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Chemistry

Theoretical chemistry & modeling

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Displaying 26 - 50 of 180

Prediction of Sustainable Aviation Fuel Properties for Liquid Hydrocarbons from Hydrotreating Biomass Catalytic Fast Pyrolysis Derived Organic Intermediates

April 11, 2023
Author(s)
Suphat Watanasiri, Kristiina Iisa, Eugene Paulechka, Earl Christensen, Chris Muzny, Abhijit Dutta
Catalytic fast pyrolysis (CFP) of wood, woody residues, and agricultural waste has the potential to produce organic liquid intermediates that can be hydroprocessed to sustainable aviation fuels (SAF). In this article we present results of property

Conformational dynamics of the hepatitis B virus pre-genomic RNA on multiple time scales: implications for viral replication

September 30, 2022
Author(s)
Lucasz T. Olenginski, Wojciech K. Kasprzak, Christina Bergonzo, Bruce A. Shapiro, Theodore Kwaku Dayie
HBV replication is initiated by the binding of polymerase (P) to epsilon (ε), a 61 nucleotide (nt) cis -acting regulatory stem-loop RNA located at the 5′-end of the pregenomic RNA (pgRNA). This interaction triggers protein-primed reverse transcription and

PrepareForLeap: An automated tool for fast PDB-to-parameter generation

March 23, 2022
Author(s)
Daniel R. Roe, Christina Bergonzo
Setting up molecular dynamics simulations from experimentally determined structures is often complicated by a variety of factors, particularly the inclusion of carbohydrates, since these have several forms which can be linked in a variety of ways. Here we

Path-integral calculation of the third dielectric virial coefficient of noble gases

December 15, 2021
Author(s)
Giovanni Garberoglio, Allan H. Harvey, Bogumil Jeziorski
We present a rigorous framework for fully quantum calculation of the third dielectric virial coefficient C_eps(T) of noble gases, including exchange effects. The quantum efects are taken into account with the path-integral Monte Carlo method. Calculations

HDX-MS and MD simulations provide evidence for stabilization of the IgG1- FcgRIa (CD64a) immune complex through intermolecular glycoprotein bonds

December 8, 2021
Author(s)
Kyle Anderson, Kerry Scott, Christina Bergonzo, Ioannis Karageorgos, Elyssia Gallagher, Venkata Tayi, Michael Butler, Jeffrey W. Hudgens
Previous reports present different models for the stabilization of the Fc—FcγRI immune complex. Although accord exists on the importance of L235 in IgG1 and some hydrophobic contacts for complex stabilization, discord exists regarding the existence of

Dual current anomalies and quantum transport within extended reservoir simulations

October 19, 2021
Author(s)
Gabriela Wojtowicz, Justin E. Elenewski, Marek Rams, Michael P. Zwolak
Quantum transport simulations are rapidly evolving, including the development of well–controlled tensor network techniques for many– body transport calculations. One particularly powerful approach combines matrix product states with extended reservoirs —

Performance of Reservoir Discretizations in Quantum Transport Simulations

September 29, 2021
Author(s)
Justin E. Elenewski, Gabriela Wojtowicz, Marek Rams, Michael P. Zwolak
Quantum transport simulations require a level of discretization, often achieved through an explicit representation of the electronic reservoirs. These representations should converge to the same continuum limit, though there is a trade-off between a given
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