The determination of molecular properties from MULTIMODE with an application to the calculation of Franck-Condon factors for photoionization of CF3 to CF3+

Extensions to the code MULTIMODE to obtain rovibrational wave functions and properties are described. An application of these new capabilities is made to a calculation of the Franck-Condon factors for photoionization of CF3 to CF3+. These calculations make use of a new, full-dimensional ab initio potential energy surface, which is also described here.

Characterization of wheat puroindoline proteins

Puroindoline proteins were purified from selected UK-grown hexaploid wheats. Their identities were confirmed on the basis of capillary electrophoresis mobilities, relative molecular mass and N-terminal amino acid sequencing. Only one form of puroindoline-a protein was found in those varieties, regardless of endosperm texture. Three allelic forms of puroindoline-b protein were identified. Nucleotide sequencing of cDNA produced by RT-PCR of isolated mRNA indicated that these were the 'wild-type', found in soft wheats, puroindoline-b containing a Gly -> Ser amino acid substitution (position 46) and puroindoline-b containing a Trp -> Arg substitution (position 44). The latter two were found in hard wheats. Microheterogeneity, due to short extensions and/or truncations at the N-terminus and C-terminus, was detected for both puroindoline-a and puroindoline-b. The type of microheterogeneity observed was more consistent for puroindoline-a than for puroindoline-b, and may arise through slightly different post-translational processing pathways. A puroindoline-b allele corresponding to a Leu -> Pro substitution (position 60) was identified from the cDNA sequence of the hard variety Chablis, but no mature puroindoline-b protein was found in this or two other European varieties known to possess this puroindoline-b allele. Wheats possessing the puroindoline-b proteins with point mutations appeared to contain lower amounts of puroindoline protein. Such wheats have a hard endosperm texture, as do wheats from which puroindoline-a or puroindoline-b are absent. Our results suggest that point mutations in puroindoline-b genes may confer hard endosperm texture through accumulation of allelic forms of puroindoline-b proteins with altered functional properties and/or through lower amounts of puroindoline proteins.

A cost-effective high-throughput digital system for observation and acquisition of animal behavioral data

We have designed and implemented a low-cost digital system using closed-circuit television cameras coupled to a digital acquisition system for the recording of in vivo behavioral data in rodents and for allowing observation and recording of more than 10 animals simultaneously at a reduced cost, as compared with commercially available solutions. This system has been validated using two experimental rodent models: one involving chemically induced seizures and one assessing appetite and feeding. We present observational results showing comparable or improved levels of accuracy and observer consistency between this new system and traditional methods in these experimental models, discuss advantages of the presented system over conventional analog systems and commercially available digital systems, and propose possible extensions to the system and applications to non-rodent studies.

Extending the friction cone algorithm for arbitrary polygon based haptic objects

Most haptic environments are based on single point interactions whereas in practice, object manipulation requires multiple contact points between the object, fingers, thumb and palm. The Friction Cone Algorithm was developed specifically to work well in a multi-finger haptic environment where object manipulation would occur. However, the Friction Cone Algorithm has two shortcomings when applied to polygon meshes: there is no means of transitioning polygon boundaries or feeling non-convex edges. In order to overcome these deficiencies, Face Directed Connection Graphs have been developed as well as a robust method for applying friction to non-convex edges. Both these extensions are described herein, as well as the implementation issues associated with them.

Force shading and bump mapping using the friction cone algorithm

Previous work has presented the friction cone algorithm, a generalised method to resolve forces on a simulated haptic object when two or more fingers are in contact. Two extensions to the friction cone algorithm are presented: force shading and bump mapping. Force shading removes the discontinuities that are present when transitioning from one face to the next, whilst bump mapping provides a mechanism for rendering haptic textures on polygonal surfaces. Both these extensions can be combined whilst still maintaining the friction cone algorithm's intrinsic ability to simulate arbitrarily complex friction models.

Perspex machine IX: transreal analysis

We introduce transreal analysis as a generalisation of real analysis. We find that the generalisation of the real exponential and logarithmic functions is well defined for all transreal numbers. Hence, we derive well defined values of all transreal powers of all non-negative transreal numbers. In particular, we find a well defined value for zero to the power of zero. We also note that the computation of products via the transreal logarithm is identical to the transreal product, as expected. We then generalise all of the common, real, trigonometric functions to transreal functions and show that transreal (sin x)/x is well defined everywhere. This raises the possibility that transreal analysis is total, in other words, that every function and every limit is everywhere well defined. If so, transreal analysis should be an adequate mathematical basis for analysing the perspex machine - a theoretical, super-Turing machine that operates on a total geometry. We go on to dispel all of the standard counter "proofs" that purport to show that division by zero is impossible. This is done simply by carrying the proof through in transreal arithmetic or transreal analysis. We find that either the supposed counter proof has no content or else that it supports the contention that division by zero is possible. The supposed counter proofs rely on extending the standard systems in arbitrary and inconsistent ways and then showing, tautologously, that the chosen extensions are not consistent. This shows only that the chosen extensions are inconsistent and does not bear on the question of whether division by zero is logically possible. By contrast, transreal arithmetic is total and consistent so it defeats any possible "straw man" argument. Finally, we show how to arrange that a function has finite or else unmeasurable (nullity) values, but no infinite values. This arithmetical arrangement might prove useful in mathematical physics because it outlaws naked singularities in all equations.

