Temperature, ordering, and equilibrium with time-dependent confining forces

The concepts of temperature and equilibrium are not well defined in systems of particles with time-varying external forces. An example is a radio frequency ion trap, with the ions laser cooled into an ordered solid, characteristic of sub-mK temperatures, whereas the kinetic energies associated with the fast coherent motion in the trap are up to 7 orders of magnitude higher. Simulations with 1,000 ions reach equilibrium between the degrees of freedom when only aperiodic displacements (secular motion) are considered. The coupling of the periodic driven motion associated with the confinement to the nonperiodic random motion of the ions is very small at low temperatures and increases quadratically with temperature.

Modeling and optimization of populations subject to time-dependent mutation.

It has become clear that many organisms possess the ability to regulate their mutation rate in response to environmental conditions. So the question of finding an optimal mutation rate must be replaced by that of finding an optimal mutation schedule. We show that this task cannot be accomplished with standard population-dynamic models. We then develop a "hybrid" model for populations experiencing time-dependent mutation that treats population growth as deterministic but the time of first appearance of new variants as stochastic. We show that the hybrid model agrees well with a Monte Carlo simulation. From this model, we derive a deterministic approximation, a "threshold" model, that is similar to standard population dynamic models but differs in the initial rate of generation of new mutants. We use these techniques to model antibody affinity maturation by somatic hypermutation. We had previously shown that the optimal mutation schedule for the deterministic threshold model is phasic, with periods of mutation between intervals of mutation-free growth. To establish the validity of this schedule, we now show that the phasic schedule that optimizes the deterministic threshold model significantly improves upon the best constant-rate schedule for the hybrid and Monte Carlo models.

Difference schemes for time-dependent heat conduction models with delay

Different non-Fourier models of heat conduction, that incorporate time lags in the heat flux and/or the temperature gradient, have been increasingly considered in the last years to model microscale heat transfer problems in engineering. Numerical schemes to obtain approximate solutions of constant coefficients lagging models of heat conduction have already been proposed. In this work, an explicit finite difference scheme for a model with coefficients variable in time is developed, and their properties of convergence and stability are studied. Numerical computations showing examples of applications of the scheme are presented.

Basic studies in heat transfer and fluid flow.

"Quarterly progress report".

Basic experimental studies on boiling fluid flow and heat transfer at elevated pressures for month of ...

"Monthly progress report".

Time-dependent descriptors for the Poisson queue.

Bibliography: p. 67-68.

Heat transfer and fluid flow; a bibliography of selected report literature.

"TID-3305 (Supplement 1)"

Fluid flow through a spherical vessel containing distributed heat sources.

"Work performed under contract no. W-7405-Eng-26"

Determination of chromophore charge states in the low pH color transition of the fluorescent protein Rtms5(H146S) via time-dependent DFT

The red fluorescent protein Rtms5H146S displays a transition from blue (absorbance λmax 590 nm) to yellow (absorbance λmax not, vert, similar453 nm) upon titration to low pH. The pKa of the reaction depends on the concentration of halide, offering promise for new expressible halide sensors. The protonation state involved in the low pH form of the chromophore remains, however, ambiguous. We report calculated excitation energies of different protonation states of an RFP chromophore model. These suggest that the relevant titration site is the phenoxy moiety of the chromophore, and the relevant base and conjugate acid are anionic and neutral chromophore species, respectively.

Timing and chemistry of fluid-flow events in the Lawn Hill Platform, Northern Australia

