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We investigate wavelet-like localized solutions in nonlinear waveguides, enabled by complementary propagation constants embedded in domains of anomalous dispersion. They are carrier-envelope-phase stable and independent of fine details of the dispersion profile. Their spectra extend over vast ranges and they are also robust against nonlinear perturbations, providing properties highly demanded in ultrafast science. In the limits of low and high energies, approximate representations are given by modified Morlet wavelets and Gaussian pulses, respectively. We demonstrate their special features by exploiting general principles of quantum scattering theory and solid-state physics, realizing interlocked chains of wavelets analog to photonic time crystals.

We study solitary wave solutions for the nonlinear Schr\"odinger equation perturbed by the effects of third-, and fourth-order dispersion, maintaining a wavenumber gap between the solitary waves and the propagation constant. We numerically construct members of a family of such solitary waves, including Kruglov and Harvey's exact solution, using the spectral renormalization method and establish empirical relations between the pulse parameters. A deeper insight into the properties of solitary waves and solitons can be obtained through collisions. Therefore we perform pulse propagation simulations demonstrating different collision regimes. Depending on the pulses initial phase difference, this can lead to the formation of short-lived two-pulse bound states. While these collisions are generally inelastic, singular phase values exist at which they are elastic. Finally, we detail the properties of Kruglov and Harvey's soliton solution under loss, verifying earlier predictions of perturbation theory and suggesting a convergence to the soliton solution of the standard nonlinear Schr\"odinger equation in the limit of large propagation distances.

We present a detailed overview of the physics of two-color soliton molecules in nonlinear waveguides, i.e. bound states of localized optical pulses which are held together due to an incoherent interaction mechanism. The mutual confinement, or trapping, of the subpulses, which leads to a stable propagation of the pulse compound, is enabled by the nonlinear Kerr effect. Special attention is paid to the description of the binding mechanism in terms of attractive potential wells, induced by the refractive index changes of the subpulses, exerted on one another through cross-phase modulation. Specifically, we discuss nonlinear-photonics meta atoms, given by pulse compounds consisting of a strong trapping pulse and a weak trapped pulse, for which trapped states of low intensity are determined by a Schr\"odinger-type eigenproblem. We discuss the rich dynamical behavior of such meta-atoms, demonstrating that an increase of the group-velocity mismatch of both subpulses leads to an ionization-like trapping-to-escape transition. We further demonstrate that if both constituent pulses are of similar amplitude, molecule-like bound-states are formed. We show that z-periodic amplitude variations permit a coupling of these pulse compound to dispersive waves, resulting in the resonant emission of Kushi-comb-like multi-frequency radiation.

We study incoherently coupled two-frequency pulse compounds in waveguides with single zero-dispersion and zero-nonlinearity points. In such waveguides, supported by a negative nonlinearity, soliton dynamics can be obtained even in domains of normal dispersion. We demonstrate trapping of weak pulses by solitary-wave wells, forming nonlinear-photonics meta-atoms, and molecule-like bound-states of pulses. We study the impact of Raman effect on these pulse compounds, finding that, depending on the precise subpulse configuration, they decelerate, accelerate, or are completely unaffected. Our results extend the range of systems in which two-frequency pulse compounds can be expected to exist and demonstrate further unique and unexpected behavior.

We numerically explore synthetic crystal diamond for realizing novel light sources in ranges which are up to now difficult to achieve with other materials, such as sub-10-fs pulse durations and challenging spectral ranges. We assess the performance of on-chip diamond waveguides for controlling light generation by means of nonlinear soliton dynamics. Tailoring the cross-section of such diamond waveguides allows to design dispersion profiles with custom zero-dispersion points and anomalous dispersion ranges exceeding an octave. Various propagation dynamics, including supercontinuum generation by soliton fission, can be realized in diamond photonics. In stark contrast to usual silica-based optical fibers, where such processes occur on the scale of meters, in diamond millimeter-scale propagation distances are sufficient. Unperturbed soliton-dynamics prior to soliton fission allow to identify a pulse self-compression scenario that promises record-breaking compression factors on chip-size propagation lengths.

