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MPI@LHC Talk.
https://cds.cern.ch/record/2129370
Draft version of talk for MPI@LHC, regarding the topic of "Monte Carlo Tuning @ ATLAS". The talk introduces the event generator chain, concepts of tuning, issues/problems with over tuning, and then proceeds to explain 3(4) tunes performed at ATLAS. A 4th tune known as A15-MG5aMC@NLO(-TTBAR) is also included, but is awaiting note approval.Jiggins, StephenThe ATLAS collaborationSun, 07 Feb 2016 06:16:18 GMT07 Feb 2016ATL-PHYS-SLIDE-2016-051https://cds.cern.ch/record/21293702016051ECAL Energy Flow CalibrationMichigan CERN Research Abroad Program
https://cds.cern.ch/record/2129363
My talk will be covering my work as a whole over the course of the semester. The focus will be on using energy flow calibration in ECAL to check the precision of the corrections made by the light monitoring system used to account for transparency loss within ECAL crystals due to radiation damage over time. CERN. GenevaWIMPEE, Zachary PaulSat, 06 Feb 2016 13:30:16 GMT2015-12-10https://cds.cern.ch/record/2129363['']Further Research with HGamma GroupMichigan CERN Research Abroad Program
https://cds.cern.ch/record/2129362
CERN. GenevaPETERSON-HALL, Rebecca HelenSat, 06 Feb 2016 12:25:30 GMT2015-12-10https://cds.cern.ch/record/2129362['']Chaos in QFT and black holes 4CERN Winter School on Supergravity, Strings, and Gauge Theory 2016
https://cds.cern.ch/record/2129361
CERN. GenevaSTANFORD, DouglasSat, 06 Feb 2016 11:05:01 GMT2016-02-05https://cds.cern.ch/record/2129361['']Exploiting plume structure to decode gas source distance using metal-oxide gas sensors
https://cds.cern.ch/record/2129357
Estimating the distance of a gas source is important in many applications of chemical sensing, like e.g. environmental monitoring, or chemically-guided robot navigation. If an estimation of the gas concentration at the source is available, source proximity can be estimated from the time-averaged gas concentration at the sensing site. However, in turbulent environments, where fast concentration fluctuations dominate, comparably long measurements are required to obtain a reliable estimate. A lesser known feature that can be exploited for distance estimation in a turbulent environment lies in the relationship between source proximity and the temporal variance of the local gas concentration - the farther the source, the more intermittent are gas encounters. However, exploiting this feature requires measurement of changes in gas concentration on a comparably fast time scale, that have up to now only been achieved using photo-ionisation detectors. Here, we demonstrate that by appropriate signal processing, off-the-shelf metal-oxide sensors are capable of extracting rapidly fluctuating features of gas plumes that strongly correlate with source distance. We show that with a straightforward analysis method it is possible to decode events of large, consistent changes in the measured signal, so-called 'bouts'. The frequency of these bouts predicts the distance of a gas source in wind-tunnel experiments with good accuracy. Our results offer an alternative approach to estimating gas source proximity that is largely independent of gas concentration, using off-the-shelf metal-oxide sensors. The analysis method we employ demands very few computational resources and is suitable for low-power microcontrollers.Schmuker, MichaelBahr, ViktorHuerta, RamónSat, 06 Feb 2016 06:37:34 GMT03 Feb 2016arXiv:1602.01815https://cds.cern.ch/record/2129357['arXiv:1602.01815']arXiv:1602.01815A Multiscale Diffuse-Interface Model for Two-Phase Flow in Porous Media
https://cds.cern.ch/record/2129356
