arXiv subjects

Christoph Best

Publications and source records attributed to Christoph Best.

8 recordsLinked to original sources

arXiv2005

Probabilistic methods for predicting protein functions in protein-protein interaction networks

We discuss probabilistic methods for predicting protein functions from protein-protein interaction networks. Previous work based on Markov Randon Fields is extended and compared to a general machine-learning theoretic approach. Using actual protein interaction networks for yeast from the MIPS database and GO-SLIM function assignments, we compare the predictions of the different probabilistic methods and of a standard support vector machine. It turns out that, with the currently available networks, the simple methods based on counting frequencies perform as well as the more sophisticated approaches.

q-bio.MN↗

arXiv2000

Algebraic Multigrid for Disordered Systems and Lattice Gauge Theories

The construction of multigrid operators for disordered linear lattice operators, in particular the fermion matrix in lattice gauge theories, by means of algebraic multigrid and block LU decomposition is discussed. In this formalism, the effective coarse-grid operator is obtained as the Schur complement of the original matrix. An optimal approximation to it is found by a numerical optimization procedure akin to Monte Carlo renormalization, resulting in a generalized (gauge-path dependent) stencil that is easily evaluated for a given disorder field. Applications to preconditioning and relaxation methods are investigated.

hep-lat↗

arXiv1999

Visualizing Conformations in Molecular Dynamics

The Monte Carlo simulation of the dynamics of complex molecules produces trajectories with a large number of different configurations to sample configuration space. It is expected that these configurations can be classified into a small number of conformations representing essential changes in the shape of the molecule. We present a method to visualize these conformations by point sets in the plane based on a geometrical distance measure between individual configurations. It turns out that different conformations appear as well-separated point sets. The method is further improved by performing a cluster analysis of the data set. The point-cluster representation is used to control a three-dimensional molecule viewer application to show individual configurations and conformational changes. The extraction of essential coordinates and visualization of molecular shape is discussed.

physics.comp-ph↗

arXiv1999

Wavelet-induced renormalization group for the Landau-Ginzburg model

The scale hierarchy of wavelets provides a natural frame for renormalization. Expanding the order parameter of the Landau-Ginzburg/$Φ^4$ model in a basis of compact orthonormal wavelets explicitly exhibits the coupling between scales that leads to non-trivial behavior. The locality properties of Daubechies' wavelets enable us to derive the qualitative renormalization flow of the Landau-Ginzburg model from Gaussian fluctuations in wavelet space.

hep-lat↗

arXiv1999

A simple C++ library for manipulating scientific data sets as structured data

Representing scientific data sets efficiently on external storage usually involves converting them to a byte string representation using specialized reader/writer routines. The resulting storage files are frequently difficult to interpret without these specialized routines as they do not contain information about the logical structure of the data. Avoiding such problems usually involves heavy-weight data format libraries or data base systems. We present a simple C++ library that allows to create and access data files that store structured data. The structure of the data is described by a data type that can be built from elementary data types (integer and floating-point numbers, byte strings) and composite data types (arrays, structures, unions). An abstract data access class presents the data to the application. Different actual data file structures can be implemented under this layer. This method is particularly suited to applications that require complex data structures, e.g. molecular dynamics simulations. Extensions such as late type binding and object persistence are discussed.

cs.CE↗

arXiv1996

A microscopic semiclassical confining field equation for $U(1)$ lattice gauge theory in 2+1 dimensions

We present a semiclassical nonlinear field equation for the confining field in 2+1--dimensional $U(1)$ lattice gauge theory (compact QED). The equation is derived directly from the underlying microscopic quantum Hamiltonian by means of truncation. Its nonlinearities express the dynamic creation of magnetic monopole currents leading to the confinement of the electric field between two static electric charges. We solve the equation numerically and show that it can be interpreted as a London relation in a dual superconductor.

hep-lat↗

arXiv1994

U(1) flux tube profiles from Hamiltonian lattice gauge theory using a random walk ground-state projector

We use a self-guided random walk to solve the ground-state problem of Hamiltonian U(1) pure gauge theory in 2+1 dimensions in the string sector. By making use of the electric-field representation, we argue that the spatial distribution of the electric field can be more easily measured than in ordinary Monte Carlo simulations.

hep-lat↗

arXiv1994

Variational description of statistical field theories using Daubechies' wavelets

We investigate the description of statistical field theories using Daubechies' orthonormal compact wavelets on a lattice. A simple variational approach is used to extend mean field theory and make predictions for the fluctuation strengths of wavelet coefficients and thus for the correlation function. The results are compared to Monte Carlo simulations. We find that wavelets provide a reasonable description of critical phenomena with only a small number of variational parameters. This lets us hope for an implementation of the renormalization group in wavelet space.

hep-lat↗