Nonlinear waveguides with two distinct domains of anomalous dispersion can support the formation of molecule-like two-color pulse compounds. They consist of two tightly bound subpulses with frequency loci separated by a vast frequency gap. Perturbing such a two-color pulse compound triggers periodic amplitude and width variations, reminiscent of molecular vibrations. With increasing strength of perturbation, the dynamics of the pulse compound changes from harmonic to nonlinear oscillations. The periodic amplitude variations enable coupling of the pulse compound to dispersive waves, resulting in the resonant emission of multi-frequency radiation. We demonstrate that the location of the resonances can be precisely predicted by phase-matching conditions. If the pulse compound consists of a pair of identical subpulses, inherent symmetries lead to degeneracies in the resonance spectrum. Weak perturbations lift existing degeneracies and cause a splitting of the resonance lines into multiple lines. Strong perturbations result in more complex emission spectra, characterized by well separated spectral bands caused by resonant Cherenkov radiation and additional four-wave mixing processes.

We provide Python tools enabling numerical simulation and analysis of the propagation dynamics of ultrashort laser pulses in nonlinear waveguides. The modeling approach is based on the widely used generalized nonlinear Schr\"odinger equation for the pulse envelope. The presented software implements the effects of linear dispersion, pulse self-steepening, and the Raman effect. The focus lies on the implementation of input pulse shot noise, i.e. classical background fields that mimick quantum noise, which are often not thoroughly presented in the scientific literature. We discuss and implement commonly adopted quantum noise models based on pure spectral phase noise, as well as Gaussian noise. Coherence properties of the resulting spectra can be calculated. We demonstrate the functionality of the software by reproducing results for a supercontinuum generation process in a photonic crystal fiber, documented in the scientific literature. The presented Python tools are are open-source and released under the MIT license in a publicly available software repository.

We present a flexible, open-source Python package for the accurate simulation of the $z$-propagation dynamics of ultrashort optical pulses in nonlinear waveguides, especially valid for few-cycle pulses and their interaction. The simulation approach is based on unidirectional propagation equations for the analytic signal. The provided software allows to account for dispersion, attenuation, four-wave mixing processes including, e.g., third-harmonic generation, and features various models for the Raman response. The propagation equations are solved on a periodic temporal domain. For $z$-propagation, a selection of pseudospectral methods is available. Propagation scenarios for a custom propagation constant and initial field pulses can either be specified in terms of a HDF5 based input file format or by direct implementation using a python script. We demonstrate the functionality for a test-case for which an exact solution is available, by reproducing exemplary results documented in the scientific literature, and a complex propagation scenario involving multiple pulses. The py-fmas code, its reference manual, an extended user guide, and further usage examples are available online at https://github.com/omelchert/py-fmas.

A Python package for the calculation of spectrograms with optimized time and frequency resolution for application in the analysis of numerical simulations on ultrashort pulse propagation is presented. Gabor's uncertainty principle prevents both resolutions from being optimal simultaneously for a given window function employed in the underlying short-time Fourier analysis. Our aim is to yield a time-frequency representation of the input signal with marginals that represent the original intensities per unit time and frequency similarly well. As use-case we demonstrate the implemented functionality for the analysis of simulations on ultrashort pulse propagation in a nonlinear waveguide., Comment: 7 pages, 1 figure, supplemental code at https://github.com/omelchert/optfrog.git

We present a simple electromechanical finite difference model to study the response of a piezoelectric polyvinylidenflourid (PVDF) transducer to optoacoustic (OA) pressure waves in the acoustic nearfield prior to thermal relaxation of the OA source volume. The assumption of nearfield conditions, i.e. the absence of acoustic diffraction, allows to treat the problem using a one-dimensional numerical approach. Therein, the computational domain is modeled as an inhomogeneous elastic medium, characterized by its local wave velocities and densities, allowing to explore the effect of stepwise impedance changes on the stress wave propagation. The transducer is modeled as a thin piezoelectric sensing layer and the electromechanical coupling is accomplished by means of the respective linear constituting equations. Considering a low-pass characteristic of the full experimental setup, we obtain the resulting transducer signal. Complementing transducer signals measured in a controlled laboratory experiment with numerical simulations that result from a model of the experimental setup, we find that, bearing in mind the apparent limitations of the one-dimensional approach, the simulated transducer signals can be used very well to predict and interpret the experimental findings., Comment: 9 pages, 3 figures, 1 table, 6 code listings; supplementary code at https://github.com/omelchert/LEPM-1DFD.git

We present numerical simulations for modelling optoacoustic (OA) signals observed in PVA hydrogel tissue phantoms. We review the computational approach to model the underlying mechanisms, i.e. optical absorption of laser energy and acoustic propagation of mechanical stress, geared towards experiments that involve absorbing media only. We apply the numerical procedure to model signals observed in the acoustic near- and farfield in both, forward and backward detection mode, in PVA hydrogel tissue phantoms (i.e. an elastic solid). Further, we illustrate the computational approach by modeling OA signal for several experiments on dye solution (i.e. a liquid) reported in the literature, and benchmark the research code by comparing our fully 3D procedure to limiting cases described in terms of effectively 1D approaches., Comment: 18 pages, 5 figures

