns with two pairs of large scale vortices near opposing parallel walls.…"

"The modeling of complex systems such as ecological or socio-economic systems can be very challenging. Although various modeling approaches exist, they are generally not compatible and mutually consistent, and empirical data often do not allow one to decide what model is the right one, the best one, or most appropriate one. Moreover, as the recent financial and economic crisis shows, relying on a single, idealized model can be very costly. This contribution tries to shed new light on problems that arise when complex systems are modeled. While the arguments can be transferred to many different systems, the related scientific challenges are illustrated for social, economic, and traffic systems. The contribution discusses issues that are sometimes overlooked and tries to overcome some frequent misunderstandings and controversies of the past.…"

"We address the problem of estimating unknown model parameters and state variables in stochastic reaction processes when only sparse and noisy measurements are available. Using an asymptotic system size expansion for the backward equation we derive an efficient approximation for this problem. We demonstrate the validity of our approach on model systems and generalize our method to the case when some state variables are not observed."

"While the concept of clusters arises when viewing quasicrystalline surfaces at close range, long range quasiperiodic order as seen in diffraction studies is perhaps more naturally described in terms of quasiperiodic tilings. These are the analogs of the “Bravais lattices” for periodic systems, and give a good description of the orientational order and positional long range order seen in quasicrystal diffraction patterns. Tilings are constructed from a small num- ber of tiles arranged so as to avoid overlapping or holes. Quasiperiodic tilings usually possess a hierarchically organised structure, where tilings can be ”in- flated”(”deflated”) so as to obtain a similar tiling on a larger(smaller) length scale."

"Much recent interest has focused on "open" dynamical systems, in which a classical map or flow is considered only until the trajectory reaches a "hole", at which the dynamics is no longer considered. Here we consider questions pertaining to the survival probability as a function of time, given an initial measure on phase space. We focus on the case of billiard dynamics, namely that of a point particle moving with constant velocity except for mirror-like reflections at the boundary, and give a number of recent results, physical applications and open problems."

"Storage optimization in distributed environments is a major concern when talking about reliability in this kind of schemes. Although replication is the most used option, erasure coding is a more optimized one.
However, erasure coding uses a lot of bandwidth to replace one node. In a dynamic scheme, where nodes enter and leave the system frequently, bandwidth use could be an important drawback.
Regenerating Codes introduced by Dimakis et al. minimize the code repair problem by applying Network Coding to the distributed storage scheme. However finding the coefficients for the linear combinations used to replace a node is not easy, specially for the systematic case, and must be calculated for each new node fail.…"

"In this paper, we perform a minimalistic quantization of the classical game of tic-tac-toe, by allowing superpositions of classical moves. In order for the quantum game to reduce properly to the classical game, we require legal quantum moves to be orthogonal to all previous moves. We also admit interference effects, by squaring the sum of amplitudes over all moves by a player to compute his or her occupation level of a given site. A player wins when the sums of occupations along any of the eight straight lines we can draw in the $3 \times 3$ grid is greater than three.…"

"Actual accounting systems are based on transactions. But in the current, knowledge-based economy much of the value creation precedes, sometimes by years, the occurrence of transactions. Until then, the accounting system does not register any value created in contrast to the investments made into R&D, which are fully expensed. This difference, between how the accounting system is handling value created and is handling investments into value creation, is the major reason for the growing disconnect between market values and financial information."

Makes me want to write a simple agent-based model in which a few people have almost all the money and most everybody else are allowed to move a bit around, for a fee.

"This is a short commentary piece that discusses how the methods used in the natural sciences can apply to economics in general and financial markets specifically."

"In real communication and transportation networks, the geographical positions of nodes are very important for the efficiency and the tolerance of connectivity. Considering spatially inhomogeneous positions of nodes according to a population, we introduce a multi-scale quartered (MSQ) network that is stochastically constructed by recursive subdivision of polygonal faces as a self-similar tiling. It has several advantages: the robustness of connectivity, the bounded short path lengths, and the shortest distance routing algorithm in a distributive manner. Furthermore, we show that the MSQ network is more efficient with shorter link lengths and more suitable with lower load for avoiding traffic congestion than other geographical networks which have various topologies ranging from river to scale-free networks. These results will be useful for providing an insight into the future design of ad hoc network infrastructures."

"We describe computer algorithms that produce the complete set of isohedral tilings by n-omino or n-iamond tiles in which the tiles are fundamental domains and the tilings have 3-, 4-, or 6-fold rotational symmetry. The symmetry groups of such tilings are of types p3, p31m, p4, p4g, and p6. There are no isohedral tilings with symmetry groups p3m1, p4m, or p6m that have polyominoes or polyiamonds as fundamental domains. We display the algorithms' output and give enumeration tables for small values of n.…"

I ♡ pragmatic physics. "We propose a simple rubber friction law, which can be used, e.g., in models of tire (and vehicle) dynamics."

"It features generic data abstraction through Collections, a Visualization API allowing the creation of pluggable visualizations, and a Scene Graph implementation on top of HTML 5 Canvas. See the GitHub project, the documentation, and an example."

"For a set of n points in the plane, we consider the axis–aligned (p,k)-Box Covering problem: Find p axis-aligned, pairwise-disjoint boxes that together contain n-k points. In this paper, we consider the boxes to be either squares or rectangles, and we want to minimize the area of the largest box. For general p we show that the problem is NP-hard for both squares and rectangles. For a small, fixed number p, we give algorithms that find the solution in the following running times:
For squares we have O(n+k log k) time for p=1, and O(n log n+k^p log^p k time for p = 2,3. For rectangles we get O(n + k^3) for p = 1 and O(n log n+k^{2+p} log^{p-1} k) time for p = 2,3. In all cases, our algorithms use O(n) space."

