One-way quantum computing in a decoherence-free subspace

We introduce a novel scheme for one-way quantum computing (QC) based on the use of information encoded qubits in an effective cluster state resource. With the correct encoding structure, we show that it is possible to protect the entangled resource from phase damping decoherence, where the effective cluster state can be described as residing in a decoherence-free subspace (DFS) of its supporting quantum system. One-way QC then requires either single or two-qubit adaptive measurements. As an example where this proposal can be realized, we describe an optical lattice set-up where the scheme provides robust quantum information processing. We also outline how one can adapt the model to provide protection from other types of decoherence.

Origin of Ferroelastic domains in Free-Standing Single Crystal Ferroelectric Films

The origin of the unusual 90 degrees ferroelectric/ferroelastic domains, consistently observed in recent studies on mesoscale and nanoscale free-standing single crystals of BaTiO3 [Schilling , Phys. Rev. B 74, 024115 (2006); Schilling , Nano Lett. 7, 3787 (2007)], has been considered. A model has been developed which postulates that the domains form as a response to elastic stress induced by a surface layer which does not undergo the paraelectric-ferroelectric cubic-tetragonal phase transition. This model was found to accurately account for the changes in domain periodicity as a function of size that had been observed experimentally. The physical origin of the surface layer might readily be associated with patterning damage, seen in experiment; however, when all evidence of physical damage is removed from the BaTiO3 surfaces by thermal annealing, the domain configuration remains practically unchanged. This suggests a more intrinsic origin, such as the increased importance of surface tension at small dimensions. The effect of surface tension is also shown to be proportional to the difference in hardness between the surface and the interior of the ferroelectric. The present model for surface-tension induced twinning should also be relevant for finely grained or core-shell structured ceramics.

Discovery of novel Agonists and antagonists of the free fatty acid receptor 1 (FFAR1) using virtual screening

The G-protein-coupled receptor free fatty acid receptor 1 (FFAR1), previously named GPR40, is a possible novel target for the treatment of type 2 diabetes. In an attempt to identify new ligands for this receptor, we performed virtual screening (VS) based on two-dimensional (2D) similarity, three-dimensional (3D) pharmacophore searches, and docking studies by using the structure of known agonists and our model of the ligand binding site, which was validated by mutagenesis. VS of a database of 2.6 million compounds followed by extraction of structural neighbors of functionally confirmed hits resulted in identification of 15 compounds active at FFAR1 either as full agonists, partial agonists, or pure antagonists. Site-directed mutagenesis and docking studies revealed different patterns of ligand-receptor interactions and provided important information on the role of specific amino acids in binding and activation of FFAR1.

Modelling the mechanical response of the Reed-mouthpiece-lip system of a clarinet. Part I. A one-dimensional distributed model

The motion of a clarinet reed that is clamped to a mouthpiece and supported by a lip is simulated in the time-domain using finite difference methods. The reed is modelled as a bar with non-uniform cross section, and is described using a one-dimensional, fourth-order partial differential equation. The interactions with the mouthpiece Jay and the player's lip are taken into account by incorporating conditional contact forces in the bar equation. The model is completed by clamped-free boundary conditions for the reed. An implicit finite difference method is used for discretising the system, and values for the physical parameters are chosen both from laboratory measurements and by accurate tuning of the numerical simulations. The accuracy of the numerical system is assessed through analysis of frequency warping effects and of resonance estimation. Finally, the mechanical properties of the system are studied by analysing its response to external driving forces. In particular, the effects of reed curling are investigated.

