arXiv subjects

Won Kyu Kim

Publications and source records attributed to Won Kyu Kim.

At least 19 recordsLinked to original sources

arXiv2025

Confinement-Driven Acceleration of First-Passage Rates

We demonstrate that confinement geometry can act as a rectifier in passive diffusion, optimally accelerating first-passage rates beyond free diffusion. Using analytic theory based on the Fick-Jacobs approach and Brownian dynamics simulations, we find nonmonotonic mean first-passage rates driven by entropy. Through the transmission probability, our findings highlight how confinement optimizes transport dynamics in trap-and-escape processes, with implications for molecular translocation and reaction kinetics in soft matter and biological systems.

physics.bio-ph↗

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

Active Diffusion of Self-Propelled Particles in Semi-Flexible Polymer Networks

Mesh-like structures, such as mucus gel or cytoskeleton networks, are ubiquitous in biological systems. These intricate structures are composed of cross-linked, semi-flexible bio-filaments, crucial to numerous biological processes. In many biological systems, active self-propelled particles like motor proteins or bacteria navigate these intricate polymer networks. In this study, we develop a computational model of three-dimensional cubic-topological, swollen polymer networks of semi-flexible filaments. We perform Langevin dynamics simulations to investigate the diffusion of active tracer particles navigating through these networks. By analyzing various physical observables, we investigate the effects of mesh-to-particle size ratio, Péclet number of active particles, and bending stiffness of the polymer networks upon active trapped-and-hopping diffusion of the tracer. When the tracer size is equal to or larger than the mesh size, the polymer stiffness substantially enhances trapping while suppressing the hopping process. Notably, the mean trapped time exhibits an exponential growth law to the bending stiffness with an activity-dependent slope. An analytic theory based on the mean first-passage time of active particles in a harmonic potential is developed. Our findings deepen the comprehension of the intricate interplay between the polymer's bending stiffness, tracer size, and the activity of tracer particles. This knowledge can shed light on important biological processes, such as motor-driven cargo transport or drug delivery, which hinge on the behavior of active particles within biological gels.

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

Multidimensional entropic bound: Estimator of entropy production for general Langevin dynamics with an arbitrary time-dependent protocol

Entropy production (EP) is a key quantity in thermodynamics, and yet measuring EP has remained a challenging task. Here we introduce an EP estimator, called multidimensional entropic bound (MEB), utilizing an ensemble of trajectories without knowing the details of a given system. MEB is a unified method in the sense that it is applicable to both overdamped and underdamped Langevin dynamics, irrespective of the time dependence of the driving protocol. In addition, MEB is computationally efficient because optimization is unnecessary. We apply our developed estimator to three physical systems driven by time-dependent protocols pertaining to experiments using optical tweezers: a dragged Brownian particle, a pulling process of a harmonic chain, and an unfolding process of an RNA hairpin. Numerical simulations confirm the validity and efficiency of our method.

cond-mat.stat-mech↗

arXiv2022

Feedback-controlled solute transport through chemo-responsive polymer membranes

Polymer membranes are typically assumed to be inert and nonresponsive to the flux and density of the permeating particles in transport processes. Here, we study theoretically the consequences of membrane responsiveness and feedback on the steady-state force--flux relations and membrane permeability using a nonlinear-feedback solution-diffusion model of transport through a slab-like membrane. Therein, the solute concentration inside the membrane depends on the bulk concentration, $c_0$, the driving force, $f$, and the polymer volume fraction, $ϕ$. In our model, solute accumulation in the membrane causes a sigmoidal volume phase transition of the polymer, changing its permeability, which, in return, affects the membrane's solute uptake. This feedback leads to nonlinear force--flux relations, $j(f)$, which we quantify in terms of the system's differential permeability, $\mathcal{P}_\text{sys}^Δ\propto {\mathrm{d}j}/{\mathrm{d}f}$. We find that the membrane feedback can increase or decrease the solute flux by orders of magnitude, triggered by a small change in the driving force, and largely tunable by attractive versus repulsive solute--membrane interactions. Moreover, controlling the input, $c_0$ and $f$, can lead to steady-state bistability of $ϕ$ and hysteresis in the force--flux relations. This work advocates that the fine-tuning of the membrane's chemo-responsiveness will enhance the nonlinear transport control features, providing great potential for future (self-)regulating membrane devices.

