Simplified Variants Research Articles

Excitation Energies with Cost-Reduced Variant of the Active-Space EOMCCSDT Method: The EOMCCSDt-3̅ Approach.

In this paper, we discuss the performance of several simplified variants of equation-of-motion coupled cluster method (EOMCC) with iterative inclusion of singles, doubles, and active-space triples (EOMCCSDt). In particular, we explore simplified EOMCCSDt approaches that enable one to generate the triply excited amplitudes in an on-the-fly manner. The original EOMCCSDt formulation has already demonstrated great success in encapsulating the most important excited-state correlation effects due to triples. In analogy to the original EOMCCSDT-3 formulation, the proposed approach can bypass the typical bottlenecks associated with the need for storing triply excited amplitudes. In this paper, we illustrate the performance of several approximate EOMCCSDt methods, named EOMCCSDt-3̅ and EOMCCSDt-3̅, on typical benchmark systems including C2, N2, ozone, ethene, and E-butadiene molecules. These new methods yield excitation energies close to the EOMCCSDt ones. The extrapolation of excitation energies for basis sets ranging from cc-pVDZ to cc-pV6Z for N2 and C2 shows very good convergence to the experimental results for states dominated by single excitations. The performance of the EOMCCSDt-3̅x approach is also compared with the results obtained with popular CCSDR(3) and CC3 approaches.

Еще раз о роли английского языка как глобального в развитии европейского образования

The article considers the status of English as a global means of communication in the light of modern approaches to the development of language teaching and studies the motives for learning the language in European countries. The author analyses the attempts to develop simplified variants of English the possibility of using them in the classroom. She concludes that neither Globish, nor the variant of English devoid of the cultural component can be used in the classroom either at school or at university. The author further underlined that English does not act as a dominant language in Europe and it does not oust other languages, but is widely used as an auxiliary means of communication.

Integrating evolution into ecological modelling: accommodating phenotypic changes in agent based models.

Evolutionary change is a characteristic of living organisms and forms one of the ways in which species adapt to changed conditions. However, most ecological models do not incorporate this ubiquitous phenomenon. We have developed a model that takes a ‘phenotypic gambit’ approach and focuses on changes in the frequency of phenotypes (which differ in timing of breeding and fecundity) within a population, using, as an example, seasonal breeding. Fitness per phenotype calculated as the individual’s contribution to population growth on an annual basis coincide with the population dynamics per phenotype. Simplified model variants were explored to examine whether the complexity included in the model is justified. Outputs from the spatially implicit model underestimated the number of individuals across all phenotypes. When no phenotype transitions are included (i.e. offspring always inherit their parent’s phenotype) numbers of all individuals are always underestimated. We conclude that by using a phenotypic gambit approach evolutionary dynamics can be incorporated into individual based models, and that all that is required is an understanding of the probability of offspring inheriting the parental phenotype.

The influence of migrating bed forms on the velocity-intermittency structure of turbulent flow over a gravel bed

[1] Modeling turbulent flows at high Reynolds number requires solving simplified variants of the Navier-Stokes equations. The methods used to close the resulting Reynolds-averaged, or eddy simulation equations usually follow classical theory and, at small enough scales, postulate universal scaling for turbulence that is independent of the velocity itself. This may not be the best way to conceptualize geophysical turbulence. Turbulent intermittency may be defined in terms of the local “roughness” of the velocity signal as measured by pointwise Holder exponents. This study investigates the joint velocity-intermittency structure of flow over a gravel-bed surface with migrating bed forms. We report clear velocity-intermittency dependence and quantify its nature above the moving bed form profile. Our results imply differences in energy transfer close to bed forms at shorter wavelengths than those forced directly. Hence, progress in modeling flows of geophysical relevance may require a reconsideration of the principles on which turbulence closures are based.

Inverse Kinematics Using Particle Swarm Optimization, A Statistical Analysis

This paper investigates the relative performances of PSO variants when used to solve inverse kinematics. Inverse kinematics is a key issue in robotics; for problems such as path planning, motion generation or trajectories optimization, they are classically involved. In the specific case of articulated robotics, inverse kinematics is needed to generate the joint motions, correspondent to a known target position. Articulated systems are very important in humanoid robotics, since arms and legs belong typically to this kind of mechanisms. In this paper the IK-PSO, Inverse Kinematics PSO, is applied to a double link articulated system. A statistical analysis is conducted to survey the convergence and relative performances of the main PSO variants when applied to solve IK; the PO variants tested are: Inertia weight PSO, Constriction factor PSO, linear decreasing weight and two simplified PSO variants.