An understanding of chemoselective hydrogenation on crotonaldehyde over Pt(111) in the free energy landscape: The microkinetics study based on first-principles calculations

Microkinetic model is developed in the free energy landscape based on density functional theory (DFT) to quantitatively investigate the reaction mechanism of chemoselective partial hydrogenation of crotonaldehyde to crotyl alcohol over Pt(1 1 1) at the temperature of 353 K. Three different methods (mobile, immobile and collision theory models) were carried out to obtain free energy barrier of adsorption/desorption processes. The results from mobile and collision theory models are similar. The calculated TOFs from both models are close to the experiment value. However, for the immobile model, in which the free energy barrier of desorption approaches the energy barrier, the calculated TOF is 2 orders of magnitude lower than the other models. The difficulty of adsorption/ desorption may be overestimated in the immobile model. In addition, detailed analyses show that for the surface hydrogenation elementary steps, the entropy and internal energy effects are small under the reaction condition, while the zero-point-energy (ZPE) correction is significant, especially for the multi-step hydrogenation reaction. The total energy with the ZPE correction approaches to the full free energy calculation for the surface reaction under the reaction condition. (c) 2011 Elsevier B.V. All rights reserved.

Artemisinins act through at least two targets in a yeast model

Artemisinin and related compounds are potent and widely used antimalarial drugs but their biochemical mode of action is not clear. There is strong evidence that ATP-dependent calcium transporters are a key target in the malarial parasite. However, work using Saccharomyces cerevisiae suggests that disruption of mitochondrial function is critical in the cell killing activity of these compounds. Here it is shown that, in the absence of reducing agents, artemisinin and artesunate targeted the S. cerevisiae calcium channels Pmr1p and Pmc1p. Both compounds affected the growth of yeast on fermentable and nonfermentable media. This growth inhibition was not seen in a yeast strain in which the genes encoding both calcium channels were deleted. In the presence of reducing agents, which break the endoperoxide bridge in the drugs, growth inhibition was only observed in nonfermentable media. This inhibition could be partially relieved by the addition of a free radical scavenger. These results suggest that the drugs have two biochemical modes of action - one acting by specific binding to calcium channels and one involving free radical production in the mitochondria.

Decay of Cystalline Order and Equilibration during the Solid-to-Plasma Transition Induced by 20-fs Microfocused 92-eV Free-Electron-Laser Pulses

We have studied a solid-to-plasma transition by irradiating Al foils with the FLASH free electron laser at intensities up to 10(16) W/cm(2). Intense XUV self-emission shows spectral features that are consistent with emission from regions of high density, which go beyond single inner-shell photoionization of solids. Characteristic features of intrashell transitions allowed us to identify Auger heating of the electrons in the conduction band occurring immediately after the absorption of the XUV laser energy as the dominant mechanism. A simple model of a multicharge state inverse Auger effect is proposed to explain the target emission when the conduction band at solid density becomes more atomiclike as energy is transferred from the electrons to the ions. This allows one to determine, independent of plasma simulations, the electron temperature and density just after the decay of crystalline order and to characterize the early time evolution.

The role of non-protein sulphydryls in determining the chemical repair rates of free radical precursors of DNA damage and cell killing in Chinese hamster V79 cells. I

Chinese hamster V79 fibroblasts were irradiated in the gas explosion apparatus and the chemical repair rates of the oxygen-dependent free radical precursors of DNA double-strand breaks (dsb) and lethal lesions measured using filter elution (pH 9.6) and a clonogenic assay. Depletion of cellular GSH levels, from 4.16 fmol/cell to 0.05 fmol/cell, by treatment with buthionine sulphoximine (50 mumol dm-3; 18 h), led to sensitization as regards DNA dsb induction and cell killing. This was evident at all time settings but was particularly pronounced when the oxygen shot was given 1 ms after the irradiation pulse. A detailed analysis of the chemical repair kinetics showed that depletion of GSH led to a reduction in the first-order rate constant for dsb precursors from 385 s-1 to 144 s-1, and for lethal lesion precursors from 533 s-1 to 165 s-1. This is generally consistent with the role of GSH in the repair-fixation model of radiation damage at the critical DNA lesions. However, the reduction in chemical repair rate was not proportional to the severe thiol depletion (down to almost-equal-to 1% for GSH) and a residual repair capacity remained (almost-equal-to 30%). This was found not to be due to compartmentalization of residual GSH in the nucleus, as the repair rate for dsb precursors in isolated nuclei, washed virtually free of GSH, was identical to that found in GSH-depleted cells (144 s-1), also the OER remained substantially above unity. This suggests that other reducing agents may have a role to play in the chemical repair of oxygen-dependent damage. One possible candidate is the significant level of protein sulphydryls present in isolated nuclei.

