arXiv subjects

Changbong Hyeon

Publications and source records attributed to Changbong Hyeon.

At least 19 recordsLinked to original sources

arXiv2026

Physical Constraints on the Rhythmicity of the Biological Clock

Circadian rhythms in living organisms are temporal orders emerging from biochemical circuits driven out of equilibrium. Here, considering the KaiABC system, a minimal model in the synthetic biology, we study how the oscillation emerges from the circuit made of three Kai proteins and ATP alone. The phase diagram constructed in terms of KaiC and KaiA concentrations reveals a narrowly bounded oscillatory phase, which naturally explains arrhythmia upon protein over-expression. As dictated by the cost-precision trade-offs of the thermodynamic uncertainty relations, the presence of intrinsic noise, amplified in small systems, demands higher free energy cost to achieve greater rhythmic precision. The cost-minimizing condition within the oscillatory phase is found to generate $\sim$21-hr rhythm, which is entrained to 24-hr environmental signals as long as the forcing amplitude is greater than $\sim 10$ \% of the metabolic rate. An optimal level of intrinsic noise can also induce oscillations even beyond the Hopf bifurcation, effectively expanding the oscillatory phase. Our study clarifies how the physical factors, such as regulatory mechanism, energy cost, and stochastic noise contribute to the operation of biological clocks.

cond-mat.stat-mech↗

arXiv2026

A simple fourth order propagator based on the Magnus expansion in the Liouville space: Application to a $Λ$-system and assessment of the rotating wave approximation

A simple 4th order propagator [Ture and Jang, {\it J. Phys. Chem. A.} {\bf 128}, 2871 (2024)] based on the Magnus expansion (ME) is extended to the Liouville space for both closed-system and Lindbladian open-system quantum dynamics. For both dynamics, commutator free versions of 4th order propagators are provided as well. These propagators are then applied to the dynamics of a driven $Λ$-system, where Lindblad terms represent the effect of a photonic bath. For both dynamics, the accuracy of the rotating wave approximation (RWA) for the matter-radiation interaction is assessed. We confirmed reasonable performance of RWA for weak and resonant fields. However, small errors appear for moderate fields and substantial errors can be found for strong fields where coherent population trapping can still be expected. We also found that the presence of bath for open system quantum dynamics consistently reduces the errors of the RWA. These results provide a quantitative information on how the RWA breaks down beyond weak field or for non-resonant cases. Major results are benchmarked against results of our 6th order ME-based propagator. We also provide numerical comparison of our algorithms with other 4th order algorithms for the $Λ$-system. These confirm reasonable performance of our simple propagators and the improvement gained through commutator-free expressions.

quant-ph↗

arXiv2025

Depletion interaction between cylindrical inclusions in polymer brushes

Inclusions in mobile brushes experience apparent (depletion) attraction, which arises from a tendency to minimize the volume of depletion zones around the inclusions, thereby to maximize the entropy of the surrounding polymers. Here, we study the brush-induced depletion attraction between cylindrical inclusions using molecular dynamics simulations and the Asakura-Oosawa theory. Our considerations find that the correlation blobs defined in the brush environment serve as the fundamental units of the attraction. In tall brushes, however, the entropy of the overgrown polymer competes with the depletion attraction between the inclusions. As a result, the brush-induced depletion interaction displays non-monotonic variations with the brush height. Our study not only expands the repertoire of colloid-polymer mixtures to depletion interactions in brushes, but also suggests the brush-induced depletion interaction as a previously unappreciated mechanism for glycocalyx-induced protein cluster formation on cell surfaces.

cond-mat.soft↗

arXiv2025

The thermodynamic uncertainty relation of a quantum-mechanically coupled two-qubit system

The minimal bound of the thermodynamic uncertainty relation (TUR) is modulated from that of the classical counterpart ($\mathcal{Q}_{\rm min}=2$) when a quantumness is present in the dynamical process far from equilibrium. A recent study on a dissipative two-level system (TLS) subject to an external field indicates that quantum coherence can suppress the fluctuations of the irreversible current and loosens the TUR bound to $\mathcal{Q}_{\rm min}^{\rm TLS}\approx 1.25$. Here, we extend on the field-driven single TLS % in a photonic bath to a quantum-mechanically coupled two-qubit system (TQS), and explore how the quantum coupling between the two qubits, an additional complexity introduced to the probem of TLS, affects the photon current, fluctuations, and the TUR bound. We find that the TUR bound of TQS depends on the strength of coupling, such that $\mathcal{Q}_{\rm min}^{\rm TQS}=\mathcal{Q}_{\rm min}^{\rm TLS}\approx 1.25$ when the two qubits are effectively decoupled under weak coupling, whereas another loose bound $\mathcal{Q}_{\rm min}^{\rm TQS}\approx 1.36$ is identified for two strongly coupled qubits under strong fields. By contrasting the TQS against two coupled noisy oscillators, we illuminate the quantumness unique to the TQS and its effect on the TUR. Our findings from the study of TQS form the basis for understanding the TUR of more general $N$-qubit systems.

