arXiv subjects

Amity Andersen

Publications and source records attributed to Amity Andersen.

3 recordsLinked to original sources

arXiv2025

Tracking Electron, Proton, and Solvent Motion in Proton-Coupled Electron Transfer with Ultrafast X-rays

Proton-coupled electron transfer (PCET) is foundational to catalysis, bioenergetics, and energy conversion, yet capturing and disentangling the coupled motions of electrons, protons, and solvent has remained a major experimental challenge. We combine femtosecond optical spectroscopy, site-specific ultrafast soft X-ray absorption spectroscopy, and time-resolved X-ray scattering with advanced calculations to disentangle the elementary steps of PCET in solution. Using a ruthenium polypyridyl model complex, we directly resolve photoinduced electron redistribution, ligand-site protonation within 100 ps, and the accompanying solvent reorganization. This unified multi-modal approach provides an orbital-level, atomistic picture of PCET, showing how electronic, nuclear, and solvation degrees of freedom can be separated experimentally. Our results establish a general X-ray framework for understanding and ultimately controlling PCET in catalysis, artificial photosynthesis, and biological energy flow.

physics.chem-ph↗

arXiv2025

PTM-Psi on the Cloud

We developed an advanced computational framework to accelerate the study of the impact of post-translational modifications on protein structures and interactions (PTM-Psi) using asynchronous, loosely coupled workflows on the Azure Quantum Elements Cloud platform. We seamlessly integrate emerging cloud computing assets that further expand the scope and capability of PTM-Psi Python package by refactoring it into a cloud-compatible library. We employed a "workflow of workflows" approach wherein a parent workflow spawns one or more child workflows, managing them, and acting on their results. This approach enabled us to optimize resource allocation according to each workflow's needs, and allowed us to use the cloud heterogeneous architecture for the computational investigation of a combinatorial explosion of thiol protein PTMs on an exemplary protein megacomplex critical to the Calvin-Benson cycle of light-dependent sugar production in cyanobacteria. With PTM-Psi on the cloud, we transformed the pipeline for the thiol PTM analysis to achieve high throughput by leveraging the strengths of the cloud service. \ptmpsi\ on the cloud reduces operational complexity and lowers entry barriers to data interpretation with structural modeling for a redox proteomics mass spectrometry specialist.

physics.bio-ph↗

arXiv2016

Self-Learning Kinetic Monte Carlo Simulations of Al Diffusion in Mg

Vacancy-mediated diffusion of an Al atom in pure Mg matrix is studied using the atomistic, on-lattice self-learning kinetic Monte Carlo (SLKMC) method. Activation barriers for vacancy-Mg and vacancy-Al atom exchange processes are calculated on-the-fly using the climbing image nudged-elastic band method and binary Mg-Al modified embedded-atom method interatomic potential. Diffusivities of an Al atom obtained from SLKMC simulations show the same behavior as observed in experimental and theoretical studies available in the literature, that is, Al atom diffuses faster within the basal plane than along the c-axis. Although, the effective activation barriers for Al-atom diffusion from SLKMC simulations are close to experimental and theoretical values, the effective prefactors are lower than those obtained from experiments. We present all the possible vacancy-Mg and vacancy-Al atom exchange processes and their activation barriers identified in SLKMC simulations. A simple mapping scheme to map an HCP lattice on to a simple cubic lattice is described, which enables the simulation of HCP lattice using on-lattice framework. We also present the pattern recognition scheme which is used in SLKMC simulations to identify the local Al atom configuration around a vacancy.

cond-mat.mtrl-sci↗