Molecular modelling in structural biology

Molecular modelling is a powerful methodology for analysing the three dimensional structure of biological macromolecules. There are many ways in which molecular modelling methods have been used to address problems in structural biology. It is not widely appreciated that modelling methods are often an integral component of structure determination by NMR spectroscopy and X-ray crystallography. In this review we consider some of the numerous ways in which modelling can be used to interpret and rationalise experimental data and in constructing hypotheses that can be tested by experiment. Genome sequencing projects are producing a vast wealth of data describing the protein coding regions of the genome under study. However, only a minority of the protein sequences thus identified will have a clear sequence homology to a known protein. In such cases valuable three-dimensional models of the protein coding sequence can be constructed by homology modelling methods. Threading methods, which used specialised schemes to relate protein sequences to a library of known structures, have been shown to be able to identify the likely protein fold even in cases where there is no clear sequence homology. The number of protein sequences that cannot be assigned to a structural class by homology or threading methods, simply because they belong to a previously unidentified protein folding class, will decrease in the future as collaborative efforts in systematic structure determination begin to develop. For this reason, modelling methods are likely to become increasingly useful in the near future. The role of the blind prediction contests, such as the Critical Assessment of techniques for protein Structure Prediction (CASP), will be briefly discussed. Methods for modelling protein-ligand and protein-protein complexes are also described and examples of their applications given.     

Modelling photonic crystal fibers with localized functions

In this paper we present an overview of of the standard methods used when modelling photonic crystal fibers with Hermite-Gaussian functions, as well as a new variant of this modelling scheme, based solely on Hermite-Gaussian expansion series, which introduces the possibility of directly modelling fibers with finite claddings. We investigate the challenges and advantages of such a model and compare it to a proven modelling tool, namely the plane wave method.     

A hybrid EDC/Flamelet approach for modelling biomass combustion of grate-firing furnace

This paper proposes a new combustion model for the simulation of biomass combustion. It is developed based on the framework of the well-known Eddy Dissipation Concept (EDC) approach, which has the ability to incorporate chemical kinetics in turbulent reacting flows and thus makes it suitable for modelling gas-phase combustion. However, its high computational cost when using detailed chemistry has made it impractical for modelling large/industrial setups. To address this handicap, the proposed approach decouples the real-time calculation of chemical and mixing processes by importing a pre-calculated steady laminar flamelet library into EDC. The development of this new model is performed based on a modified version of EDC (called Extended EDC), which is capable of modelling the gas-phase of biomass combustion over a wide range of turbulent flow conditions. The proposed model is validated by simulating the well-documented experiment of the piloted jet flames of Barlow and Frank. The performance of the model is then evaluated by simulating a small-scale grate firing biomass furnace. The results show that, overall, the proposed model can be used to model biomass combustion at substantially low computational cost.     

Quantum-Like Tunnelling and Levels of Arbitrage

We apply methods of wave mechanics to financial modelling. We proceed by assigning a financial interpretation to wave numbers. This paper makes a plea for the use of the concept of ‘tunnelling’ (in the mathematical formalism of quantum mechanics) in the modelling of financial arbitrage. Financial arbitrage is a delicate concept to model in social science (i.e. in this case economics and finance) as its presence affects the precision of benchmark financial asset prices. In this paper, we attempt to show how ‘tunnelling’ can be used to positive effect in the modelling of arbitrage in a financial asset pricing context.     

Cellular automata simulation of traffic including cars and bicycles

As ‘greening’ of all aspects of human activity becomes mainstream, transportation science is also increasingly focused around sustainability. Modal co-existence between motorised and non-motorised traffic on urban networks is, in this context, of particular interest for traffic flow modelling. The main modelling problems here are posed by the heterogeneity of vehicles, including size and dynamics, and by the complex interactions at intersections. Herein we address these with a novel technique, based on one-dimensional cellular automata components, for modelling network infrastructure and its occupancy by vehicles. We use this modelling approach, together with a corresponding vehicle behaviour model, to simulate combined car and bicycle traffic for two elemental scenarios—examples of components that would be used in the building of an arbitrary network. Results of simulations performed on these scenarios, (i) a stretch of road and (ii) an intersection causing conflict between cars and bicycles sharing a lane, are presented and analysed.     

Applying colour science in colour design

Although colour science has been widely used in a variety of industries over the years, it has not been fully explored in the field of product design. This paper will initially introduce the three main application fields of colour science: colour specification, colour-difference evaluation and colour appearance modelling. By integrating these advanced colour technologies together with modern colour imaging devices such as display, camera, scanner and printer, some computer systems have been recently developed to assist designers for designing colour palettes through colour selection by means of a number of widely used colour order systems, for creating harmonised colour schemes via a categorical colour system, for generating emotion colours using various colour emotional scales and for facilitating colour naming via a colour-name library. All systems are also capable of providing accurate colour representation on displays and output to different imaging devices such as printers.     

