arXiv subjects

Ji-Hyun Kim

Publications and source records attributed to Ji-Hyun Kim.

10 recordsLinked to original sources

arXiv2026

Effects of Divalent Cations on Diffusion Dynamics of Biological Water Confined between Lipid Membranes

Biological water is an ionic solution containing both monovalent and divalent ions. However, the effects of divalent ions on the dynamics of biological water remain largely unknown. Here, we investigate how the transport dynamics of water molecules nanoconfined between lipid membranes depends on the concentration of calcium (Ca2+) and magnesium (Mg2+) ions by using molecular dynamics simulations and the generalized transport equation for biological water. We find that the diffusion coefficient of biological water monotonically increases with Ca2+ ion concentration but exhibits a largely opposite, non-monotonic dependence on Mg2+ concentration. The deviation of the water molecules' displacement distribution from the Gaussian also shows distinct dependence on the concentrations of Mg2+ and Ca2+. These contrasting behaviors originate from the different hydration radii of these divalent ions and their distinct effects on the interfacial structure and dynamics of biological water. The relaxation of the lateral displacement distribution of water molecules toward a Gaussian is determined by the time-correlation function of diffusion coefficient fluctuations, whose relaxation time increases with salt concentrations. The primary source of the lateral diffusion coefficient fluctuation is thermal motion of water molecules in the longitudinal direction, along which microscopic environments surrounding a water molecule, including the functional groups of lipid membrane and ion concentrations, drastically change.

cond-mat.soft↗

arXiv2024

Hyperphosphorylation-Induced Phase Transition in Vesicle Delivery Dynamics of Motor Proteins in Neuronal Cells

Synaptic vesicle transport by motor proteins along microtubules is a crucial active process underlying neuronal communication. It is known that microtubules are destabilized by tau-hyperphosphorylation, which causes tau proteins to detach from microtubules and form neurofibril tangles. However, how tau-phosphorylation affects transport dynamics of motor proteins on the microtubule remains unknown. Here, we discover that long-distance unidirectional motion of vesicle-motor protein multiplexes (VMPMs) in living cells is suppressed under tau-hyperphosphorylation, with the consequent loss of fast vesicle-transport along the microtubule. The VMPMs in hyperphosphorylated cells exhibit seemingly bidirectional random motion, with dynamic properties far different from VMPM motion in normal cells. We establish a parsimonious physicochemical model of VMPM's active motion that provides a unified, quantitative explanation and predictions for our experimental results. Our analysis reveals that, under hyperphosphorylation conditions, motor-protein-multiplexes have both static and dynamic motility fluctuations. The loss of the fast vesicle-transport along the microtubule can be a mechanism of neurodegenerative disorders associated with tau-hyperphosphorylation.

physics.bio-ph↗

arXiv2024

Transport Dynamics of Water Molecules Confined between Lipid Membranes

Water molecules confined between biological membranes exhibit a distinctive non-Gaussian displacement distribution, far different from bulk water. Here, we introduce a new transport equation for water molecules in the intermembrane space, quantitatively explaining molecular dynamics simulation results. We find the unique transport dynamics of water molecules stems from the lateral diffusion coefficient fluctuation caused by their longitudinal motion. We also identify an interfacial region where water possesses distinct physical properties, unaffected by changes in the intermembrane separation.

cond-mat.soft↗

arXiv2019

Observation time dependent mean first passage time of diffusion and sub-diffusion processes

The mean first passage time, one of the important characteristics for a stochastic process, is often calculated assuming the observation time is infinite. However, in practice, the observation time, T, is always finite and the mean first passage time (MFPT) is dependent on the length of the observation time. In this work, we investigate the observation time dependence of the MFPT of a particle freely moving in the interval [-L,L] for a simple diffusion model and four different models of subdiffusion, the fractional diffusion equation (FDE), scaled Brown motion (SBM), fractional Brownian motion (FBM), and stationary Markovian approximation model of SBM and FBM. We find that the MFPT is linearly dependent on T in the small T limit for all the models investigated, while the large-T behavior of the MFPT is sensitive to stochastic properties of the transport model in question. We also discuss the relationship between the observation time, T, dependence and the travel-length, L, dependence of the MFPT. Our results suggest the observation time dependency of the MFPT can serve as an experimental measure that is far more sensitive to stochastic properties of transport processes than the mean square displacement.

cond-mat.stat-mech↗

arXiv2018

Frequency spectrum of biological noise: a probe of reaction dynamics in living cells

Even in the steady-state, the number of biomolecules in living cells fluctuates dynamically; and the frequency spectrum of this chemical fluctuation carries valuable information about the mechanism and the dynamics of the intracellular reactions creating these biomolecules. Although recent advances in single-cell experimental techniques enable the direct monitoring of the time-traces of the biological noise in each cell, the development of the theoretical tools needed to extract the information encoded in the stochastic dynamics of intracellular chemical fluctuation is still in its adolescence. Here, we present a simple and general equation that relates the power-spectrum of the product number fluctuation to the product lifetime and the reaction dynamics of the product creation process. By analyzing the time traces of the protein copy number using this theory, we can extract the power spectrum of the mRNA number, which cannot be directly measured by currently available experimental techniques. From the power spectrum of the mRNA number, we can further extract quantitative information about the transcriptional regulation dynamics. Our power spectrum analysis of gene expression noise is demonstrated for the gene network model of luciferase expression under the control of the Bmal 1a promoter in mouse fibroblast cells. Additionally, we investigate how the non-Poisson reaction dynamics and the cell-to-cell heterogeneity in transcription and translation affect the power-spectra of the mRNA and protein number.