cond-mat.stat-mech↗

arXiv2025

Iterative Annealing Mechanism for Protein and RNA Chaperones

Molecular chaperones are machines that consume copious amount of ATP to drive misfolded proteins or RNA to fold into functionally competent native states. Because the folding landscapes of biomolecules with complex native state topology are rugged consisting of multiple minima that are separated by large free energy barriers, folding occurs by the kinetic partitioning mechanism according to which only a small fraction of the molecules reach the folded state in biologically viable times. The rescue of such proteins and RNA require chaperones. Although the protein and RNA chaperones are profoundly different in their structure and action, the principles underlying their activity to produce the folded structures can be understood using a unified theoretical framework based on iterative annealing mechanism (IAM). Our theory shows that both these machines have evolved to the maximize the production of the steady state yield on biological times. Strikingly, theory predicts that only at a moderate level of RNA chaperone activity is the yield of the self-splicing pre-RNA is maximized in \textit{in vivo}.

physics.bio-ph↗

arXiv2024

Organization and Dynamics of Chromosomes

How long threadlike eukaryotic chromosomes fit tidily in the small volume of the nucleus without significant entanglement is just beginning to be understood, thanks to major advances in experimental techniques. Several polymer models, which reproduce contact maps that measure the probabilities that two loci are in spatial contact, have predicted the three-dimensional structures of interphase chromosomes. Data-driven approaches, using contact maps as input, predict that mitotic helical chromosomes are characterized by switch in handedness, referred to as "perversion". By using experimentally derived effective interactions between chromatin loci in simulations, structures of conventional and inverted nuclei have been accurately predicted. Polymer theory and simulations show that the dynamics of individual loci in chromatin exhibit subdiffusive behavior but the diffusion exponents are broadly distributed, which accords well with experiments. Although coarse-grained models are successful, many challenging problems remain, which require the creation of new experimental and computational tools to understand genome biology.

cond-mat.soft↗

arXiv2024

Emergence of metachronal waves in a chain of symmetrically beating filaments

Recent experiments have shown that metachronal waves (MCWs) can emerge from a chain of symmetrically beating nematodes aligned at the edge of sessile droplets. Our study, employing a coupled elastohydrodynamic model of active filaments, elucidates that a misalignment caused by a tilt against the bounding wall disrupts the synchronization and generates a constant time lag between adjacent filaments, giving rise to MCWs. The MCWs, enhancing the fluid circulation, achieve their maximum thermodynamic efficiency over the same range of tilt angles observed in the nematode experiments.

cond-mat.soft↗

arXiv2024

Anomalous Water Penetration in $\text{Al}^{3+}$ Dissolution

The physicochemical characterization of trivalent ions is limited due to a lack of accurate force fields. By leveraging the latest machine learning force field to model aqueous $\text{AlCl}_{3}$, we discover that upon dissolution of $\text{Al}^{3+}$, water molecules beyond the second hydration shell involve in the hydration process. A combination of scissoring of coordinating water is followed by synchronized secondary motion of water in the second solvation shell due to hydrogen bonding. Consequently, the water beyond the second solvation penetrates through the second solvation shell and coordinates to the $\text{Al}^{3+}$. Our study reveals a novel microscopic understanding of solvation dynamics for trivalent ion.

physics.chem-ph↗

arXiv2023

Irregularity of polymer domain boundaries in two-dimensional polymer solution

Polymer chains composing a polymer solution in strict two dimensions (2D) are characterized with irregular domain boundaries, whose fractal dimension ($\mathcal{D}^{\partial}$) varies with the area fraction of the solution and the solvent quality. {\color{black}Our analysis of numerical simulations of polymer solutions finds} that $\mathcal{D}^{\partial}$ in good solvents changes non-monotonically from $\mathcal{D}^{\partial}=4/3$ in dilute phase to $\mathcal{D}^{\partial}=5/4$ in dense phase, maximizing to $\mathcal{D}^{\partial}\approx 3/2$ at a crossover area fraction $ϕ_{\rm cr}\approx 0.2$, whereas for polymers in $Θ$ solvents $\mathcal{D}^{\partial}$ remains constant at $\mathcal{D}^{\partial}=4/3$ from dilute to semi-dilute phase. Using polymer physics arguments, we rationalize these values, and show that the maximum irregularity of $\mathcal{D}^\partial\approx 3/2$ is due to "fjord"-like corrugations formed along the domain boundaries which also maximize at the same crossover area fraction. Our finding of $\mathcal{D}^\partial\approx 3/2$ is, in fact, in perfect agreement with the upper bound for the fractal dimension of the external perimeter of 2D random curves at scaling limit, which is predicted by the Schramm-Loewner evolution (SLE).