A combinatorial sample-preparation robot system using the volumetric-weighing method

We have developed a new automatic sample-preparation robot system with use of the volumetric-weighing method. In this system, slurries, aqueous solutions, and other wet reagents are employed as starting materials and 64 (8×8) samples at the maximum are prepared on a library plate of 35 mm × 35 mm size. Volumetric-weighing and mixing of the starting materials and distributing reaction mixtures to the library plate are automatically performed by computer-controlled mechanisms with an easy-to-use programming software interface. While this robot is designed in terms of space saving and portability, it is able to equip with an atmosphere-controlled furnace to sinter the samples on the library plate. Typical preparation time for a library plate of 36 (6×6) samples is less than 40 min. This robot system is promising in enhancing throughput of wet-chemically synthesized materials researches.     

DISCRETE HUYGENS' MODELLING APPROACH TO WAVE PROPAGATIONS IN A HOMOGENEOUS ELASTIC FIELD

The application of the discrete Huygens' modelling has been discussed for acoustic wave propagation problems, in which the scalar wave field problems have been focused. The present paper extends the application of the modelling to the elastic wave propagation in a homogeneous elastic medium in which two types of waves, the longitudinal wave and the shear wave, are independent except at the boundary. Each wave can be treated like a scalar wave until the two waves reach the boundary where they couple so as to satisfy the displacement or stress boundary condition. We propose the approach confining ourselves to the two-dimensional field. Some examples are demonstrated, whose solutions are compared with the vectorial wave modelling and finite difference modelling solutions whenever they are available.     

Modelling of the ultrasonic field by the angular spectrum method in presence of interface

We present a numerical modelling of the harmonic sound in two isotropic media, one liquid and the other solid separated by a plane interface. This numerical modelling is carried out by the angular spectrum method. This latter is applied to calculate the displacement potential generated by a rectangular transducer with a Gaussian profile and with an uniform profile. The rigorous modelling of the field needed to find the optimal parameters of the decomposition according to the transducer aperture and the ultrasonic wave frequency.     

Sensitivity of trace gas abundances retrievals from infrared limb emission spectra to simplifying approximations in radiative transfer modelling

The accuracy of trace gas abundances retrieved from spectrally resolved infrared limb emission measurements relies, among other things, on the appropriate modelling of radiative transfer through the actual atmosphere. We quantify the mapping of several commonly applied simplifications in radiative transfer modelling on the trace gas abundances retrieval error at the example of the Michelson interferometer for passive atmospheric sounding (MIPAS)/environmental satellite (ENVISAT) space borne Fourier transform infra-red limb emission experiment. The Karlsruhe optimized and precise radiative transfer algorithm (KOPRA) which was used as a tool for this study will be introduced. KOPRA supports accurate modelling of the particular instrument requirements of MIPAS and the observation scenarios during the ENVISAT mission, in particular with respect to its viewing direction and its altitude coverage of the atmosphere. We show that disregarding of horizontal temperature inhomogeneities and non-local thermodynamic equilibrium effects, insufficient accuracy in modelling of field-of-view and apodisation effects, and disregarding individual profiles of isotopic species play the key roles in radiative transfer modelling and lead to systematic retrieval errors which can by far exceed the expected random retrieval error caused by measurement noise.     

High-pressure neutron diffraction and models of titan

Saturn's largest moon Titan is the only planetary satellite to have a significant atmosphere. The nature of this atmosphere and the origins of the ～5% of methane in it are a source of longstanding debate. The high-pressure properties of the icy components - ammonia monohydrate and methane hydrate - from which Titan formed are crucial to modelling of Titan and yet until recently were poorly known. We have now carried out neutron diffraction studies of both systems across the entire pressure and temperature range relevant to Titan. We found several new phases in ammonia monohydrate and have been able to construct an equation of state for this material. And we have shown that methane hydrate does not decompose into ice and methane at 1.2 GPa as had been calculated. These results move modelling of Titan onto new ground.     

Average‐atom model calculations of dense‐plasma opacities: Review and potential applications to white‐dwarf stars

Methods using average‐atom models in order to calculate dense‐plasma opacities and conductivities are reviewed. Dense plasmas at moderate temperatures, of interest in white‐dwarf modelling, are considered. Due to their relative simplicity of implementation, compared to more detailed models (detailed‐level accounting, detailed configuration accounting, etc.), average‐atom models are a privileged framework for the application of the most involved dense‐plasma statistical modelling. Moreover, the average‐atom models are well suited to the calculation of some thermodynamic properties, such as the equation of state. They can also be used in order to estimate broadband radiative properties of dense plasmas. After an introduction to the opacity issue in the modelling of white dwarfs, we make a short review of average‐atom models. We then address the methods of calculating the opacity starting from the average‐atom model, see some of their limitations, and briefly discuss some problems that remain open, such as the modelling of fluctuations, or the accounting for channel mixing and collective phenomena in the photoabsorption.     