In this paper we consider a multiscale phase-field model for capillarity-driven flows in porous media. The presented model constitutes a reduction of the conventional Navier-Stokes-Cahn-Hilliard phase-field model, valid in situations where interest is restricted to dynamical and equilibrium behavior in an aggregated sense, rather than a precise description of microscale flow phenomena. The model is based on averaging of the equation of motion, thereby yielding a significant reduction in the complexity of the underlying Navier-Stokes-Cahn-Hilliard equations, while retaining its macroscopic dynamical and equilibrium properties. Numerical results are presented for the representative 2-dimensional capillary-rise problem pertaining to two closely spaced vertical plates with both identical and disparate wetting properties. Comparison with analytical solutions for these test cases corroborates the accuracy of the presented multiscale model. In addition, we present results for a capillary-rise problem with a non-trivial geometry corresponding to a porous medium.Roudbari, Mahnaz Shokrpourvan Brummelen, E HaraldVerhoosel, Clemens VSat, 06 Feb 2016 06:37:34 GMT03 Feb 2016arXiv:1602.01809https://cds.cern.ch/record/2129356['arXiv:1602.01809']arXiv:1602.01809Conformity-Driven Agents Support Ordered Phases in the Spatial Public Goods Game
https://cds.cern.ch/record/2129355
We investigate the spatial Public Goods Game in the presence of conformity-driven agents on a bi-dimensional lattice with periodic boundary conditions. The present setting usually considers fitness-driven agents, i.e., agents that tend to imitate the strategy of their fittest neighbors. Here, fitness is a general property usually adopted to quantify the extent to which individuals are able to succeed, or at least to survive, in a competitive environment. However, when social systems are considered, the evolution of a population might be affected also by social behaviors as conformity, stubbornness, altruism, and selfishness. Although the term evolution can assume different meanings depending on the considered domain, here it corresponds to the set of processes that lead a system towards an equilibrium or a steady-state. In doing so, we use two types of strategy update rules: fitness-driven and conformity-driven. We map fitness to the agents' payoff so that richer agents are those most imitated by fitness-driven agents, while conformity-driven agents tend to imitate the strategy assumed by the majority of their neighbors. Numerical simulations aim to identify critical phenomena, on varying the amount of the relative density of conformity-driven agents in the population, and to study the nature of related equilibria. Remarkably, we find that conformity fosters ordered phases and may also lead to bistable behaviors.Javarone, Marco AlbertoAntonioni, AlbertoCaravelli, FrancescoSat, 06 Feb 2016 06:37:34 GMT04 Feb 2016arXiv:1602.01808https://cds.cern.ch/record/2129355['arXiv:1602.01808']arXiv:1602.01808Long-range attraction of particles adhered to lipid vesicles
https://cds.cern.ch/record/2129354
Many biological systems fold thin sheets of lipid membrane into complex three-dimensional structures. This microscopic origami is often mediated by the adsorption and self-assembly of proteins on a membrane. As a model system to study adsorption-mediated interactions, we study the collective behavior of micrometric particles adhered to a lipid vesicle. We estimate the colloidal interactions using a maximum likelihood analysis of particle trajectories. When the particles are highly wrapped by a tense membrane, we observe strong long-range attractions with a typical binding energy of 150 $k_B T$ and significant forces extending a few microns.Sarfati, RaphaelDufresne, Eric RSat, 06 Feb 2016 06:37:34 GMT04 Feb 2016arXiv:1602.01802https://cds.cern.ch/record/2129354['arXiv:1602.01802']arXiv:1602.01802Two-vector representation of a nondepolarizing Mueller matrix
https://cds.cern.ch/record/2129353
A geometric view of the polarimetric properties of a nondepolarizing medium is presented by means of a pair of vectors in the Poincar\'e sphere. An alternative representation constituted by a set of vectors contained in the equatorial plane of the Poincar\'e sphere is also defined and interpreted. The analyses of the magnitudes and relative orientations of the constitutive vectors of such simple representations allow for a classification of nondepolarizing media.Gil, José JJosé, Ignacio SanSat, 06 Feb 2016 06:37:34 GMT04 Feb 2016arXiv:1602.01794https://cds.cern.ch/record/2129353['arXiv:1602.01794']arXiv:1602.01794Dynamics of Plant Growth; A Theory Based on Riemannian Geometry
https://cds.cern.ch/record/2129352
