SP Model Research Articles

Reconstruction and analysis of genome-scale metabolic model of a photosynthetic bacterium.

BackgroundSynechocystis sp. PCC6803 is a cyanobacterium considered as a candidate photo-biological production platform - an attractive cell factory capable of using CO2 and light as carbon and energy source, respectively. In order to enable efficient use of metabolic potential of Synechocystis sp. PCC6803, it is of importance to develop tools for uncovering stoichiometric and regulatory principles in the Synechocystis metabolic network.ResultsWe report the most comprehensive metabolic model of Synechocystis sp. PCC6803 available, iSyn669, which includes 882 reactions, associated with 669 genes, and 790 metabolites. The model includes a detailed biomass equation which encompasses elementary building blocks that are needed for cell growth, as well as a detailed stoichiometric representation of photosynthesis. We demonstrate applicability of iSyn669 for stoichiometric analysis by simulating three physiologically relevant growth conditions of Synechocystis sp. PCC6803, and through in silico metabolic engineering simulations that allowed identification of a set of gene knock-out candidates towards enhanced succinate production. Gene essentiality and hydrogen production potential have also been assessed. Furthermore, iSyn669 was used as a transcriptomic data integration scaffold and thereby we found metabolic hot-spots around which gene regulation is dominant during light-shifting growth regimes.ConclusionsiSyn669 provides a platform for facilitating the development of cyanobacteria as microbial cell factories.

Super-parameterization in ocean modeling: Application to deep convection

We explore the efficacy of “super parameterization” ( SP) in ocean modeling in which local 2-d non-hydrostatic plume-resolving fine-grained ( FG) models are embedded at each vertical column of a coarse-grained ( CG) hydrostatic model. A general multi-scale algorithm is described in which tendencies from the FG models are projected onto the CG model which in turn constrains the average state of the FG models, coupling the two models together. The approach is tested in the context of models of open ocean deep convection and compared with a pure hydrostatic, coarse resolution model using convective adjustment ( HYD) and a full 3-d non-hydrostatic plume-resolving simulation ( NH). The SP model is found to be greatly superior to HYD at much less computational cost than the fully non-hydrostatic calculation.

3D RFEC simulations for the in-service inspection of steam generator tubes in fast breeder reactors

Three-dimensional numeric simulations, based on the finite element model, are conducted to simulate the In-Service Inspection of magnetic steam generator tubes of a Fast Breeder Reactor using remote field eddy current probes. The influen ce of sodium in the gap SP-tube and outer defect detectability is computed for a large SP model with multiple SG tubes using the 3D-RFECT code.

Component identification of electron transport chains in curdlan-producing Agrobacterium sp. ATCC 31749 and its genome-specific prediction using comparative genome and phylogenetic trees analysis

Agrobacterium sp. ATCC 31749 (formerly named Alcaligenes faecalis var. myxogenes) is a non-pathogenic aerobic soil bacterium used in large scale biotechnological production of curdlan. However, little is known about its genomic information. DNA partial sequence of electron transport chains (ETCs) protein genes were obtained in order to understand the components of ETC and genomic-specificity in Agrobacterium sp. ATCC 31749. Degenerate primers were designed according to ETC conserved sequences in other reported species. DNA partial sequences of ETC genes in Agrobacterium sp. ATCC 31749 were cloned by the PCR method using degenerate primers. Based on comparative genomic analysis, nine electron transport elements were ascertained, including NADH ubiquinone oxidoreductase, succinate dehydrogenase complex II, complex III, cytochrome c, ubiquinone biosynthesis protein ubiB, cytochrome d terminal oxidase, cytochrome bo terminal oxidase, cytochrome cbb (3)-type terminal oxidase and cytochrome caa (3)-type terminal oxidase. Similarity and phylogenetic analyses of these genes revealed that among fully sequenced Agrobacterium species, Agrobacterium sp. ATCC 31749 is closest to Agrobacterium tumefaciens C58. Based on these results a comprehensive ETC model for Agrobacterium sp. ATCC 31749 is proposed.

