Penn State Harrisburg

Classical normal mode analysis (cNMA) is a standard method for studying the equilibrium vibrations of macromolecules. A major limitation of cNMA is that it requires a cumbersome step of energy minimization that also alters the input structure significantly. Variants of normal mode analysis (NMA) exist that perform NMA directly on PDB structures without energy minimization, while maintaining most of the accuracy of cNMA. Spring-based NMA (sbNMA) is such a model. sbNMA uses an all-atom force field as cNMA does, which includes bonded terms such as bond stretching, bond angle bending, torsional, improper, and non-bonded terms such as van der Waals interactions. Electrostatics was not included in sbNMA because it introduced negative spring constants. In this work, we present a way to incorporate most of the electrostatic contributions in normal mode computations, which marks another significant step toward a free-energy-based elastic network model (ENM) for NMA. The vast majority of ENMs are entropy models. One significance of having a free energy-based model for NMA is that it allows one to study the contributions of both entropy and enthalpy. As an application, we apply this model to study the binding stability between SARS-COV2 and angiotensin converting enzyme 2 (or ACE2). Our results show that the stability at the binding interface is contributed nearly equally by hydrophobic interactions and hydrogen bonds.

Improving pellet quality (PQ) by increasing the percentage of pellets in finished feed is complicated.The hurdles of feed manufacturing are well documented.Researchers continue to investigate the effects of PQ on various performance parameters, yet addnl. PQ benefits must be presented to stimulate change in feed manufacturing practices.Therefore, the aim of this study was to investigate the effects of PQ on nutrient segregation in com. broiler houses differing in feed line length.Four experiments (Exp) were performed, each including 4 replicate feed lines segmented into 8 regions.A com. broiler finisher diet was manufactured using techniques to create either poor pellet quality (PPQ) or improved pellet quality (IPQ) feeds.Exp1 and Exp2 were conducted to investigate how PPQ and IPQ feed contributes to nutrient segregation in a 152-m feed line, resp.Exp3 and Exp4 used the same PPQ and IPQ feed but were carried out in a 152-m house with split feed lines, 76-m long.Feed samples were taken from each feed pan per Exp.Pellets and fines were analyzed sep. to determine pellet-to-fine ratio (P:F), pellet survivability, and nutrient concentrationsSegregation of amino acids and phytase were apparent in Exp1 (PPQ-152m), demonstrated by varying concentrations of amino acids and phytase activity across the 8 regions of the feed line (P < 0.05).Phytase segregation was not apparent in Exp2 (IPQ-152m) (P > 0.05).Threonine and phytase segregation occurred in Exp3 (PPQ-76m) (P < 0.05), whereas no evidence of nutrient segregation was observed in Exp4 (IPQ-76m) (P > 0.05).These data suggest that investing in PQ improvements provides a more uniform distribution of nutrients throughout the house.

Elemental mercury emitted by anthropogenic processes is oxidized in the atm. by halogens, ozone or nitro species.The oxidized mercury then deposits in the surface environment or reduces back to elemental mercury.The aqueous phase atm. photoreduction of oxidized mercury can also take place in the clouds.Thus, the oxidation, reduction and surface deposition control the overall mercury budget and its distribution in the atm.In this study, the structural and vibrational properties of all oxidized mercury mols. both in gas and aqueous phases are studied using the first principle d.-functional method.A correlation of bond distance, vibrational frequency, stability and solvation free energy with the electronegativity of non-metal atoms has emerged from the calculationsThe bond distances between mercury and first elements depend on the electronegativity of the second elements; the more electroneg. the second element is, the shorter the bond between mercury and the first element.The wave number of stretching frequency is inversely related to the bond distances.Importantly, the mercury - halogen bond distances lengthen in the aqueous phase from the corresponding gas phase distances in all mols.Interestingly, the increment of distances in halide mols. is higher than mols. that contain oxygen and nitrogen atoms.For isomers, the mols. with mercury-oxygen bonds are more stable than those with mercury-halogen bonds both in the gas and aqueous phases.The relative stability, however, decreases in the aqueous phase.Solvation free energy is higher for mols. where oxygen is a terminal atom than that for mols. where oxygen is a bridging atom.