Pre- and post-processing for Cosmic/NASTRAN on personal computers and mainframes

An interface between Cosmic/NASTRAN and GIFTS has recently been released, combining the powerful pre- and post-processing capabilities of GIFTS with Cosmic/NASTRAN's analysis capabilities. The interface operates on a wide range of computers, even linking Cosmic/NASTRAN and GIFTS when the two are on different computers. GIFTS offers a wide range of elements for use in model construction, each translated by the interface into the nearest Cosmic/NASTRAN equivalent; and the options of automatic or interactive modelling and loading in GIFTS make pre-processing easy and effective. The interface itself includes the programs GFTCOS, which creates the Cosmic/NASTRAN input deck (and, if desired, control deck) from the GIFTS Unified Data Base, COSGFT, which translates the displacements from the Cosmic/NASTRAN analysis back into GIFTS; and HOSTR, which handles stress computations for a few higher-order elements available in the interface, but not supported by the GIFTS processor STRESS. Finally, the versatile display options in GIFTS post-processing allow the user to examine the analysis results through an especially wide range of capabilities, including such possibilities as creating composite loading cases, plotting in color and animating the analysis

Polarized light field under dynamic ocean surfaces: Numerical modeling compared with measurements

As part of the Radiance in a Dynamic Ocean (RaDyO) program, we have developed a numerical model for efficiently simulating the polarized light field under highly dynamic ocean surfaces. Combining the advantages of the three-dimensional Monte Carlo and matrix operator methods, this hybrid model has proven to be computationally effective for simulations involving a dynamic air-sea interface. Given water optical properties and ocean surface wave slopes obtained from RaDyO field measurements, model-simulated radiance and polarization fields under a dynamic surface are found to be qualitatively comparable to their counterparts from field measurements and should be quantitatively comparable if the light field measurement and the wave slope/water optical property measurements are appropriately collocated and synchronized. This model serves as a bridge to connect field measurements of water optical properties, wave slopes and polarized light fields. It can also be used as a powerful yet convenient tool to predict the temporal underwater polarized radiance in a real-world situation. When appropriate surface measurements are available, model simulation is shown to reveal more dynamic features in the underwater light field than direct measurements

Актуальність впровадження систем газового обліку в сучасних умовах

Free energy calculation has long been an important goal for molecular dynamics simulation and force field development, but historically it has been challenged by limited performance, accuracy, and creation of topologies for arbitrary small molecules. This has made it difficult to systematically compare different sets of parameters to improve existing force fields, but in the past few years several authors have developed increasingly automated procedures to generate parameters for force fields such as Amber, CHARMM, and OPLS. Here, we present a new framework that enables fully automated generation of GROMACS topologies for any of these force fields and an automated setup for parallel adaptive optimization of high-throughput free energy calculation by adjusting lambda point placement on the fly. As a small example of this automated pipeline, we have calculated solvation free energies of 50 different small molecules using the GAFF, OPLS-AA, and CGenFF force fields and four different water models, and by including the often neglected polarization costs, we show that the common charge models are somewhat underpolarized.QC 20150505</p

Effect of the integration method on the accuracy and computational efficiency of free energy calculations using thermodynamic integration

Although calculations of free energy using molecular dynamics simulations have gained significant importance in the chemical and biochemical fields, they still remain quite computationally intensive. Furthermore, when using thermodynamic integration, numerical evaluation of the integral of the Hamiltonian with respect to the coupling parameter may introduce unwanted errors in the free energy. In this paper, we compare the performance of two numerical integration techniques-the trapezoidal and Simpson's rules and propose a new method, based on the analytic integration of physically based fitting functions that are able to accurately describe the behavior of the data. We develop and test our methodology by performing detailed studies on two prototype systems, hydrated methane and hydrated methanol, and treat Lennard-Jones and electrostatic contributions separately. We conclude that the widely used trapezoidal rule may introduce systematic errors in the calculation, but these errors are reduced if Simpson's rule is employed, at least for the electrostatic component. Furthermore, by fitting thermodynamic integration data, we are able to obtain precise free energy estimates using significantly fewer data points (5 intermediate states for the electrostatic component and 11 for the Lennard-Jones term), thus significantly decreasing the associated computational cost. Our method and improved protocol were successfully validated by computing the free energy of more complex systems hydration of 2-methylbutanol and of 4-nitrophenol-thus paving the way for widespread use in solvation free energy calculations of drug molecules

Diode laser based light sources for biomedical applications

Diode lasers are by far the most efficient lasers currently available. With the ever-continuing improvement in diode laser technology, this type of laser has become increasingly attractive for a wide range of biomedical applications. Compared to the characteristics of competing laser systems, diode lasers simultaneously offer tunability, high-power emission and compact size at fairly low cost. Therefore, diode lasers are increasingly preferred in important applications, such as photocoagulation, optical coherence tomography, diffuse optical imaging, fluorescence lifetime imaging, and terahertz imaging. This review provides an overview of the latest development of diode laser technology and systems and their use within selected biomedical applications

