Symmetry contaminations in reactive scattering through long-lived collision complexes

We extend our Lanczos subspace time-independent wave packet method [J. Chem. Phys. 116 (2002) 2354] to investigate the issue of symmetry contaminations for the challenging deep-well H + O-2 reaction. Our central objective is to address the issue of whether significant symmetry contamination can occur if a wavepacket initially possessing the correct O-O exchange symmetry is propagated over tens of thousands of recursive steps using a basis which does not explicitly enforce the correct symmetry, and if so how seriously this affects the results. We find that symmetry contamination does exist where the symmetry constraint is not explicitly enforced in the basis. While it affects individual resonances and the associated peak amplitudes, the overall shape of the more averaged quantities such as total reaction probabilities and vibrational branching ratios are not seriously affected. (C) 2004 Elsevier B.V. All rights reserved.

Spin boson models for quantum decoherence of electronic excitations of biomolecules and quantum dots in a solvent

We give a theoretical treatment of the interaction of electronic excitations (excitions) in biomolecules and quantum dots with the surrounding polar solvent. Significant quantum decoherence occurs due to the interaction of the electric dipole moment of the solute with the fluctuating electric dipole moments of the individual molecules in the solvent. We introduce spin boson models which could be used to describe the effects. of decoherence on the quantum dynamics of biomolecules which undergo light-induced conformational change and on biomolecules or quantum dots which are coupled by Forster resonant energy transfer.

Post-hatching growth and development of the pectoral and pelvic limbs in the black noddy, Anous minutus

The black tern (Anous minutus) uses a semi-precocial growth strategy. Terrestrial locomotor capacity occurs soon after hatching, but pectoral limb development is delayed and flight is not possible until about post-hatching day 50. A growth series (hatchlings to fledglings) was used to explore how limb musculoskeletal development varied with body mass. In the pelvic limb, bone lengths scaled isometrically or with negative allometry. Gastrocnemius muscle mass and the failure load and stiffness of the tibiotarsus scaled isometrically. In the pectoral limb, pectoralis and supracoracoideus muscle masses increased with strong positive allometry that was mirrored by increases in wing bone strength and stiffness. Bending strength (σult) and modulus (E) remained fairly constant throughout development to fledging for all limb bones. The moment of inertia (I) scaled with negative allometry for the tibiotarsus and with strong positive allometry in the wing bones. Differences in σult and E of the tibiotarsus between pre-fledged chicks and adults was due, primarily, to increases in bone density rather than increases in the moment of inertia of the skeletal elements, whereas σult of wing bones was a function of increases in both bone density and I. Early development of functional pelvic limbs in tree-nesting birds is relatively unusual, and presumably reflects a familial trait that does not appear to compromise breeding success in this species.

Molecular dynamics characterization of n-octyl-beta-D-glucopyranoside micelle structure in aqueous solution

n-Octyl-beta-D-glueopyranoside (OG) is a non-ionic glycolipid, which is used widely in biotechnical and biochemical applications. All-atom molecular dynamics simulations from two different initial coordinates and velocities in explicit solvent have been performed to characterize the structural behaviour of an OG aggregate at equilibrium conditions. Geometric packing properties determined from the simulations and small angle neutron scattering experiment state that OG micelles are more likely to exist in a non-spherical shape, even at the concentration range near to the critical micelle concentration (0.025 M). Despite few large deviations in the principal moment of inertia ratios, the average micelle shape calculated from both simulations is a prolate ellipsoid. The deviations at these time scales are presumably the temporary shape change of a micelle. However, the size of the micelle and the accessible surface areas were constant during the simulations with the micelle surface being rough and partially elongated. Radial distribution functions computed for the hydroxyl oxygen atoms of an OG show sharper peaks at a minimum van der Waals contact distance than the acetal oxygen, ring oxygen, and anomeric carbon atoms. This result indicates that these atoms are pointed outwards at the hydrophilic/hydrophobic interface, form hydrogen bonds with the water molecules, and thus hydrate the micelle surface effectively. (c) 2005 Elsevier Inc. All rights reserved.

Comparison of the Berman Intubating Airway and the Williams Airway Intubator for fibreoptic orotracheal intubation in anaesthetised patients

Sixty patients with no clinical indicators of a difficult airway were selected to undergo a fibreoptic assessment after induction of general anaesthesia using both the Berman Intubating Airway and the Williams Airway Intubator. The bronchoscopic view and ease of railroading a tracheal tube during fibreoptic orotracheal intubation were studied. The bronchoscopic views obtained by the Berman Airway and the Williams Airway were significantly different (p < 0.008, test of symmetry). The estimated odds ratio of obtaining an obstructed path was 3.06 times higher for the Berman than the Williams Airway. However, if the glottis could be reached with the bronchoscope, there was no significant difference in the degree of ease of intubation between the two airways.

