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At least 613 records · Page 34Linked to original sources
PubMed2004

Automated clustering of ensembles of alternative models in protein structure databases.

Experimentally determined protein structures have been classified in different public databases according to their structural and evolutionary relationships. Frequently, alternative structural models, determined using X-ray crystallography or NMR spectroscopy, are available for a protein. These models can present significant structural dissimilarity. Currently there is no classification available for these alternative structures. In order to classify them, we developed STRuster, an automated method for clustering ensembles of structural models according to their backbone structure. The method is based on the calculation of carbon alpha (Calpha) distance matrices. Two filters are applied in the calculation of the dissimilarity measure in order to identify both large and small (but significant) backbone conformational changes. The resulting dissimilarity value is used for hierarchical clustering and partitioning around medoids (PAM). Hierarchical clustering reflects the hierarchy of similarities between all pairs of models, while PAM groups the models into the 'optimal' number of clusters. The method has been applied to cluster the structures in each SCOP species level and can be easily applied to any other sets of conformers. The results are available at: http://bioinf.mpi-sb.mpg.de/projects/struster/.

Aldehyde-Lyases↗
PubMed2003

Entanglement and quantum teleportation with multi-atom ensembles.

Atomic ensembles containing a large number of atoms have been proved to be an effective medium for quantum-state (quantum information) engineering and processing via their coupling with multi-photon light pulses. The general mechanism of this coupling, which involves continuous quantum variables for light and atoms, is described. The efficient quantum interface between light and atoms has led to the recent demonstration of an entangled state of two macroscopic atomic objects, more precisely two caesium gas samples. Based on this result, a proposal for teleportation of an entangled state of two atomic samples (entanglement swapping) is presented.

Journal Article↗
PubMed2000

Preferential relaxation of positively supercoiled DNA by E. coli topoisomerase IV in single-molecule and ensemble measurements.

We show that positively supercoiled [(+) SC] DNA is the preferred substrate for Escherichia coli topoisomerase IV (topo IV). We measured topo IV relaxation of (-) and (+) supercoils in real time on single, tethered DNA molecules to complement ensemble experiments. We find that the preference for (+) SC DNA is complete at low enzyme concentration. Otherwise, topo IV relaxed (+) supercoils at a 20-fold faster rate than (-) supercoils, due primarily to about a 10-fold increase in processivity with (+) SC DNA. The preferential cleavage of (+) SC DNA in a competition experiment showed that substrate discrimination can take place prior to strand passage in the presence or absence of ATP. We propose that topo IV discriminates between (-) and (+) supercoiled DNA by recognition of the geometry of (+) SC DNA. Our results explain how topo IV can rapidly remove (+) supercoils to support DNA replication without relaxing the essential (-) supercoils of the chromosome. They also show that the rate of supercoil relaxation by topo IV is several orders of magnitude faster than hitherto appreciated, so that a single enzyme may suffice at each replication fork.

DNA Topoisomerase IV↗
PubMed2004

The Ensembl core software libraries.

Systems for managing genomic data must store a vast quantity of information. Ensembl stores these data in several MySQL databases. The core software libraries provide a practical and effective means for programmers to access these data. By encapsulating the underlying database structure, the libraries present end users with a simple, abstract interface to a complex data model. Programs that use the libraries rather than SQL to access the data are unaffected by most schema changes. The architecture of the core software libraries, the schema, and the factors influencing their design are described. All code and data are freely available.

Animals↗
PubMed2004

ESTGenes: alternative splicing from ESTs in Ensembl.

We describe a novel algorithm for deriving the minimal set of nonredundant transcripts compatible with the splicing structure of a set of ESTs mapped on a genome. Sets of ESTs with compatible splicing are represented by a special type of graph. We describe the algorithms for building the graphs and for deriving the minimal set of transcripts from the graphs that are compatible with the evidence. These algorithms are part of the Ensembl automatic gene annotation system, and its results, using ESTs, are provided at www.ensembl.org as ESTgenes for the mosquito, Caenorhabditis briggsae, C. elegans, zebrafish, human, mouse, and rat genomes. Here we also report on the results of this method applied to the human and mouse genomes.

Alternative Splicing↗
PubMed2004

The Ensembl computing architecture.

Ensembl is a software project to automatically annotate large eukaryotic genomes and release them freely into the public domain. The project currently automatically annotates 10 complete genomes. This makes very large demands on compute resources, due to the vast number of sequence comparisons that need to be executed. To circumvent the financial outlay often associated with classical supercomputing environments, farms of multiple, lower-cost machines have now become the norm and have been deployed successfully with this project. The architecture and design of farms containing hundreds of compute nodes is complex and nontrivial to implement. This study will define and explain some of the essential elements to consider when designing such systems. Server architecture and network infrastructure are discussed with a particular emphasis on solutions that worked and those that did not (often with fairly spectacular consequences). The aim of the study is to give the reader, who may be implementing a large-scale biocompute project, an insight into some of the pitfalls that may be waiting ahead.

Computational Biology↗
PubMed1999

Solution of lattice gas models in the generalized ensemble on the Bethe lattice.

We present the exact Bethe lattice solution for a lattice gas Potts model defined in the generalized ensemble which was previously studied in elucidating the anomalous thermodynamic properties of water. For this model the locus of density maxima (TMD), the locus of isothermal compressibility extrema, (TEC), the spinodal curve, and the percolation curve for four hydrogen bonded molecules are calculated using the Bethe lattice solution. The results confirm qualitative relationships between the TMD, the TEC, and the percolation curve obtained previously from a mean field calculation.