Low-energy effective-field theories of Sp(4) spin systems

We study the classical and quantum phase transitions of Sp(4) spin systems on three-dimensional stacked square and triangular lattices. We present general Ginzburg-Landau field theories for various types of Sp(4) spin orders with different ground-state manifolds such as CP(3), ${S}^{7}/{Z}_{2}$, Grassmann manifold ${G}_{2,5}$, ${G}_{2,6}$, and so on, based on which the nature of the classical phase transitions are studied, and a global phase diagram is presented. The classical phase transitions close to quantum phase transitions toward spin-liquid states are also discussed based on renormalization group flow. Our results can be directly applied to the simplest Sp(4) and SU(4) Heisenberg models which can be realized using spin-3/2 atoms and alkaline-earth atoms trapped in optical lattice.

Green chemistry volumetric titration kit for pharmaceutical formulations: Econoburette

Stopcock SC and Spring Sp models of Econoburette (Calibrated, RTC (NR), Ministry of Small Scale Industries, Government of India), developed for semimicro volumetric titration of pharmaceutical formulations are reported. These are economized and risk free titration where pipette is replaced by an inbuilt pipette and conical flask by inbuilt bulb. A step of pipetting of stock solution by mouth is deleted. It is used to allow solution exposure to user’s body. This risk is removed and even volatile and toxic solutions are titrated with full proof safety. Econoburette minimizes use of materials and time by 90 % and prevent discharge of polluting effluent to environment. Few acid and base samples are titrated and an analysis of experimental expenditure isdescribed in the papers.

Evaluation of Heavy Metals Loading of River Ijana in Ekpan – Warri, Nigeria

The concentration of Cadmium (Cd), Chromium (Cr), Copper (Cu), Iron (Fe), Nickel (Ni), Lead (Pb) and Zinc (Zn) which may affect human health and the “health” of the aquatic ecosystem were determine in the River Ijana Ekpan, using a pye unicam Atomic Absorption Spectrometry SP model 2900. The level of heavy metal in the study area varied between Cd (0.010 ± 0.004mgl-1) and (0.100 ±0.014mg1-1); Cr (0.037 ± 0.006mg1-1) and (0.067 ± 0.020mg1-1), Cu (0.020 ± 0.004mg1-1) and (0.050 ± 0.029mg1-1); Fe (0.046 ± 0.007 mg1-1) and (0.229 ± 0.008mg1-1); Ni (0.030 ± 0.004mg1-1) and (0.080 ± 0.010mg1-1); Pb (0.025 ± 0.006mg1-1) and (0.058 ± 0.008mg1-1) and Zn (0.088 ± 0.012mg1-1) and (0.122 ± 0.007mg1-1). The concentration of these parameters of pollution contained in the study area (SS1 – SS3) indicated that the River is fairly polluted. The possible sources of these parameters of pollution are diverse: originating from anthropogenic / natural and point sources. @JASEM

Modelling the demand for medium distance air travel with the mixed data estimation method

A stated preference experiment is developed looking at airplane and a fictitious high-speed train trips between Santiago and Concepción in Chile. Four variables are used – travel time, fare, comfort, and service delay; a factorial fractional design allowed the experimental size to be reduced to nine pairs of options. Trip characteristics and socio-economic information were also gathered for each respondent. With the purpose of overcoming the potential imperfections that pure SP models are known to have, we incorporated revealed preference data, obtained in a previous study, including bus, train and airplane travellers. Mixed stated and revealed preference models were estimated and compared with those obtained from the stated preference data alone. Finally, a second group of stated preference data is added. Different specifications were tested with mixed stated and revealed preference data. Moreover, by segmenting the sample we were able to derive subjective values of time for different kinds of individuals.