We discuss efficient algorithms for the accurate forward and reverse evaluation of the discrete Fourier-Bessel transform (dFBT) as numerical tools to assist in the 2D polar convolution of two radially symmetric functions, relevant, e.g., to applications in computational biophotonics. In our survey of the numerical procedure we account for the circumstance that the objective function might result from a more complex measurement process and is, in the worst case, known on a finite sequence of coordinate values, only. We contrast the performance of the resulting algorithms with a procedure based on a straight forward numerical quadrature of the underlying integral transform and asses its efficienty for two benchmark Fourier-Bessel pairs. An application to the problem of finite-size beam-shape convolution in polar coordinates, relevant in the context of tissue optics and optoacoustics, is used to illustrate the versatility and computational efficiency of the numerical procedure., Comment: 15 pages, 6 figures, 1 table; supplementary code at https://github.com/omelchert/dFBT-FJ.git

In this letter we address the numeric inversion of optoacoustic signals to initial stress profiles. Therefore we put under scrutiny the optoacoustic kernel reconstruction problem in the paraxial approximation of the underlying wave-equation. We apply a Fourier-series expansion of the optoacoustic Volterra kernel and obtain the respective expansion coefficients for a given "apparative" setup by performing a gauge procedure using synthetic input data. The resulting effective kernel is subsequently used to solve the optoacoustic source reconstruction problem for general signals. We verify the validity of the proposed inversion protocol for synthetic signals and explore the feasibility of our approach to also account for the diffraction transformation of signals beyond the paraxial approximation., Comment: 5 pages, 2 figures, supplementary code at https://github.com/omelchert/INVERT.git

The direct problem of optoacoustic signal generation in biological media consists of solving the inhomogeneous optoacoustic wave equation for an initial acoustic stress profile. In contrast, the mathematically challenging inverse problem requires the reconstruction of the initial stress profile from a proper set of observed signals. In this article, we consider the particular case of a Gaussian transverse irradiation source profile in the paraxial approximation of the wave equation, for which the direct problem along the beam axis can be cast into a linear Volterra integral equation of the second kind. This integral equation can be used in two ways: as a forward solver to predict optoacoustic signals in terms of the direct problem, and as an inverse solver for which we here devise highly efficient numerical schemes used for the reconstruction of initial pressure profiles from observed signals, constituting a methodical progress of computational aspects of optoacoustics. In this regard, we explore the validity as well as the limits of the inversion scheme via numerical experiments, with parameters geared towards actual optoacoustic problem instances. The considered inversion input consists of synthetic data, obtained by means of forward solvers based on the Volterra integral, and, more generally, the optoacoustic Poisson integral. Regarding the latter, we numerically invert signals that correspond to different detector-to-sample distances and assess the convergence to the true initial stress profiles upon approaching the far-field. Finally, we also address the effect of noise on the quality of the reconstructed pressure profiles., Comment: 17 pages, 7 figures

In this article we characterize optoacoustic signals generated from layered tissue phantoms via short laser pulses by experimental and numerical means. In particular, we consider the case where scattering is effectively negligible and the absorbed energy density follows Beer-Lambert's law, i.e. is characterized by an exponential decay within the layers and discontinuities at interfaces. We complement experiments on samples with multiple layers, where the material properties are known a priori, with numerical calculations for a pointlike detector, tailored to suit our experimental setup. Experimentally, we characterize the acoustic signal observed by a piezoelectric detector in the acoustic far-field in backward mode and we discuss the implication of acoustic diffraction on our measurements. We further attempt an inversion of an OA signal in the far-field approximation., Comment: 10 pages, 6 figures, supplementary code at https://github.com/omelchert/SONOS.git

We estimate the critical thresholds of bond and site percolation on nonplanar, effectively two-dimensional graphs with chimera like topology. The building blocks of these graphs are complete and symmetric bipartite subgraphs of size $2n$, referred to as $K_{n,n}$ graphs. For the numerical simulations we use an efficient union-find based algorithm and employ a finite-size scaling analysis to obtain the critical properties for both bond and site percolation. We report the respective percolation thresholds for different sizes of the bipartite subgraph and verify that the associated universality class is that of standard two-dimensional percolation. For the canonical chimera graph used in the D-Wave Systems Inc.~quantum annealer ($n = 4$), we discuss device failure in terms of network vulnerability, i.e., we determine the critical fraction of qubits and couplers that can be absent due to random failures prior to losing large-scale connectivity throughout the device., Comment: 9 pages, 5 figures