A Packet/Frame sync detector based on statistical mode with application to wireless-USB

Wireless Personal Area Networks (WPANs) are offering high data rates suitable for interconnecting high bandwidth personal consumer devices (Wireless HD streaming, Wireless-USB and Bluetooth EDR). ECMA-368 is the Physical (PHY) and Media Access Control (MAC) backbone of many of these wireless devices. WPAN devices tend to operate in an ad-hoc based network and therefore it is important to successfully latch onto the network and become part of one of the available piconets. This paper presents a new algorithm for detecting the Packet/Fame Sync (PFS) signal in ECMA-368 to identify piconets and aid symbol timing. The algorithm is based on correlating the received PFS symbols with the expected locally stored symbols over the 24 or 12 PFS symbols, but selecting the likely TFC based on the highest statistical mode from the 24 or 12 best correlation results. The results are very favorable showing an improvement margin in the order of 11.5dB in reference sensitivity tests between the required performance using this algorithm and the performance of comparable systems.

Wiener-System subspace identification for mobile wireless mm-wave networks

We discuss the feasibility of wireless terahertz communications links deployed in a metropolitan area and model the large-scale fading of such channels. The model takes into account reception through direct line of sight, ground and wall reflection, as well as diffraction around a corner. The movement of the receiver is modeled by an autonomous dynamic linear system in state space, whereas the geometric relations involved in the attenuation and multipath propagation of the electric field are described by a static nonlinear mapping. A subspace algorithm in conjunction with polynomial regression is used to identify a single-output Wiener model from time-domain measurements of the field intensity when the receiver motion is simulated using a constant angular speed and an exponentially decaying radius. The identification procedure is validated by using the model to perform q-step ahead predictions. The sensitivity of the algorithm to small-scale fading, detector noise, and atmospheric changes are discussed. The performance of the algorithm is tested in the diffraction zone assuming a range of emitter frequencies (2, 38, 60, 100, 140, and 400 GHz). Extensions of the simulation results to situations where a more complicated trajectory describes the motion of the receiver are also implemented, providing information on the performance of the algorithm under a worst case scenario. Finally, a sensitivity analysis to model parameters for the identified Wiener system is proposed.

Uniformization of affine dependence programs for parallel embedded system design

This paper is concerned with the uniformization of a system of afine recurrence equations. This transformation is used in the design (or compilation) of highly parallel embedded systems (VLSI systolic arrays, signal processing filters, etc.). In this paper, we present and implement an automatic system to achieve uniformization of systems of afine recurrence equations. We unify the results from many earlier papers, develop some theoretical extensions, and then propose effective uniformization algorithms. Our results can be used in any high level synthesis tool based on polyhedral representation of nested loop computations.

Uniformization tool for systolic array designs

The paper is concerned with the uniformization of a system of affine recurrence equations. This transformation is used in the design (or compilation) of highly parallel embedded systems (VLSI systolic arrays, signal processing filters, etc.). We present and implement an automatic system to achieve uniformization of systems of affine recurrence equations. We unify the results from many earlier papers, develop some theoretical extensions, and then propose effective uniformization algorithms. Our results can be used in any high level synthesis tool based on polyhedral representation of nested loop computations.

A climate change risk analysis for world ecosystems

We quantify the risks of climate-induced changes in key ecosystem processes during the 21st century by forcing a dynamic global vegetation model with multiple scenarios from 16 climate models and mapping the proportions of model runs showing forest/nonforest shifts or exceedance of natural variability in wildfire frequency and freshwater supply. Our analysis does not assign probabilities to scenarios or weights to models. Instead, we consider distribution of outcomes within three sets of model runs grouped by the amount of global warming they simulate: <2°C (including simulations in which atmospheric composition is held constant, i.e., in which the only climate change is due to greenhouse gases already emitted), 2–3°C, and >3°C. High risk of forest loss is shown for Eurasia, eastern China, Canada, Central America, and Amazonia, with forest extensions into the Arctic and semiarid savannas; more frequent wildfire in Amazonia, the far north, and many semiarid regions; more runoff north of 50°N and in tropical Africa and northwestern South America; and less runoff in West Africa, Central America, southern Europe, and the eastern U.S. Substantially larger areas are affected for global warming >3°C than for <2°C; some features appear only at higher warming levels. A land carbon sink of ≈1 Pg of C per yr is simulated for the late 20th century, but for >3°C this sink converts to a carbon source during the 21st century (implying a positive climate feedback) in 44% of cases. The risks continue increasing over the following 200 years, even with atmospheric composition held constant.

