Interacting with the biomolecular solvent accessible surface via a haptic feedback device

Background: From the 1950s computer based renderings of molecules have been produced to aid researchers in their understanding of biomolecular structure and function. A major consideration for any molecular graphics software is the ability to visualise the three dimensional structure of the molecule. Traditionally, this was accomplished via stereoscopic pairs of images and later realised with three dimensional display technologies. Using a haptic feedback device in combination with molecular graphics has the potential to enhance three dimensional visualisation. Although haptic feedback devices have been used to feel the interaction forces during molecular docking they have not been used explicitly as an aid to visualisation. Results: A haptic rendering application for biomolecular visualisation has been developed that allows the user to gain three-dimensional awareness of the shape of a biomolecule. By using a water molecule as the probe, modelled as an oxygen atom having hard-sphere interactions with the biomolecule, the process of exploration has the further benefit of being able to determine regions on the molecular surface that are accessible to the solvent. This gives insight into how awkward it is for a water molecule to gain access to or escape from channels and cavities, indicating possible entropic bottlenecks. In the case of liver alcohol dehydrogenase bound to the inhibitor SAD, it was found that there is a channel just wide enough for a single water molecule to pass through. Placing the probe coincident with crystallographic water molecules suggests that they are sometimes located within small pockets that provide a sterically stable environment irrespective of hydrogen bonding considerations. Conclusion: By using the software, named HaptiMol ISAS (available from http://​www.​haptimol.​co.​uk), one can explore the accessible surface of biomolecules using a three-dimensional input device to gain insights into the shape and water accessibility of the biomolecular surface that cannot be so easily attained using conventional molecular graphics software

The Influence of Socioindexical Information on the Speech Perception-Production Link: Evidence from a Shadowing Task

The body of work on speech perception demonstrates the ability of listeners to utilize both visual and acoustic information in their processing of a given speech signal. More recent studies have established that listeners are sensitive to cues in both these modalities which inform their perception of a speaker\u27s identity in parallel with the linguistic message, but the relationship between social information in perception and production together is unclear. This study reports the results of an experiment designed to test the hypothesis that expectations about a speakers identity is able to influence a listener\u27s perception and production of speech in tandem. The shadowing task addresses the degree to which listeners faithfully reproduce L2 accented English when presented with four ethnically distinct faces in congruent and incongruent auditory-visual pairs in a within-subject design. Analyses of the degree of acoustic similarity to model talkers in speakers\u27 imitations revealed a slight average trend toward convergence on vowel spectra, vowel duration, and average fundamental frequency. Significant predictors of the degree of change in a speaker\u27s production were shown to be the vowel quality measured and the voice presented, but these predictors were agnostic with respect to whether these changes represented phonetic convergence or divergence. The variance in degree of similarity suggests that speakers\u27 convergence is subject to linguistic selectivity, but it is less clear the role social selectivity plays when presented with unfamiliar varieties. Overall these findings are consistent with exemplar models which consider the inherent coupling of individuals\u27 speech perception and production, but that the visual stimuli had no significant effect on these analyses may be reflective of listeners\u27 adaptive processes during perception of L2-accented speech

Creation of collective many-body states and single photons from two-dimensional Rydberg lattice gases

The creation of collective many-body quantum states from a two-dimensional lattice gas of atoms is studied. Our approach relies on the van-der-Waals interaction that is present between alkali metal atoms when laser excited to high-lying Rydberg s-states. We focus on a regime in which the laser driving is strong compared to the interaction between Rydberg atoms. Here energetically low-lying many-particle states can be calculated approximately from a quadratic Hamiltonian. The potential usefulness of these states as a resource for the creation of deterministic single-photon sources is illustrated. The properties of these photon states are determined from the interplay between the particular geometry of the lattice and the interatomic spacing.Comment: 12 pages, 8 figure

Monitoring and Discovering X-ray Pulsars in the Small Magellanic Cloud

Regular monitoring of the SMC with RXTE has revealed a huge number of X-ray pulsars. Together with discoveries from other satellites at least 45 SMC pulsars are now known. One of these sources, a pulsar with a period of approximately 7.8 seconds, was first detected in early 2002 and since discovery it has been found to be in outburst nine times. The outburst pattern clearly shows a period of 45.1 +/- 0.4 d which is thought to be the orbital period of this system. Candidate outburst periods have also been obtained for nine other pulsars and continued monitoring will enable us to confirm these. This large number of pulsars, all located at approximately the same distance, enables a wealth of comparative studies. In addition, the large number of pulsars found (which vastly exceeds the number expected simply by scaling the relative mass of the SMC and the Galaxy) reveals the recent star formation history of the SMC which has been influenced by encounters with both the LMC and the Galaxy.Comment: 5 pages, 4 figures, AIP conference proceedings format. Contribution to "X-ray Timing 2003: Rossi and Beyond." meeting held in Cambridge, MA, November, 200