The Palomar Testbed Interferometer

The Palomar Testbed Interferometer (PTI) is a long-baseline infrared interferometer located at Palomar Observatory, California. It was built as a testbed for interferometric techniques applicable to the Keck Interferometer. First fringes were obtained in July 1995. PTI implements a dual-star architecture, tracking two stars simultaneously for phase referencing and narrow-angle astrometry. The three fixed 40-cm apertures can be combined pair-wise to provide baselines to 110 m. The interferometer actively tracks the white-light fringe using an array detector at 2.2 um and active delay lines with a range of +/- 38 m. Laser metrology of the delay lines allows for servo control, and laser metrology of the complete optical path enables narrow-angle astrometric measurements. The instrument is highly automated, using a multiprocessing computer system for instrument control and sequencing.Comment: ApJ in Press (Jan 99) Fig 1 available from http://huey.jpl.nasa.gov/~bode/ptiPicture.html, revised duging copy edi

Factors regulating the Great Calcite Belt in the Southern Ocean and its biogeochemical significance

The Great Calcite Belt (GCB) is a region of elevated surface reflectance in the Southern Ocean (SO) covering ~16% of the global ocean and is thought to result from elevated, seasonal concentrations of coccolithophores. Here we describe field observations and experiments from two cruises that crossed the GCB in the Atlantic and Indian sectors of the SO. We confirm the presence of coccolithophores, their coccoliths, and associated optical scattering, located primarily in the region of the subtropical, Agulhas, and Subantarctic frontal regions. Coccolithophore-rich regions were typically associated with high-velocity frontal regions with higher seawater partial pressures of CO2 (pCO2) than the atmosphere, sufficient to reverse the direction of gas exchange to a CO2 source. There was no calcium carbonate (CaCO3) enhancement of particulate organic carbon (POC) export, but there were increased POC transfer efficiencies in high-flux particulate inorganic carbon regions. Contemporaneous observations are synthesized with results of trace-metal incubation experiments, 234Th-based flux estimates, and remotely sensed observations to generate a mandala that summarizes our understanding about the factors that regulate the location of the GCB

Satellite estimates of wide-range suspended sediment concentrations in Changjiang (Yangtze) estuary using MERIS data

The Changjiang (Yangtze) estuarine and coastal waters are characterized by suspended sediments over a wide range of concentrations from 20 to 2,500 mg l-1. Suspended sediment plays important roles in the estuarine and coastal system and environment. Previous algorithms for satellite estimates of suspended sediment concentration (SSC) showed a great limitation in that only low to moderate concentrations (up to 50 mg l-1) could be reliably estimated. In this study, we developed a semi-empirical radiative transfer (SERT) model with physically based empirical coefficients to estimate SSC from MERIS data over turbid waters with a much wider range of SSC. The model was based on the Kubelka–Munk two-stream approximation of radiative transfer theory and calibrated using datasets from in situ measurements and outdoor controlled tank experiments. The results show that the sensitivity and saturation level of remote-sensing reflectance to SSC are dependent on wavelengths and SSC levels. Therefore, the SERT model, coupled with a multi-conditional algorithm scheme adapted to satellite retrieval of wide-range SSC, was proposed. Results suggest that this method is more effective and accurate in the estimation of SSC over turbid water

Costly mating delays drive female ornamentation in a capital breeder

How fecundity might be traded off with mate attraction and other aspects of reproduction in females remains poorly understood. We investigated these allocation trade-offs using the common glowworm (Lampyris noctiluca), a lampyrid beetle, in which flightless, sedentary females only use resources gathered during the larval stage to attract flying males by glowing. While sexual signaling was not found to have a significant fecundity cost, a delay in successfully attracting a mate greatly increased the risk of reproductive failure, with fecundity losses being more severe in small females. These findings are among the first to show that failure to quickly attract a mate can decrease female fecundity. The results also show how the length of delay before mating can drive the evolution of female sexual ornamentation.Peer reviewe

NGF effects on developing forebrain cholinergic neurons are regionally specific

Nerve growth factor (NGF) has been shown to have an effect on neurons in the central nervous system (CNS). A number of observations suggest that NGF acts as a trophic factor for cholinergic neurons of the basal forebrain and the caudate-putamen. We sought to further characterize the CNS actions of NGF by examining its effect on choline acetyltransferase (ChAT) activity in the cell bodies and fibers of developing neurons of the septum and caudate-putamen. ChAT activity was increased after even a single NGF injection. Interestingly, the magnitude of the effect of multiple NGF injections suggested that repeated treatments may augment NGF actions on these neurons. The time-course of the response to NGF was followed after a single injection on postnatal day (PD) 2. NGF treatment produced long-lasting increases in ChAT activity in septum, hippocampus and caudate-putamen. The response in cell body regions (septum, caudate-putamen) was characterized by an initial lag period of approximately 24 hr, a rapid rise to maximum values, a plateau phase and a return to baseline. The response in hippocampus was delayed by 48 hr relative to that in septum, indicating that NGF actions on ChAT were first registered in septal cell bodies. Finally, developmental events were shown to have a regionally specific influence on the response of neurons to NGF. For though the septal response to a single NGF injection was undiminished well into the third postnatal week, little or no response was detected in caudate-putamen at that time. In highlighting the potency and regional specificity of NGF effects, these observations provide additional, support for the hypothesis that NGF is a trophic factor for CNS cholinergic neurons.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/45403/1/11064_2004_Article_BF00970927.pd