In this work, a new model for macroscopic plant tissue growth based on dynamical Riemannian geometry is presented. We treat 1D and 2D tissues as continuous, deformable, growing geometries for sizes larger than 1mm. The dynamics of the growing tissue are described by a set of coupled tensor equations in non-Euclidean (curved) space. These coupled equations represent a novel feedback mechanism between growth and curvature dynamics. For 1D growth, numerical simulations are compared to two measures of root growth. First, modular growth along the simulated root shows an elongation zone common to many species of plant roots. Second, the relative elemental growth rate (REGR) calculated in silico exhibits temporal dynamics recently characterized in high-resolution root growth studies but which thus far lack a biological hypothesis to explain them. Namely, the REGR can evolve from a single peak localized near the root tip to a double-peak structure. In our model, this is a direct consequence of considering growth as both a geometric reaction-diffusion process and expansion due to a distributed source of new materials. In 2D, we study a circularly symmetric growing disk with emergent negative curvatures. These results are compared against thin disk experiments, which are a proxy model for plant leaves. These results also apply to the curvature evolution and the inhomogeneous growth pattern of the Acetabularia cap. Lastly, we extend the model to anisotropic disks and predict the growth dynamics for a 2D curved surface which develops an elongated shape with localized ruffling. Our model also provides several measures of the dynamics of tissue growth. These include the time evolution of the metric and velocity field, which are dynamical variables in the model, as well as expansion, shear and rotation which are deformation tensors characterizing the growth of the tissue.Pulwicki, JuliaSat, 06 Feb 2016 06:37:34 GMTarXiv:1602.01778https://cds.cern.ch/record/2129352['arXiv:1602.01778']arXiv:1602.01778Diverse anisotropy of phonon transport in two-dimensional IV-VI compounds: A first-principles study
https://cds.cern.ch/record/2129351
New class two-dimensional (2D) materials beyond graphene, including layered and non-layered, and their heterostructures, are currently attracting increasing interest due to their promising applications in nanoelectronics, optoelectronics and clean energy, where thermal transport property is one of the fundamental physical parameters. In this paper, we systematically investigated the phonon transport properties of 2D orthorhombic IV-VI compounds of $GeS$, $GeSe$, $SnS$ and $SnSe$ by solving the Boltzmann transport equation (BTE) based on first-principles calculations. Despite the similar puckered (hinge-like) structure along the armchair direction as phosphorene, the four monolayer compounds possess diverse anisotropic properties in many aspects, such as group velocity, Young's modulus and lattice thermal conductivity ($\kappa$), etc. Especially, the $\kappa$ along the zigzag and armchair directions of monolayer $GeS$ shows the strongest anisotropy while monolayer $SnS$ and $SnSe$ shows an almost isotropy in phonon transport, despite the similar characteristics of their structures. Based on the analysis of the frequency dependent $\kappa$ and average phonon group velocity, we find that, the anisotropy mainly arises from the phonon modes below the gap in the phonon dispersions. The larger the gap, the stronger the anisotropy. This mechanism is explained from the coupling between the phonon modes on both sides of the gap and is further confirmed by the phonon scattering channels. We further show that the anisotropic behavior of the electron localization functions (ELF) reflecting the bonding characteristics is the physical origin of the anisotropic properties. Our study offers fundamental understanding of the anisotropic phonon transport properties of 2D compounds with hinge-like structure, and would be helpful for further modulation and applications in emerging technologies.Qin, GuangzhaoQin, ZhenzhenFang, Wu-ZhangZhang, Li-ChuanYue, Sheng-YingYan, Qing-BoHu, MingSu, GangSat, 06 Feb 2016 06:37:34 GMT04 Feb 2016arXiv:1602.01766https://cds.cern.ch/record/2129351['arXiv:1602.01766']arXiv:1602.01766Reforming the international system of units: On our way to redefine the base units solely from fundamental constants and beyond