Optimally Orienting Physical Networks

In a network orientation problem, one is given a mixed graph, consisting of directed and undirected edges, and a set of source-target vertex pairs. The goal is to orient the undirected edges so that a maximum number of pairs admit a directed path from the source to the target. This NP-complete problem arises in the context of analyzing physical networks of protein-protein and protein-DNA interactions. While the latter are naturally directed from a transcription factor to a gene, the direction of signal flow in protein-protein interactions is often unknown or cannot be measured en masse. One then tries to infer this information by using causality data on pairs of genes such that the perturbation of one gene changes the expression level of the other gene. Here we provide a first polynomial-size ILP formulation for this problem, which can be efficiently solved on current networks. We apply our algorithm to orient protein-protein interactions in yeast and measure our performance using edges with known orientations. We find that our algorithm achieves high accuracy and coverage in the orientation, outperforming simplified algorithmic variants that do not use information on edge directions. The obtained orientations can lead to a better understanding of the structure and function of the network.

Rapid and sensitive detection of cytokines using functionalized gold nanoparticle-based immuno-PCR, comparison with immuno-PCR and ELISA

Reliable and simple methods are required for detection of low concentrations of cytokines and some other proteins in complex biological fluids. This is especially important when monitoring the immune responses under various physiological and pathophysiological conditions in vivo or following production of these compounds in in vitro systems. Cytokines and other immunologically active molecules are being predominantly detected by enzyme-linked immunosorbent assays (ELISA) and newly also by immuno-polymerase chain reactions (iPCR). New simplified variants of iPCR have recently been described where antibodies are connected with multiple DNA templates through gold nanoparticles (Au-NPs) to form a new class of detection reagents. In this study we compared functionalized Au-NP-based iPCR (Nano-iPCR) with standard ELISA and iPCR for the detection of interleukin (IL)-3 and stem cell factor (SCF). The same immunoreagents (IL-3- and SCF-specific polyclonal antibodies and their biotinylated forms) were used throughout the assays. The obtained data indicate that both Nano-iPCR and iPCR are superior in sensitivity and detection range than ELISA. Furthermore, Nano-iPCR is easier to perform than the other two methods. Nano-iPCR was used for monitoring changes in concentration of free SCF during growth of mast cells in SCF-conditioned media. The results show that growing cultures gradually reduce the amount of SCF in supernatant to 25% after 5days. The combined data indicate that Nano-iPCR assays may be preferable for rapid detection of low concentrations of cytokines in complex biological fluids.

Efficient Business Service Consumption by Customization with Variability Modelling

The establishment of service orientation in industry determines the need for efficient engineering technologies that properly support the whole life cycle of service provision and consumption. A central challenge is adequate support for the efficient employment of komplex services in their individual application context. This becomes particularly important for large-scale enterprise technologies where generic services are designed for reuse in several business scenarios. In this article we complement our work regarding Service Variability Modelling presented in a previous publication. There we presented an approach for the customization of services for individual application contexts by creating simplified variants, based on model-driven variability management. That work presents our revised service variability metamodel, new features of the variability tools and an applicability study, which reveals that substantial improvements on the efficiency of standard business service consumption under both usability and economic aspects can be achieved.

Failure of unrestrained lightly reinforced concrete slabs under fire, Part II: Verification and application

The simplified analytical models developed in the companion paper for the failure assessment of simply supported composite floor slabs without planar restraints are investigated further in this paper. In addition to taking account of membrane action and the material response at elevated temperature, these models allow for the bond developed between the reinforcement and the surrounding concrete. This is an essential requirement for defining a rational performance-based failure criterion for composite floor slabs at elevated temperatures, since the bond along with the characteristics of the reinforcement response govern failure by rupture of the reinforcement across full depth cracks. The kinematic assumptions inherent in the formulation of the complete and simplified variants of the models are first verified against detailed finite element analysis, and comparisons are made against a previously proposed model to identify common features and important benefits. Subsequently, the models are utilised in several examples which demonstrate their applicability, and the treatment of important factors related to boundary conditions and geometric configuration is discussed, highlighting in the process any restrictions on the application of the proposed models.

A new structural class of S-adenosylhomocysteine hydrolase inhibitors

Effective inhibitors of S-adenosylhomocysteine hydrolase hold promise towards becoming useful therapeutic agents. Since most efforts have focused on the development of nucleoside analog inhibitors, issues regarding bioavailability and selectivity have been major challenges. Considering the marine sponge metabolite ilimaquinone was found to be a competitive inhibitor of S-adenosylhomocysteine hydrolase, new opportunities for developing selective new inhibitors of this enzyme have become available. Based on the activities of various hybrid analogs, SAR studies, pharmacophore modeling, and computer docking studies have lead to a predictive understanding of ilimaquinone’s S-adenosylhomocysteine hydrolase inhibitory activities. These studies have allowed for the design and preparation of simplified structural variants possessing new furanoside bioisosteres with 100-fold greater inhibitory activities than that of the natural product.