In this work we consider information-theoretical observables to analyze short symbolic sequences, comprising time-series that represent the orientation of a single spin in a $2D$ Ising ferromagnet on a square lattice of size $L^2=128^2$, for different system temperatures $T$. The latter were chosen from an interval enclosing the critical point $T_{\rm c}$ of the model. At small temperatures the sequences are thus very regular, at high temperatures they are maximally random. In the vicinity of the critical point, nontrivial, long-range correlations appear. Here, we implement estimators for the entropy rate, excess entropy (i.e. "complexity") and multi-information. First, we implement a Lempel-Ziv string parsing scheme, providing seemingly elaborate entropy rate and multi-information estimates and an approximate estimator for the excess entropy. Furthermore, we apply easy-to-use black-box data compression utilities, providing approximate estimators only. For comparison and to yield results for benchmarking purposes we implement the information-theoretic observables also based on the well-established M-block Shannon entropy, which is more tedious to apply compared to the the first two "algorithmic" entropy estimation procedures. To test how well one can exploit the potential of such data compression techniques, we aim at detecting the critical point of the $2D$ Ising ferromagnet. Among the above observables, the multi-information, which is known to exhibit an isolated peak at the critical point, is very easy to replicate by means of both efficient algorithmic entropy estimation procedures. Finally, we assess how good the various algorithmic entropy estimates compare to the more conventional block entropy estimates and illustrate a simple modification that yields enhanced results., Comment: 12 pages, 6 figures, 2 tables, supersedes arXiv:1206.7032

The principle characteristics of biased greedy random walks (BGRWs) on two-dimensional lattices with real-valued quenched disorder on the lattice edges are studied. Here, the disorder allows for negative edge-weights. In previous studies, considering the negative-weight percolation (NWP) problem, this was shown to change the universality class of the existing, static percolation transition. In the presented study, four different types of BGRWs and an algorithm based on the ant colony optimization (ACO) heuristic were considered. Regarding the BGRWs, the precise configurations of the lattice walks constructed during the numerical simulations were influenced by two parameters: a disorder parameter rho that controls the amount of negative edge weights on the lattice and a bias strength B that governs the drift of the walkers along a certain lattice direction. Here, the pivotal observable is the probability that, after termination, a lattice walk exhibits a total negative weight, which is here considered as percolating. The behavior of this observable as function of rho for different bias strengths B is put under scrutiny. Upon tuning rho, the probability to find such a feasible lattice walk increases from zero to one. This is the key feature of the percolation transition in the NWP model. Here, we address the question how well the transition point rho_c, resulting from numerically exact and "static" simulations in terms of the NWP model can be resolved using simple dynamic algorithms that have only local information available, one of the basic questions in the physics of glassy systems., Comment: 14 pages, 7 figures

We perform numerical simulations to study the optimal path problem on disordered hierarchical graphs with effective dimension d=2.32. Therein, edge energies are drawn from a disorder distribution that allows for positive and negative energies. This induces a behavior which is fundamentally different from the case where all energies are positive, only. Upon changing the subtleties of the distribution, the scaling of the minimum energy path length exhibits a transition from self-affine to self-similar. We analyze the precise scaling of the path length and the associated ground-state energy fluctuations in the vincinity of the disorder critical point, using a decimation procedure for huge graphs. Further, using an importance sampling procedure in the disorder we compute the negative-energy tails of the ground-state energy distribution up to 12 standard deviations away from its mean. We find that the asymptotic behavior of the negative-energy tail is in agreement with a Tracy-Widom distribution. Further, the characteristic scaling of the tail can be related to the ground-state energy flucutations, similar as for the directed polymer in a random medium., Comment: 10 pages, 10 figures, 3 tables

In the presented article, statistical properties regarding the topology and standard percolation on relative neighborhood graphs (RNGs) for planar sets of points, considering the Euclidean metric, are put under scrutiny. RNGs belong to the family of ``proximity graphs'', i.e. their edge-set encodes proximity information regarding the close neighbors for the terminal nodes of a given edge. Therefore they are, e.g., discussed in the context of the construction of backbones for wireless ad-hoc networks that guarantee connectedness of all underlying nodes. Here, by means of numerical simulations, we determine the asymptotic degree and diameter of RNGs and we estimate their bond and site percolation thresholds, which were previously conjectured to be nontrivial. We compare the results to regular 2D graphs for which the degree is close to that of the RNG. Finally, we deduce the common percolation critical exponents from the RNG data to verify that the associated universality class is that of standard 2D percolation., Comment: 7 pages, 5 figures, 1 table