A multiple-radical model for radiation action on DNA and the dependence of OER on LET

We have a developed a multiple-radical model of the chemical modification reactions involving oxygen and thiols relevant to the interactions of ionizing radiations with DNA. The treatment is based on the Alper and Howard-Flanders equation but considers the case where more than one radical may be involved in the production of lesions in DNA. This model makes several predictions regarding the induction of double strand breaks in DNA by ionizing radiation and the role of sensitizers such as oxygen and protectors such as thiols which act at the chemical phase of radiation action via the involvement of free radicals. The model predicts a decreasing OER with increasing LET on the basis that as radical multiplicity increases so will the probability that, even under hypoxia, damage will be fixed and lead to lesion production. The model can be considered to provide an alternative hypothesis to those of 'interacting radicals' or of 'oxygen-in-the-track'.

A Monte Carlo model of DNA double-strand break clustering and rejoining kinetics for the analysis of pulsed-field gel electrophoresis data

In studies of radiation-induced DNA fragmentation and repair, analytical models may provide rapid and easy-to-use methods to test simple hypotheses regarding the breakage and rejoining mechanisms involved. The random breakage model, according to which lesions are distributed uniformly and independently of each other along the DNA, has been the model most used to describe spatial distribution of radiation-induced DNA damage. Recently several mechanistic approaches have been proposed that model clustered damage to DNA. In general, such approaches focus on the study of initial radiation-induced DNA damage and repair, without considering the effects of additional (unwanted and unavoidable) fragmentation that may take place during the experimental procedures. While most approaches, including measurement of total DNA mass below a specified value, allow for the occurrence of background experimental damage by means of simple subtractive procedures, a more detailed analysis of DNA fragmentation necessitates a more accurate treatment. We have developed a new, relatively simple model of DNA breakage and the resulting rejoining kinetics of broken fragments. Initial radiation-induced DNA damage is simulated using a clustered breakage approach, with three free parameters: the number of independently located clusters, each containing several DNA double-strand breaks (DSBs), the average number of DSBs within a cluster (multiplicity of the cluster), and the maximum allowed radius within which DSBs belonging to the same cluster are distributed. Random breakage is simulated as a special case of the DSB clustering procedure. When the model is applied to the analysis of DNA fragmentation as measured with pulsed-field gel electrophoresis (PFGE), the hypothesis that DSBs in proximity rejoin at a different rate from that of sparse isolated breaks can be tested, since the kinetics of rejoining of fragments of varying size may be followed by means of computer simulations. The problem of how to account for background damage from experimental handling is also carefully considered. We have shown that the conventional procedure of subtracting the background damage from the experimental data may lead to erroneous conclusions during the analysis of both initial fragmentation and DSB rejoining. Despite its relative simplicity, the method presented allows both the quantitative and qualitative description of radiation-induced DNA fragmentation and subsequent rejoining of double-stranded DNA fragments. (C) 2004 by Radiation Research Society.

Label-free detection of nanomolar unmodified single- and double-stranded dna by using surface-enhanced raman spectroscopy on Ag and Au colloids

Unlabelled single- and double-stranded DNA (ssDNA and dsDNA, respectively) has been detected at concentrations =10-9?M by surface-enhanced Raman spectroscopy. Under appropriate conditions the sequences spontaneously adsorbed to the surface of both Ag and Au colloids through their nucleobases; this allowed highly reproducible spectra with good signal-to-noise ratios to be recorded on completely unmodified samples. This eliminated the need to promote absorption by introducing external linkers, such as thiols. The spectra of model ssDNA sequences contained bands of all the bases present and showed systematic changes when the overall base composition was altered. Initial tests also showed that small but reproducible changes could be detected between oligonucleotides with the same bases arranged in a different order. The spectra of five ssDNA sequences that correspond to different strains of the Escherichia coli bacterium were found to be sufficiently composition-dependent so that they could be differentiated without the need for any advanced multivariate data analysis techniques.