Mudrocks and carbonates of the Isa superbasin in the Lawn Hill platform in northern Australia host major base metal sulfide mineralization, including the giant strata-bound Century Zn-Pb deposit. Mineral paragenesis, stable isotope, and K-Ar dating studies demonstrate that long-lived structures such as the Termite Range fault acted as hot fluid conduits several times during the Paleoproterozoic and Mesoproterozoic in response to major tectonic events. Illite and chlorite crystallinity studies suggest the southern part of the platform has experienced higher temperatures (up to 300 degrees C) than similar stratigraphic horizons in the north. The irregular downhole variation of illite crystallinity values provides further information oil the thermal regime in the basin and shows that clay formation was controlled not only by temperature increase with depth but also by high water/rock ratios along relatively permeable zones. K-Ar dating of illite, in combination with other data, may indicate three major thermal events in the central and northern Lawn Hill platform Lit 1500, 1440 to 1400, and 1250 to 1150 Ma. This study did not detect the earlier Century base metal mineralizing event at 1575 Ma. 1500 Ma ages are recorded only in the south and correspond to the age of the Late Isan orogeny and deposition of the Lower Roper superbasin. They may reflect exhumation of a provenance region. The 1440 to 1300 Ma ages are related to fault reactivation and a thermal pulse at similar to 1440 to 1400 Ma possibly accompanied by fluid flow, with subsequent enhanced cooling possibly due to thermal relaxation or further crustal exhumation. The youngest thermal and/or fluid-flow event at 1250 to 1150 Ma is recorded mainly to the cast of the Tern-lite Range fault and may be related to the assembly of the Rodinian supercontinent. Fluids in equilibrium with illite that formed over a range of temperatures, at different times in different parts of the platform. have relatively uniform oxygen isotope compositions and more variable hydrogen isotope compositions (delta O-18 = 3.5-9.7 parts per thousand V-SMOW; delta D = -94 to -36 parts per thousand V-SMOW). The extent of the 180 enrichment and the variably depleted hydrogen isotope compositions suggest the illite interacted with deep-basin hypersaline brines that were composed of evaporated seawater and/or highly evolved meteoric water. Siderite is the most abundant iron-rich gangue phase in the Century Zn-Pb deposit, which is surrounded by all extensive ferroan carbonate alteration halo. Modeling suggests that the ore siderite formed at temperatures of 120 degrees to 150 degrees C, whereas siderite and ankerite in the alteration halo formed at temperatures of 150 degrees to 180 degrees C. The calculated isotopic compositions of the fluids are consistent with O-18-rich basinal brines and mixed inorganic and organic carbon Sources (6180 = 3-10 parts per thousand V-SMOW, delta C-13 = -7 to -3 parts per thousand V-PDB). in the northeast Lawn Hill platform carbonate-rich rocks preserve marine to early diagenetic carbon and oxygen isotope compositions, whereas ferroan carbonate cements in siltstones and shales in the Desert Creek borehole are O-18 and C-13 depleted relative to the sedimentary carbonates. The good agreement between temperature estimates from illite crystallinity and organic reflectance (160 degrees-270 degrees C) and inverse correlation with carbonate delta O-18 values indicates that organic maturation and carbonate precipitation in the northeast Lawn Hill platform resulted from interaction with the 1250 to 1150 Ma fluids. The calculated isotopic compositions of the fluid are consistent with evolved basinal brine (delta O-18 = 5.1-9.4 parts per thousand V-SMOW; delta C-13 = -13.2 to -3.7 parts per thousand V-PDB) that contained a variable organic carbon component from the oxidation and/or hydrolysis of organic matter in the host sequence. The occurrence of extensive O-18- and C-13-depleted ankerite and siderite alteration in Desert Creek is related to the high temperature of the 1250 to 1150 Ma fluid-flow event in the northeast Lawn Hill platform, in contrast to the lower temperature fluids associated with the earlier Century Zn-Pb deposit in the central Lawn Hill platform.

In vivo demonstration of load-induced fluid flow in the rat tibia and its potential implications for processes associated with functional adaptation

Load-induced extravascular fluid flow has been postulated to play a role in mechanotransduction of physiological loads at the cellular level. Furthermore, the displaced fluid serves as a carrier for metabolites, nutrients, mineral precursors and osteotropic agents important for cellular activity. We hypothesise that load-induced fluid flow enhances the transport of these key substances, thus helping to regulate cellular activity associated with processes of functional adaptation and remodelling. To test this hypothesis, molecular tracer methods developed previously by our group were applied in vivo to observe and quantify the effects of load-induced fluid flow under four-point-bending loads. Preterminal tracer transport studies were carried out on 24 skeletally mature Sprague Dawley rats. Mechanical loading enhanced the transport of both small- and larger-molecular-mass tracers within the bony tissue of the tibial mid-diaphysis. Mechanical loading showed a highly significant effect on the number of periosteocytic spaces exhibiting tracer within the cross section of each bone. For all loading rates studied, the concentration of Procion Red tracer was consistently higher in the tibia subjected to pure bending loads than in the unloaded, contralateral tibia, Furthermore, the enhancement of transport was highly site-specific. In bones subjected to pure bending loads, a greater number of periosteocytic spaces exhibited the presence of tracer in the tension band of the cross section than in the compression band; this may reflect the higher strains induced in the tension band compared with the compression band within the mid-diaphysis of the rat tibia. Regardless of loading mode, the mean difference between the loaded side and the unloaded contralateral control side decreased with increasing loading frequency. Whether this reflects the length of exposure to the tracer or specific frequency effects cannot be determined by this set of experiments. These in vivo experimental results corroborate those of previous ex vivo and in vitro studies, Strain-related differences in tracer distribution provide support for the hypothesis that load-induced fluid flow plays a regulatory role in processes associated with functional adaptation.