arXiv subjects

Yun Kyung Shin

Publications and source records attributed to Yun Kyung Shin.

4 recordsLinked to original sources

arXiv2026

ReaxKit: A Modular Python Toolkit for Preparing, Parsing, and Analyzing ReaxFF Molecular Dynamics Simulations

Empirical reactive force field (RFF) molecular dynamics enables atomistic simulation of bond breaking, bond formation, charge redistribution, and structural evolution in chemically complex systems. The ReaxFF method is arguably the most popular and transferable of the currently available RFF methods. However, routine use of ReaxFF often requires substantial manual effort to prepare inputs, interpret engine-specific outputs, organize simulation artifacts, and develop custom analysis scripts, limiting reproducibility and scalability. Here, we present ReaxKit, a modular Python toolkit for preparing, parsing, analyzing, and managing ReaxFF molecular dynamics simulations. ReaxKit uses a separation-of-concerns architecture that distinguishes engine-specific input/output handling, canonical domain data models, scientific analysis, workflow orchestration, presentation, storage, and graphical interaction. Engine adapters convert outputs from supported simulation environments into typed, engine-independent data structures, allowing analysis modules to operate independently of native file formats. User requests are executed through consistent command-line, functional Python, and browser-based graphical interfaces, while a dedicated workspace preserves raw data, normalized datasets, analysis settings, results, logs, caches, and provenance information. Representative applications demonstrate the breadth of the toolkit, including automated generation of elastic and equation-of-state training data from Materials Project structures and mechanical properties, characterization of active sites and local structural environments, and execution of simulation campaigns through YAML-defined study workflows. These capabilities show that ReaxKit supports all essential stages of the ReaxFF workflow.

physics.chem-ph↗

arXiv2026

Third-Body Stabilization of Supercritical CO2 in CO Oxidation: Development and Application of a ReaxFF Force Field for the CO/O/CO2 System

Supercritical CO2 (scCO2) plays a crucial role as a solvent in separation processes, advanced power cycles, and materials processing. Nonetheless, the atomistic comprehension of how the dense scCO2 matrix influences the fundamental reaction of carbon monoxide (CO) is still insufficiently explored. Experimental studies and molecular dynamics (MD) simulations frequently fail to detect the highly reactive, transient intermediates, such as atomic oxygen (O), that drive these reactions. To address this issue, we have developed a novel ReaxFF reactive force field for the CO2/CO/O system. The force field parameters were calibrated using density functional theory and second-order Moller-Plesset calculations to model CO2 crystal properties, intermolecular interactions, bond dissociation curves, and reaction energy barriers. The force field reproduces the cohesive energy of the CO2 crystal, the pressure characteristics of bulk scCO2, the equation-of-state behavior over a wide pressure-density range, the pressure dependence of the C-O bond length under compression, and the structural properties of liquid and scCO2, as documented by experiments, ab-initio MD, and prominent non-reactive models. The force field was subsequently applied to study the CO + O -> CO2 reaction. In a dilute environment, the reaction is inefficient as the newly formed CO2 rapidly dissociates due to excess kinetic and potential energy acquired from the exothermic reaction. Conversely, in a dense scCO2 environment, the surrounding matrix acts as an efficient third body, stabilizing the emerging CO2 product via molecular collisions. Statistical analysis confirms an average excess energy dissipation of 133.9 +/- 3.6 kcal/mol over 112.4 +/- 17.9 ps. Kinetic energy decomposition reveals that approximately 92% of the excess kinetic energy is stored in internal (rotational and vibrational) degrees of freedom.

cond-mat.mtrl-sci↗

arXiv2024

Development and Application of a ReaxFF Reactive Force Field for Ni-Doped MoS$_2$

The properties of $\mathrm{MoS_2}$ can be tuned or optimized through doping. In particular, Ni doping has been shown to improve the performance of $\mathrm{MoS_2}$ for various applications, including catalysis and tribology. To enable investigation of Ni-doped $\mathrm{MoS_2}$ with reactive molecular dynamics simulations, we developed a new ReaxFF force field to describe this material. The force field parameters were optimized to match a large set of density-functional theory (DFT) calculations of 2H-$\mathrm{MoS_2}$ doped with Ni, at four different sites (Mo-substituted, S-substituted, octahedral intercalation, and tetrahedral intercalation), under uniaxial, biaxial, triaxial, and shear strain. The force field was evaluated by comparing ReaxFF- and DFT-relaxed structural parameters, the tetrahedral/octahedral energy difference in doped 2H, energies of doped 1H and 1T monolayers, and doped 2H structures with vacancies. We demonstrated the application of the force field with reactive simulations of sputtering deposition and annealing of Ni-doped $\mathrm{MoS_2}$ films. Results show that the developed force field can successfully model the phase transition of Ni-doped $\mathrm{MoS_2}$ from amorphous to crystalline. The newly developed force field can be used in subsequent investigations to study the properties and behavior of Ni-doped $\mathrm{MoS_2}$ using reactive molecular dynamics simulations.

cond-mat.mtrl-sci↗

arXiv2023

Development of an eReaxFF Force Field for BZY20 Solid Oxide Electrocatalysis

Electrocatalysis is a catalytic process where the rate of an electrochemical reaction occurring at the electrode-electrolyte interface can be controlled by varying the electrical potential. Electrocatalysis can be applied to generate hydrogen which can be stored for future use in fuel cells for clean electricity. The use of solid oxide in electrocatalysis specially in hydrogen evolution reaction is promising. However, further improvements are essential in order to meet the ever-increasing global energy demand. Improvement of the performance of these high energy chemical systems is directly linked to the understanding and improving the complex physical and chemical phenomena and exchanges that take place at their different interfaces. To enable large length and time scale atomistic simulations of solid oxide electrocatalysis for hydrogen generation, we developed an eReaxFF force field for barium zirconate doped with 20 mol% of yttrium (BZY20). All parameters for the eReaxFF were optimized to reproduce quantum mechanical (QM) calculations on relevant condensed phase and cluster systems describing oxygen vacancies, vacancy migrations, water adsorption, water splitting and hydrogen generation on the surfaces of the BZY20 solid oxide. Using the developed force field, we performed zero-voltage molecular dynamics simulations to observe water adsorption and the eventual hydrogen production. Based on our simulation results, we conclude that this force field sets a stage for the introduction of explicit electron concept in order to simulate electron conductivity, electron leakage and non-zero-voltage effects on hydrogen generation. Overall, we demonstrate how atomistic-scale simulations can enhance our understanding of processes at interfaces in solid oxide materials.

physics.chem-ph↗