Stochastic protein folding simulation in the three-dimensional HP-model

We present results from three-dimensional protein folding simulations in the HP-model on ten benchmark problems. The simulations are executed by a simulated annealing-based algorithm with a time-dependent cooling schedule. The neighbourhood relation is determined by the pull-move set. The results provide experimental evidence that the maximum depth D of local minima of the underlying energy landscape can be upper bounded by D < n(2/3). The local search procedure employs the stopping criterion (In/delta)(D/gamma) where m is an estimation of the average number of neighbouring conformations, gamma relates to the mean of non-zero differences of the objective function for neighbouring conformations, and 1-delta is the confidence that a minimum conformation has been found. The bound complies with the results obtained for the ten benchmark problems. (c) 2008 Elsevier Ltd. All rights reserved.

Three-Dimensional Analysis of Seepage below and around Hydraulic Structures

This paper investigates the problem of seepage under the floor of hydraulic structures considering the compartment of flow that seeps through the surrounding banks of the canal. A computer program, utilizing a finite-element method and capable of handling three-dimensional (3D) saturated–unsaturated flow problems, was used. Different ratios of canal width/differential head applied on the structure were studied. The results produced from the two-dimensional (2D) analysis were observed to deviate largely from that obtained from 3D analysis of the same problem, despite the fact that the porous medium was isotropic and homogeneous. For example, the exit gradient obtained from 3D analysis was as high as 2.5 times its value obtained from 2D analysis. Uplift force acting upwards on the structure has also increased by about 46% compared with its value obtained from the 2D solution. When the canal width/ differential head ratio was 10 or higher, the 3D results were comparable to the 2D results. It is recommended to construct a core of low permeability soil in the banks of canal to reduce the seepage losses, uplift force, and exit gradient.

Confirming the Existence of Gaps and Depletions in the Irish Oak Tree-Ring Record

In the course of building the 7000 year Belfast long oak chronology a series of depletion problems were encountered. These problems were overcome by 1984 when the completion of the long chronology was announced. The solution to the bridging of the various ‘gaps’ in the Irish chronology lay in the use of long sections of oak chronology from Britain. Now that a quarter of a century has elapsed and large numbers of additional oak samples, and site assemblages, have been accumulated it seems reasonable to review the ‘gaps’ in order to see if the Irish chronology could now be constructed without the use of British material. That is, are the depletion periods in the Irish chronology still evident, and if so, what might they imply about past conditions and human populations? The perhaps surprising conclusion is that the original depletions are still evident after 25 years of quasi-random sampling by archaeologists and palaeoecologists throughout Ireland.

Two-dimensional hygrothermal transfer in porous building materials

A two-dimensional mathematical model for evaluating the simultaneous heat and moisture migration in porous building materials was proposed. Vapor content and temperature were chosen as the principal driving potentials. The numerical solution was based on the control volume finite difference technique with fully implicit scheme in time. Two validation experiments were developed in this study. The evolution of transient moisture distributions in both one-dimensional and two-dimensional cases was measured. A comparison between experimental results and those obtained by the numerical model proves that they are fully consistent with each other. The model can be easily integrated into a whole building heat, air and moisture transfer model. Another main advantage of the present numerical method lies in the fact that the required moisture transport properties are comparatively simple and easy to determine.

Twist localizes three-dimensional patterns

A mechanism or the localization of spatially periodic,self-oganized patterns in anisotropic media which requires systems extended in all three spatial dimensions is presented: When the anisotropy axis is twisted, the pattern becomes localized in planes parallel to the anisotropy axis. An analytical description of the effect is developed, and used to interpret recent experiments in the high-frequency regime of electroconvection by Bohatsch and Stannarius [Phys. Rev. E 60, 5591 (1999)]. The localization width is found to be of the order of magnitude of the geometrical average of the pattern wavelength and the inverse twist.

On the mobility of a one-dimensional damped Frenkel-Kontorova chain: Commensurate versus incommensurate

The mobility of a one-dimensional damped Frenkel-Kontorova chain under a de driving force is studied numerically and analytically For the commensurate case, the particles in the chain me synchronized st high driving force. For the incommensurate chain, a single mode solution dominates st high mobility regime. We are able to calculate the mobilities for both the cases analytically, and a good agreement with numerical results is found. The mobility hysteresis for the incommensurate chain is explained by the existence of two branches of physical solutions, and transitions occur when one of them breaks up.

Buckling and Postbuckling Structures: Experimental, Analytical and Numerical Studies

This book provides an in-depth treatment of the study of the stability of engineering structures. Contributions from internationally recognized leaders in the field ensure a wide coverage of engineering disciplines in which structural stability is of importance, in particular the analytical and numerical modelling of structural stability applied to aeronautical, civil, marine and offshore structures. The results from a number of comprehensive experimental test programs are also presented, thus enhancing our understanding of stability phenomena as well as validating the analytical and computational solution schemes presented. A variety of structural materials are investigated with special emphasis on carbon-fibre composites, which are being increasingly utilized in weight-critical structures. Instabilities at the meso- and micro-scales are also discussed. This book will be particularly relevant to professional engineers, graduate students and researchers interested in structural stability.

