ChemTS: An Efficient Python Library for de novo Molecular Generation

Automatic design of organic materials requires black-box optimization in a vast chemical space. In conventional molecular design algorithms, a molecule is built as a combination of predetermined fragments. Recently, deep neural network models such as variational auto encoders (VAEs) and recurrent neural networks (RNNs) are shown to be effective in de novo design of molecules without any predetermined fragments. This paper presents a novel python library ChemTS that explores the chemical space by combining Monte Carlo tree search (MCTS) and an RNN. In a benchmarking problem of optimizing the octanol-water partition coefficient and synthesizability, our algorithm showed superior efficiency in finding high-scoring molecules. ChemTS is available at https://github.com/tsudalab/ChemTS

Ocean current energy resource assessment for the United States

Ocean currents are an attractive source of clean energy due to their inherent reliability, persistence and sustainability. The Gulf Stream system is of particular interest as a potential energy resource to the United States with significant currents and proximity to the large population on the U.S. east coast. To assess the energy potential from ocean currents for the United States, the characterization of ocean currents along the U.S. coastline is performed in this dissertation. A GIS database that maps the ocean current energy resource distribution for the entire U.S. coastline and also provides joint velocity magnitude and direction probability histograms is developed. Having a geographical constraint by Florida and the Bahamas, the Florida Current has the largest ocean current resource which is fairly stable with prevalent seasonal variability in the upper layer of the water column (~200m). The core of the Florida Current features higher stability than the edges as a result of the meandering and seasonal broadening of the current flow. The variability of the Gulf Stream significantly increases as it flows past the Cape Hatteras. The theoretical energy balance in the Gulf Stream system is examined using the two-dimensional ocean circulation equations based on the assumptions of the Stommel model for quasi-geostrophic subtropical gyres. Additional turbine drag is formulated and incorporated in the model to represent power extraction by turbines. Parameters in the model are calibrated against ocean observational data such that the model can reproduce the volume and kinetic energy fluxes in the Gulf Stream. The results show that considering extraction over a region comprised of the entire Florida Current portion of the Gulf Stream system, the theoretical upper bound of averaged power dissipation is around 5.1 GW, or 45 TWh/yr. If the extraction area comprises the entire portion of the Gulf Stream within 200 miles of the U.S. coastline, the theoretical upper bound of averaged power dissipation becomes approximately 18.6 GW or 163 TWh/yr. The impact of the power extraction is primarily constrained in the vicinity of the turbine region, and includes a significant reduction of flow strength and water level drop in the power extraction site. The turbines also significantly reduce residual energy fluxes in the flow, and cause redirection of the Gulf Stream. A full numerical simulation of the ocean circulation in the Atlantic Ocean is performed using Hybrid Coordinate Ocean Model (HYCOM) and power extraction from the Florida Current is modeled as additional momentum sink. Effects of power extraction are shown to include flow rerouting from the Florida Strait channel to the east side of the Bahamas. Flow redirection is stronger during peak summer flow resulting in less seasonal variability in both power extraction and residual fluxes in the Florida Current. A significant water level drop is shown at the power extraction site, and so is a slight water level rise along the coasts of Florida and the Gulf. The sum of extracted power and the residual energy flux in the Florida Current is lower than the original energy flux in the baseline case, indicating a net loss of energy reserve in the Florida Current channel due to flow redirection. The impact from power extraction on the mean flow field is concentrated in the near field of the power extraction site, while shifts in the far flow field in time and space have little impact on the overall flow statistics.Ph.D