cond-mat.soft↗

arXiv2022

Proton-transfer spectroscopy beyond the normal-mode scenario

A stochastic theory is developed to predict the spectral signature of proton-transfer processes and applied to infrared spectra computed from ab initio molecular-dynamics simulations of a single H$_5$O$_2{}^{+}$ cation. By constraining the oxygen atoms to a fixed distance, this system serves as a tunable model for general proton-transfer processes with variable barrier height. Three spectral contributions at distinct frequencies are identified and analytically predicted: the quasi-harmonic motion around the most probable configuration, amenable to normal-mode analysis, the contribution due to transfer paths when the proton moves over the barrier and a shoulder for low frequencies stemming from the stochastic transfer-waiting-time distribution; the latter two contributions are not captured by normal-mode analysis but exclusively report on the proton-transfer kinetics. In accordance with reaction kinetic theory, the transfer-waiting-contribution frequency depends inverse exponentially on the barrier height, whereas the transfer-path-contribution frequency is rather insensitive to the barrier height.

physics.chem-ph↗

arXiv2022

Active diffusion of self-propelled particles in flexible polymer networks

Biopolymer networks having a meshwork topology, e.g., extracellular matrix and mucus gels, are ubiquitous. It is an open question to understand how self-propelled agents such as Janus colloidal particles diffuse through such a biopolymer network. Here, we computationally explore this issue in-depth by explicitly modeling three-dimensional biopolymer networks and performing Langevin dynamics simulations of active diffusion of the self-propelled tracers therein. We show that the active tracer performs distinct diffusion dynamics depending on the mesh-to-particle size and Péclet number (Pe). When the particle is smaller than the mesh size, it moves as if in free space with a decreased mobility depending on the polymer occupation density and Pe. However, when the particle size is increased to be comparable to the mesh size, the active particles explore the polymer network using the trapped-and-hopping mechanism. We study the trapped time distribution, flight length distribution, the mean-squared displacement, and the long-time diffusivity at varying Pe. If the particle is larger than the mesh, it captures the collective viscoelastic dynamics from the polymer network at short times and the simple diffusion of the total system at large times. Finally, we discuss the scaling behavior of the long-time diffusivity with Pe, where we find a range of Pe that yields a nontrivial power law. The latter turns out to arise from a large fluctuation of trapped, activated tracers in conjugation with responsive polymer networks.

cond-mat.soft↗

arXiv2021

Nanochannels and nanodroplets in polymer membranes controlling ionic transport

Polymer materials with low water uptake exhibit a highly heterogeneous interior, characterized by water clusters in the form of nanodroplets and nanochannels. Here, based on our recent insights from computer simulations, we argue that water cluster structure has large implications for ionic transport and selective permeability in polymer membranes. Importantly, we demonstrate that the two key quantities for transport, the ion diffusion and the solvation free energy inside the polymer, are extremely sensitive to molecular details of the water clusters. In particular, we highlight the significance of water droplet interface potentials and the nature of hopping diffusion through transient water channels. These mechanisms can be harvested and fine-tuned to optimize selectivity in ionic transport in a wide range of applications.

cond-mat.soft↗

arXiv2021

Transport in polymer membranes beyond linear response: Controlling permselectivity by the driving force

In the popular solution-diffusion picture, the membrane permeability is defined as the product of the partition ratio and the diffusivity of penetrating solutes inside the membrane in the linear response regime, i.e., in equilibrium. However, of practical importance is the penetrants' flux across the membrane driven by external forces. Here, we study nonequilibrium membrane permeation orchestrated by a uniform external driving field using molecular computer simulations and continuum (Smoluchowski) theory in the stationary state. In the simulations, we explicitly resolve the penetrants' transport across a finite monomer-resolved polymer network, addressing one-component penetrant systems and mixtures. We introduce and discuss possible definitions of nonequilibrium, force-dependent permeability, representing `system' and `membrane' permeability. In particular, we present for the first time a definition of the differential permeability response to the force. We demonstrate that the latter turns out to be significantly nonlinear for low-permeable systems, leading to a high amount of selectiveness in permeability, called `permselectivity', and is tunable by the driving force. Our continuum-level analytical solutions exhibit remarkable qualitative agreement with the penetrant- and polymer-resolved simulations, thereby allowing us to characterize the underlying mechanism of permeabilities and steady-state transport beyond the linear response level.

cond-mat.soft↗

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

Coverage Fluctuations and Correlations in Nanoparticle-Catalyzed Diffusion-Influenced Bimolecular Reactions