cond-mat.soft↗

arXiv2023

General Chemical Reaction Network Theory for Olfactory Sensing Based on G-Protein-Coupled Receptors : Elucidation of Odorant Mixture Effects and Agonist-Synergist Threshold

This work presents a general chemical reaction network theory for olfactory sensing processes that employ G-protein-coupled receptors as olfactory receptors (ORs). The theory is applicable to general mixtures of odorants and an arbitrary number of ORs. Reactions of ORs with G-proteins, both in the presence and the absence of odorants, are explicitly considered. A unique feature of the theory is the definition of an odor activity vector consisting of strengths of odorant-induced signals from ORs relative to those due to background G-protein activity in the absence of odorants. It is demonstrated that each component of the odor activity defined this way reduces to a Michaelis-Menten form capable of accounting for cooperation or competition effects between different odorants. The main features of the theory are illustrated for a two-odorant mixture. Known and potential mixture effects, such as suppression, shadowing, inhibition, and synergy are quantitatively described. Effects of relative values of rate constants, basal activity, and G-protein concentration are also demonstrated.

q-bio.MN↗

arXiv2023

Fundamental trade-off between the speed of light and the Fano factor of photon current in three-level lambda systems

Electromagnetically induced slow-light medium is a promising system for quantum memory devices, but controlling its noise level remains a major challenge to overcome. This work considers the simplest model for such medium, comprised of three-level $Λ$-systems interacting with bosonic bath, and provides a new fundamental trade-off relation in light-matter interaction between the group velocity of light and the Fano factor of photon current due to radiative transitions. Considering the steady state limits of a newly derived Lindblad-type equation, we find that the Fano factor of the photon current maximizes to 3 at the minimal group velocity of light, which holds true universally regardless of detailed values of parameters characterizing the medium.

quant-ph↗

arXiv2022

Solvent quality dependent osmotic pressure of polymer solutions in two dimensions

Confined in two dimensional planes, polymer chains comprising dense monolayer solution are segregated from each other due to topological interaction. Although the segregation is inherent in two dimensions (2D), the solution may display different properties depending on the solvent quality. Among others, it is well known in both theory and experiment that the osmotic pressure ($Π$) in the semi-dilute regime displays solvent quality-dependent increases with the area fraction ($ϕ$) (or monomer concentration, $ρ$), that is, $Π\sim ϕ^3$ for good solvent and $Π\sim ϕ^8$ for $Θ$ solvent. The osmotic pressure can be associated with the Flory exponent (or the correlation length exponent) for the chain size and the pair distribution function of monomers; however, they do not necessarily offer a detailed microscopic picture leading to the difference. To gain microscopic understanding into the different surface pressure isotherms of polymer solution under the two distinct solvent conditions, we study the chain configurations of polymer solution based on our numerical simulations that semi-quantitatively reproduce the expected scaling behaviors. Notably, at the same value of $ϕ$, polymer chains in $Θ$ solvent occupy the surface in a more \emph{inhomogeneous} manner than the chains in good solvent, yielding on average a greater and more heterogeneous interstitial void size, which is related to the fact that the polymer in $Θ$ solvent has a greater correlation length. The polymer configurations and interstitial voids visualized and quantitatively analyzed in this study offer microscopic understanding to the origin of the solvent quality dependent osmotic pressure of 2D polymer solutions.

cond-mat.soft↗

arXiv2021

The origin of loose bound of the thermodynamic uncertainty relation in a dissipative two-level quantum system

The thermodynamic uncertainty relations (TURs), originally discovered for classical systems, dictate the trade-off between dissipation and fluctuations of irreversible current, specifying a minimal bound that constrains the two quantities. In a series of effort to extend the relation to the one under more generalized conditions, it has been noticed that the bound is less tight in open quantum processes. To study the origin of the loose bounds, we consider an external field-driven transition dynamics of two-level quantum system weakly coupled to the bosonic bath as a model of open quantum system. The model makes it explicit that the imaginary part of quantum coherence, which contributes to dissipation to the environment, is responsible for loosening the TUR bound by suppressing the relative fluctuations in the irreversible current of transitions, whereas the real part of the coherence tightens it. Our study offers a better understanding of how quantum nature affects the TUR bound.