The information theoretic observables entropy (a measure of disorder), excess entropy (a measure of complexity) and multi information are used to analyze ground-state spin configurations for disordered and frustrated model systems in 2D and 3D. For both model systems, ground-state spin configurations can be obtained in polynomial time via exact combinatorial optimization algorithms, which allowed us to study large systems with high numerical accuracy. Both model systems exhibit a continuous transition from an ordered to a disordered ground state as a model parameter is varied. By using the above information theoretic observables it is possible to detect changes in the spatial structure of the ground states as the critical point is approached. It is further possible to quantify the scaling behavior of the information theoretic observables in the vicinity of the critical point. For both model systems considered, the estimates of critical properties for the ground-state phase transitions are in good agreement with existing results reported in the literature., Comment: 11 pages, 7 figures, paper summary available at http://www.papercore.org/Melchert2012

We consider the "Touch and Stop" cluster growth percolation (CGP) model on the two dimensional square lattice. A key-parameter in the model is the fraction p of occupied "seed" sites that act as nucleation centers from which a particular cluster growth procedure is started. Here, we consider two growth-styles: rhombic and disk-shaped cluster growth. For intermediate values of p the final state, attained by the growth procedure, exhibits a cluster of occupied sites that spans the entire lattice. Using numerical simulations we investigate the percolation probability and the order parameter and perform a finite-size scaling analysis for lattices of side length up to L=1024 in order to carefully determine the critical exponents that govern the respective transition. In contrast to previous studies, reported in [Tsakiris et al., Phys. Rev. E 82 (2010) 041108], we find strong numerical evidence that the CGP model is in the standard percolation universality class., Comment: 8 pages, 7 figures, 1 table

In this lecture we will consider the minimum weight spanning tree (MST) problem, i.e., one of the simplest and most vital combinatorial optimization problems. We will discuss a particular greedy algorithm that allows to compute a MST for undirected weighted graphs, namely Kruskal's algorithm, and we will study the structure of MSTs obtained for weighted scale free random graphs. This is meant to clarify whether the structure of MSTs is sensitive to correlations between edge weights and topology of the underlying scale free graphs., Comment: 10 pages, 5 figures, Lecture notes related to the summer school "Modern Computational Science 2012 - Optimization", the example programs can be downloaded at http://www.mcs.uni-oldenburg.de/58424.html

In these lecture notes, a selection of frequently required statistical tools will be introduced and illustrated. They allow to post-process data that stem from, e.g., large-scale numerical simulations (aka sequence of random experiments). From a point of view of data analysis, the concepts and techniques introduced here are of general interest and are, at best, employed by computational aid. Consequently, an exemplary implementation of the presented techniques using the Python programming language is provided. The contents of these lecture notes is rather selective and represents a computational experimentalist's view on the subject of basic data analysis, ranging from the simple computation of moments for distributions of random variables to more involved topics such as hierarchical cluster analysis and the parallelization of Python code., Comment: 62 pages, 10 figures, Lecture notes related to the summer school "Modern Computational Science 2012 - Optimization", the example programs can be downloaded at http://www.mcs.uni-oldenburg.de/58424.html

We consider the negative weight percolation (NWP) problem on hypercubic lattice graphs with fully periodic boundary conditions in all relevant dimensions from d=2 to the upper critical dimension d=6. The problem exhibits edge weights drawn from disorder distributions that allow for weights of either sign. We are interested in in the full ensemble of loops with negative weight, i.e. non-trivial (system spanning) loops as well as topologically trivial ("small") loops. The NWP phenomenon refers to the disorder driven proliferation of system spanning loops of total negative weight. While previous studies where focused on the latter loops, we here put under scrutiny the ensemble of small loops. Our aim is to characterize -using this extensive and exhaustive numerical study- the loop length distribution of the small loops right at and below the critical point of the hypercubic setups by means of two independent critical exponents. These can further be related to the results of previous finite-size scaling analyses carried out for the system spanning loops. For the numerical simulations we employed a mapping of the NWP model to a combinatorial optimization problem that can be solved exactly by using sophisticated matching algorithms. This allowed us to study here numerically exact very large systems with high statistics., Comment: 7 pages, 4 figures, 2 tables, paper summary available at http://www.papercore.org/Kajantie2000. arXiv admin note: substantial text overlap with arXiv:1003.1591, arXiv:1005.5637, arXiv:1107.1742