The kinetic processes in nanoparticle-based catalysis are dominated by large fluctuations and spatiotemporal heterogeneities, in particular for diffusion-influenced reactions which are far from equilibrium. Here, we report results from particle-resolved reaction-diffusion simulations of steady-state bimolecular reactions catalyzed on the surface of a single, perfectly spherical nanoparticle. We study various reactant adsorption and diffusion regimes, in particular considering the crowding effects of the reaction products. Our simulations reveal that fluctuations, significant coverage cross-correlations, transient self-poisoning, related domain formation, and excluded-volume effects on the nanoparticle surface lead to a complex kinetic behavior, sensitively tuned by the balance between adsorption affinity, mixed 2D and 3D diffusion, and chemical reaction propensity. The adsorbed products are found to influence the correlations and fluctuations, depending on overall reaction speed, thereby going beyond conventional steric (e.g., Langmuir-like) product inhibition mechanisms. We summarize our findings in a state diagram depicting the nonlinear kinetic regimes by an apparent surface reaction order in dependence of the intrinsic reaction propensity and adsorption strength. Our study using a simple, perfectly spherical, and inert nanocatalyst demonstrates that spatiotemporal heterogeneities are intrinsic to the reaction-diffusion problem and not necessarily caused by any dynamical surface effects from the catalyst (e.g., dynamical surface reconstruction), as often argued.

physics.chem-ph↗

arXiv2020

Tuning the Selective Permeability of Polydisperse Polymer Networks

We study the permeability and selectivity (`permselectivity') of model membranes made of polydisperse polymer networks for molecular penetrant transport, using coarse-grained, implicit-solvent computer simulations. The permeability $\mathcal P$ is determined on the linear-response level using the solution-diffusion model, $\mathcal P = {\mathcal K}D_\text{in}$, $\textit{i.e.}$, by calculating the equilibrium penetrant partition ratio $\mathcal K$ and penetrant diffusivity $D_\text{in}$ inside the membrane. We vary two key parameters, namely the monomer-monomer interaction, which controls the degree of swelling and collapse of the network, and the monomer-penetrant interaction, which tunes the penetrant uptake and microscopic energy landscape for diffusive transport. The results for the partition ratio $\mathcal K$ cover four orders of magnitude and are non-monotonic versus the parameters, which is well interpreted by a second-order virial expansion of the free energy of transferring one penetrant from bulk into the polymeric medium. We find that the penetrant diffusivity $D_\text{in}$ in the polydisperse networks, in contrast to highly ordered membrane structures, exhibits relatively simple exponential decays and obeys well-known free-volume and Kramers' escape scaling laws. The eventually resulting permeability $\mathcal P$ thus resembles the qualitative functional behavior (including maximization and minimization) of the partitioning. However, partitioning and diffusion are anti-correlated, yielding large quantitative cancellations, controlled and fine-tuned by the network density and interactions as rationalized by our scaling laws. As a consequence, we finally demonstrate that even small changes of penetrant-network interactions, $\textit{e.g.}$, by half a $k_\text{B}T$, modify the permselectivity of the membrane by almost one order of magnitude.

cond-mat.soft↗

arXiv2020

Aqueous Nanoclusters Govern Ion Partitioning in Dense Polymer Membranes

The uptake and sorption of charged molecules by responsive polymer membranes and hydrogels in aqueous solutions is of key importance for the development of soft functional materials. Here we investigate the partitioning of simple monoatomic (Na$^+$, K$^+$, Cs$^+$, Cl$^-$, I$^-$) and one molecular ion (4-nitrophenolate; NP$^-$) within a dense, electroneutral poly($N$-isopropylacrylamide) membrane using explicit-water molecular dynamics simulations. Inside the predominantly hydrophobic environment water distributes in a network of polydisperse water nanoclusters. The average cluster size determines the mean electrostatic self-energy of the simple ions, which preferably reside deeply inside them; we therefore find substantially larger partition ratios $K\simeq\>$10$^{-1}$ than expected from a simple Born picture using a uniform dielectric constant. Despite their irregular shapes we observe that the water clusters possess a universal negative electrostatic potential with respect to their surrounding, as is known for aqueous liquid-vapor interfaces. This potential, which we find concealed in cases of symmetric monoatomic salts, can dramatically impact the transfer free energies of larger charged molecules because of their weak hydration and increased affinity to interfaces. Consequently, and in stark contrast to the simple ions, the molecular ion NP$^-$ can have a partition ratio much larger than unity, $K\simeq\>$10-30 (depending on the cation type) or even $10^3$ in excess of monovalent salt, which explains recent observations of enhanced reaction kinetics of NP$^-$ reduction catalyzed within dense polymer networks. These results also suggest that ionizing a molecule can even enhance the partitioning in a collapsed, rather hydrophobic gel, which strongly challenges the traditional simplistic reasoning.

