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One of the challenges and a significant part of a protein structure’s prediction in three-dimensional space is a side chain prediction/packing. This area of research has a large importance, due to its various applications in protein design. In recent years, many methodologies and techniques have been crafted for side chain prediction such as DLPacker, FASPR, SCWRL4 and OPUS-Rota4. In this research, we address the problem from a different perspective. We employed a machine learning model to predict the side chain packing of protein molecules given only the Cα trace. We analyzed 32,000 protein molecules to extract important geometrical features that can distinguish between different orientations of side chain rotamers. We designed and implemented a Random Forest model to tackle this problem. Given the accuracy of existing state-of-the-art approaches, our model represents an improvement from among other models. The results of our experiment show that Random Forest is highly effective, achieving a total average accuracy of 73.7% for proteins and 73.3% for individual amino acids. 

Hurricane storm surges are influenced by wind intensity, forward speed, width and slope of the ocean bottom, central pressure, angle of approach, shape of coastal lines, local features, and storm size. A numerical experiment is conducted using the Advanced Circulation + Simulation and Simulating Waves Nearshore (ADCIRC + SWAN) coupled model for understanding the effects of wind intensity, forward speed, and wave on the storm surges caused by Hurricane Harvey. The ADCIRC + SWAN is used to simulate hurricane storm surges and waves. The wind fields of Hurricane Harvey were reconstructed from observed data, aided by a variety of methodologies and analyses conducted by Ocean Weather Inc (OWI) after the event. These reconstructed wind fields were used as the meteorological forcing in the base case in ADCIRC+SWAN to investigate the storm surges caused by the hurricane. Hurricane Harvey was the second most costly hurricane in the United States, causing severe urban flooding by dropping more than 60 inches of rainfall in Texas. The hurricane made three landfalls, with its first landfall as a Category 4 based on the Saffir–Simpson Hurricane Wind Scale (SSHWS), with wind intensities of 212.98 km/h (59 m/s). The storm surges caused by Hurricane Harvey were unique due to the slow speed, crooked tracks, triple landfalls in the USA, and excessive rain. The model’s storm surge and wave results were compared against observed data. High water marks at 21 locations and time series at 12 National Oceanic and Atmospheric Administration (NOAA) gauges were compared with the generated results. Several cases were investigated by increasing or decreasing the wind intensity or hurricane forward speed by 25% of the OWI wind and pressure data. The effects of the wave were analyzed by comparing the results obtained from ADCIRC + SWAN (with waves) and ADCIRC (without waves) models. The study found that the changes in wind intensity had the most significant effect on storm surges, followed by wave and forward speed changes. This study signifies the importance of considering these factors to enhance accuracy in predicting storm surges. 

Hurricane storm surges are influenced by several factors, including wind intensity, surface pressure, forward speed, size, angle of approach, ocean bottom depth and slope, shape and geographical features of the coastline. The relative influence of each factor may be amplified or abated by other factors that are acting at the time of the hurricane’s approach to the land. To understand the individual and combined influence of wind intensity, surface pressure and forward speed, a numerical experiment is conducted using Advanced CIRCulation + Simulating Waves Nearshore (ADCIRC + SWAN) by performing hindcasts of Hurricane Rita storm surges. The wind field generated by Ocean Weather Inc. (OWI) is used as the base meteorological forcing in ADCIRC + SWAN. All parameters are varied by certain percentages from those in the OWI wind field. Simulation results are analyzed for maximum wind intensity, wind vector pattern, minimum surface pressure, forward speed, maximum water elevation, station water elevation time series, and high water marks. The results for different cases are compared against each other, as well as with observed data. Changes in the wind intensity have the greatest impact, followed by the forward speed and surface pressure. The combined effects of the wind intensity and forward speed are noticeably different than their individual effects.