Immunogenic, antigenic, fibrillogenic and inflammatory properties of new simplified β-amyloid peptides

The most promising approach in Alzheimer disease immunotherapy is represented by amyloid β derivatives with low intrinsic neurotoxicity and minimal overall T cell responses. To avoid toxicity and autoimmune response, we have designed a new class of Aβ derivatives through segmentation of the original Aβ[1–42] peptide and application of the glycine substitution modification technology. Aβ[1–16], Aβ[13–28] and Aβ[25–42] fragments were selected in order to retain the major immunogenic sites of the Aβ[1–42] peptide. All peptides showed comparable immunogenicity, and raised antibodies were all able to cross-recognize both Aβ[1–42] and Aβ[1–40] synthetic amyloid forms. Polyclonal antibodies produced against the simplified variants were able to recognize the parent peptide, but not the opposite simplified forms, in strict agreement with the model of independent surfaces of recognition. All Aβ simplified derivatives showed reduced fibrillogenic properties, thus underlining that the introduction of glycine residues in alternating positions allows to obtain modified peptides maintaining the main immunogenic properties of the parent peptides, but with reduced ability to adopt a β-sheet conformation and therefore a much lower risk of toxicity in humans. In addition, in vitro studies on peripheral blood mononuclear cells (PBMCs) from healthy donors showed that only the Aβ[13–28]+G peptide failed to induce IFN-γ production, thus suggesting that this molecule could represent a good candidate for potentially safer vaccine therapy to reduce amyloid burden in Alzheimer's disease instead of using toxic Aβ[1–42].

On the fulfillment of the energy conservation law in mathematical models of evolution of single spherical bubble

The problem of the evolution of a single spherical bubble in an infinite liquid is considered, as the result of a variation of the pressure in the liquid at an infinite distance from the bubble. It has been assumed the bubble is filled with vapor from the surrounding liquid or insoluble gas. The question of the fulfillment of the integral energy conservation law is investigated using different ways of describing the hydrodynamic and heat and mass exchange processes in both the bubble and surrounding liquid and at the bubble interface. Kinetic and internal energy of vapor (gas) in the bubble, kinetic and internal energy of the liquid, and energy of surface tension are taken into account in the energy balance. The liquid is assumed to be incompressible, viscous and heat-conducting, the vapor (gas) to be nonviscous, heat-conducting and obeying the Clapeyron equation. Thermal–physical properties, exclusive of specific heats, are allowed to be temperature-dependent. For the above suppositions and assumptions, a mathematical model ensuring exact fulfillment of the integral energy conservation law has been developed. It has been shown that the conservation integral can be fulfilled by the given model. As simplified variants of the principal model, models of the uniform bubble and pressure uniform bubble, have been proposed which ensure the exact fulfillment of the integral energy balance disregarding the relatively small vapor kinetic energy. A relation defining the imbalance in the integral energy conservation law for some often-used extra simplifications has been derived.

Thermodynamic Properties of BPTI Variants with Highly Simplified Amino Acid Sequences

We report the first detailed thermodynamic analysis of simplified proteins by differential scanning calorimetry (DSC). The experiments were carried out with five simplified BPTI variants, whose structures and activities have been reported, in which several residues not essential for specifying the tertiary structure were replaced by alanine. In most aspects, the thermodynamics of simplified proteins were very similar to, if not essentially identical with, those of natural proteins. In particular, they undergo a highly cooperative two-state thermal unfolding process with a large enthalpy change, which is a thermodynamic hallmark of the native state of natural globular proteins. Furthermore, the specific enthalpy and entropy changes upon unfolding at 110 °C were close to values invariably observed for small natural globular proteins (55 J g − 1 and ~16 J K − 1 g − 1 , respectively). On the other hand, two simplified BPTI variants, BPTI-21 and BPTI-22 (containing 21 and 22 alanine residues), were enthalpically stabilized while entropically destabilized with respect to the reference BPTI-[5,55] molecule. This peculiar type of entropy–enthalpy compensation is in sharp contrast to the usual enthalpy destabilization/entropy stabilization observed in mutational studies of natural proteins. Overall, we conclude that a thermodynamic native state can be achieved by proteins encoded with extensively simplified sequences.

An Active Enzyme Constructed from a 9-Amino Acid Alphabet

Nature employs a set of 20 amino acids to produce a repertoire of protein structures endowed with sophisticated functions. Here, we combined design and selection to create an enzyme composed entirely from a set of only 9 amino acids that can rescue auxotrophic cells lacking chorismate mutase. The simplified protein captures key structural features of its natural counterpart but appears to be somewhat less stable and more flexible. The potential of a dramatically reduced amino acid alphabet to produce an active catalyst supports the notion that primordial enzymes may have possessed low amino acid diversity and suggests that combinatorial engineering strategies, such as the one used here, may be generally applied to create enzymes with novel structures and functions.

