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

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. Element C: Fuel injector-air swirl characterization

The main objectives of the NASA-sponsored Aerothermal Modeling Program, Phase 2--Element C, are experimental evaluation of the air swirler interaction with a fuel injector in a simulated combustor chamber, assessment of the current two-phase models, and verification of the improved spray evaporation/dispersion models. This experimental and numerical program consists of five major tasks. Brief descriptions of the five tasks are given

Aerothermal modeling program, Phase 2, Element C: Fuel injector-air swirl characterization

The main objectives of the NASA sponsored Aerothermal Modeling Program, Phase 2, Element C, are to collect benchmark quality data to quantify the fuel spray interaction with the turbulent swirling flows and to validate current and advanced two phase flow models. The technical tasks involved in this effort are discussed

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

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

Exact Solutions of the Two-Dimensional Discrete Nonlinear Schr\"odinger Equation with Saturable Nonlinearity

We show that the two-dimensional, nonlinear Schr\"odinger lattice with a saturable nonlinearity admits periodic and pulse-like exact solutions. We establish the general formalism for the stability considerations of these solutions and give examples of stability diagrams. Finally, we show that the effective Peierls-Nabarro barrier for the pulse-like soliton solution is zero

Design Concepts for Co-Production of Power, Fuels & Chemicals Via Coal/Biomass Mixtures

The overall goal of the program is to develop design concepts, incorporating advanced technologies in areas such as oxygen production, feed systems, gas cleanup, component separations and gas turbines, for integrated and economically viable coal and biomass fed gasification facilities equipped with carbon capture and storage for the following scenarios: (i) coproduction of power along with hydrogen, (ii) coproduction of power along with fuels, (iii) coproduction of power along with petrochemicals, and (iv) coproduction of power along with agricultural chemicals. To achieve this goal, specifically the following objectives are met in this proposed project: (i) identify advanced technology options and innovative preliminary design concepts that synergistically integrate plant subsections, (ii) develop steady state system simulations to predict plant efficiency and environmental signature, (iii) develop plant cost estimates by capacity factoring major subsystems or by major equipment items where required, and then capital, operating and maintenance cost estimates, and (iv) perform techno- economic analyses for the above described coproduction facilities. Thermal efficiencies for the electricity only cases with 90% carbon capture are 38.26% and 36.76% (HHV basis) with the bituminous and the lignite feedstocks respectively. For the coproduction cases (where 50% of the energy exported is in the form of electricity), the electrical efficiency, as expected, is highest for the hydrogen coproduction cases while lowest for the higher alcohols (ethanol) coproduction cases. The electrical efficiencies for Fischer-Tropsch coproduction cases are slightly higher than those for the methanol coproduction cases but it should be noted that the methanol (as well as the higher alcohol) coproduction cases produce the finished coproduct while the Fischer-Tropsch coproduction cases produce a coproduct that requires further processing in a refinery. The cross comparison of the thermal performance between the various coproduct cases is further complicated by the fact that the carbon footprint is not the same when carbon leaving with the coproduct are accounted for. The economic analysis and demand for a particular coproduct in the market place is a more meaningful comparison of the various coproduction scenarios. The first year cost of electricity calculated for the bituminous coal is $102.9/MWh while that for the lignite is$108.1/MWh. The calculated cost of hydrogen ranged from $1.42/kg to$2.77/kg depending on the feedstock, which is lower than the DOE announced hydrogen cost goal of $3.00/kg in July 14, 2005. Methanol cost ranged from$345/MT to $617/MT, while the market price is around$450/MT. For Fischer-Tropsch liquids, the calculated cost ranged from $65/bbl to$112/bbl, which is comparable to the current market price of crude oil at around $100/bbl. It should be noted, however, that F-T liquids contain no sulfur and nitrogen compounds. The calculated cost of alcohol ranged from$4.37/gal to $5.43/gal, while it ranged from$2.20/gal to $3.70/gal in a DOE funded study conducted by Louisiana State University. The Louisiana State University study consisted of a significantly larger plant than our study and benefited from economies of scale. When the plant size in our study is scaled up to similar size as in the Louisiana State University study, cost of alcohol is then reduced to a range of$3.24/gal to $4.28/gal, which is comparable. Urea cost ranged from$307/MT to $428/MT, while the market price is around$480/MT