Transferable neural networks for enhanced sampling of protein dynamics

Variational auto-encoder frameworks have demonstrated success in reducing complex nonlinear dynamics in molecular simulation to a single non-linear embedding. In this work, we illustrate how this non-linear latent embedding can be used as a collective variable for enhanced sampling, and present a simple modification that allows us to rapidly perform sampling in multiple related systems. We first demonstrate our method is able to describe the effects of force field changes in capped alanine dipeptide after learning a model using AMBER99. We further provide a simple extension to variational dynamics encoders that allows the model to be trained in a more efficient manner on larger systems by encoding the outputs of a linear transformation using time-structure based independent component analysis (tICA). Using this technique, we show how such a model trained for one protein, the WW domain, can efficiently be transferred to perform enhanced sampling on a related mutant protein, the GTT mutation. This method shows promise for its ability to rapidly sample related systems using a single transferable collective variable and is generally applicable to sets of related simulations, enabling us to probe the effects of variation in increasingly large systems of biophysical interest.Comment: 20 pages, 10 figure

Extended Water Quality Monitoring of the Lincoln Lake Watershed

For seven years, the Lincoln Lake (Moores Creek and Beatty Branch) watershed was monitored for improvements in water quality resulting from agricultural best management practices (BMP) implemented to reduce nutrient transport. During the first three years of monitoring (1991 to 1994), nitrogen transport declined significantly (Edwards et al., 1994, 1996, and 1997) under both base and storm flow conditions. This decline in nitrogen transport was again observed in the three-year period following 1994 (Vendrell et al. 1998). This monitoring effort has demonstrated that water quality bas improved in the Lincoln Lake watershed. However, since the nitrogen transport continued to decline and there was some indication that phosphorus may begin to decline, monitoring was extended for another year (1998)

Land use change detection with LANDSAT-2 data for monitoring and predicting regional water quality degradation

The author has identified the following significant results. Comparison between LANDSAT 1 and 2 imagery of Arkansas provided evidence of significant land use changes during the 1972-75 time period. Analysis of Arkansas historical water quality information has shown conclusively that whereas point source pollution generally can be detected by use of water quality data collected by state and federal agencies, sampling methodologies for nonpoint source contamination attributable to surface runoff are totally inadequate. The expensive undertaking of monitoring all nonpoint sources for numerous watersheds can be lessened by implementing LANDSAT change detection analyses

Variation between European eel Anguilla anguilla (L.) stocks in five marshes of the Thames Estuary (United Kingdom)

The European eel (Anguilla anguilla, L.) was historically widely distributed throughout the United Kingdom, in coastal waters, lakes, rivers and wetlands. Recruitment has declined in recent decades and the species is now listed as ‘Critically Endangered’ on the International Union for Conservation of Nature and Natural Resources (IUCN) Red List. Management of suitable wetland habitats may contribute to species recovery; however, little is known about the stocks in these areas. In this study, yellow (adult stage > 300 mm) eels were sampled in ditches in five marshes bordering the Thames Estuary in England, UK. Ecological variables, including ditch characteristics, invertebrate abundance and water quality parameters were measured. Habitat features were also observed and recorded, including access, land use and water management regimes. Eels were found in all marshes, but at varying catch-per-unit-effort (CPUE). There were no significant correlations between CPUE and the ecological variables, except ditch width. However, a significant difference in CPUE was found between two of the marshes, which may be explained by variations in local habitat management. Mean lengths showed a high proportion of females and mean body condition of four of the marshes was also found to be greater than in three rivers in the same region. These findings suggest that the marshes are potentially favourable eel habitats and that factors influencing habitat quality, such as land use and water management, may affect eel abundance, production of females and body condition. Effective management of such wetlands may therefore contribute to the conservation of European eel

Wind Symphony

Bone Student Center Ballroom Sunday Afternoon November 22, 1998 3:00 p.m

NLTT5306: The shortest Period Detached White Dwarf + Brown Dwarf Binary

We have spectroscopically confirmed a brown dwarf mass companion to the hydrogen atmosphere white dwarf NLTT5306. The white dwarf's atmospheric parameters were measured using Sloan Digital Sky Survey and X-Shooter spectroscopy as T_eff=7756+/-35K and log(g)=7.68+/-0.08, giving a mass for the primary of M_WD=0.44+/-0.04 M_sun, at a distance of 71+/-4 pc with a cooling age of 710+/-50 Myr. The existence of the brown dwarf secondary was confirmed through the near-infrared arm of the X-Shooter data and a spectral type of dL4-dL7 was estimated using standard spectral indices. Combined radial velocity measurements from the Sloan Digital Sky Survey, X-Shooter and the Hobby-Eberly Telescope's High Resolution Spectrograph of the white dwarf gives a minimum mass of 56+/-3 M_jup for the secondary, confirming the substellar nature. The period of the binary was measured as 101.88+/-0.02 mins using both the radial velocity data and i'-band variability detected with the INT. This variability indicates 'day' side heating of the brown dwarf companion. We also observe H{\alpha} emission in our higher resolution data in phase with the white dwarf radial velocity, indicating this system is in a low level of accretion, most likely via a stellar wind. This system represents the shortest period white dwarf + brown dwarf binary and the secondary has survived a stage of common envelope evolution, much like its longer period counterpart, WD0137-349. Both systems likely represent bona-fide progenitors of cataclysmic variables with a low mass white dwarf and a brown dwarf donor.Comment: 9 pages, 11 figures, accepted for publication in MNRA