Publications de Sophia Kathryn Johnson

Publications associées (6)

Oxidative Defect Detection Within Free and Packed DNA Systems: A Quantum Mechanical/Molecular Mechanics (QM/ MM) Approach

Ursula Röthlisberger, Sophia Kathryn Johnson

Base excision repair enzymes (BERs) detect and repair oxidative DNA damage with efficacy despite the small size of the defects and their often only minor structural impact. A charge transfer (CT) model for rapid scanning of DNA stretches has been evoked to ...

Swiss Chemical Soc2024

Computational investigation of functionalized carbenes on dinitrogen activation

Sophia Kathryn Johnson

Activation of the dinitrogen triple bond is a crucial step in the overall fixation of atmospheric nitrogen into usable forms for industrial and biological applications. Current synthetic catalysts incorporate metal ions to facilitate the activation and cle ...

2022

Making Puzzle Pieces Fit or Reshaping MiMiC for Multiscale Simulations with CP2K and More

Ursula Röthlisberger, Sophia Kathryn Johnson, Andrea Levy, Andrej Antalik

MiMiC is a framework for modeling large-scale chemical processes that require treatment at multiple resolutions. It does not aim to implement single-handedly all methods required to treat individual subsystems, but instead, it relegates this task to specia ...

American Chemical Society (ACS)2025

MiMiCPy: An Efficient Toolkit for MiMiC-Based QM/MM Simulations

Ursula Röthlisberger, Sophia Kathryn Johnson, Andrea Levy

MiMiC is a highly flexible, extremely scalable multiscale modeling framework. It couples the CPMD (quantum mechanics, QM) and GROMACS (molecular mechanics, MM) codes. The code requires preparing separate input files for the two programs with a selection of ...

AMER CHEMICAL SOC2023

Redox-Based Defect Detection in Packed DNA: Insights from Hybrid Quantum Mechanical/Molecular Mechanics Molecular Dynamics Simulations

Oliver Daniel Toth, Ursula Röthlisberger, Polydefkis Diamantis, Murat Kiliç, Sophia Kathryn Johnson

The impact of an 8-oxoguanine (8oxoG) defect on the redox properties of DNA within the nucleosome core particle (NCP) was investigated employing hybrid quantum mechanical/molecular mechanics (QM/MM) molecular dynamics simulations of native and 8oxoG-contai ...

Amer Chemical Soc2023

MiMiC: A high-performance framework for multiscale molecular dynamics simulations

Ursula Röthlisberger, Sophia Kathryn Johnson, François Louis Mouvet, Andrea Levy, Andrej Antalik

MiMiC is a framework for performing multiscale simulations in which loosely coupled external programs describe individual subsystems at different resolutions and levels of theory. To make it highly efficient and flexible, we adopt an interoperable approach ...

2024