Crystallographic B-Factors Highlight Energetic Frustration in Aldolase Folding

Kinetic simulations of the folding and unfolding of the mammalian TIM barrel protein aldolase were conducted to determine if a minimalist monomeric Gō model, using the native structure to determine attractive energies in the protein chain, could capture the experimentally determined folding pathway. The folding order, that is, the order in which different secondary structures fold, between the Gō model simulations and that from hydrogen-deuterium exchange experiments, did not agree. To explain this discrepancy, two alternate variant of the basic Gō model were simulated: (1) a monomer Gō model with native contact energies weighted by a statistical potential (SP model) and (2) a monomer Gō model with native contact energies inversely weighted by crystallographic B factors (B model). The B model demonstrated the best agreement between simulation and experiments. The success of the B model is attributed to the ability of B factors to highlight local energetic frustration in the aldolase structure which results in weaker native contacts in these frustrated regions. The predictive success of the B model also reveals the potential use of B factor information for energetic weighting in general protein modeling.

The scheduling of deliveries in a production-distribution system with multiple buyers

In a real production and distribution business environment with one supplier and multiple heterogeneous buyers, the differences in buyers’ ordering cycles have influence on production arrangements. Consequently, the average inventory level (AIL) at the supplier’s end is affected by both the production policy and the ordering policy, typically by the scheduling of deliveries. Consequently, the average inventory holding cost is most deeply affected. In this paper, it is proposed that the scheduling of deliveries be formulated as a decision problem to determine the time point at which deliveries are made to buyers in order to minimize the supplier’s average inventory. A formulation of the average inventory level (AIL) in a production cycle at the supplier’s end using a lot-for-lot policy is developed. Under the lot-for-lot policy, the scheduling of deliveries (SP) is formulated as a nonlinear programming model used to determine the first delivery point for each buyer with an objective to minimize the sum of the product of the individual demand quantity and the first delivery time for each buyer. Thus, the SP model determines not only the sequence of the first deliveries to individual buyers, but also the time when the deliveries are made. An iterative heuristic procedure (IHP) is developed to solve the SP model assuming a given sequence of buyers. Six sequence rules are considered and evaluated via simulation.

Stellar polytropes and Navarro–Frenk–White halo models: comparison with observations

Motivated by the possible conflict between the Navarro–Frenk–White (NFW) modelpredictions for the dark matter contents of galactic systems and its correlation withbaryonic surface density, we will explore an alternative paradigm for the description of darkmatter halos. Such an alternative emerges from Tsallis’ non-extensive thermodynamicsapplied to self-gravitating systems and leads to the so-called ‘stellar polytrope’ (SP) model.We consider that this could be a better approach to real structures rather than theisothermal model, given the fact that the first one takes into account the non-extensivity ofenergy and entropy present in these type of systems characterized by long-rangeinteractions. We compare a halo based on the Navarro–Frenk–White (NFW) modeland one which follows the SP description. Analysing the dark matter contentsestimated by means of global physical parameters of galactic discs, obtained from asample of actual galaxies, with the ones of the unobserved dark matter halos, weconclude that the SP model is favoured over the NFW model in such a comparison.

Towards an intelligent database system founded on the SP theory of computing and cognition

The SP theory of computing and cognition, described in previous publications, is an attractive model for intelligent databases because it provides a simple but versatile format for different kinds of knowledge, it has capabilities in artificial intelligence, it can function effectively in the face of errors in its input data, and it can function like established database models when that is required. This paper first describes the SP theory in outline and the computer models in which it is expressed. The main sections of the paper describe, with examples from the SP62 computer model, how the SP framework can emulate other abstract models used in database applications: the relational model (including retrieval of information in the manner of query-by-example, creating a join between two or more tables, and aggregation), object-oriented models (including class-inclusion hierarchies, part-whole hierarchies and their integration, inheritance of attributes, cross-classification and multiple inheritance), and hierarchical and network models (including discrimination networks). Comparisons are made between the SP model and those other models. The artificial intelligence capabilities of the SP model are briefly reviewed: representation and integration of diverse kinds of knowledge in one versatile format; fuzzy pattern recognition and recognition at multiple levels of abstraction; best-match and semantic forms of information retrieval; various kinds of exact reasoning and probabilistic reasoning; analysis and production of natural language; planning; problem solving; and unsupervised learning. Also considered are ways in which current prototypes may be translated into an ‘industrial strength’ working system.

