Chemical structure matching using correlation matrix memories

This paper describes the application of the Relaxation By Elimination (RBE) method to matching the 3D structure of molecules in chemical databases within the frame work of binary correlation matrix memories. The paper illustrates that, when combined with distributed representations, the method maps well onto these networks, allowing high performance implementation in parallel systems. It outlines the motivation, the neural architecture, the RBE method and presents some results of matching small molecules against a database of 100,000 models

From isovists to visibility graphs: a methodology for the analysis of architectural space

An isovist, or viewshed, is the area in a spatial environment directly visible from a location within the space. Here we show how a set of isovists can be used to generate a graph of mutual visibility between locations. We demonstrate that this graph can also be constructed without reference to isovists and that we are in fact invoking the more general concept of a visibility graph. Using the visibility graph, we can extend both isovist and current graph-based analyses of architectural space to form a new methodology for the investigation of configurational relationships. The measurement of local and global characteristics of the graph, for each vertex or for the system as a whole, is of interest from an architectural perspective, allowing us to describe a configuration with reference to accessibility and visibility, to compare from location to location within a system, and to compare systems with different geometries. Finally we show that visibility graph properties may be closely related to manifestations of spatial perception, such as way-finding, movement, and space use

Extrema statistics in the dynamics of a non-Gaussian random field

When the equations that govern the dynamics of a random field are nonlinear, the field can develop with time non-Gaussian statistics even if its initial condition is Gaussian. Here, we provide a general framework for calculating the effect of the underlying nonlinear dynamics on the relative densities of maxima and minima of the field. Using this simple geometrical probe, we can identify the size of the non-Gaussian contributions in the random field, or alternatively the magnitude of the nonlinear terms in the underlying equations of motion. We demonstrate our approach by applying it to an initially Gaussian field that evolves according to the deterministic KPZ equation, which models surface growth and shock dynamics.Comment: 9 pages, 3 figure

Fluctuating observation time ensembles in the thermodynamics of trajectories

The dynamics of stochastic systems, both classical and quantum, can be studied by analysing the statistical properties of dynamical trajectories. The properties of ensembles of such trajectories for long, but fixed, times are described by large-deviation (LD) rate functions. These LD functions play the role of dynamical free-energies: they are cumulant generating functions for time-integrated observables, and their analytic structure encodes dynamical phase behaviour. This "thermodynamics of trajectories" approach is to trajectories and dynamics what the equilibrium ensemble method of statistical mechanics is to configurations and statics. Here we show that, just like in the static case, there is a variety of alternative ensembles of trajectories, each defined by their global constraints, with that of trajectories of fixed total time being just one of these. We show that an ensemble of trajectories where some time-extensive quantity is constant (and large) but where total observation time fluctuates, is equivalent to the fixed-time ensemble, and the LD functions that describe one ensemble can be obtained from those that describe the other. We discuss how the equivalence between generalised ensembles can be exploited in path sampling schemes for generating rare dynamical trajectories.Comment: 12 pages, 5 figure

Collisionless heating in capacitive discharges enhanced by dual-frequency excitation

We discuss collisionless electron heating in capacitive discharges excited by a combination of two disparate frequencies. By developing an analytical model, we find, contrary to expectation, that the net heating in this case is much larger than the sum of the effects occurring when the two frequencies act separately. This prediction is substantiated by kinetic simulations, which are also in excellent general quantitative agreement with the model for discharge parameters that are typical of recent experiments

Parameterization of Dark-Energy Properties: a Principal-Component Approach

Considerable work has been devoted to the question of how to best parameterize the properties of dark energy, in particular its equation of state w. We argue that, in the absence of a compelling model for dark energy, the parameterizations of functions about which we have no prior knowledge, such as w(z), should be determined by the data rather than by our ingrained beliefs or familiar series expansions. We find the complete basis of orthonormal eigenfunctions in which the principal components (weights of w(z)) that are determined most accurately are separated from those determined most poorly. Furthermore, we show that keeping a few of the best-measured modes can be an effective way of obtaining information about w(z).Comment: Unfeasibility of a truly model-independent reconstruction of w at z>1 illustrated. f(z) left out, and w(z) discussed in more detail. Matches the PRL versio

QSO's from Galaxy Collisions with Naked Black Holes

In the now well established conventional view (see Rees [1] and references therein), quasi-stellar objects (QSOs) and related active galactic nuclei (AGN) phenomena are explained as the result of accretion of plasma onto giant black holes which are postulated to form via gravitational collapse of the high density regions in the centers of massive host galaxies. This model is supported by a wide variety of indirect evidence and seems quite likely to apply at least to some observed AGN phenomena. However, one surprising set of new Hubble Space Telescope (HST) observations [2-4] directly challenges the conventional model, and the well known evolution of the QSO population raises some additional, though not widely recognized, difficulties. We propose here an alternative possibility: the Universe contains a substantial independent population of super-massive black holes, and QSO's are a phenomenon that occurs due to their collisions with galaxies or gas clouds in the intergalactic medium (IGM). This hypothesis would naturally explain why the QSO population declines very rapidly towards low redshift, as well as the new HST data.Comment: plain TeX file, no figures, submitted to Natur