Elastic Deformation of Dispersely Failing Unidirectionally Reinforced Composites

A phenomenological model is proposed for describing the elastic deformation of a unidirectionally reinforced composite capable of accumulating scattered microdamages during its loading. The composite is considered as a homogeneous transversely isotropic solid. Its damaged state at every point is characterized by a centrally symmetric scalar function on the unit sphere (the damage function), which is used to account for variations in the elastic properties of the material during its deformation. The damage itself depends on the history of some equivalent strain, for which four simplified variants are suggested. The relation between strains and stresses is defined in a differential form. Dependences are presented for determining all unknown constants from simple mechanical experiments. As an example, an actual unidirectionally reinforced GFRP is considered, for which the main two-dimensional sections of corresponding failure surfaces are also constructed.

Adaptive integration of molecular dynamics.

This article presents a particle method framework for simulating molecular dynamics. For time integration, the implicit trapezoidal rule is employed, where an explicit predictor enables large time steps. Error estimators for both the temporal and spatial discretization are advocated, and facilitate a fully adaptive propagation. The framework is developed and exemplified in the context of the classical Liouville equation, where Gaussian phase-space packets are used as particles. Simplified variants are discussed briefly. The concept is illustrated by numerical examples for one-dimensional dynamics in double well potential.

Cost-optimal topology planning of hierarchical access networks

This paper deals with the problem of cost-optimal hierarchical topology planning for telecommunications access networks. The generalized problem is computationally hard and only its substantially simplified variants have been studied before. We propose a heuristic algorithm relying on iterative problem decomposition, clustering methods and local optimization. The main idea of the approach is to combine clustering and local optimization operators and to apply the combined operators iteratively within the levels of the hierarchy. By an extensive empirical analysis it is shown that the presented method efficiently solves the underlying optimization problem for instances of practical size, furthermore, it is robust to handle flexibility in the problem statement and in the cost function.

Algorithmic strategies for the single nucleotide polymorphism haplotype assembly problem.

With the consensus human genome sequenced and many other sequencing projects at varying stages of completion, greater attention is being paid to the genetic differences among individuals and the abilities of those differences to predict phenotypes. A significant obstacle to such work is the difficulty and expense of determining haplotypes--sets of variants genetically linked because of their proximity on the genome--for large numbers of individuals for use in association studies. This paper presents some algorithmic considerations in a new approach for haplotype determination: inferring haplotypes from localised polymorphism data gathered from short genome 'fragments.' Formalised models of the biological system under consideration are examined, given a variety of assumptions about the goal of the problem and the character of optimal solutions. Some theoretical results and algorithms for handling haplotype assembly given the different models are then sketched. The primary conclusion is that some important simplified variants of the problem yield tractable problems while more general variants tend to be intractable in the worst case.

A Procedure for classifying textural facies in gravel‐bed rivers

Textural patches (i.e., grain‐size facies) are commonly observed in gravel‐bed channels and are of significance for both physical and biological processes at subreach scales. We present a general framework for classifying textural patches that allows modification for particular study goals, while maintaining a basic degree of standardization. Textures are classified using a two‐tier system of ternary diagrams that identifies the relative abundance of major size classes and subcategories of the dominant size. An iterative procedure of visual identification and quantitative grain‐size measurement is used. A field test of our classification indicates that it affords reasonable statistical discrimination of median grain size and variance of bed‐surface textures. We also explore the compromise between classification simplicity and accuracy. We find that statistically meaningful textural discrimination requires use of both tiers of our classification. Furthermore, we find that simplified variants of the two‐tier scheme are less accurate but may be more practical for field studies which do not require a high level of textural discrimination or detailed description of grain‐size distributions. Facies maps provide a natural template for stratifying other physical and biological measurements and produce a retrievable and versatile database that can be used as a component of channel monitoring efforts.

Modelling of short-pulse generation in rare-gas halide excimer lasers I. The model and its verification

In part I of this paper, a comprehensive model of a short-pulse rare-gas halide excimer (RGHE) laser consisting of excimer systems with the ground state both unbound and bound is presented. It takes into account the most important fast relaxation processes occurring in the active medium, variable cavity losses programmed externally, practical layout of the cavity elements, and also nonlinear saturable and non-saturable absorption in the laser. General equations for a short-pulse RGHE laser as well as their simplified variants for KrF and XeCl lasers are formulated. Good correspondence of the model to the results of numerous experiments described in the literature is demonstrated. In part II, the model will be applied in numerical investigations of short-pulse generation in KrF and XeCl lasers by fast mode locking using a square-wave-driven Pockels modulator.