Non-competitive phenotypic differences can have a strong effect on ideal free distributions

1. We present a model of the ideal free distribution (IFD) where differences between phenotypes other than those involved in direct competition for resources are considered. We show that these post-acquisitional differences can have a dramatic impact on the predicted distributions of individuals.

2. Specifically, we predict that, when the relative abilities of phenotypes are independent of location, there will be a continuum of mixed evolutionarily stable strategy (ESS) distributions (where all phenotypes are present in all patches).

3, When the relative strengths of the post-acquisitional trait in the two phenotypes differ between patches, however, we predict only a single ESS at equilibrium. Further, this distribution may be fully or partially segregated (with the distribution of at least one phenotype being spatially restricted) but it will never be mixed.

4, Our results for post-acquisitional traits mirror those of Parker (1982) for direct competitive traits. This comparison illustrates that it does not matter whether individual differences are expressed before or after competition for resources, they will still exert considerable influence on the distribution of the individuals concerned.

How do grazers achieve their distribution? A continuum of models from random diffusion to the ideal free distribution using biased random walks

A conceptual model is described for generating distributions of grazing animals, according to their searching behavior, to investigate the mechanisms animals may use to achieve their distributions. The model simulates behaviors ranging from random diffusion, through taxis and cognitively aided navigation (i.e., using memory), to the optimization extreme of the Ideal Free Distribution. These behaviors are generated from simulation of biased diffusion that operates at multiple scales simultaneously, formalizing ideas of multiple-scale foraging behavior. It uses probabilistic bias to represent decisions, allowing multiple search goals to be combined (e.g., foraging and social goals) and the representation of suboptimal behavior. By allowing bias to arise at multiple scales within the environment, each weighted relative to the others, the model can represent different scales of simultaneous decision-making and scale-dependent behavior. The model also allows different constraints to be applied to the animal's ability (e.g., applying food-patch accessibility and information limits). Simulations show that foraging-decision randomness and spatial scale of decision bias have potentially profound effects on both animal intake rate and the distribution of resources in the environment. Spatial variograms show that foraging strategies can differentially change the spatial pattern of resource abundance in the environment to one characteristic of the foraging strategy.</

Beyond the ideal free distribution: More general models of predator distribution

The ideal free distribution model which relates the spatial distribution of mobile consumers to that of their resource is shown to be a limiting case of a more general model which we develop using simple concepts of diffusion. We show how the ideal free distribution model can be derived from a more general model and extended by incorporating simple models of social influences on predator spacing. First, a free distribution model based on patch switching rules, with a power-law interference term, which represents instantaneous biased diffusion is derived. A social bias term is then introduced to represent the effect of predator aggregation on predator fitness, separate from any effects which act through intake rate. The social bias term is expanded to express an optimum spacing for predators and example solutions of the resulting biased diffusion models are shown. The model demonstrates how an empirical interference coefficient, derived from measurements of predator and prey densities, may include factors expressing the impact of social spacing behaviour on fitness. We conclude that empirical values of log predator/log prey ratio may contain information about more than the relationship between consumer and resource densities. Unlike many previous models, the model shown here applies to conditions without continual input. (C) 1997 Academic Press Limited.</p>

Element-Free Galerkin modelling of composite damage

Delamination and matrix cracking are routine damage mechanisms, observed by post-mortem analysis of laminated structures containing geometrical features such as notches or bolts. Current finite element tools cannot explicitly model an intralaminar matrix microcrack, except if the location of the damage is specified a priori. In this work, a meshless technique, the Element-Free Galerkin (EFG) method, is utilized for the first time to simulate delamination (interlaminar) and intralaminar matrix microcracking in composite laminates.