Darwinian Data Structure Selection

Data structure selection and tuning is laborious but can vastly improve an application's performance and memory footprint. Some data structures share a common interface and enjoy multiple implementations. We call them Darwinian Data Structures (DDS), since we can subject their implementations to survival of the fittest. We introduce ARTEMIS a multi-objective, cloud-based search-based optimisation framework that automatically finds optimal, tuned DDS modulo a test suite, then changes an application to use that DDS. ARTEMIS achieves substantial performance improvements for \emph{every} project in $5$ Java projects from DaCapo benchmark, $8$ popular projects and $30$ uniformly sampled projects from GitHub. For execution time, CPU usage, and memory consumption, ARTEMIS finds at least one solution that improves \emph{all} measures for $86\%$ ($37/43$) of the projects. The median improvement across the best solutions is $4.8\%$, $10.1\%$, $5.1\%$ for runtime, memory and CPU usage. These aggregate results understate ARTEMIS's potential impact. Some of the benchmarks it improves are libraries or utility functions. Two examples are gson, a ubiquitous Java serialization framework, and xalan, Apache's XML transformation tool. ARTEMIS improves gson by $16.5$\%, $1\%$ and $2.2\%$ for memory, runtime, and CPU; ARTEMIS improves xalan's memory consumption by $23.5$\%. \emph{Every} client of these projects will benefit from these performance improvements.Comment: 11 page

Parametric ordering of complex systems

Cellular automata (CA) dynamics are ordered in terms of two global parameters, computable {\sl a priori} from the description of rules. While one of them (activity) has been used before, the second one is new; it estimates the average sensitivity of rules to small configurational changes. For two well-known families of rules, the Wolfram complexity Classes cluster satisfactorily. The observed simultaneous occurrence of sharp and smooth transitions from ordered to disordered dynamics in CA can be explained with the two-parameter diagram

The short-time Dynamics of the Critical Potts Model

The universal behaviour of the short-time dynamics of the three state Potts model in two dimensions at criticality is investigated with Monte Carlo methods. The initial increase of the order is observed. The new dynamic exponent $\theta$ as well as exponent $z$ and $\beta/\nu$ are determined. The measurements are carried out in the very beginning of the time evolution. The spatial correlation length is found to be very short compared with the lattice size.Comment: 6 pages, 3 figure

Models for Monolayers Adsorbed on a Square Substrate

Motivated by recent experimental studies of Hg and Pb monolayers on Cu(001) we introduce a zero temperature model of a monolayer adsorbed on a square substrate. Lennard-Jones potentials are used to describe the interaction between pairs of adlayer-adlayer and adlayer-substrate atoms. We study a special case in which the monolayer atoms form a perfect square structure and the lattice constant, position and orientation with respect to the substrate can vary to minimize the energy. We introduce a rule based on the Farey tree construction to generate systematically the most energetically favored phases and use it to calculate the phase diagram in this model.Comment: 14 pages, Table (included), Two Figures (available upon request). SU-92-150

Determination of the Critical Point and Exponents from short-time Dynamics

The dynamic process for the two dimensional three state Potts model in the critical domain is simulated by the Monte Carlo method. It is shown that the critical point can rigorously be located from the universal short-time behaviour. This makes it possible to investigate critical dynamics independently of the equilibrium state. From the power law behaviour of the magnetization the exponents $\beta / (\nu z)$ and $1/ (\nu z)$ are determined.Comment: 6 pages, 4 figure

Conformal Dimension of the Brownian Graph

Conformal dimension of a metric space $X$, denoted by $\dim_C X$, is the infimum of the Hausdorff dimension among all its quasisymmetric images. If conformal dimension of $X$ is equal to its Hausdorff dimension, $X$ is said to be minimal for conformal dimension. In this paper we show that the graph of the one dimensional Brownian motion is almost surely minimal for conformal dimension. We also give many other examples of minimal sets for conformal dimension, which we call Bedford-McMullen type sets. In particular we show that Bedford-McMullen self-affine sets with uniform fibers are minimal for conformal dimension. The main technique in the proofs is the construction of ``rich families of minimal sets of conformal dimension one''. The latter concept is quantified using Fuglede's modulus of measures.Comment: 42 pages, 6 figure

On computability of equilibrium states

Equilibrium states are natural dynamical analogs of Gibbs states in thermodynamic formalism. This paper is devoted to the study of their computability in the sense of Computable Analysis. We show that the unique equilibrium state associated to a pair of a computable, topologically exact, distance-expanding, open map $T\colon X\rightarrow X$ and a computable H\"older continuous potential $\varphi\colon X\rightarrow\mathbb{R}$ is always computable. Furthermore, the Hausdorff dimension of the Julia set and the equilibrium state for the geometric potential of a computable hyperbolic rational map are computable. On the other hand, we introduce a mechanism to establish non-uniqueness of equilibrium states. We also present some computable dynamical systems whose equilibrium states are all non-computable.Comment: 41 pages. Reformatted, polished, typos corrected, Theorems D and E reformulated with Section 6 adjusted accordingl

Universality and Scaling in Short-time Critical Dynamics

Numerically we simulate the short-time behaviour of the critical dynamics for the two dimensional Ising model and Potts model with an initial state of very high temperature and small magnetization. Critical initial increase of the magnetization is observed. The new dynamic critical exponent $\theta$ as well as the exponents $z$ and $2\beta/\nu$ are determined from the power law behaviour of the magnetization, auto-correlation and the second moment. Furthermore the calculation has been carried out with both Heat-bath and Metropolis algorithms. All the results are consistent and therefore universality and scaling are confirmed.Comment: 14 pages, 14 figure

Critical Behaviour of the 3D XY-Model: A Monte Carlo Study

We present the results of a study of the three-dimensional $XY$-model on a simple cubic lattice using the single cluster updating algorithm combined with improved estimators. We have measured the susceptibility and the correlation length for various couplings in the high temperature phase on lattices of size up to $L=112$. At the transition temperature we studied the fourth-order cumulant and other cumulant-like quantities on lattices of size up to $L=64$. From our numerical data we obtain for the critical coupling \coup_c=0.45420(2), and for the static critical exponents $\gamma /\nu=1.976(6)$ and $\nu=0.662(7)$.Comment: 24 pages (4 PS-Figures Not included, Revtex 3.O file), report No.: CERN-TH.6885/93, KL-TH-93/1

Physico-chemical foundations underpinning microarray and next-generation sequencing experiments

Hybridization of nucleic acids on solid surfaces is a key process involved in high-throughput technologies such as microarrays and, in some cases, next-generation sequencing (NGS). A physical understanding of the hybridization process helps to determine the accuracy of these technologies. The goal of a widespread research program is to develop reliable transformations between the raw signals reported by the technologies and individual molecular concentrations from an ensemble of nucleic acids. This research has inputs from many areas, from bioinformatics and biostatistics, to theoretical and experimental biochemistry and biophysics, to computer simulations. A group of leading researchers met in Ploen Germany in 2011 to discuss present knowledge and limitations of our physico-chemical understanding of high-throughput nucleic acid technologies. This meeting inspired us to write this summary, which provides an overview of the state-of-the-art approaches based on physico-chemical foundation to modeling of the nucleic acids hybridization process on solid surfaces. In addition, practical application of current knowledge is emphasized