Toward construction of an inexpensive brain computer interface for goal oriented applications

The paper describes the implementation of an offline, low-cost Brain Computer Interface (BCI) alternative to more expensive commercial models. Using inexpensive general purpose clinical EEG acquisition hardware (Truscan32, Deymed Diagnostic) as the base unit, a synchronisation module was constructed to allow the EEG hardware to be operated precisely in time to allow for recording of automatically time stamped EEG signals. The synchronising module allows the EEG recordings to be aligned in stimulus time locked fashion for further processing by the classifier to establish the class of the stimulus, sample by sample. This allows for the acquisition of signals from the subject’s brain for the goal oriented BCI application based on the oddball paradigm. An appropriate graphical user interface (GUI) was constructed and implemented as the method to elicit the required responses (in this case Event Related Potentials or ERPs) from the subject.

Generic control interface for networked haptic virtual environments

As Virtual Reality pushes the boundaries of the human computer interface new ways of interaction are emerging. One such technology is the integration of haptic interfaces (force-feedback devices) into virtual environments. This modality offers an improved sense of immersion to that achieved when relying only on audio and visual modalities. The paper introduces some of the technical obstacles such as latency and network traffic that need to be overcome for maintaining a high degree of immersion during haptic tasks. The paper describes the advantages of integrating haptic feedback into systems, and presents some of the technical issues inherent in a networked haptic virtual environment. A generic control interface has been developed to seamlessly mesh with existing networked VR development libraries.

Empirical impact of cache effects for vision system design

Computer vision applications generally split their problem into multiple simpler tasks. Likewise research often combines algorithms into systems for evaluation purposes. Frameworks for modular vision provide interfaces and mechanisms for algorithm combination and network transparency. However, these don’t provide interfaces efficiently utilising the slow memory in modern PCs. We investigate quantitatively how system performance varies with different patterns of memory usage by the framework for an example vision system.

Collaborative grid infrastructure for molecular simulations: The eMinerals minigrid as a prototype integrated computer and data grid

This paper describes a prototype grid infrastructure, called the eMinerals minigrid, for molecular simulation scientists. which is based on an integration of shared compute and data resources. We describe the key components, namely the use of Condor pools, Linux/Unix clusters with PBS and IBM's LoadLeveller job handling tools, the use of Globus for security handling, the use of Condor-G tools for wrapping globus job submit commands, Condor's DAGman tool for handling workflow, the Storage Resource Broker for handling data, and the CCLRC dataportal and associated tools for both archiving data with metadata and making data available to other workers.

Suprathermal electron flux peaks at stream interfaces: Signature of solar wind dynamics or tracer for open magnetic flux transport on the Sun?

The high variability of the intensity of suprathermal electron flux in the solar wind is usually ascribed to the high variability of sources on the Sun. Here we demonstrate that a substantial amount of the variability arises from peaks in stream interaction regions, where fast wind runs into slow wind and creates a pressure ridge at the interface. Superposed epoch analysis centered on stream interfaces in 26 interaction regions previously identified in Wind data reveal a twofold increase in 250 eV flux (integrated over pitch angle). Whether the peaks result from the compression there or are solar signatures of the coronal hole boundary, to which interfaces may map, is an open question. Suggestive of the latter, some cases show a displacement between the electron and magnetic field peaks at the interface. Since solar information is transmitted to 1 AU much more quickly by suprathermal electrons compared to convected plasma signatures, the displacement may imply a shift in the coronal hole boundary through transport of open magnetic flux via interchange reconnection. If so, however, the fact that displacements occur in both directions and that the electron and field peaks in the superposed epoch analysis are nearly coincident indicate that any systematic transport expected from differential solar rotation is overwhelmed by a random pattern, possibly owing to transport across a ragged coronal hole boundary.

CAMCR: Computer-Assisted Mixture model analysis for Capture–Recapture count data

Population size estimation with discrete or nonparametric mixture models is considered, and reliable ways of construction of the nonparametric mixture model estimator are reviewed and set into perspective. Construction of the maximum likelihood estimator of the mixing distribution is done for any number of components up to the global nonparametric maximum likelihood bound using the EM algorithm. In addition, the estimators of Chao and Zelterman are considered with some generalisations of Zelterman’s estimator. All computations are done with CAMCR, a special software developed for population size estimation with mixture models. Several examples and data sets are discussed and the estimators illustrated. Problems using the mixture model-based estimators are highlighted.

