Immersive Projection for biochemical pattern matching

In all biological processes, protein molecules and other small molecules interact to function and form transient macromolecular complexes. This interaction of two or more molecules can be described by a docking event. Docking is an important phase for structure-based drug design strategies, as it can be used as a method to simulate protein-ligand interactions. Various docking programs exist that allow automated docking, but most of them have limited visualization and user interaction. It would be advantageous if scientists could visualize the molecules participating in the docking process, manipulate their structures and manually dock them before submitting the new conformations to an automated docking process in an immersive environment, which can help stimulate the design/docking process. This also could greatly reduce docking time and resources. To achieve this, we propose a new virtual modelling/docking program, whereby the advantages of virtual modelling programs and the efficiency of the algorithms in existing docking programs will be merged.

Cue combination for 3D location judgements

Cue combination rules have often been applied to the perception of surface shape but not to judgements of object location. Here, we used immersive virtual reality to explore the relationship between different cues to distance. Participants viewed a virtual scene and judged the change in distance of an object presented in two intervals, where the scene changed in size between intervals (by a factor of between 0.25 and 4). We measured thresholds for detecting a change in object distance when there were only 'physical' (stereo and motion parallax) or 'texture-based' cues (independent of the scale of the scene) and used these to predict biases in a distance matching task. Under a range of conditions, in which the viewing distance and position of the tarte relative to other objects was varied, the ration of 'physical' to 'texture-based' thresholds was a good predictor of biases in the distance matching task. The cue combination approach, which successfully accounts for our data, relies on quite different principles from those underlying geometric reconstruction.

Optimal inverter design for an induction machine using resonant frequency matching

The frequency responses of two 50 Hz and one 400 Hz induction machines have been measured experimentally over a frequency range of 1 kHz to 400 kHz. This study has shown that the stator impedances of the machines behave in a similar manner to a parallel resonant circuit, and hence have a resonant point at which the Input impedance of the machine is at a maximum. This maximum impedance point was found experimentally to be as low as 33 kHz, which is well within the switching frequency ranges of modern inverter drives. This paper investigates the possibility of exploiting the maximum impedance point of the machine, by taking it into consideration when designing an inverter, in order to minimize ripple currents due to the switching frequency. Minimization of the ripple currents would reduce torque pulsation and losses, increasing overall performance. A modified machine model was developed to take into account the resonant point, and this model was then simulated with an inverter to demonstrate the possible advantages of matching the inverter switching frequency to the resonant point. Finally, in order to experimentally verify the simulated results, a real inverter with a variable switching frequency was used to drive an induction machine. Experimental results are presented.

The radial width of a coronal mass ejection between 0.1 and 0.4 AU estimated from the heliospheric imager on STEREO

On 15-17 February 2008, a CME with an approximately circular cross section was tracked through successive images obtained by the Heliospheric Imager (HI) instrument onboard the STEREO-A spacecraft. Reasoning that an idealised flux rope is cylindrical in shape with a circular cross-section, best fit circles are used to determine the radial width of the CME. As part of the process the radial velocity and longitude of propagation are determined by fits to elongation-time maps as 252±5 km/s and 70±5° respectively. With the longitude known, the radial size is calculated from the images, taking projection effects into account. The radial width of the CME, S (AU), obeys a power law with heliocentric distance, R, as the CME travels between 0.1 and 0.4 AU, such that S=0.26 R0.6±0.1. The exponent value obtained is compared to published studies based on statistical surveys of in situ spacecraft observations of ICMEs between 0.3 and 1.0 AU, and general agreement is found. This paper demonstrates the new opportunities provided by HI to track the radial width of CMEs through the previously unobservable zone between the LASCO field of view and Helios in situ measurements.

A solar storm observed from the Sun to Venus using the STEREO, Venus Express, and MESSENGER spacecraft

The suite of SECCHI optical imaging instruments on the STEREO-A spacecraft is used to track a solar storm, consisting of several coronal mass ejections (CMEs) and other coronal loops, as it propagates from the Sun into the heliosphere during May 2007. The 3-D propagation path of the largest interplanetary CME (ICME) is determined from the observations made by the SECCHI Heliospheric Imager (HI) on STEREO-A (HI-1/2A). Two parts of the CME are tracked through the SECCHI images, a bright loop and a V-shaped feature located at the rear of the event. We show that these two structures could be the result of line-of-sight integration of the light scattered by electrons located on a single flux rope. In addition to being imaged by HI, the CME is observed simultaneously by the plasma and magnetic field experiments on the Venus Express and MESSENGER spacecraft. The imaged loop and V-shaped structure bound, as expected, the flux rope observed in situ. The SECCHI images reveal that the leading loop-like structure propagated faster than the V-shaped structure, and a decrease in in situ CME speed occurred during the passage of the flux rope.We interpret this as the result of the continuous radial expansion of the flux rope as it progressed outward through the interplanetary medium. An expansion speed in the radial direction of ~30 km s-1 is obtained directly from the SECCHI-HI images and is in agreement with the difference in speed of the two structures observed in situ. This paper shows that the flux rope location can be determined from white light images, which could have important space weather applications.