https://cds.cern.ch/record/2129350
Our purpose is to offer a logical analysis of the system of units and to explore possible paths towards a consistent and unified system with an original perspective. The path taken here builds on the fact that, thanks to optical or matter-wave interferometry, any measurement can be reduced to a dimensionless phase measurement and we follow this simple guiding line. We finally show how one could progress even further on the path of a synthetic framework for fundamental metrology based upon pure geometry in five dimensions.Bordé, Christian JSat, 06 Feb 2016 06:37:34 GMT29 Jan 2016arXiv:1602.01752https://cds.cern.ch/record/2129350['arXiv:1602.01752']arXiv:1602.01752The deterministic Kermack-McKendrick model bounds the general stochastic epidemic
https://cds.cern.ch/record/2129349
We prove that, for Poisson transmission and recovery processes, the classic Susceptible $\to$ Infected $\to$ Recovered (SIR) epidemic model of Kermack and McKendrick provides, for any given time t>0, a strict lower bound on the expected number of suscpetibles and a strict upper bound on the expected number of recoveries in the general stochastic SIR epidemic. The proof is based on the recent message passing representation of SIR epidemics applied to a complete graph. We also obtain an approximation for the variance of the number of susceptibles in the general stochastic epidemic.Wilkinson, Robert RBall, Frank GSharkey, Kieran JSat, 06 Feb 2016 06:37:33 GMT04 Feb 2016arXiv:1602.01730https://cds.cern.ch/record/2129349['arXiv:1602.01730']arXiv:1602.01730Breather solitons in highly nonlocal media
https://cds.cern.ch/record/2129348
We investigate the breathing of optical spatial solitons in highly nonlocal media. Generalizing the Ehrenfest theorem, we demonstrate that oscillations in beam width obey a fourth-order ordinary differential equation. Moreover, in actual highly nonlocal materials, the original accessible soliton model by Snyder and Mitchell [Science \textbf{276}, 1538 (1997)] cannot accurately describe the dynamics of self-confined beams as the transverse size oscillations have a period which not only depends on power but also on the initial width. Modeling the nonlinear response by a Poisson equation driven by the beam intensity we verify the theoretical results against numerical simulations.Alberucci, AlessandroJisha, Chandroth PAssanto, GaetanoSat, 06 Feb 2016 06:37:33 GMT04 Feb 2016arXiv:1602.01722https://cds.cern.ch/record/2129348['arXiv:1602.01722']arXiv:1602.01722The effect of ambipolar electric fields on the electron heating in capacitive RF plasmas
https://cds.cern.ch/record/2129347
We investigate the electron heating dynamics in electropositive argon and helium capacitively coupled RF discharges driven at 13.56 MHz by Particle in Cell simulations and by an analytical model. The model allows to calculate the electric field outside the electrode sheaths, space and time resolved within the RF period. Electrons are found to be heated by strong ambipolar electric fields outside the sheath during the phase of sheath expansion in addition to classical sheath expansion heating. By tracing individual electrons we also show that ionization is primarily caused by electrons that collide with the expanding sheath edge multiple times during one phase of sheath expansion due to backscattering towards the sheath by collisions. A synergistic combination of these different heating events during one phase of sheath expansion is required to accelerate an electron to energies above the threshold for ionization. The ambipolar electric field outside the sheath is found to be time modulated due to a time modulation of the electron mean energy caused by the presence of sheath expansion heating only during one half of the RF period at a given electrode. This time modulation results in more electron heating than cooling inside the region of high electric field outside the sheath on time average. If an electric field reversal is present during sheath collapse, this time modulation and, thus, the asymmetry between the phases of sheath expansion and collapse will be enhanced. We propose that the ambipolar electron heating should be included in models describing electron heating in capacitive RF plasmas.Schulze, JDonko, ZDerzsi, AKorolov, ISchuengel, ESat, 06 Feb 2016 06:37:33 GMT04 Feb 2016arXiv:1602.01719https://cds.cern.ch/record/2129347['arXiv:1602.01719']arXiv:1602.01719Building blocks of the basin stability of power grids