Influence of the solvent on the self-assembly of a modified amyloid beta peptide fragment. II. NMR and computer simulation investigation

The conformation of a model peptide AAKLVFF based on a fragment of the amyloid beta peptide A beta 16-20, KLVFF, is investigated in methanol and water via solution NMR experiments and Molecular dynamics computer simulations. In previous work, we have shown that AAKLVFF forms peptide nanotubes in methanol and twisted fibrils in water. Chemical shift measurements were used to investigate the solubility of the peptide as a function of concentration in methanol and water. This enabled the determination of critical aggregation concentrations, The Solubility was lower in water. In dilute solution, diffusion coefficients revealed the presence of intermediate aggregates in concentrated solution, coexisting with NMR-silent larger aggregates, presumed to be beta-sheets. In water, diffusion coefficients did not change appreciably with concentration, indicating the presence mainly of monomers, coexisting with larger aggregates in more concentrated solution. Concentration-dependent chemical shift measurements indicated a folded conformation for the monomers/intermediate aggregates in dilute methanol, with unfolding at higher concentration. In water, an antiparallel arrangement of strands was indicated by certain ROESY peak correlations. The temperature-dependent solubility of AAKLVFF in methanol was well described by a van't Hoff analysis, providing a solubilization enthalpy and entropy. This pointed to the importance of solvophobic interactions in the self-assembly process. Molecular dynamics Simulations constrained by NOE values from NMR suggested disordered reverse turn structures for the monomer, with an antiparallel twisted conformation for dimers. To model the beta-sheet structures formed at higher concentration, possible model arrangements of strands into beta-sheets with parallel and antiparallel configurations and different stacking sequences were used as the basis for MD simulations; two particular arrangements of antiparallel beta-sheets were found to be stable, one being linear and twisted and the other twisted in two directions. These structures Were used to simulate Circular dichroism spectra. The roles of aromatic stacking interactions and charge transfer effects were also examined. Simulated spectra were found to be similar to those observed experimentally.(in water or methanol) which show a maximum at 215 or 218 nm due to pi-pi* interactions, when allowance is made for a 15-18 nm red-shift that may be due to light scattering effects.

Non-stoichiometric oxide and metal interfaces and reactions

We have employed a combination of experimental surface science techniques and density functional calculations to study the reduction of TiO2(110) surfaces through the doping with submonolayer transition metals. We concentrate on the role of Ti adatoms in self doping of rutile and contrast the behaviour to that of Cr. DFT+U calculations enable identification of probable adsorption structures and their spectroscopic characteristics. Adsorption of both metals leads to a broken symmetry and an asymmetric charge transfer localised around the defect site of a mixed localised/delocalised character. Charge transfer creates defect states with Ti 3d character in the band gap at similar to 1-eV binding energy. Cr adsorption, however, leads to a very large shift in the valence-band edge to higher binding energy and the creation of Cr 3d states at 2.8-eV binding energy. Low-temperature oxidation lifts the Ti-derived band-gap states and modifies the intensity of the Cr features, indicative of a change of oxidation state from Cr3+ to Cr4+. Higher temperature processing leads to a loss of Cr from the surface region, indicative of its substitution into the bulk.

Ferric and ferrous iron in nitroso-myoglobin: computer simulations of stable and metastable states and their infrared spectra

The binding of NO to iron is involved in the biological function of many heme proteins. Contrary to ligands like CO and O-2, which only bind to ferrous (Fe-II) iron, NO binds to both ferrous and ferric (Fe-II) iron. In a particular protein, the natural oxidation state can therefore be expected to be tailored to the required function. Herein, we present an ob initio potential-energy surface for ferric iron interacting with NO. This potential-energy surface exhibits three minima corresponding to eta'-NO coordination (the global minimum), eta(1)-ON coordination and eta(2) coordination. This contrasts with the potential-energy surface for Fe-II-NO, which ex- hibits only two minima (the eta(2) coordination mode for Fe-II is a transition state, not a minimum). In addition, the binding energies of NO are substantially larger for Fe-III than for Fe-II. We have performed molecular dynamics simulations for NO bound to ferric myoglobin (Mb(III)) and compare these with results obtained for Mb(II). Over the duration of our simulations (1.5 ns), all three binding modes are found to be stable at 200 K and transiently stable at 300 K, with eventual transformation to the eta(1)-NO global-minimum conformation. We discuss the implication of these results related to studies of rebinding processes in myoglobin.