First imaging of corotating interaction regions using the STEREO spacecraft

Plasma parcels are observed propagating from the Sun out to the large coronal heights monitored by the Heliospheric Imagers (HI) instruments onboard the NASA STEREO spacecraft during September 2007. The source region of these out-flowing parcels is found to corotate with the Sun and to be rooted near the western boundary of an equatorial coronal hole. These plasma enhancements evolve during their propagation through the HI cameras’ fields of view and only becoming fully developed in the outer camera field of view. We provide evidence that HI is observing the formation of a Corotating Interaction Region(CIR) where fast solar wind from the equatorial coronal hole is interacting with the slow solar wind of the streamer belt located on the western edge of that coronal hole. A dense plasma parcel is also observed near the footpoint of the observed CIR at a distance less than 0.1AU from the Sun where fast wind would have not had time to catch up slow wind. We suggest that this low-lying plasma enhancement is a plasma parcel which has been disconnected from a helmet streamer and subsequently becomes embedded inside the corotating interaction region.

Stereo and motion parallax cues in human 3D vision: can they vanish without a trace?

In an immersive virtual reality environment, subjects fail to notice when a scene expands or contracts around them, despite correct and consistent information from binocular stereopsis and motion parallax, resulting in gross failures of size constancy (A. Glennerster, L. Tcheang, S. J. Gilson, A. W. Fitzgibbon, & A. J. Parker, 2006). We determined whether the integration of stereopsis/motion parallax cues with texture-based cues could be modified through feedback. Subjects compared the size of two objects, each visible when the room was of a different size. As the subject walked, the room expanded or contracted, although subjects failed to notice any change. Subjects were given feedback about the accuracy of their size judgments, where the “correct” size setting was defined either by texture-based cues or (in a separate experiment) by stereo/motion parallax cues. Because of feedback, observers were able to adjust responses such that fewer errors were made. For texture-based feedback, the pattern of responses was consistent with observers weighting texture cues more heavily. However, for stereo/motion parallax feedback, performance in many conditions became worse such that, paradoxically, biases moved away from the point reinforced by the feedback. This can be explained by assuming that subjects remap the relationship between stereo/motion parallax cues and perceived size or that they develop strategies to change their criterion for a size match on different trials. In either case, subjects appear not to have direct access to stereo/motion parallax cues.

Humans ignore motion and stereo cues in favor of a fictional stable world

As we move through the world, our eyes acquire a sequence of images. The information from this sequence is sufficient to determine the structure of a three-dimensional scene, up to a scale factor determined by the distance that the eyes have moved [1, 2]. Previous evidence shows that the human visual system accounts for the distance the observer has walked [3,4] and the separation of the eyes [5-8] when judging the scale, shape, and distance of objects. However, in an immersive virtual-reality environment, observers failed to notice when a scene expanded or contracted, despite having consistent information about scale from both distance walked and binocular vision. This failure led to large errors in judging the size of objects. The pattern of errors cannot be explained by assuming a visual reconstruction of the scene with an incorrect estimate of interocular separation or distance walked. Instead, it is consistent with a Bayesian model of cue integration in which the efficacy of motion and disparity cues is greater at near viewing distances. Our results imply that observers are more willing to adjust their estimate of interocular separation or distance walked than to accept that the scene has changed in size.

Cross validation and segment support for stereo belief propagation

Typically, algorithms for generating stereo disparity maps have been developed to minimise the energy equation of a single image. This paper proposes a method for implementing cross validation in a belief propagation optimisation. When tested using the Middlebury online stereo evaluation, the cross validation improves upon the results of standard belief propagation. Furthermore, it has been shown that regions of homogeneous colour within the images can be used for enforcing the so-called "Segment Constraint". Developing from this, Segment Support is introduced to boost belief between pixels of the same image region and improve propagation into textureless regions.

Efficient FPGA-based regular expression pattern matching

An approach to the automatic generation of efficient Field Programmable Gate Arrays (FPGAs) circuits for the Regular Expression-based (RegEx) Pattern Matching problems is presented. Using a novel design strategy, as proposed, circuits that are highly area-and-time-efficient can be automatically generated for arbitrary sets of regular expressions. This makes the technique suitable for applications that must handle very large sets of patterns at high speed, such as in the network security and intrusion detection application domains. We have combined several existing techniques to optimise our solution for such domains and proposed the way the whole process of dynamic generation of FPGAs for RegEX pattern matching could be automated efficiently.