Journal Article↗
PubMed2000

Inequivalence of dynamical ensembles in a generalized driven diffusive lattice gas

We generalize the driven diffusive lattice gas model by using a combination of Kawasaki and Glauber dynamics. We find via Monte Carlo simulations and perturbation studies that the simplest possible generalization of the equivalence of the canonical and grand-canonical ensembles, which holds in equilibrium, does not apply for this class of nonequilibrium systems.

Journal Article↗
PubMed2000

Temperature and density extrapolations in canonical ensemble monte carlo simulations

We show how to use the multiple histogram method to combine canonical ensemble Monte Carlo simulations made at different temperatures and densities. The method can be applied to study systems of particles with arbitrary interaction potential and to compute the thermodynamic properties over a range of temperatures and densities. The calculation of the Helmholtz free energy relative to some thermodynamic reference state enables us to study phase coexistence properties. We test the method on the Lennard-Jones fluids for which many results are available.

Journal Article↗
PubMed2000

Spontaneous symmetry breaking in U(N) invariant ensembles with a soft confinement potential

A solution is provided to the problem of finding the probability distribution of elements of a random matrix in terms of the distribution of eigenvalues and eigenvectors. It is then proved that completely isotropic eigenvectors can become localized when the eigenvalues increase exponentially. This general result confirms the prediction of a spontaneous breaking of the unitary transformation, U(N), invariance of random matrix ensembles, in the limit of extremely soft confinement. An algorithm is implemented to generate eigenvectors with broken symmetry. The theory is then verified numerically.

Journal Article↗
PubMed2000

Information coding via spontaneous oscillations in neural ensembles.

How information is encoded and decoded via spontaneous oscillations is investigated by using an ensemble of Hodgkin-Huxley neurons. A signal can be encoded in spontaneous and highly irregular spike trains via high-order rate coding with the second-order statistics being relevant, in which the temporal structure and the correlation between the spikes are taken into account. Although the encoded information is implicitly contained in the spike train, it can be retrieved in the post-synaptic potential. The spontaneous oscillation is filtered and the irregularity of the spike train is suppressed. In particular, we show that an arbitrary signal can be transmitted reliably through spontaneous and highly irregular spike trains, and then be reconstructed downstream in the information transmission pathway.

Action Potentials↗
PubMed2000

Distribution of the determinant of a random real-symmetric matrix from the gaussian orthogonal ensemble

The Mellin transform of the probability density of the determinant of NxN random real-symmetric matrices from the Gaussian orthogonal ensemble is calculated. The determinant probability density is given by a single Meijer G function for odd N. The distribution of the potential at the origin, within the Coulomb gas interpretation, is investigated from the Mellin transform of the determinant distribution and is shown to be asymptotically Gaussian.

Journal Article↗
PubMed2000

Equivalence of two approaches for the inhomogeneous density in the canonical ensemble

In this Brief Report we show that the inhomogeneous density obtained from a density-functional theory of classical fluids in the canonical ensemble (CE), recently presented by White et al. [Phys. Rev. Lett. 84, 1220 (2000)], is equivalent to first order to the result of the series expansion of the CE inhomogeneous density introduced by Gonzalez et al. [Phys. Rev. Lett. 79, 2466 (1997)].

Journal Article↗
PubMed2000

Gaussian unitary ensemble statistics in a time-reversal invariant microwave triangular billiard

The spectrum of a chaotic two-dimensional quantum billiard with threefold symmetry has been studied in an experiment with a superconducting microwave cavity. In total 622 eigenvalues were identified experimentally and compared with numerical calculations. The statistical analysis of the data shows that Gaussian unitary ensemble statistics can be observed for a spectrum of a time-reversal invariant system.

Journal Article↗
PubMed2001

Chaos-nonchaos phase transitions induced by external noise in ensembles of nonlinearly coupled oscillators.

Nonlinear dynamical behaviors of ensembles of nonlinearly coupled oscillators subjected to external noise are studied on the basis of nonlinear Fokker-Planck equations. The effects of two kinds of noise, the Langevin noise and the noise introduced in the coupling strength, are investigated, and phase transitions involving chaos-nonchaos bifurcations are found to occur as the noise level is changed. An H theorem is proposed for the nonlinear Fokker-Planck equation to ensure stability of the Gaussian type solution that is approached for large times.

Journal Article↗
PubMed2001

Spectral properties of a generalized chiral Gaussian unitary ensemble.

We consider a generalized chiral Gaussian Unitary ensemble (chGUE) based on a weak confining potential. We study the spectral correlations close to the origin in the thermodynamic limit. We show that for eigenvalues separated up to the mean level spacing, the spectral correlations coincide with those of chGUE. Beyond this point, the spectrum is described by an oscillating number variance centered around a constant value. We argue that the origin of such a rigid spectrum is due to the breakdown of the translational invariance of the spectral kernel in the bulk of the spectrum. Finally, we compare our results with the ones obtained from a critical chGUE recently reported in the literature. We conclude that our generalized chGUE does not belong to the same class of universality as the above mentioned model.

Journal Article↗
PubMed2002

Group symmetries in two-body random matrix ensembles generating order out of complexity.

The two-body random matrix ensembles with spin TBRE-s and in a single j shell TBRE-j introduced recently in the context of ground state structures in complex interacting particle systems, possess U(N) superset U(N/2)multiply sign in circle SU(2) and U(N)superset O(3) group symmetries, respectively, with N the number of single particle states. It is shown that both these group symmetries give rise to simplicities in the ground state structures but in different ways.

Journal Article↗