physics.bio-ph↗

arXiv2018

Universal Transport Dynamics of Complex Fluids

Thermal motion in complex fluids is a complicated stochastic process but ubiquitously exhibits initial ballistic, intermediate sub-diffusive, and long-time non-Gaussian diffusive motion, unless interrupted. Despite its relevance to numerous dynamical processes of interest in modern science, a unified, quantitative understanding of thermal motion in complex fluids remains a long-standing problem. Here, we present a new transport equation and its solutions, which yield a unified quantitative explanation of the mean square displacement (MSD) and the non-Gaussian parameter (NGP) of various fluid systems. We find the environment-coupled diffusion kernel and its time correlation function are two essential quantities determining transport dynamics of complex fluids. From our analysis, we construct a general, explicit model of the complex fluid transport dynamics. This model quantitatively explains not only the MSD and NGP, but also the time-dependent relaxation of the displacement distribution for various systems. We introduce the concepts of intrinsic disorder and extrinsic disorder that have distinct effects on transport dynamics and different dependencies on temperature and density. This work presents a new paradigm for quantitative understanding of transport and transport-coupled processes in complex disordered media.

cond-mat.dis-nn↗

arXiv2018

Gravity model for dyadic Olympic competitions

In the Olympic Games, professional athletes representing their nations compete regardless of economic, political and cultural differences. In this study, we apply gravity model to observe characteristics, represented by distances among nations that directly compete against one another in the Summer Olympics. We use dyadic data consisting of medal winning nations in the Olympic Games from 1952 to 2016. To compare how the dynamics changed during and after the Cold War period, we partitioned our data into two time periods (1952-1988 and 1992-2016). Our research is distinguishable from previous studies in that we newly introduce application of gravity model in observing the dynamics of the Olympic Games. Our results show that for the entire study period, countries that engaged each other in competition in the finals of an Olympic event tend to be similar in economic size. After the Cold War, country pairs that compete more frequently tend to be similar in genetic origin.

physics.soc-ph↗

arXiv2017

Comments on Nonrenewal Statistics in the Catalytic Activity of Enzyme Molecules at Mesoscopic Concentrations

It is well known in enzyme kinetics that the Michaelis-Menten (MM) equation is applicable only to enzymes in the steady state. We show that the result obtained in the previous work [Phys. Rev. Lett. 107, 218301 (2011)] is inconsistent with the MM equation, not because the authors considered the enzyme system at mesoscopic concentrations but because they considered the enzyme system in the non-stationary state. The substrate concentration dependence of the mean turnover time is, in fact, consistent with the MM equation in the steady state, regardless of the number of enzymes in the system.

physics.bio-ph↗

arXiv2011

Ultrathin BaTiO3 templates for multiferroic nanostructures

Structural, electronic and dielectric properties of high-quality ultrathin BaTiO3 films are investigated. The films, which are grown by ozone-assisted molecular beam epitaxy on Nb-doped SrTiO3 (001) substrates and having thicknesses as thin 8 unit cells (3.2 nm), are unreconstructed and atomically smooth with large crystalline terraces. A strain-driven transition to 3D island formation is observed for films of of 13 unit cells thickness (5.2 nm). The high structural quality of the surfaces, together with the dielectric properties similar to bulk BaTiO3 and dominantly TiO2 surface termination, make these films suitable templates for the synthesis of high-quality metal-oxide multiferroic heterostructures for the fundamental study and exploitation of magneto-electric effects, such as a recently proposed interface effect in Fe/BaTiO3 heterostructures based on Fe-Ti interface bonds.

cond-mat.mtrl-sci↗

arXiv2010

Optimal Efficiency of Self-Assembling Light-Harvesting Arrays

Using a classical master equation that describes energy transfer over a given lattice, we explore how energy transfer efficiency along with the photon capturing ability depends on network connectivity, on transfer rates, and on volume fractions - the numbers and relative ratio of fluorescence chromophore components, e.g., donor (D), acceptor (A), and bridge (B) chromophores. For a one-dimensional AD array, the exact analytical expression for efficiency shows a steep increase with a D-to-A transfer rate when a spontaneous decay is sufficiently slow. This result implies that the introduction of B chromophores can be a useful method for improving efficiency for a two-component AD system with inefficient D-to-A transfer and slow spontaneous decay. Analysis of this one-dimensional system can be extended to higher-dimensional systems with chromophores arranged in structures such as a helical or stacked-disk rod, which models the self-assembling monomers of the tobacco mosaic virus coat protein. For the stacked-disk rod, we observe the following: (1) With spacings between sites fixed, a staggered conformation is more efficient than an eclipsed conformation. (2) For a given ratio of A and D chromophores, the uniform distribution of acceptors that minimizes the mean first passage time to acceptors is a key point to designing the optimal network for a donor-acceptor system with a relatively small D-to-A transfer rate. (3) For a three-component ABD system with a large B-to-A transfer rate, a key design strategy is to increase the number of the pathways in accordance with the directional energy flow from D to B to A chromophores.

cond-mat.stat-mech↗