PRESENTATIONS OF WESS–ZUMINO–WITTEN FUSION RINGS

The fusion rings of the Wess–Zumino–Witten models are re-examined. Attention is drawn to the difference between fusion rings over ℤ (which are often of greater importance in applications) and fusion algebras over ℂ. Complete proofs are given by characterizing the fusion algebras (over ℂ) of the SU (r+1) and Sp (2r) models in terms of the fusion potentials, and it is shown that the analagous potentials cannot describe the fusion algebras of the other models. This explains why no other representation-theoretic fusion potentials have been found. Instead, explicit generators are then constructed for general WZW fusion rings (over ℤ). The Jacobi–Trudy identity and its Sp (2r) analogue are used to derive the known fusion potentials. This formalism is then extended to the WZW models over the spin groups of odd rank, and explicit presentations of the corresponding fusion rings are given. The analogues of the Jacobi–Trudy identity for the spinor representations (for all ranks) are derived for this purpose, and may be of independent interest.

SP기법을 이용한 마산항 컨테이너 터미널의 고객선호도 분석

최근 마산항에서는 마산항 개발(1-1단계) 민간투자시설사업을 통해 2011년 개장을 목표로 총 새로운 컨테이너 터미널 개발에 착수하였다. 그러나 인근의 부산신항을 비롯한 울산항 역시 동일한 시기에 새로운 컨테이너 항만의 개장을 예정하고 있어 마산항은 향후 이러한 경쟁항만들과의 치열한 경쟁을 대비한 전략수립이 요구된다. 이러한 배경에서 본 연구에서는 소비자 행동분석에 많이 활용되고 있는 SP기법을 활용하여 향후 마산항을 비롯한 경쟁 항만들의 이용여건 변화 시 고객(화주 및 선사)들의 선호도 변화를 분석하고 그에 따른 전략적 시사점을 도출하였다. Recently, the development construction of New Masan Container Terminal (1-1 Phase) with private investment would be set for opening in the 2011 year in Masan Port, Korea However, as new container terminals of the Pusan New Port and 'the New Ulsan Container Terminal neighboring Masan Port will be also planned to open around the time, the strategy establishment for Masan Port is required for a keen competition among these ports. To provide it with strategic points, we applied SP model used for customers' behavior method to analyze customer's preference changes with the shifts of the ports' conditions for customers.

Isospin symmetry breaking in an algebraic pairing Sp(4) model

An exactly solvable $\mathfrak{sp}(4)$ algebraic approach extends beyond the traditional isospin-conserving nuclear interaction to bring forward effects of isospin symmetry breaking and isospin mixing resulting from a two-body nuclear interaction that includes proton-neutron (pn) and like-particle isovector pairing correlations plus significant isoscalar pn interactions. The model yields an estimate for the extent to which isobaric analog ${0}^{+}$ states in light and medium-mass nuclei may mix with one another and reveals possible, but still extremely weak, nonanalog $\ensuremath{\beta}$-decay transitions.

Comparison of the coefficients of RP and SP models for modal choice (a case study of Karachi City, Pakistan)

This study attempted to find out the comparison between the coefficients of the similar exogenous variables of the two multinomial logit models. These models were developed for the city of Karachi, the business capital of Pakistan. The two models were developed with the Revealed Preference and Stated Preference data. The choice set for the model developed with PR data was car, motorcycle, Para transit, bus and coach. All the information about these modes was directly asked from the commuters in the survey carried out for modeling the travel behavior. However in the SP data model, the new mode of magnetic train was included in the choice set and the surveyors gave all the information to the commuters and they were asked about their preference. The coefficients of variables used in the utility functions were calibrated by using the HIELOW software. Chi-Square analysis was carried out to find out the difference between the coefficients of the similar exogenous variables of the two models. It was revealed that the difference between the coefficients of travel time public, car ownership, motorcycle ownership, income coach, age bus and age Para transit and household public for RP and SP data was found to be significant at 95 % confidence level. It was found that mostly variables of the RP data set related with public transportation were significantly different from the same variables of the SP data set, except car ownership and sex Para transit. As the magnetic train was included in the public mode and as it was observed that the major share from the (Bus and Coach users) will shift to the new magnetic train so the parameters related to public transportation were found to be significant. The reason for this unexpected result of car ownership was that it was related with the modal constant of car, which was comparatively high in the SP data set. For the covering abstract see ITRD E129315.