Adaptive modelling, estimation and fusion from data: a neurofuzzy approach

In a world of almost permanent and rapidly increasing electronic data availability, techniques of filtering, compressing, and interpreting this data to transform it into valuable and easily comprehensible information is of utmost importance. One key topic in this area is the capability to deduce future system behavior from a given data input. This book brings together for the first time the complete theory of data-based neurofuzzy modelling and the linguistic attributes of fuzzy logic in a single cohesive mathematical framework. After introducing the basic theory of data-based modelling, new concepts including extended additive and multiplicative submodels are developed and their extensions to state estimation and data fusion are derived. All these algorithms are illustrated with benchmark and real-life examples to demonstrate their efficiency. Chris Harris and his group have carried out pioneering work which has tied together the fields of neural networks and linguistic rule-based algortihms. This book is aimed at researchers and scientists in time series modeling, empirical data modeling, knowledge discovery, data mining, and data fusion.

Resource allocation analysis of the stochastic diffusion search

The Stochastic Diffusion Search (SDS) was developed as a solution to the best-fit search problem. Thus, as a special case it is capable of solving the transform invariant pattern recognition problem. SDS is efficient and, although inherently probabilistic, produces very reliable solutions in widely ranging search conditions. However, to date a systematic formal investigation of its properties has not been carried out. This thesis addresses this problem. The thesis reports results pertaining to the global convergence of SDS as well as characterising its time complexity. However, the main emphasis of the work, reports on the resource allocation aspect of the Stochastic Diffusion Search operations. The thesis introduces a novel model of the algorithm, generalising an Ehrenfest Urn Model from statistical physics. This approach makes it possible to obtain a thorough characterisation of the response of the algorithm in terms of the parameters describing the search conditions in case of a unique best-fit pattern in the search space. This model is further generalised in order to account for different search conditions: two solutions in the search space and search for a unique solution in a noisy search space. Also an approximate solution in the case of two alternative solutions is proposed and compared with predictions of the extended Ehrenfest Urn model. The analysis performed enabled a quantitative characterisation of the Stochastic Diffusion Search in terms of exploration and exploitation of the search space. It appeared that SDS is biased towards the latter mode of operation. This novel perspective on the Stochastic Diffusion Search lead to an investigation of extensions of the standard SDS, which would strike a different balance between these two modes of search space processing. Thus, two novel algorithms were derived from the standard Stochastic Diffusion Search, ‘context-free’ and ‘context-sensitive’ SDS, and their properties were analysed with respect to resource allocation. It appeared that they shared some of the desired features of their predecessor but also possessed some properties not present in the classic SDS. The theory developed in the thesis was illustrated throughout with carefully chosen simulations of a best-fit search for a string pattern, a simple but representative domain, enabling careful control of search conditions.

Head-controlled assistive telerobot with extended physiological proprioception capability

People with disabilities such as quadriplegia can use mouth-sticks and head-sticks as extension devices to perform desired manipulations. These extensions provide extended proprioception which allows users to directly feel forces and other perceptual cues such as texture present at the tip of the mouth-stick. Such devices are effective for two principle reasons: because of their close contact with the user's tactile and proprioceptive sensing abilities; and because they tend to be lightweight and very stiff, and can thus convey tactile and kinesthetic information with high-bandwidth. Unfortunately, traditional mouth-sticks and head-sticks are limited in workspace and in the mechanical power that can be transferred because of user mobility and strength limitations. We describe an alternative implementation of the head-stick device using the idea of a virtual head-stick: a head-controlled bilateral force-reflecting telerobot. In this system the end-effector of the slave robot moves as if it were at the tip of an imaginary extension of the user's head. The design goal is for the system is to have the same intuitive operation and extended proprioception as a regular mouth-stick effector but with augmentation of workspace volume and mechanical power. The input is through a specially modified six DOF master robot (a PerForceTM hand-controller) whose joints can be back-driven to apply forces at the user's head. The manipulation tasks in the environment are performed by a six degree-of-freedom slave robot (the Zebra-ZEROTM) with a built-in force sensor. We describe the prototype hardware/software implementation of the system, control system design, safety/disability issues, and initial evaluation tasks.

Velocity-based moving mesh methods for nonlinear partial differential equations

This article describes a number of velocity-based moving mesh numerical methods formultidimensional nonlinear time-dependent partial differential equations (PDEs). It consists of a short historical review followed by a detailed description of a recently developed multidimensional moving mesh finite element method based on conservation. Finite element algorithms are derived for both mass-conserving and non mass-conserving problems, and results shown for a number of multidimensional nonlinear test problems, including the second order porous medium equation and the fourth order thin film equation as well as a two-phase problem. Further applications and extensions are referenced.