Phase behaviour of DNA in presence of DNA-binding proteins

To characterize the thermodynamical equilibrium of DNA chains interacting with a solution of non-specific binding proteins, a Flory-Huggins free energy model was implemented. We explored the dependence on DNA and protein concentrations of the DNA collapse. For physiologically relevant values of the DNA-protein affinity, this collapse gives rise to a biphasic regime with a dense and a dilute phase; the corresponding phase diagram was computed. Using an approach based on Hamiltonian paths, we show that the dense phase has either a molten globule or a crystalline structure, depending on the DNA bending rigidity, which is influenced by the ionic strength. These results are valid at the thermodynamical equilibrium and should therefore be consistent with many biological processes, whose characteristic timescales range typically from 1 ms to 10 s. Our model may thus be applied to biological phenomena that involve DNA-binding proteins, such as DNA condensation with crystalline order, which occurs in some bacteria to protect their chromosome from detrimental factors; or transcription initiation, which occurs in clusters called transcription factories that are reminiscent of the dense phase characterized in this study.Comment: 20 pages, 9 figures, accepted for publication at The Biophysical Journa

On Restricting Real-Valued Genotypes in Evolutionary Algorithms

Real-valued genotypes together with the variation operators, mutation and crossover, constitute some of the fundamental building blocks of Evolutionary Algorithms. Real-valued genotypes are utilized in a broad range of contexts, from weights in Artificial Neural Networks to parameters in robot control systems. Shared between most uses of real-valued genomes is the need for limiting the range of individual parameters to allowable bounds. In this paper we will illustrate the challenge of limiting the parameters of real-valued genomes and analyse the most promising method to properly limit these values. We utilize both empirical as well as benchmark examples to demonstrate the utility of the proposed method and through a literature review show how the insight of this paper could impact other research within the field. The proposed method requires minimal intervention from Evolutionary Algorithm practitioners and behaves well under repeated application of variation operators, leading to better theoretical properties as well as significant differences in well-known benchmarks

Theoretical analysis of a novel integrated energy system formed by a microturbine and a exhaust fired single-double effect absorption chiller

Integrated Energy Systems (IES) combine a distributed power generation system (DG) such as a microturbine generator (MTG) or a fuel cell with thermally activated technologies (TAT) such as absorption cooling. This integration maximizes the efficiency of energy use by utilizing on-site most of the waste heat generated by DG, and reduces harmful emissions to the environment. This study investigates the energy and exergy performance of an IES. This system is comprised of an MTG with internal recuperator and a novel absorption cooling cycle. The absorption cycle is a single-double effect exhaust fired cycle, which recuperates the heat exchanged from the MTG exhaust gases using two generators at two different levels of temperature. The selection of the DG element, the TAT element and their internal configurations is based upon a real IES commercial unit that has been tested in the APEP-UCI DG testing facilities in Irvine, California. This unit has an electrical power capacity of 28 kW and a cooling capacity of 14 refrigeration tons (49.2 kW). Inputs for the thermodynamic models developed for the MTG and for the absorption cycle are derived from experimental variables that will be controlled in the testing phase. The MTG model is using empirical correlations for key model parameters (pressure ratio, turbine inlet temperature, etc.) from previous studies in order to predict the observed change in performance with part load operation. The calculated mass flow rate and temperature of the exhaust gases are inputs for the absorption cycle model, together with cooling and chilled water inlet temperatures and flow rates. Heat and mass transferefficiencies along with heat transfer coefficients for the suite of heat exchangers comprising the single-double effect absorption cycle are determined from proprietary testing data provided by the manufacturers

Fuel injector: Air swirl characterization aerothermal modeling, phase 2, volume 1

A well integrated experimental/analytical investigation was conducted to provide benchmark quality relevant to a prefilming type airblast fuel nozzle and its interaction with the combustor dome air swirler. The experimental investigation included a systematic study of both single-phase flows that involved single and twin co-axial jets with and without swirl. A two-component Phase Doppler Particle Analyzer (PDPA) was used to document the interaction of single and co-axial air jets with glass beads that simulate nonevaporating spray and simultaneously avoid the complexities associated with fuel atomization processes and attendant issues about the specification of relevant boundary conditions. The interaction of jets with methanol spray produced by practical airblast nozzle was also documented in the spatial domain of practical interest. Model assessment activities included the use of three turbulence models (k-epsilon, algebraic second moment (ASM), and differential second moment (DSM)) for the carrier phase, deterministic or stochastic Lagrangian treatment of the dispersed phase, and advanced numerical schemes. Although qualitatively good comparison with data was obtained for most of the cases investigated, the model deficiencies in regard to modeled dissipation rate transport equation, single length scale, pressure-strain correlation, and other critical closure issues need to be resolved before one can achieve the degree of accuracy required to analytically design combustion systems

Optimization of circular orifice jets mixing into a heated cross flow in a cylindrical duct

To examine the mixing characteristics of circular jets in an axisymmetric can geometry, temperature measurements were obtained downstream of a row of cold jet injected into a heated cross stream. The objective was to obtain uniform mixing within one duct radius downstream of the leading edge of the jet orifices. An area weighted standard deviation of the mixture fraction was used to help quantify the degree of mixedness at a given plane. Non-reacting experiments were conducted to determine the influence of the number of jets on the mixedness in a cylindrical configuration. Results show that the number of orifices significantly impacts the mixing characteristics of jets injected from round hole orifices in a can geometry. Optimum mixing occurs when the mean jet trajectory aligns with the radius which divides the cross sectional area of the can into two equal parts at one mixer radius downstream of the leading edge of the orifice. The optimum number of holes at momentum-flux ratios of 25 and 52 is 10 and 15 respectively