Contemporaneous XMM-Newton investigation of a giant X-ray flare and quiescent state from a cool M-class dwarf in the local cavity

We report the serendipitous detection of a giant X-ray flare from the source 2XMM J043527.2-144301 during an XMM-Newton observation of the high latitude molecular cloud MBM20. The source has not been previously studied at any wavelength. The X-ray flux increases by a factor of more than 52 from quiescent state to peak of flare. A 2MASS counterpart has been identified (2MASS J04352724-1443017), and near-infrared colors reveal a spectral type of M8-M8.5 and a distance of (67\pm 13) pc, placing the source in front of MBM20. Spectral analysis and source luminosity are also consistent with this conclusion. The measured distance makes this object the most distant source (by about a factor of 4) at this spectral type detected in X-rays. The X-ray flare was characterized by peak X-ray luminosity of ~8.2E28 erg s-1 and integrated X-ray energy of ~2.3E32 erg. The flare emission has been characterized with a 2-temperature model with temperatures of ~10 and 46 MK (0.82 and 3.97 keV), and is dominated by the higher temperature component.Comment: 19 pages, 5 figures; Accepted for publication on Ap

The binary period and outburst behaviour of the SMC X-ray binary pulsar system SXP504

A probable binary period has been detected in the optical counterpart to the X-ray source CXOU J005455.6-724510 = RX J0054.9-7245 = AXJ0054.8-7244 = SXP504 in the Small Magellanic Cloud. This source was detected by Chandra on 04 Jul 2002 and subsequently observed by XMM-Newton on 18 Dec 2003. The source is coincident with an Optical Gravitational Lensing (OGLE) object in the lightcurves of which several optical outburst peaks are visible at ~ 268 day intervals. Timing analysis shows a period of 268.6 +/- 0.1 days at > 99% significance. Archival Rossi X-ray Timing Explorer (RXTE) data for the 504s pulse-period has revealed detections which correspond closely with predicted or actual peaks in the optical data. The relationship between this orbital period and the pulse period of 504s is within the normal variance found in the Corbet diagram.Comment: Accepted by MNRAS. 1 LATEX page. 4 figure

Towards the production of radiotherapy treatment shells on 3D printers using data derived from DICOM CT and MRI: preclinical feasibility studies

Background: Immobilisation for patients undergoing brain or head and neck radiotherapy is achieved using perspex or thermoplastic devices that require direct moulding to patient anatomy. The mould room visit can be distressing for patients and the shells do not always fit perfectly. In addition the mould room process can be time consuming. With recent developments in three-dimensional (3D) printing technologies comes the potential to generate a treatment shell directly from a computer model of a patient. Typically, a patient requiring radiotherapy treatment will have had a computed tomography (CT) scan and if a computer model of a shell could be obtained directly from the CT data it would reduce patient distress, reduce visits, obtain a close fitting shell and possibly enable the patient to start their radiotherapy treatment more quickly. Purpose: This paper focuses on the first stage of generating the front part of the shell and investigates the dosimetric properties of the materials to show the feasibility of 3D printer materials for the production of a radiotherapy treatment shell. Materials and methods: Computer algorithms are used to segment the surface of the patient’s head from CT and MRI datasets. After segmentation approaches are used to construct a 3D model suitable for printing on a 3D printer. To ensure that 3D printing is feasible the properties of a set of 3D printing materials are tested. Conclusions: The majority of the possible candidate 3D printing materials tested result in very similar attenuation of a therapeutic radiotherapy beam as the Orfit soft-drape masks currently in use in many UK radiotherapy centres. The costs involved in 3D printing are reducing and the applications to medicine are becoming more widely adopted. In this paper we show that 3D printing of bespoke radiotherapy masks is feasible and warrants further investigation

Testing the durability of limestone for Cathedral façade restoration

This research aimed to specify an optimum replacement stone for Truro Cathedral. A variety of petrographically and visually similar material to the original Bath stone was initially selected. The stones were subjected to three different durability tests; Sodium sulphate crystallisation and large scale testing with both accelerated and climatic freeze-thaw cyclic loading. The most suitable stone was determined as the one with the best performance characteristics overall