"We study the problem of reconstructing a sparse signal from a limited number of its linear projections when a part of its support is known, although the known part may contain some errors. The “known" part of the support, denoted T, may be available from prior knowledge. Alternatively, in a problem of recursively reconstructing time sequences of sparse spatial signals, one may use the support estimate from the previous time instant as the “known" part. The idea of our proposed solution (modified-CS) is to solve a convex relaxation of the following problem: find the signal that satisfies the data constraint and is sparsest outside of T.…"

"We present a form of algebraic reasoning for computational objects which are expressed as graphs. Edges describe the flow of data between primitive operations which are represented by vertices. These graphs have an interface made of half-edges (edges which are drawn with an unconnected end) and enjoy rich compositional principles by connecting graphs along these half-edges. In particular, this allows equations and rewrite rules to be specified between graphs. Particular computational models can then be encoded as an axiomatic set of such rules. Further rules can be derived graphically and rewriting can be used to simulate the dynamics of a computational system, e.g. evaluating a program on an input. Examples of models which can be formalised in this way include traditional electronic circuits as well as recent categorical accounts of quantum information."

"This expository review is devoted to fish swimming and bird/insect flight.…"

"We analyze over 500 million Twitter messages from an eight month period and find that tracking a small number of flu-related keywords allows us to forecast future influenza rates with high accuracy, obtaining a 95% correlation with national health statistics. We then analyze the robustness of this approach to spurious keyword matches, and we propose a document classification component to filter these misleading messages. We find that this document classifier can reduce error rates by over half in simulated false alarm experiments, though more research is needed to develop methods that are robust in cases of extremely high noise."

"We propose a degree-based coarse graining approach that not just accelerates the evaluation of dynamics on complex networks, but also satisfies the consistency conditions for both equilibrium statistical distributions and nonequilibrium dynamical flows. For the Ising model and susceptible-infected-susceptible epidemic model, we introduce these required conditions explicitly and further prove that they are satisfied by our coarse-grained network construction within the annealed network approximation. Finally, we numerically show that the phase transitions and fluctuations on the coarse-grained network are all in good agreements with those on the original one."

"Bacteria are the unseen majority on our planet, with millions of species and comprising most of the living protoplasm. While current methods enable in-depth study of a small number of communities, a simple tool for breadth studies of bacterial population composition in a large number of samples is lacking. We propose a novel approach for reconstruction of the composition of an unknown mixture of bacteria using a single Sanger-sequencing reaction of the mixture. This method is based on compressive sensing theory, which deals with reconstruction of a sparse signal using a small number of measurements. Utilizing the fact that in many cases each bacterial community is comprised of a small subset of the known bacterial species, we show the feasibility of this approach for determining the composition of a bacterial mixture.…"

"The Fermi Paradox is the apparent contradiction between the high probability extraterrestrial civilizations' existence and the lack of contact with such civilizations. In general, solutions to Fermi's paradox come down to either estimation of Drake equation parameters i.e. our guesses about the potential number of extraterrestrial civilizations or simulation of civilizations development in the universe. We consider a new type of cellular automata, that allows to analyze Fermi paradox. We introduce bonus stimulation model (BS-model) of development in cellular space (Universe) of objects (Civilizations). When civilizations get in touch they stimulate development each other, increasing their life time. We discovered nonlinear threshold behaviour of total volume of civilizations in universe and on the basis of our model we built analogue of Drake equation."

"In this paper, we investigate a conjecture by von Haeseler concerning the Maximum Parsimony method for phylogenetic estimation, which was published by the Newton Institute in Cambridge on a list of open phylogenetic problems in 2007. This conjecture deals with the question whether Maximum Parsimony trees are hereditary. The conjecture suggests that a Maximum Parsimony tree for a particular (DNA) alignment necessarily has subtrees of all possible sizes which are most parsimonious for the corresponding subalignments. We answer the conjecture affirmatively for binary alignments on five taxa but also show how to construct examples for which Maximum Parsimony trees are not hereditary. …we also show that compatible most parsimonious quartets do not have to provide a most parsimonious supertree. Last, we show that our results can be generalized to Maximum Likelihood for certain nucleotide substitution models."

"Laboratory investigations have shown that a formal theory of fault-tolerance will be essential to harness nanoscale self-assembly as a medium of computation. Several researchers have voiced an intuition that self-assembly phenomena are related to the field of distributed computing. This paper formalizes some of that intuition. We construct tile assembly systems that are able to simulate the solution of the wait-free consensus problem in some distributed systems. (For potential future work, this may allow binding errors in tile assembly to be analyzed, and managed, with positive results in distributed computing, as a "blockage" in our tile assembly model is analogous to a crash failure in a distributed computing model.) …We show that solution of this strengthened consensus problem can be simulated by a two-dimensional tile assembly model only for two processes, whereas a three-dimensional tile assembly model can simulate its solution in a distributed system with any number of processes

"Genetic oscillators are a major theme of interest in the emerging field of synthetic biology. Until recently, most work has been carried out using intra-cellular oscillators, but this approach restricts the broader applicability of such systems. Motivated by a desire to develop large-scale, spatially-distributed cell-based computational systems, we present an initial design for a population-level oscillator which uses three different bacterial strains. Our system is based on the client-server model familiar to computer science, and uses quorum sensing for communication between nodes. We present the results of extensive in silico simulation tests, which confirm that our design is both feasible and robust."

Frankly, I've alway thought this, especially after some early "confusing" experiments that never got published because they were part of my first Ph.D. thesis research: "…We argue that the presence of only the frozen phase in the work of Kauffman et al. was due simply to the specific parametrization used, and is not an inherent feature of this class of functions. However, these networks are significantly more stable than the variants where all possible Boolean functions are allowed."