U.S. flag

An official website of the United States government

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Secure .gov websites use HTTPS
A lock ( ) or https:// means you’ve safely connected to the .gov website. Share sensitive information only on official, secure websites.

Chemistry

Theoretical chemistry and modeling

Search Publications

Search Title, Abstract, Conference, Citation, Keyword or Author
Published Date
Displaying 26 - 50 of 194

Anisotropic coarse-grain Monte Carlo simulations of lysozyme, lactoferrin, and NISTmAb by precomputing atomistic models

September 5, 2024
Author(s)
Harold Hatch, Christina Bergonzo, Marco Blanco, Guangcui Yuan, Sergei Grudinin, Mikael Lund, Joseph E. Curtis, Alexander Grishaev, Yun Liu, Vincent K. Shen
We develop a multiscale coarse-grain model of the NIST Monoclonal Antibody Reference Material 8671 (NISTmAb) to enable systematic computational investigations of high-concentration physical instabilities such as phase separation, clustering, and

Monte Carlo molecular simulations with FEASST version 0.25.1

September 5, 2024
Author(s)
Harold Hatch, Daniel Siderius, Vincent K. Shen
FEASST is an open-source Monte Carlo software for particle-based simulations. This software, which was released in 2017, has been used to study phase equilibrium, self-assembly, aggregation or gelation in biological materials, colloids, polymers, ionic

Evaluation of Formation Enthalpies of C3 and C4 Brominated Hydrocarbons: Bringing Together Classical Thermodynamics, Modern Mass-Spectroscopy, and High-Level Ab Initio Calculations

February 7, 2024
Author(s)
Eugene Paulechka, Andrei F. Kazakov
The enthalpies of formation of brominated C3–C4 hydrocarbons were critically evaluated using experimental data sources ranging from classical thermodynamics methods to modern high-precision mass spectrometry and reported in a time span of a century. The

Divalent ions as mediators of carbonylation in cardiac myosin binding protein C

November 1, 2023
Author(s)
Christina Bergonzo, Baikuntha Aryal, Ashutosh Rao
The dosing and efficacy of chemotherapeutic drugs can be limited by toxicity caused by off-pathway reactions. One hypothesis for how such toxicity arises is via metal-catalyzed oxidative damage of cardiac myosin binding protein C (cMyBP-C) found in cardiac

Effects of Glycans and Hinge on Dynamics in the IgG1 Fc

October 28, 2023
Author(s)
Christina Bergonzo, J. Todd Hoopes, Zvi Kelman, David Travis Gallagher
The crystallizable fragment (Fc) domain of immunoglobulin subclass IgG1 antibodies is engineered for a wide variety of pharmaceutical applications. Two important structural variables in Fc constructs are the hinge region connecting the Fc to the antigen

One-Step Traceability with NIST on a Chip: A Case for the Emergence of Quantum-Based Methods for Metrology and Sensing of Pressure, Vacuum, Temperature, Electric Fields, Mass, Force, and Torque, all enabled by the New SI

May 8, 2023
Author(s)
Jay Hendricks, Barbara Goldstein, Alexandra Artusio-Glimpse, Christopher Holloway, Matthew Simons, Nikunjkumar Prajapati, Andrew Rotunno, Samuel Berweger, Kaleb Campbell, Maitreyi Jayaseelan, Nikolai Klimov, Zeeshan Ahmed, Daniel Barker, Stephen Eckel, James Fedchak, Jacob Ricker, Kevin Douglass, Tobias Herman, Michal Chojnacky, Julia Scherschligt, Stephan Schlamminger, Leon Chao, Zane Comden, John-Edward Draganov, Thinh Bui
The world is changing. Measurements are everywhere. As sensors are embedded into everyday products and electronics, the importance of sensors that give "the right answer" or "none at all" is of growing importance. The traditional role of the national

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
Was this page helpful?