arXiv subjects

Ju-Yeon Jo

Publications and source records attributed to Ju-Yeon Jo.

5 recordsLinked to original sources

arXiv2025

Single-View Tomographic Reconstruction Using Learned Primal Dual

The Learned Primal Dual (LPD) method has shown promising results in various tomographic reconstruction modalities, particularly under challenging acquisition restrictions such as limited viewing angles or a limited number of views. We investigate the performance of LPD in a more extreme case: single-view tomographic reconstructions of axially-symmetric targets. This study considers two modalities: the first assumes low-divergence or parallel X-rays. The second models a cone-beam X-ray imaging testbed. For both modalities, training data is generated using closed-form integral transforms, or physics-based ray-tracing software, then corrupted with blur and noise. Our results are then compared against common numerical inversion methodologies.

eess.IV↗

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↗

arXiv2024

Network analysis with quantum dynamics clarifies why photosystem II exploits both chlorophyll a and b

In green plants, chlorophyll-a and chlorophyll-b are the predominant pigments bound to light-harvesting proteins. While the individual characteristics of these chlorophylls are well understood, the advantages of their coexistence remain unclear. In this study, we establish a method to simulate excitation energy transfer within the entire photosystem II supercomplex by employing network analysis integrated with quantum dynamic calculations. We then investigate the effects of the coexistence of chlorophyll-a and chlorophyll-b by comparing various chlorophyll compositions. Our results reveal that the natural chlorophyll composition allows the excited energy to preferentially flow through specific domains that act as safety valves, preventing downstream overflow. Our findings suggest that the light-harvesting proteins in a photosystem II supercomplex achieve evolutionary advantages with the natural chlorophyll-a/b ratio, capturing light energy efficiently and safely across various light intensities. Using our framework, one can better understand how green plants harvest light energy and adapt to changing environmental conditions.

physics.data-an↗

arXiv2021

Full molecular dynamics simulations of molecular liquids for single-beam spectrally controlled two-dimensional Raman spectroscopy

Single-beam spectrally controlled (SBSC) two-dimensional (2D) Raman spectroscopy is a unique 2D vibrational measurement technique utilizing trains of short pulses that are generated from a single broadband pulse by pulse shaping. This approach overcomes the difficulty of 2D Raman spectroscopy in dealing with small-signal extraction and avoids complicated low-order cascading effects, thus providing a new possibility for measuring the intramolecular and intermolecular modes of molecular liquids using fifth-order 2D Raman spectroscopy. Recently, for quantitatively investigating the mode-mode coupling mechanism, Hurwitz et al. [Optics Express 28, 3803 (2020)] have developed a new pulse design for this measurement to separate the contributions of the fifth- and third-order polarizations, which are often overlapped in the original single-beam measurements. Here, we describe a method for simulating these original measurements and the new 2D Raman measurements on the basis of a second-order response function approach. We carry out full molecular dynamics simulations for carbon tetrachloride and liquid water using an equilibrium-nonequilibrium hybrid algorithm, with the aim of explaining the key features of the SBSC 2D Raman spectroscopic method from a theoretical point of view. The predicted signal profiles and intensities provide valuable information that can be applied to 2D spectroscopy experiments, allowing them to be carried out more efficiently.

physics.chem-ph↗

arXiv2016

Full molecular dynamics simulations of liquid water and carbon tetrachloride for two-dimensional Raman spectroscopy in the frequency domain

Frequency-domain two-dimensional Raman signals, which are equivalent to coherent two-dimensional Raman scattering (COTRAS) signals, for liquid water and carbon tetrachloride were calculated using an equilibrium-nonequilibrium hybrid MD simulation algorithm. We elucidate mechanisms governing the 2D signal profiles involving anharmonic mode-mode coupling and the nonlinearities of the polarizability for the intermolecular and intramolecular vibrational modes. The predicted signal profiles and intensities can be utilized to analyze recently developed single-beam 2D spectra, whose signals are generated from a coherently controlled pulse, allowing the single-beam measurement to be carried out more efficiently.

physics.chem-ph↗