Determination of the orientational distribution and orientation factor for transfer between membrane-bound fluorophores using a confocal microscope

Orientational fluorophores have been a useful tool in physical chemistry, biochemistry, and more recently structural biology due to the polarized nature of the light they emit and that fact that energy can be transferred between them. We present a practical scheme in which measurements of the intensity of emitted fluorescence can be used to determine limits on the mean and distribution of orientation of the absorption transition moment of membrane-bound. uorophores. We demonstrate how information about the orientation of. uorophores can be used to calculate the orientation factor k(2) required for use in FRET spectroscopy. We illustrate the method using images of AlexaFluor probes bound to MscL mechanosensitive transmembrane channel proteins in spherical liposomes.

Optical trapping of a cube

The successful development and optimisation of optically-driven micromachines will be greatly enhanced by the ability to computationally model the optical forces and torques applied to such devices. In principle, this can be done by calculating the light-scattering properties of such devices. However, while fast methods exist for scattering calculations for spheres and axisymmetric particles, optically-driven micromachines will almost always be more geometrically complex. Fortunately, such micromachines will typically possess a high degree of symmetry, typically discrete rotational symmetry. Many current designs for optically-driven micromachines are also mirror-symmetric about a plane. We show how such symmetries can be used to reduce the computational time required by orders of magnitude. Similar improvements are also possible for other highly-symmetric objects such as crystals. We demonstrate the efficacy of such methods by modelling the optical trapping of a cube, and show that even simple shapes can function as optically-driven micromachines.

Time-Frequency Distribution Moments of Heart Rate Variability for Neonatal Seizure Detection

In this paper, we propose features extracted from the heart rate variability (HRV) based on the first and second conditional moments of time-frequency distribution (TFD) as an additional guide for seizure detection in newborn. The features of HRV in the low frequency band (LF: 0-0.07 Hz), mid frequency band (MF: 0.07-0.15 Hz), and high frequency band (HF: 0.15-0.6 Hz) have been obtained by means of the time-frequency analysis using the modified-B distribution (MBD). Results of ongoing time-frequency research are presented. Based on our preliminary results, the first conditional moment of HRV which is also known as the mean/central frequency in the LF band and the second conditional moment of HRV which is also known as the variance/instantaneous bandwidth (IB) in the HF band can be used as a good feature to discriminate the newborn seizure from the non-seizure

Finite-size effects in on-line learning of multilayer neural networks

We complement recent advances in thermodynamic limit analyses of mean on-line gradient descent learning dynamics in multi-layer networks by calculating fluctuations possessed by finite dimensional systems. Fluctuations from the mean dynamics are largest at the onset of specialisation as student hidden unit weight vectors begin to imitate specific teacher vectors, increasing with the degree of symmetry of the initial conditions. In light of this, we include a term to stimulate asymmetry in the learning process, which typically also leads to a significant decrease in training time.

Failure of steel gusset plates

This thesis examines the parameters associated with the failure of triangular steel gusset plates. Eighty two results are presented investigating the position of the applied load, the gusset plate height to length ratio, size, thickness, internal angle and the removal of the inside corner. The thickness of the loaded plate and its influence on the gusset plates failure is also investigated. Twenty two similar gusset plates were tested to investigate the welds connecting the gusset plate to the adjacent loaded and support edges. The experimental results are compared with existing methods, none of which cover all the variables tested. Some methods do not consider buckling and most of those that do are inadequate. Most of the methods do not accurately take account of the load position. An alternative method based on experimental observations is presented for design purposes. The method covers any combination of the variables tested. To test assumptions made in the theoretical work forty seven strut tests took place to investigate buckling characteristics and fifteen special gusset plates were also tested. The gusset plates were found to fail in an elastic-plastic buckling manner. A gusset plate has a specific moment of resistance capacity about it’s inside corner and the ultimate load that can be applied is dependent upon the position of the load relative to the supported edge. There is an optimum height to length ratio for strength and any increase in the internal angle from 90 degrees produces little change in moment capacity. The removal of small portions of the inside corner of a gusset plate has little effect upon its moment capacity. The loaded plate does not provide any significant moment of resistance to the applied load at failure. The main functions of the loaded and supported edge welds is to prevent the gusset plate from slipping from between the plates.

Design of sway frames

The aim of the work presented in this thesis is to produce a direct method to design structures subject to deflection constraints at the working loads. The work carried out can be divided into four main parts. In the first part, a direct design procedure for plane steel frames subjected to sway limitations is proposed. The stiffness equations are modified so that the sway in each storey is equal to some specified values. The modified equations are then solved by iteration to calculate the cross-sectional properties of the columns as well as the other joint displacements. The beam sections are selected initially and then altered in an effort to reduce the total material cost of the frame. A linear extrapolation technique is used to reduce this cost. In this design, stability functions are used so that the effect of axial loads in the members are taken into consideration. The final reduced cost design is checked for strength requirements and the members are altered accordingly. In the second part, the design method is applied to the design of reinforced concrete frames in which the sway in the columns play an active part in the design criteria. The second moment of area of each column is obtained by solving the modified stiffness equations and then used to calculate the mlnlmum column depth required. Again the frame has to be checked for all the ultimate limit state load cases. In the third part, the method is generalised to design pin-jointed space frames for deflection limitatlions. In these the member areas are calculated so that the deflection at a specified joint is equal to its specified value. In the final part, the Lagrange multiplier technique is employed to obtain an optimum design for plane rigidly jointed steel frames. The iteration technique is used here to solve the modified stiffness equations as well as derivative equations obtained in accordance to the requirements of the optimisation method.