https://cds.cern.ch/record/2129346
Given a power grid and a transmission (coupling) strength, basin stability is a measure of synchronization stability for individual nodes. Earlier studies have focused on the basin stability's dependence of the position of the nodes in the network for single values of transmission strength. Basin stability grows from zero to one as transmission strength increases, but often in a complex, non-monotonous way. In this study, we investigate the entire functional form of basin stability's dependence on transmission strength. To be able to perform a systematic analysis, we restrict ourselves to small networks. We scan all isomorphically distinct networks with an equal number of power producers and consumers of six nodes or less. We find that the shapes of the basin stability falls into a few, rather well-defined classes, that could be characterized by the number of edges and the betweenness of the nodes, whereas other network positional quantities matters less.Kim, HeetaeLee, Sang HoonHolme, PetterSat, 06 Feb 2016 06:37:33 GMT04 Feb 2016arXiv:1602.01712https://cds.cern.ch/record/2129346['arXiv:1602.01712']arXiv:1602.01712On thermodynamic aspects of information transfer in complex dynamical systems
https://cds.cern.ch/record/2129345
From the Horowitz-Esposito stochastic thermodynamical description of information flows in dynamical systems [J. M. Horowitz and M. Esposito, Phys. Rev. X4, 031015 (2014)], it is known that while the second law of thermodynamics is satisfied by a joint system, the entropic balance for the subsystems is adjusted by a term related to the mutual information exchange rate between the two subsystems. In this article, we present a quantitative discussion of the conceptual link between the Horowitz-Esposito analysis and the Liang-Kleeman work on information transfer between dynamical system components [X. S. Liang and R. Kleeman, Phys. Rev. Lett. 95, 244101 (2005)]. In particular, the entropic balance arguments employed in the two approaches are compared. Notwithstanding all differences between the two formalisms, our work strengthens the Liang-Kleeman heuristic balance reasoning by showing its formal analogy with the recent Horowitz-Esposito thermodynamic balance arguments.Cafaro, CarloAli, Sean AlanGiffin, AdomSat, 06 Feb 2016 06:37:33 GMT04 Feb 2016arXiv:1602.01693https://cds.cern.ch/record/2129345['arXiv:1602.01693']arXiv:1602.01693A quantum protective mechanism in photosynthesis
https://cds.cern.ch/record/2129344
Since the emergence of oxygenic photosynthesis, living systems have developed protective mechanisms against reactive oxygen species. During charge separation in photosynthetic reaction centres, triplet states can react with molecular oxygen generating destructive singlet oxygen. The triplet product yield in bacteria is observed to be reduced by weak magnetic fields. Reaction centres from plants' photosystem II share many features with bacterial reaction centres, including a high-spin iron whose function has remained obscure. To explain observations that the magnetic field effect is reduced by the iron, we propose that its fast-relaxing spin plays a protective role in photosynthesis by generating an effective magnetic field. We consider a simple model of the system, derive an analytical expression for the effective magnetic field and analyse the resulting triplet yield reduction. The protective mechanism is robust for realistic parameter ranges, constituting a clear example of a quantum effect playing a macroscopic role vital for life.Marais, AdrianaSinayskiy, IlyaPetruccione, Francescovan Grondelle, RienkSat, 06 Feb 2016 06:37:33 GMT04 Feb 2016arXiv:1602.01689https://cds.cern.ch/record/2129344['arXiv:1602.01689']arXiv:1602.01689Phonon Boltzmann equation-based discrete unified gas kinetic scheme for multiscale heat transfer
https://cds.cern.ch/record/2129343