quant-ph↗

arXiv2021

Thermodynamic optimality of glycolytic oscillations

Temporal order in living matters reflects the self-organizing nature of dynamical processes driven out of thermodynamic equilibrium. Because of functional reason, the period of a biochemical oscillation must be tuned to a specific value with precision; however, according to the thermodynamic uncertainty relation (TUR), the precision of oscillatory period is constrained by the thermodynamic cost of generating it. After reviewing the basics of chemical oscillations using Brusselator as a model system, we study the glycolytic oscillation generated by octameric phosphofructokinase (PFK), which is known to display a period of several minutes. By exploring the phase space of glycolytic oscillations, we find that the glycolytic oscillation under the cellular condition is realized in a cost effective manner. Specifically, over the biologically relevant range of parameter values of glycolysis and octameric PFK, the entropy production from the glycolytic oscillation is minimal when the oscillation period is (5 - 10) minutes. Further, the glycolytic oscillation is found at work near the phase boundary of limit cycles, suggesting that a moderate increase of glucose injection rate leads to the loss of oscillatory dynamics, which is reminiscent of the loss of pulsatile insulin release resulting from elevated blood glucose level.

physics.bio-ph↗

arXiv2021

Thermodynamic uncertainty relation to assess biological processes

We review the trade-offs between speed, fluctuations, and thermodynamic cost involved with biological processes in nonequilibrium states, and discuss how optimal these processes are in light of the universal bound set by the thermodynamic uncertainty relation (TUR). The values of the uncertainty product $\mathcal{Q}$ of TUR, which can be used as a measure of the precision of enzymatic processes realized for a given thermodynamic cost, are suboptimal when the substrate concentration $[S]$ is at the Michaelis constant ($K_\text{M}$), and some of the key biological processes are found to work around this condition. We illustrate the utility of $\mathcal{Q}$ in assessing how close the molecular motors and biomass producing machineries are to the TUR bound, and for the cases of biomass production (or biological copying processes) we discuss how their optimality quantified in terms of $\mathcal{Q}$ is balanced with the error rate in the information transfer process. We also touch upon the trade-offs in other error-minimizing processes in biology, such as gene regulation and chaperone-assisted protein folding. A spectrum of $\mathcal{Q}$ recapitulating the biological processes surveyed here provides glimpses into how biological systems are evolved to optimize and balance the conflicting functional requirements.

physics.bio-ph↗

arXiv2021

Polymer brush-induced depletion interactions and clustering of membrane proteins

We investigate the effect of mobile polymer brushes on proteins embedded in biological membranes by employing both Asakura-Oosawa type of theoretical model and coarse-grained molecular dynamics simulations. The brush polymer-induced depletion attraction between proteins changes non-monotonically with the size of brush. The depletion interaction, which is determined by the ratio of protein size to the grafting distance between brush polymers, increases linearly with brush size as long as the polymer brush height is shorter than the protein size. When the brush height exceeds the protein size, however, the depletion attraction among proteins is slightly reduced. We also explore the possibility of brush polymer-induced assembly of a large protein cluster, which can be related to one of many molecular mechanisms underlying recent experimental observations of integrin nanocluster formation and signaling.

cond-mat.soft↗

arXiv2020

Thermodynamic cost, speed, fluctuations, and error reduction of biological copy machines

Due to large fluctuations in cellular environments, transfer of information in biological processes without regulation is inherently error-prone. The mechanistic details of error-reducing mechanisms in biological copying processes have been a subject of active research; however, how error reduction of a process is balanced with its thermodynamic cost and dynamical properties remain largely unexplored. Here, we study the error reducing strategies in light of the recently discovered thermodynamic uncertainty relation (TUR) that sets a physical bound to the cost-precision trade-off relevant in general dissipative processes. We found that the two representative copying processes, DNA replication by the exonuclease-deficient T7 DNA polymerase and mRNA translation by the \textit{E. coli} ribosome, reduce the error rates to biologically acceptable levels while also optimizing the processes close to the physical limit dictated by TUR.

physics.bio-ph↗

arXiv2020

Thermodynamic cost of synchronizing a population of beating cilia

Synchronization among arrays of beating cilia is one of the emergent phenomena in biological processes at meso-scopic scales. Strong inter-ciliary couplings modify the natural beating frequencies, $ω$, of individual cilia to produce a collective motion that moves around a group frequency $ω_m$. Here we study the thermodynamic cost of synchronizing cilia arrays by mapping their dynamics onto a generic phase oscillator model. The model suggests that upon synchronization the mean heat dissipation rate is decomposed into two contributions, dissipation from each cilium's own natural driving force and dissipation arising from the interaction with other cilia, the latter of which can be interpreted as the one produced by a potential with a time-dependent protocol in the framework of our model. The spontaneous phase-synchronization of beating dynamics of cilia induced by strong inter-ciliary coupling is always accompanied with a significant reduction of dissipation for the cilia population, suggesting that organisms as a whole expend less energy by attaining a temporal order. At the level of individual cilia, however, a population of cilia with $|ω|< ω_m$ expend more amount of energy upon synchronization.

cond-mat.stat-mech↗