Børsintroduksjoner : prising av norske børsintroduksjoner med vekt på oljerelaterte selskaper

Vår utredning tar for seg 38 børsintroduksjoner i perioden 01.01.04 til 31.12.05. Vi har fokusert spesielt på de 12 oljerelaterte selskapene som ble introdusert i perioden. I analysen har vi sett på selskapenes avkastning på kort og lang sikt og sammenlignet med den generelle avkastningen i aksjemarkedet, målt ved OSEBX indeksen. De oljerelaterte selskapene har vi også sammenlignet med bransjen, målt ved OSE10 Energy indeksen. Videre har vi sett på om det er noen sammenheng mellom hvor emisjonskursen blir satt i forhold til indikert pris (indikert prisintervall) og størrelsen på startavkastningen. Til slutt har vi rangert meglerhusene (som har rollen som tilrettelegger i en børsintroduksjon) basert på antall selskaper de er tilrettelegger for i perioden og sammenholder dette med startavkastning for å undersøke om det foreligger en sammenheng. Den teoretiske delen innledes med å beskrive grunnen til at selskaper velger å gå på børs samt en beskrivelse av børsintroduksjonsprosessen. Videre legger vi forholdsvis stor vekt på å gjøre rede for ulike teorier som prøver å forklare den til dels høye startavkastningen på kort sikt og den dårlige avkastningen på lang sikt som man har observert i de fleste aksjemarkeder. I analysen har vi kommet frem til at startavkastningen, justert for den generelle markedsutviklingen, gjennomsnittlig for selskapene samlet har vært på 2,21 %. For de oljerelaterte selskapene har startavkastningen vært høyere (4,84 %), mens startavkastningen til de ikke oljerelaterte var lavere (1,12 %). Dette er resultater som er langt lavere enn det som har vært observert i tidligere studier. Vi ser også på om det er noen sammenheng mellom hvor emisjonsprisen havner i prisintervallet og startavkastningen. For de ikke-oljerelaterte selskapene ser vi at der emisjonskursen havner i den øvre delen av prisintervallet er det en positiv startavkastning, mens startavkastningen er negativ for de selskapene der emisjonsprisen havner i nedre del av prisintervallet. For de oljerelaterte selskapene er startavkastningen, noe overraskende, svært positiv når emisjonskursen havner i nedre del av intervallet. I analysen av tilretteleggers betydning for startavkastningen får vi ikke noe entydig resultat. Vi har rangert tilretteleggerne etter antall børsintroduksjoner de har gjennomført i perioden. Den tilretteleggeren med flest børsintroduksjoner har i gjennomsnitt en positiv startavkastning, mans flere av tilretteleggerne med få børsintroduksjoner har negativ startavkastning. For å sammenligne selskapenes avkastning på lengre sikt i forhold til den generelle markedsutviklingen, og for oljesektoren spesielt, har vi beregnet den markedsjusterte avkastningen etter 3 mnd, 6 mnd, 9 mnd og 12 mnd. For selskapene samlet reduseres den markedsjusterte avkastningen fra 9,96 % etter 3 mnd til 0,01 % etter 12 mnd. Det samme bilde får vi når vi kun ser på de ikke-oljerelaterte selskapene der den markedsjusterte avkastningen er -26,32 % etter 12 mnd. Dette stemmer overens med tidligere empiri. Ser vi spesielt på de oljerelaterte selskapene har de en helt annen utvikling på lang sikt. Her øker den langsiktige markedsjusterte avkastningen fra 12,57 % etter 3 mnd til 68,46 % etter 12 mnd. Sammenligner vi de oljerelaterte selskapene med bransjen, blir den markedsjusterte avkastningen redusert til 39,33 % etter 12 mnd. Det at de nye oljeselskapene har gjort det til dels mye bedre enn resten av selskapene på børsen samt bransjen, strider med tidligere empiri

Discrete Nonlinear Schrodinger Equations with arbitrarily high order nonlinearities

A class of discrete nonlinear Schrodinger equations with arbitrarily high order nonlinearities is introduced. These equations are derived from the same Hamiltonian using different Poisson brackets and include as particular cases the saturable discrete nonlinear Schrodinger equation and the Ablowitz-Ladik equation. As a common property, these equations possess three kinds of exact analytical stationary solutions for which the Peierls-Nabarro barrier is zero. Several properties of these solutions, including stability, discrete breathers and moving solutions, are investigated

Phase Locking Between Fiske and Flux-Flow Modes in Coupled Sine-Gordon Systems

We investigate nonlinear resonant modes in coupled sine-Gordon systems with open boundary conditions. The system models coupled Josephson junctions with boundary conditions representing the situation where an external magnetic field is applied. The so-called Fiske modes are found to exist in phase-locked states where the equivalent voltages across the individual coupled Josephson junctions are either identical or identical with opposite signs. The analysis covers all Fiske modes including the flux-flow region. We present a comprehensive comparison between results on analytical treatment and direct numerical simulations of the coupled field equations

Aerothermal modeling program, phase 2

The main objectives of the Aerothermal Modeling Program, Phase 2 are: to develop an improved numerical scheme for incorporation in a 3-D combustor flow model; to conduct a benchmark quality experiment to study the interaction of a primary jet with a confined swirling crossflow and to assess current and advanced turbulence and scalar transport models; and to conduct experimental evaluation of the air swirler interaction with fuel injectors, assessments of current two-phase models, and verification the improved spray evaporation/dispersion models