Numerical prediction of multiscale heat transfer is a challenging problem due to the wide range of time and length scales involved. In this work a discrete unified gas kinetic scheme (DUGKS) is developed for heat transfer in materials with different acoustic thickness based on the phonon Boltzmann equation. With discrete phonon direction, the Boltzmann equation is discretized with a second-order finite-volume formulation, in which the time-step is fully determined by the Courant-Friedrichs-Lewy (CFL) condition. The scheme has the asymptotic preserving (AP) properties for both diffusive and ballistic regimes, and can present accurate solutions in the whole transition regime as well. The DUGKS is a self-adaptive multiscale method for the capturing of local transport process. Numerical tests for both heat transfers with different Knudsen numbers are presented to validate the current method.Guo, ZhaoliXu, KunSat, 06 Feb 2016 06:37:33 GMT04 Feb 2016arXiv:1602.01680https://cds.cern.ch/record/2129343['arXiv:1602.01680']arXiv:1602.01680Irreversible Markov chain Monte Carlo algorithm for the self-avoiding walk
https://cds.cern.ch/record/2129342
We design an irreversible Markov chain Monte Carlo algorithm for the self-avoiding walk (SAW). It outperforms the Berretti-Sokal algorithm. The gained efficiency increases with the spatial dimension, from about $10$ times in two dimensions to around $40$ times in five dimensions. The algorithm violates the widely used detailed balance condition and satisfies the weaker balance condition. We employ the irreversible method to study the finite-size scaling of SAW above the upper critical dimension.Hu, HaoChen, XiaosongDeng, YoujinSat, 06 Feb 2016 06:37:33 GMT04 Feb 2016arXiv:1602.01671https://cds.cern.ch/record/2129342['arXiv:1602.01671']arXiv:1602.01671Entrainment dominates the interaction of microalgae with micron-sized objects
https://cds.cern.ch/record/2129341
The incessant activity of swimming microorganisms has a direct physical effect on surrounding microscopic objects, leading to enhanced diffusion far beyond the level of Brownian motion with possible influences on the spatial distribution of non-motile planktonic species and particulate drifters. Here we study in detail the effect of eukaryotic flagellates, represented by the green microalga Chlamydomonas reinhardtii, on microparticles. Macro- and micro-scopic experiments reveal that microorganism-colloid interactions are dominated by rare close encounters leading to large displacements through direct entrainment. Simulations and theoretical modelling show that the ensuing particle dynamics can be understood in terms of a simple jump-diffusion process, combining standard diffusion with Poisson-distributed jumps. This heterogeneous dynamics is likely to depend on generic features of the near-field of swimming microorganisms with front-mounted flagella.Jeanneret, RaphaëlKantsler, VasilyPolin, MarcoSat, 06 Feb 2016 06:37:33 GMT04 Feb 2016arXiv:1602.01666https://cds.cern.ch/record/2129341['arXiv:1602.01666']arXiv:1602.01666Dynamics of Disagreement: Large-Scale Temporal Network Analysis Reveals Negative Interactions in Online Collaboration
https://cds.cern.ch/record/2129340
Disagreement and conflict are a fact of social life and considerably affect our well-being and productivity. Such negative interactions are rarely explicitly declared and recorded and this makes them hard for scientists to study. We overcome this challenge by investigating the patterns in the timing and configuration of contributions to a large online collaboration community. We analyze sequences of reverts of contributions to Wikipedia, the largest online encyclopedia, and investigate how often and how fast they occur compared to a null model that randomizes the order of actions to remove any systematic clustering. We find evidence that individuals systematically attack the same person and attack back their attacker; both of these interactions occur at a faster response rate than expected. We also establish that individuals come to defend an attack victim but we do not find evidence that attack victims "pay it forward" or that attackers collude to attack the same individual. We further find that high-status contributors are more likely to attack many others serially, status equals are more likely to revenge attacks back, while attacks by lower-status contributors trigger attacks forward; yet, it is the lower-status contributors who also come forward to defend third parties. The method we use can be applied to other large-scale temporal communication and collaboration networks to identify the existence of negative social interactions and other social processes.Tsvetkova, MilenaGarcía-Gavilanes, RuthYasseri, TahaSat, 06 Feb 2016 06:37:33 GMT04 Feb 2016arXiv:1602.01652https://cds.cern.ch/record/2129340['arXiv:1602.01652']arXiv:1602.01652Localized plasmons in bilayer graphene nanodisks
