arXiv subjects

Kwanghee Park

Publications and source records attributed to Kwanghee Park.

7 recordsLinked to original sources

arXiv2026

sbml4md: A computational platform for System-Bath Modeling via Molecular Dynamics powered by Machine Learning

We introduce sbml4md, a newly developed algorithm implemented as a software package to extract parameters of multimode anharmonic Brownian (MAB) models from molecular dynamics (MD) trajectories for simulating nonlinear vibrational spectra of intramolecular modes of molecular liquids. By leveraging machine learning (ML) techniques to capture vibrational anharmonicity, intermolecular couplings, and bath correlation functions for each mode, sbml4md obviates empirical fitting and enables the modeling of environments with spatial and temporal heterogeneity. This work provides a set of parameters specifically tailored for the Hierarchical Equations of Motion (HEOM) framework, enabling numerically "exact" simulations of nonlinear vibrational spectra. Building upon our previous implementation for intramolecular vibrational modes [Park, Jo, and Tanimura, J. Chem. Phys. 163, 214104 (2025)], the present code enhances optimization efficiency by explicitly accounting for intermolecular vibrational contributions. This extension enables sbml4md to broaden the applicability of HEOM-based dynamical modeling by seamlessly integrating classical MD approaches, thereby providing a flexible and scalable framework for simulating both linear and nonlinear spectra under realistic conditions with minimal empirical input. The accompanying ML code, written in Python, is provided as supporting material.

physics.chem-ph↗

arXiv2026

Isotope Effects in 2D correlation infrared Spectra of Water: HEOM Analysis of Molecular Dynamics-Based Machine Learning Models

We model, simulate, and analyze the intramolecular modes of liquid H2O and D2O to elucidate how energy excitation, relaxation, and vibrational dephasing interplay through anharmonic mode-mode coupling. Our analysis employs two-dimensional (2D) correlation spectra, a representative observable in nonlinear infrared vibrational spectroscopy. Accurate reproduction of these 2D spectral profiles requires not only a precise dynamical description of intramolecular vibrations but also an appropriate treatment of thermal environmental effects arising from strong interactions with surrounding molecules, which act as thermal baths. Capturing the essential features of the 2D spectra further demands a non-Markovian, non-perturbative, and nonlinear description of the interactions between intramolecular modes and their baths. To this end, we adopt a hierarchical equations of motion (HEOM) framework to compute the 2D spectra. By comparing the resulting spectra of H2O and D2O, we explore the underlying mechanisms governing their complex energy and phase relaxation dynamics.

physics.chem-ph↗

arXiv2025

System-Bath Modeling in Vibrational Spectroscopy via Molecular Dynamics: A Machine Learning Framework for Hierarchical Equations of Motion (HEOM)

Molecular vibrations in solutions, especially OH stretching and bending in water, drive ultrafast energy relaxation and dephasing in chemical and biological systems. We present a machine learning approach for constructing system-bath models of intramolecular vibrations in solution, compatible with quantum simulations via the hierarchical equations of motion (HEOM). Using classical molecular dynamics trajectories generated with a force field specifically developed for quantum molecular dynamics, the model captures anharmonic mode coupling and non-Markovian dissipation through spectral distribution functions (SDFs). These features, in turn, enable quantum mechanical treatment of ultrafast energy relaxation, vibrational dephasing, and thermal excitation within the HEOM framework.. The trained model yields physically interpretable parameters, validated against infrared spectra. Notably, combining Brownian oscillator and Drude SDFs -- representing inter- and intramolecular vibrational modes -- significantly improves learning performance and supports rigorous simulation of nonlinear vibrational spectroscopy.