We present a numerical analysis of the entropy rate and statistical complexity related to the spin flip dynamics of the 2D Ising Ferromagnet at different temperatures T. We follow an information theoretic approach and test three different entropy estimation algorithms to asses entropy rate and statistical complexity of binary sequences. The latter are obtained by monitoring the orientation of a single spin on a square lattice of side-length L=256 at a given temperature parameter over time. The different entropy estimation procedures are based on the M-block Shannon entropy (a well established method that yields results for benchmarking purposes), non-sequential recursive pair substitution (providing an elaborate and an approximate estimator) and a convenient data compression algorithm contained in the zlib-library (providing an approximate estimator only). We propose an approximate measure of statistical complexity that emphasizes on correlations within the sequence and which is easy to implement, even by means of black-box data compression algorithms. Regarding the 2D Ising Ferromagnet simulated using Metropolis dynamics and for binary sequences of finite length, the proposed approximate complexity measure is peaked close to the critical temperature. For the approximate estimators, a finite-size scaling analysis reveals that the peak approaches the critical temperature as the sequence length increases. Results obtained using different spin-flip dynamics are briefly discussed. The suggested complexity measure can be extended to non-binary sequences in a straightforward manner., Comment: 24 pages, 9 figures, paper summary available at http://www.papercore.org/Melchert2011b

We study numerically the geometrical properties of minimally weighted paths that appear in the negative-weight percolation (NWP) model on two-dimensional lattices assuming a combination of periodic and free boundary conditions (BCs). Each realization of the disorder consists of a random fraction 1-rho of bonds with unit strength and a fraction rho of bond strengths drawn from a Gaussian distribution with zero mean and unit width. For each such sample, the path is forced to span the lattice along the direction with the free BCs. The path and a set of negatively weighted loops form a ground state (GS). A ground state on such a lattice can be determined performing a non-trivial transformation of the original graph and applying sophisticated matching algorithms. Here we examine whether the geometrical properties of the paths are in accordance with predictions of Schramm-Loewner evolution (SLE). Measuring the fractal dimension and reviewing Schramm's left passage formula indicates that the paths cannot be described in terms of SLE., Comment: 9 pages, 8 figures, paper summary available at http://papercore.org/Norrenbrock2012

The presented article attempts to characterize the encryption dynamics of delayed dynamics based block ciphers, designed for the encryption of binary data. For such encryption algorithms, the encryption process relies on a coupling dynamics with time delay between different bits in the plaintext (i.e.\ the "initial" message to be encrypted). Here, the principal dynamics of the encryption process is examined and the Hammingdistance is used to quantify the change in ciphertext (i.e.\ the plaintext after encryption) upon changing a single bit in the plaintext message or slightly perturbing the key used during encryption. More precisely, the previously proposed "encryption via delayed dynamics" (in short: EDDy) algorithm as well as its extended version (termed ExEDDy) are analyzed by means of numerical simulations. As a result it is found that while EDDy exhibits a rather poor perfomance, ExEDDy performes considerably better and hence constitutes a significant improvement over EDDy. Consequently, the results are contrasted with those obtained for a block cipher that implements the encryption/decryption dynamics by means of reversible cellular automata., Comment: 10 pages, 10 figures; paper summary available at http://www.papercore.org/Melchert2011c

We investigate both analytically and numerically the ensemble of minimum-weight loops and paths in the negative-weight percolation model on random graphs with fixed connectivity and bimodal weight distribution. This allows us to study the mean-field behavior of this model. The analytical study is based on a conjectured equivalence with the problem of self-avoiding walks in a random medium. The numerical study is based on a mapping to a standard minimum-weight matching problem for which fast algorithms exist. Both approaches yield results which are in agreement, on the location of the phase transition, on the value of critical exponents, and on the absence of any sizeable indications of a glass phase. By these results, the previously conjectured upper critical dimension of d_u=6 is confirmed., Comment: 11 pages, 10 figures, paper summary available at http://www.papercore.org/Melchert2011