https://cds.cern.ch/record/2129339
We study localized plasmonic excitations in bilayer graphene (BLG) nanodisks, comparing AA-stacked and AB-stacked BLG and contrasting the results to the case of two monolayers without electronic hybridization. The electrodynamic response of the BLG electron gas is described in terms of a spatially homogeneous surface conductivity, and an efficient alternative two-dimensional electrostatic approach is employed to carry out all the numerical calculations of plasmon resonances. Due to a unique electronic band structures, the resonance frequency of the traditional dipolar plasmonic mode in the AA-stacked BLG nanodisk is roughly doping independent in the low-doping regime, while the mode is highly damped as the Fermi level approaches the interlayer hopping energy $\gamma$ associated with tunneling of electrons between the two layers. In addition to the traditional dipolar mode, we find that the AB-stacked BLG nanodisk also hosts a new plasmonic mode with energy larger than $\gamma$. This mode can be tuned by either the doping level or structural size, and furthermore, this mode can dominate the plasmonic response for realistic structural conditions.Wang, WeihuaXiao, SanshuiMortensen, N AsgerSat, 06 Feb 2016 06:37:33 GMT04 Feb 2016arXiv:1602.01651https://cds.cern.ch/record/2129339['arXiv:1602.01651']arXiv:1602.01651Non-uniform force allocation for area preservation in spring network models
https://cds.cern.ch/record/2129338
In modelling of elastic objects in a flow such as red blood cells, white blood cells, or tumour cells, several elastic moduli are involved. One of them is the area conservation modulus. In this paper, we focus on spring network models and we introduce a new way of modeling the area preservation modulus. We take into account the current shape of the individual triangles and find the proportional allocation of area conservation forces, which would for individual triangles preserve their shapes. The analysis shows that this approach tends to regularize the triangulation. We demonstrate this effect on individual triangles as well as on the complete triangulations.Cimrak, IvanJancigova, IvetaSat, 06 Feb 2016 06:37:33 GMT04 Feb 2016arXiv:1602.01647https://cds.cern.ch/record/2129338['arXiv:1602.01647']arXiv:1602.01647Evolutionary dynamics of selfish DNA generates pseudo-linguistic features of genomes
https://cds.cern.ch/record/2129337
Since the sequencing of large genomes, many statistical features of their sequences have been found. One intriguing feature is that certain subsequences are much more abundant than others. In fact, abundances of subsequences of a given length are distributed with a scale-free power-law tail, resembling properties of human texts, such as the Zipf's law. Despite recent efforts, the understanding of this phenomenon is still lacking. Here we find that selfish DNA elements, such as those belonging to the Alu family of repeats, dominate the power-law tail. Interestingly, for the Alu elements the power-law exponent increases with the length of the considered subsequences. Motivated by these observations, we develop a model of selfish DNA expansion. The predictions of this model qualitatively and quantitatively agree with the empirical observations. This allows us to estimate parameters for the process of selfish DNA spreading in a genome during its evolution. The obtained results shed light on how evolution of selfish DNA elements shapes non-trivial statistical properties of genomes.Sheinman, MichaelRamisch, AnnaMassip, FlorianArndt, Peter FSat, 06 Feb 2016 06:37:33 GMT04 Feb 2016arXiv:1602.01612https://cds.cern.ch/record/2129337['arXiv:1602.01612']arXiv:1602.01612