Universal tight binding model for chemical reactions in solution and at surfaces. I. Organic molecules

As is now well established, a first order expansion of the Hohenberg-Kohn total energy density functional about a trial input density, namely, the Harris-Foulkes functional, can be used to rationalize a non self consistent tight binding model. If the expansion is taken to second order then the energy and electron density matrix need to be calculated self consistently and from this functional one can derive a charge self consistent tight binding theory. In this paper we have used this to describe a polarizable ion tight binding model which has the benefit of treating charge transfer in point multipoles. This admits a ready description of ionic polarizability and crystal field splitting. It is necessary in constructing such a model to find a number of parameters that mimic their more exact counterparts in the density functional theory. We describe in detail how this is done using a combination of intuition, exact analytical fitting, and a genetic optimization algorithm. Having obtained model parameters we show that this constitutes a transferable scheme that can be applied rather universally to small and medium sized organic molecules. We have shown that the model gives a good account of static structural and dynamic vibrational properties of a library of molecules, and finally we demonstrate the model's capability by showing a real time simulation of an enolization reaction in aqueous solution. In two subsequent papers, we show that the model is a great deal more general in that it will describe solvents and solid substrates and that therefore we have created a self consistent quantum mechanical scheme that may be applied to simulations in heterogeneous catalysis.

Two-dimensional images of dissolved sulfide and metals in anoxic sediments by a novel diffusive gradients in thin film probe and optical scanning techniques

A novel diffusive gradients in thin film probe developed comprises diffusive gel layer of silver iodide (AgI) and a back-up Microchelex resin gel layer. 2D high-resolution images of sulfide and trace metals were determined respectively on the AgI gel by densitometric analysis and on the Microchelex resin layer with laser-ablation-inductively-coupled plasma mass spectrometry (LA-ICP-MS).We investigated the validity of the analytical procedures used for the determination of sulfide and trace metals. We found low relative standard deviations on replicate measurements, linear trace-metal calibration curves between the LA-ICP-MS signal and the true trace-metal concentration in the resin gel, and a good agreement of the sulfide results obtained with the AgI resin gel and with other analytical methods. The method was applied on anoxic sediment pore waters in an estuarine and marine system. Simultaneous remobilization of sulfide and trace metals was observed in the marine sediment.

Detection of Low-Concentration Contaminants in Solution by Exploiting Chemical Derivatization in Surface-Enhanced Raman Spectroscopy

Analytical examination of animal remains from Borneo:the painting of bone and shell

Examination of a selection of shell and bone from archaeological assemblages excavated at Niah Cave and Gua Sireh, both of which are located in Sarawak, Borneo, has revealed the deliberate application of coloured material to one or more surfaces. Small fragments of the surface colourant were analysed using a variety of techniques, including microscopy, energy dispersive microwave analysis and infra-red spectrophotometry. These procedures established that, although red in colour, the applied coating in each instance was not red iron oxide. It is suggested that, based on the chemical components present, this coating was a tree resin or a similar organic substance. The paper further reports the presence of enhanced chloride values in the colourant recovered from the ancient human cranial fragment tested. It is suggested that elevated concentrations of this trace element may indicate that the site, the human remains or ingredients within the colourant were once in close proximity to the sea. (C) 2010 Elsevier Ltd. All rights reserved.

Arsenic-glutathione complexes - Their stability in solution and during separation by different HPLC modes

Complexes of arsenic compounds and glutathione are believed to play an essential part in the metabolism and transport of inorganic arsenic and its methylated species. Up to now, the evidence of their presence is mostly indirect. We studied the stability and Chromatographic behaviour of glutathione complexes with trivalent arsenic: i.e. As^III(GS)₃, MA ^III(GS)₂ and DMA^III(GS) under different conditions. Standard ion chromatography using PRP X-100 and carbonate or formic acid buffer disintegrated the complexes, while all three complexes are stable and separable by reversed phase chromatography (0.1% formic acid/acetonitrile gradient). As^III(GS)₃ and MA^III(GS)₂ were more stable than DMA^III(GS), which even under optimal conditions tended to degrade on the column at 25 °C. Chromatography at 6 °C can retain the integrity of the samples. These results shed more light on the interpretation of a vast number of previously published arsenic speciation studies, which have used Chromatographic separation techniques with the assumption that the integrity of the arsenic species is guaranteed. © The Royal Society of Chemistry 2004.

Cell Coverage Optimization for the Multicell Massive MIMO Uplink

We investigate the cell coverage optimization problem for the massive multiple-input multiple-output (MIMO) uplink. By deploying tilt-adjustable antenna arrays at the base stations, cell coverage optimization can become a promising technique which is able to strike a compromise between covering cell-edge users and pilot contamination suppression. We formulate a detailed description of this optimization problem by maximizing the cell throughput, which is shown to be mainly determined by the user distribution within several key geometrical regions. Then, the formulated problem is applied to different example scenarios: for a network with hexagonal shaped cells and uniformly distributed users, we derive an analytical lower bound of the ergodic throughput in the objective cell, based on which, it is shown that the optimal choice for the cell coverage should ensure that the coverage of different cells does not overlap; for a more generic network with sectoral shaped cells and non-uniformly distributed users, we propose an analytical approximation of the ergodic throughput. After that, a practical coverage optimization algorithm is proposed, where the optimal solution can be easily obtained through a simple one-dimensional line searching within a confined searching region. Our numerical results show that the proposed coverage optimization method is able to greatly increase the system throughput in macrocells for the massive MIMO uplink transmission, compared with the traditional schemes where the cell coverage is fixed.