Analysis of Seamless Transit Services in Rural Areas

This paper attempts to clarify better combinations of a new local bus system (i. e., DRT: Demand Responsive Transport) and existing regional buses at a bus terminal in order to provide convenient transfers between them in depopulated rural areas, where local buses are more frequent than regional ones. Especially, the paper focuses on how the elderly people's preferences of bus use are influenced by terminal environments, waiting time at the terminal and other level-of-service factors. For that purpose, bus use two SP models of bus use are developed to analyze the influences of seamless transfers at the terminal on the preferences of using both local and regional bus services. Furthermore, the required facilities and services when waiting at the terminal are also investigated, using the Covariance Structure Analysis method, from the perspective of improving the convenience and amenity

Modelling the extraction of essential oils with compressed carbon dioxide

Three models were used to describe the extraction of essential oils from oregano bracts using compressed carbon dioxide. They were developed on the basis of a plate-like geometry of the particles and were tested experimentally using various bract pre-treatments, pressures, temperatures and solvent flow rates. The two particle phase derived models applied, the Single Plate model (SP model) and the Simple Single Plate model (SSP model), differ only by the allowance or not for a film coefficient ( k f) and have as the only adjustable parameter the matrix diffusivity ( D m). The third model, the Fluid Phase/Simple Single Plate model (FP/SSP model), considers both the particle mass balance and a detailed description of the fluid mass balance. In addition to the matrix diffusivity the FP/SSP model may require the adjustment of the fraction of oil leached by the solvent during the pressurisation procedure ( f 0). All models gave a good fit to the experimental data though the FP/SSP model gave the best fit. However, the matrix diffusivities found correlated very poorly with the estimated diffusivity of essential oils in carbon dioxide ( D 12), which indicates a complex intraparticle transport.

Chemical Vapor Infiltration Rates of ZrO2into MoSi2Porous Bodies and Comparison with Model Calculation

Zirconia (ZrO 2 ) was chemical vapor infiltrated (CVI) into a partially sintered MoSi 2 body (preform) by using zirconium n-propoxide (Zr(OC 3 H 7 ) 4 ) as a gas precursor. Infiltration distances at different conditions were compared with the calculated results. Chemical vapor deposition (CVD) film growth rates of ZrO 2 were measured, and the data were incorporated into the model calculations. Two models were used to analyze the observed infiltration distances. Initially a conventional model assuming a pore with constant radius (SP model) was used. With this model, it was possible to predict the approximate infiltration distance. However, the model cannot predict pore closure and the infiltration distances for a variety of CVI conditions. Secondly, a newly proposed model (PC model) from a previous paper was applied to calculate the infiltration distance. Using this model, it was possible to predict the occurrence of pore closure or the formation of the deposition layer on the preform surface.

Staggering behavior of the low-lying excited states of even-even nuclei in aSp(4,R)classification scheme

We implement a high order discrete derivative analysis of the low lying collective energies of even-even nuclei with respect to the total number of valence nucleon pairs N in the framework of F- spin multiplets appearing in a symplectic sp(4,R) classification scheme. We find that for the nuclei of any given F- multiplet the respective experimental energies exhibit a Delta N=2 staggering behavior and for the nuclei of two united neighboring F- multiplets well pronounced Delta N=1 staggering patterns are observed. Those effects have been reproduced successfully through a generalized sp(4,R) model energy expression and explained in terms of the step-like changes in collective modes within the F- multiplets and the alternation of the F-spin projection in the united neighboring multiplets. On this basis we suggest that the observed Delta N=2 and Delta N=1 staggering effects carry detailed information about the respective systematic manifestation of both high order alpha - particle like quartetting of nucleons and proton (neutron) pairing interaction in nuclei.PACS number(s):21.10.Re, 21.60.Fw