In the presented article we present an algorithm for the computation of ground state spin configurations for the 2d random bond Ising model on planar triangular lattice graphs. Therefore, it is explained how the respective ground state problem can be mapped to an auxiliary minimum-weight perfect matching problem, solvable in polynomial time. Consequently, the ground state properties as well as minimum-energy domain wall (MEDW) excitations for very large 2d systems, e.g. lattice graphs with up to N=384x384 spins, can be analyzed very fast. Here, we investigate the critical behavior of the corresponding T=0 ferromagnet to spin-glass transition, signaled by a breakdown of the magnetization, using finite-size scaling analyses of the magnetization and MEDW excitation energy and we contrast our numerical results with previous simulations and presumably exact results., Comment: 5 pages, 5 figures

By means of numerical simulations we investigate the configurational properties of densely and fully packed configurations of loops in the negative-weight percolation (NWP) model. In the presented study we consider 2d square, 2d honeycomb, 3d simple cubic and 4d hypercubic lattice graphs, where edge weights are drawn from a Gaussian distribution. For a given realization of the disorder we then compute a configuration of loops, such that the configurational energy, given by the sum of all individual loop weights, is minimized. For this purpose, we employ a mapping of the NWP model to the "minimum-weight perfect matching problem" that can be solved exactly by using sophisticated polynomial-time matching algorithms. We characterize the loops via observables similar to those used in percolation studies and perform finite-size scaling analyses, up to side length L=256 in 2d, L=48 in 3d and L=20 in 4d (for which we study only some observables), in order to estimate geometric exponents that characterize the configurations of densely and fully packed loops. One major result is that the loops behave like uncorrelated random walks from dimension d=3 on, in contrast to the previously studied behavior at the percolation threshold, where random-walk behavior is obtained for d>=6., Comment: 11 pages, 7 figures

By means of numerical simulations we investigate the geometric properties of loops on hypercubic lattice graphs in dimensions d=2 through 7, where edge weights are drawn from a distribution that allows for positive and negative weights. We are interested in the appearance of system-spanning loops of total negative weight. The resulting negative-weight percolation (NWP) problem is fundamentally different from conventional percolation, as we have seen in previous studies of this model for the 2d case. Here, we characterize the transition for hypercubic systems, where the aim of the present study is to get a grip on the upper critical dimension d_u of the NWP problem. For the numerical simulations we employ a mapping of the NWP model to a combinatorial optimization problem that can be solved exactly by using sophisticated matching algorithms. We characterize the loops via observables similar to those in percolation theory and perform finite-size scaling analyses, e.g. 3d hypercubic systems with side length up to L=56 sites, in order to estimate the critical properties of the NWP phenomenon. We find our numerical results consistent with an upper critical dimension d_u=6 for the NWP problem., Comment: 9 pages, 2 tables and 6 figures

autoScale.py is a program that performs an automatic finite-size scaling analysis for given sets of simulated data. It implements a quite general scaling assumption and optimizes an initial set of scaling parameters that enforce a data collapse of the different data sets. The presented guide describes how the program works, it presents a detailed example and finally gives some hints on how to improve the results of a scaling analysis., Comment: 12 pages, 1 figure; contains supplementary archive

Sequence alignment is a tool in bioinformatics that is used to find homological relationships in large molecular databases. It can be mapped on the physical model of directed polymers in random media. We consider the finite-temperature version of local sequence alignment for proteins and study the transition between the linear phase and the biologically relevant logarithmic phase, where the free-energy grows linearly or logarithmically with the sequence length. By means of numerical simulations and finite-size scaling analysis we determine the phase diagram in the plane that is spanned by the gap costs and the temperature. We use the most frequently used parameter set for protein alignment. The critical exponents that describe the parameter driven transition are found to be explicitly temperature dependent. Furthermore, we study the shape of the (free-) energy distribution close to the transition by rare-event simulations down to probabilities of the order $10^{-64}$. It is well known that, in the logarithmic region, the optimal score distribution (T=0) is described by a modified Gumbel distribution. We confirm that this also applies for the free-energy distribution ($T>0$). However, in the linear phase, the distribution crosses over to a modified Gaussian distribution.