physics.chem-ph↗

arXiv2021

Redox and Molecular Diffusion in 2D van der Waals Space

Understanding charge transfer (CT) between two chemical entities and subsequent change in their charge densities is essential not only for molecular species but also for various low-dimensional materials. Because of their extremely high fraction of surface atoms, two-dimensional (2-D) materials are most susceptible to charge exchange and exhibit drastically different physicochemical properties depending on their charge density. In this regard, spontaneous and uncontrollable ionization of graphene in the ambient air has caused much confusion and technical difficulty in achieving experimental reproducibility since its first report in 2004. Moreover, the same ambient hole doping was soon observed in 2-D semiconductors, which implied that a common mechanism should be operative and apply to other low-dimensional materials universally. In this Account, we review our breakthroughs in unraveling the chemical origin and mechanistic requirements of the hidden CT reactions using 2-D crystals. We developed in-situ optical methods to quantify charge density using Raman and photoluminescence (PL) spectroscopy and imaging. Using gas and temperature-controlled in-situ measurements, we revealed that the electrical holes are injected by the oxygen reduction reaction (ORR): $O_{2}$ + $4H^{+}$ + $4e^{-}$ $\rightleftharpoons$ $2H_{2}O$, which was independently verified by pH dependence in HCl solutions. In addition to oxygen and water vapor, the overall CT reaction requires hydrophilic dielectric substrates, which assist hydration of the sample-substrate interface. The interface-localized reaction allowed us to visualized and control interfacial molecular diffusion and CT by varing the 2-D gap spacing and introducing defects. The complete mechanism of the fundamental charge exchange summarized in this Account will be essential in exploring material and device properties of other low dimensional materials.

cond-mat.mtrl-sci↗

arXiv2020

On-Stack Two-Dimensional Conversion of MoS2 into MoO3

Chemical transformation of existing two-dimensional (2D) materials can be crucial in further expanding the 2D crystal palette required to realize various functional heterostructures. In this work, we demonstrate a 2D 'on-stack' chemical conversion of single-layer crystalline MoS2 into MoO3 with a precise layer control that enables truly 2D MoO3 and MoO3/MoS2 heterostructures. To minimize perturbation of the 2D morphology, a nonthermal oxidation using O2 plasma was employed. The early stage of the reaction was characterized by a defect-induced Raman peak, drastic quenching of photoluminescence (PL) signals and sub-nm protrusions in atomic force microscopy images. As the reaction proceeded from the uppermost layer to the buried layers, PL and optical second harmonic generation signals showed characteristic modulations revealing a layer-by-layer conversion. The plasma-generated 2D oxides, confirmed as MoO3 by x-ray photoelectron spectroscopy, were found to be amorphous but extremely flat with a surface roughness of 0.18 nm, comparable to that of 1L MoS2. The rate of oxidation quantified by Raman spectroscopy decreased very rapidly for buried sulfide layers due to protection by the surface 2D oxides, exhibiting a pseudo-self-limiting behavior. As exemplified in this work, various on-stack chemical transformations can be applied to other 2D materials in forming otherwise unobtainable materials and complex heterostructures, thus expanding the palette of 2D material building blocks.

cond-mat.mtrl-sci↗

arXiv2020

Direction-Controlled Chemical Doping for Reversible G-Phonon Mixing in ABC Trilayer Graphene

Not only the apparent atomic arrangement but the charge distribution also defines the crystalline symmetry that dictates the electronic and vibrational structures. In this work, we report reversible and direction-controlled chemical doping that modifies the inversion symmetry of AB-bilayer and ABCtrilayer graphene. For the top-down and bottom-up hole injection into graphene sheets, we employed molecular adsorption of electronegative I2 and annealing-induced interfacial hole doping, respectively. The chemical breakdown of the inversion symmetry led to the mixing of the G phonons, Raman active Eg and Raman-inactive Eu modes, which was manifested as the two split G peaks, G- and G+. The broken inversion symmetry could be recovered by removing the hole dopants by simple rinsing or interfacial molecular replacement. Alternatively, the symmetry could be regained by double-side charge injection, which eliminated G- and formed an additional peak, Go, originating from the barely doped interior layer. Chemical modification of crystalline symmetry as demonstrated in the current study can be applied to other low dimensional crystals in tuning their various material properties.

cond-mat.mes-hall↗

arXiv2020

Redox-Governed Charge Doping Dictated by Interfacial Diffusion in Two-Dimensional Materials

Controlling extra charge carriers is pivotal in manipulating electronic, optical, and magnetic properties of various two-dimensional (2D) materials. Nonetheless, the ubiquitous hole doping of 2D materials in the air and acids has been controversial in its mechanistic details. Here we show their common origin is an electrochemical reaction driven by redox couples of oxygen and water molecules. Using real-time photoluminescence imaging of WS2 and Raman spectroscopy of graphene, we capture molecular diffusion through the 2D nanoscopic space between 2D materials and hydrophilic substrates, and show that the latter accommodate water molecules also serving as a hydrating solvent. We also demonstrate that HCl-induced doping is governed by dissolved O2 and pH in accordance with the Nernst equation. The nanoscopic electrochemistry anatomized in this work sets an ambient limit to material properties, which is universal to not only 2D but also other forms of materials.

cond-mat.mes-hall↗