OCT retinal thickness ratios and frequency of follow-up in Wet AMD

Poster Introduction: In neovascular age-related macular degeneration (nAMD), optical coherence tomography (OCT) is an important tool to determine when intravitreal injections of ranibizumab should be administered. Current guidelines recommend that patients should be reviewed four weekly and OCT indications for further treatment include subretinal fluid and intraretinal fluid or cysts. Purpose: We have reviewed the OCT scans of subjects who have successfully responded to ranibizumab to look for factors that might predict which patients will not require injection and could have extended appointments. Method: This was a prospective study in which we observed for 6 consecutive months the OCT images of 28 subjects who had received intravitreal ranibizumab for nAMD and were judged to be clinically inactive at recruitment to the study. Ratios between full retinal thickness (FRT = neurosensory retina + outer reflective band) and outer reflective band (ORB) thickness at the fovea were calculated for each subject at the moment of entering the study and at each successive visit for 6 consecutive months. Results: Patients with lower FRT/ORB ratios were found to be less likely to require an additional injection of ranibizumab and no subject with a ratio of 1.75 or less needed further injections. Conclusion: This small pilot study suggests that on macular OCT, the FRT/ORB ratio, and in particular values of 1.75 or less, may prove to be a useful, practical tool when deciding the follow up period for subjects undergoing treatment with intravitreal ranibizumab for nAMD.

Effects of syllable structure in aphasic errors:implications for a new model of speech production

Current models of word production assume that words are stored as linear sequences of phonemes which are structured into syllables only at the moment of production. This is because syllable structure is always recoverable from the sequence of phonemes. In contrast, we present theoretical and empirical evidence that syllable structure is lexically represented. Storing syllable structure would have the advantage of making representations more stable and resistant to damage. On the other hand, re-syllabifications affect only a minimal part of phonological representations and occur only in some languages and depending on speech register. Evidence for these claims comes from analyses of aphasic errors which not only respect phonotactic constraints, but also avoid transformations which move the syllabic structure of the word further away from the original structure, even when equating for segmental complexity. This is true across tasks, types of errors, and, crucially, types of patients. The same syllabic effects are shown by apraxic patients and by phonological patients who have more central difficulties in retrieving phonological representations. If syllable structure was only computed after phoneme retrieval, it would have no way to influence the errors of phonological patients. Our results have implications for psycholinguistic and computational models of language as well as for clinical and educational practices.

Dynamic complexity of chaotic transitions in high-dimensional classical dynamics:Leu-Enkephalin folding

Leu-Enkephalin in explicit water is simulated using classical molecular dynamics. A ß-turn transition is investigated by calculating the topological complexity (in the "computational mechanics" framework [J. P. Crutchfield and K. Young, Phys. Rev. Lett., 63, 105 (1989)]) of the dynamics of both the peptide and the neighbouring water molecules. The complexity of the atomic trajectories of the (relatively short) simulations used in this study reflect the degree of phase space mixing in the system. It is demonstrated that the dynamic complexity of the hydrogen atoms of the peptide and almost all of the hydrogens of the neighbouring waters exhibit a minimum precisely at the moment of the ß-turn transition. This indicates the appearance of simplified periodic patterns in the atomic motion, which could correspond to high-dimensional tori in the phase space. It is hypothesized that this behaviour is the manifestation of the effect described in the approach to molecular transitions by Komatsuzaki and Berry [T. Komatsuzaki and R.S. Berry, Adv. Chem. Phys., 123, 79 (2002)], where a "quasi-regular" dynamics at the transition is suggested. Therefore, for the first time, the less chaotic character of the folding transition in a realistic molecular system is demonstrated. © Springer-Verlag Berlin Heidelberg 2006.

Measuring complexity through average symmetry

This work introduces a complexity measure which addresses some conflicting issues between existing ones by using a new principle - measuring the average amount of symmetry broken by an object. It attributes low (although different) complexity to either deterministic or random homogeneous densities and higher complexity to the intermediate cases. This new measure is easily computable, breaks the coarse graining paradigm and can be straightforwardly generalized, including to continuous cases and general networks. By applying this measure to a series of objects, it is shown that it can be consistently used for both small scale structures with exact symmetry breaking and large scale patterns, for which, differently from similar measures, it consistently discriminates between repetitive patterns, random configurations and self-similar structures