SMLTM simulations of the diurnal tide: comparison with UARS observations

Wind and temperature observations in the mesosphere and lower thermosphere (MLT) from the Upper Atmosphere Research Satellite (UARS) reveal strong seasonal variations of tides, a dominant component of the MLT dynamics. Simulations with the Spectral mesosphere/lower thermosphere model (SMLTM) for equinox and solstice conditions are presented and compared with the observations. The diurnal tide is generated by forcing specified at the model lower boundary and by in situ absorption of solar radiation. The model incorporates realistic parameter-izations of physical processes including various dissipation processes important for propagation of tidal waves in the MLT. A discrete multi-component gravity-wave parameterization has been modified to account for seasonal variations of the background temperature. Eddy diffusion is calculated depending on the gravitywave energy deposition rate and stability of the background flow. It is shown that seasonal variations of the diurnal-tide amplitudes are consistent with observed variations of gravity-wave sources in the lower atmosphere.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/47861/1/585_1997_Article_70151187.pd

Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints

BACKGROUND: We are interested in the problem of predicting secondary structure for small sets of homologous RNAs, by incorporating limited comparative sequence information into an RNA folding model. The Sankoff algorithm for simultaneous RNA folding and alignment is a basis for approaches to this problem. There are two open problems in applying a Sankoff algorithm: development of a good unified scoring system for alignment and folding and development of practical heuristics for dealing with the computational complexity of the algorithm. RESULTS: We use probabilistic models (pair stochastic context-free grammars, pairSCFGs) as a unifying framework for scoring pairwise alignment and folding. A constrained version of the pairSCFG structural alignment algorithm was developed which assumes knowledge of a few confidently aligned positions (pins). These pins are selected based on the posterior probabilities of a probabilistic pairwise sequence alignment. CONCLUSION: Pairwise RNA structural alignment improves on structure prediction accuracy relative to single sequence folding. Constraining on alignment is a straightforward method of reducing the runtime and memory requirements of the algorithm. Five practical implementations of the pairwise Sankoff algorithm – this work (Consan), David Mathews' Dynalign, Ian Holmes' Stemloc, Ivo Hofacker's PMcomp, and Jan Gorodkin's FOLDALIGN – have comparable overall performance with different strengths and weaknesses

Cooling of the mesosphere and lower thermosphere due to doubling of CO2

A new parameterization of infrared radiative transfer in the 15-μm CO2 band has been incorporated into the Spectral mesosphere/lower thermosphere model (SMLTM). The parameterization is applicable to calculations of heating rates above approximately 15 km for arbitrary vertical profiles of the CO2 concentration corresponding to the surface mixing ratio in the range 150–720 ppm. The sensitivity of the mesosphere and lower thermosphere (MLT) to doubling of CO2 has been studied. The thermal response in the MLT is mostly negative (cooling) and much stronger than in the lower atmosphere. An average cooling at the stratopause is about 14 K. It gradually decreases to approximately 8 K in the upper mesosphere and again increases to about 40–50 K in the thermosphere. The cooling and associated thermal shrinking result in a substantial density reduction in the MLT that reaches 40–45% in the thermosphere. Various radiative, chemical, and dynamical feedbacks potentially important for the thermal response in the MLT are discussed. It is noted that the results of simulations are strikingly similar to observations of long-term trends in the MLT. This suggests that during the last 3–4 decades the thermal structure in the real upper atmosphere has undergone substantial changes driven by forcing comparable with that due to doubling of CO2.Key words. Meteorology and atmospheric dynamics (Climatology · Middle atmosphere dynamics · Thermospheric dynamics

Ortland, SMLTM simulations of the diurnal tide: comparison with UARS observation, Ann. Geophysicae, 15, this issue

Abstract. Wind and temperature observations in the mesosphere and lower thermosphere (MLT) from the Upper Atmosphere Research Satellite (UARS) reveal strong seasonal variations of tides, a dominant component of the MLT dynamics. Simulations with the Spectral mesosphere/lower thermosphere model (SMLTM) for equinox and solstice conditions are presented and compared with the observations. The diurnal tide is generated by forcing speci®ed at the model lower boundary and by in situ absorption of solar radiation. The model incorporates realistic parameterizations of physical processes including various dissipation processes important for propagation of tidal waves in the MLT. A discrete multi-component gravity-wave parameterization has been modi®ed to account for seasonal variations of the background temperature. Eddy di€usion is calculated depending on the gravitywave energy deposition rate and stability of the background ¯ow. It is shown that seasonal variations of the diurnal-tide amplitudes are consistent with observed variations of gravity-wave sources in the lower atmosphere.