Modelling language evolution: Examples and predictions

We survey recent computer modelling research of language evolution, focusing on a rule-based model simulating the lexicon–syntax coevolution and an equation-based model quantifying the language competition dynamics. We discuss four predictions of these models: (a) correlation between domain-general abilities (e.g. sequential learning) and language-specific mechanisms (e.g. word order processing); (b) coevolution of language and relevant competences (e.g. joint attention); (c) effects of cultural transmission and social structure on linguistic understandability; and (d) commonalities between linguistic, biological, and physical phenomena. All these contribute significantly to our understanding of the evolutions of language structures, individual learning mechanisms, and relevant biological and socio-cultural factors. We conclude the survey by highlighting three future directions of modelling studies of language evolution: (a) adopting experimental approaches for model evaluation; (b) consolidating empirical foundations of models; and (c) multi-disciplinary collaboration among modelling, linguistics, and other relevant disciplines.     

Early stages of silicon oxidation

Experiments have shown that the early stages of silicon oxidation proceed layer by layer, so that one layer is essentially complete before another develops. Other experiments show that the mechanism does not involve step growth, the most obvious mechanism. We use a new approach to modelling the growth to show that these two observations can be understood when there is a rate-determining step which depends strongly on the local oxide thickness. The rate in question might be the sticking probability, or the rate of incorporation of adsorbed oxygen species into the oxide network. Such mechanisms are possible when transport by an ionic species dominates, contrary to the situation for thicker films. Our modelling suggests the mechanisms are driven by the image interaction, as in earlier suggestions by Stoneham and Tasker, rather than an effect of the electric field central to the Mott-Cabrera mechanism.     

ARROW-based silicon-on-insulator photonic crystal waveguides with reduced losses

We employ an antiresonant reflecting layers arrangement with silicon-on-insulator based photonic crystal waveguides. The 3D FDTD numerical modelling reveals improved transmission in such structures with a promising potential for their application in photonic circuits.     

Directional integration on unstructured meshes via supermesh construction

Unstructured meshes are in widespread use throughout computational physics, but calculating diagnostics of simulations on such meshes can be challenging. For example, in geophysical fluid dynamics, it is frequently desirable to compute directional integrals such as vertical integrals and zonal averages; however, it is difficult to compute these on meshes with no inherent spatial structure. This is widely regarded as an obstacle to the adoption of unstructured mesh numerical modelling in this field. In this paper, we describe an algorithm by which one can exactly compute such directional integrals on arbitrarily unstructured meshes. This is achieved via the solution of a problem of computational geometry, constructing the supermesh of two meshes. We demonstrate the utility of this approach by applying it to a classical geophysical fluid dynamics system: the thermally driven rotating annulus. This addresses an important objection to the more widespread use of unstructured mesh modelling.     

Dynamically tessellating algorithm for analysis of pore size distribution in particle agglomerates

We describe a novel physical application of the OctTree data structure [P. Meagher, Comput. Graphics Image Process 19(2) (1982) 129–147] in a dynamically tessellating algorithm, in conjunction with an object-oriented, constructive solid geometry library (DOC), to efficiently determine pore size distributions in large multi-particle systems. We apply the DOC library to investigate the evolving dynamics of pore formation in multi-particle systems, such as a mixture of smooth hard cubes and spheres and a collection of frictional soft spheres. We demonstrate that the algorithm is able to provide insight into the effect of structural changes on the porosity network; for example, during the uniaxial compaction of soft spheres, we find the number density of pores increases while the mean volume of the pores decreases. This trend is responsible for a shift in the distribution of the pore volumes to favour smaller volumes. We anticipate that the DOC method will have wider applications in the area of granular materials for studying the changes in pore structure in both experimental and numerical systems as a complement to the analysis of particle packing.     

An innovative hand-held vision-based digitizing system for 3D modelling

We describe a new hand-held 3D modelling device using vision and inertial measurements. Our system allows fast and accurate acquisition of the geometry and appearance information of any 3D object. We focused our work towards an easy manipulation and operating condition.Our methods allow automatic registration with no preparation of the scene (i.e. no markers) even when the object is moved between two acquisitions.In this paper, the design of the system and the developed methods for its use are presented. The system has been evaluated, qualitatively and quantitatively, using reference measurements provided by commercial scanning devices. The results show that this new hand-held scanning device is really competitive for modelling any 3D object.