We study domain-wall excitations in two-dimensional random-bond Ising spin systems on a square lattice with side length L, subject to two different continuous disorder distributions. In both cases an adjustable parameter allows to tune the disorder so as to yield a transition from a spin-glass ordered ground state to a ferromagnetic groundstate. We formulate an auxiliary graph-theoretical problem in which domain walls are given by undirected shortest paths with possibly negative distances. Due to the details of the mapping, standard shortest-path algorithms cannot be applied. To solve such shortest-path problems we have to apply minimum-weight perfect-matching algorithms. We first locate the critical values of the disorder parameters, where the ferromagnet to spin-glass transition occurs for the two types of the disorder. For certain values of the disorder parameters close to the respective critical point, we investigate the system size dependence of the width of the the average domain-wall energy (~L^\theta) and the average domain-wall length (~L^df). Performing a finite-size scaling analysis for systems with a side length up to L=512, we find that both exponents remain constant in the spin-glass phase, i.e. \theta ~- 0.28 and df~1.275. This is consistent with conformal field theory, where it seems to be possible to relate the exponents from the analysis of Stochastic Loewner evolutions (SLEs) via df-1=3/[4(3+\theta)]. Finally, we characterize the transition in terms of ferromagnetic clusters of spins that form, as one proceeds from spin-glass ordered to ferromagnetic ground states., Comment: 10 pages, 8 figures, 2 tables; version2: additional text, added 3 references

We investigate the geometric properties of loops on two-dimensional lattice graphs, where edge weights are drawn from a distribution that allows for positive and negative weights. We are interested in the appearance of spanning loops of total negative weight. The resulting percolation problem is fundamentally different from conventional percolation, as we have seen in a previous study of this model for the undiluted case. Here, we investigate how the percolation transition is affected by additional dilution. We consider two types of dilution: either a certain fraction of edges exhibit zero weight, or a fraction of edges is even absent. We study these systems numerically using exact combinatorial optimization techniques based on suitable transformations of the graphs and applying matching algorithms. We perform a finite-size scaling analysis to obtain the phase diagram and determine the critical properties of the phase boundary. We find that the first type of dilution does not change the universality class compared to the undiluted case whereas the second type of dilution leads to a change of the universality class., Comment: 8 pages, 7 figures

We investigate the performance of the recently proposed stationary Fokker-Planck sampling method considering a combinatorial optimization problem from statistical physics. The algorithmic procedure relies upon the numerical solution of a linear second order differential equation that depends on a diffusion-like parameter D. We apply it to the problem of finding ground states of 2d Ising spin glasses for the +-J-Model. We consider square lattices with side length up to L=24 with two different types of boundary conditions and compare the results to those obtained by exact methods. A particular value of D is found that yields an optimal performance of the algorithm. We compare this optimal value of D to a percolation transition, which occurs when studying the connected clusters of spins flipped by the algorithm. Nevertheless, even for moderate lattice sizes, the algorithm has more and more problems to find the exact ground states. This means that the approach, at least in its standard form, seems to be inferior to other approaches like parallel tempering., Comment: v1: 13 pages, 7 figures; v2: extended text

We describe a percolation problem on lattices (graphs, networks), with edge weights drawn from disorder distributions that allow for weights (or distances) of either sign, i.e. including negative weights. We are interested whether there are spanning paths or loops of total negative weight. This kind of percolation problem is fundamentally different from conventional percolation problems, e.g. it does not exhibit transitivity, hence no simple definition of clusters, and several spanning paths/loops might coexist in the percolation regime at the same time. Furthermore, to study this percolation problem numerically, one has to perform a non-trivial transformation of the original graph and apply sophisticated matching algorithms. Using this approach, we study the corresponding percolation transitions on large square, hexagonal and cubic lattices for two types of disorder distributions and determine the critical exponents. The results show that negative-weight percolation is in a different universality class compared to conventional bond/site percolation. On the other hand, negative-weight percolation seems to be related to the ferromagnet/spin-glass transition of random-bond Ising systems, at least in two dimensions., Comment: v1: 4 pages, 4 figures; v2: 10 pages, 7 figures, added results, text and references

We study domain walls in 2d Ising spin glasses in terms of a minimum-weight path problem. Using this approach, large systems can be treated exactly. Our focus is on the fractal dimension $d_f$ of domain walls, which describes via $<\ell >\simL^{d_f}$ the growth of the average domain-wall length with %% systems size $L\times L$. %% 20.07.07 OM %% Exploring systems up to L=320 we yield $d_f=1.274(2)$ for the case of Gaussian disorder, i.e. a much higher accuracy compared to previous studies. For the case of bimodal disorder, where many equivalent domain walls exist due to the degeneracy of this model, we obtain a true lower bound $d_f=1.095(2)$ and a (lower) estimate $d_f=1.395(3)$ as upper bound. Furthermore, we study the distributions of the domain-wall lengths. Their scaling with system size can be described also only by the exponent $d_f$, i.e. the distributions are monofractal. Finally, we investigate the growth of the domain-wall width with system size (``roughness'') and find a linear behavior., Comment: 8 pages, 8 figures, submitted to Phys. Rev. B; v2: shortened version