cond-mat.soft↗

arXiv2020

Modeling of stimuli-responsive nanoreactors: rational rate control towards the design of colloidal enzymes

In modern applications of heterogeneous liquid-phase nanocatalysis, the catalysts (e.g., metal nanoparticles) need to be typically affixed to a colloidal carrier system for stability and easy handling. "Passive carriers" (e.g., simple polyelectrolytes) serve for a controlled synthesis of the nanoparticles and prevent coagulation during catalysis. Recently, however, hybrid conjugates of nanoparticles and synthetic thermosensitive polymers have been developed that enable to change the catalytic activity of the nanoparticles by external triggers. In particular, nanoparticles embedded in a stimuli-responsive network made from poly(N-isopropylacrylamide) (PNIPAM) have become the most-studied examples of such hybrids. It has been demonstrated that the permeability of the polymer network and thus the reactant flux can be switched and controlled by external stimuli. Such "active carriers" may thus be viewed as true nanoreactors that open up new design routes in nano-catalysis and elevate synthesis to create highly selective, programmable "colloidal enzymes". However, only a comprehensive understanding of these materials on all time and length scales can lead to a rational design of future, highly functional materials. Here we review the current state of the theoretical and multi-scale simulation approaches, aiming at a fundamental understanding of these nanoreactors. In particular, we summarize a theoretical approach for reaction rates of surface-catalyzed bimolecular reactions in responsive nanoreactors in terms of the key material parameters, the polymer shell permeability P and the reactant partition ratio K. We discuss recent computer simulation studies of both atomistic and coarse-grained polymer models in which these quantities have been characterized in some detail. We conclude with an outlook on selected open questions and future theoretical challenges in nanoreactor modeling.

physics.chem-ph↗

arXiv2019

Tuning the permeability of dense membranes by shaping nanoscale potentials

The permeability is one of the most fundamental transport properties in soft matter physics, material engineering, and nanofluidics. Here we report by means of Langevin simulations of ideal penetrants in a nanoscale membrane made of a fixed lattice of attractive interaction sites, how the permeability can be massively tuned, even minimized or maximized, by tailoring the potential energy landscape for the diffusing penetrants, depending on the membrane attraction, topology, and density. Supported by limiting scaling theories we demonstrate that the observed non-monotonic behavior and the occurrence of extreme values of the permeability is far from trivial and triggered by a strong anti-correlation and substantial (orders of magnitude) cancellation between penetrant partitioning and diffusivity, especially within dense and highly attractive membranes.

cond-mat.soft↗

arXiv2019

Transfer Free Energies and Partitioning of Small Molecules in Collapsed PNIPAM Polymers

A central quantity in the design of functional hydrogels used as nanocarrier systems, for instance for drug delivery or adaptive nanocatalysis, is the partition ratio, which quantifies the uptake of a molecular substance by the polymer matrix. By employing all-atom molecular dynamics simulations, we study the solvation and partitioning (with respect to bulk water) of small subnanometer-sized solutes in a dense matrix of collapsed Poly(N-isopropylacrylamide) (PNIPAM) polymers above the lower critical solution temperature (LCST) in aqueous solution. We examine the roles of the solute's polarity and its size on the solubility properties in the thermoresponsive polymer. We show that the transfer free energies of nonpolar solutes from bulk water into the polymer are favorable and scale in a good approximation with the solute's surface area. Even for small solute size variation, partitioning can vary over orders of magnitude. A polar nature of the solute, on the other hand, generally opposes the transfer, at least for alkyl solutes. Finally, we find a strong correlation between the transfer free energies in the gel and the adsorption free energies on a single extended polymer chain, which enables us to relate the partition ratios in the swollen and collapsed state of a PNIPAM gel.

cond-mat.soft↗

arXiv2018

Selective molecular transport in thermo-responsive polymer membranes: role of nanoscale hydration and fluctuations

For a wide range of modern soft functional materials the selective transport of sub-nanometer-sized molecules (`penetrants') through a stimuli-responsive polymeric membrane is key to the desired function. In this study, we investigate the diffusion properties of penetrants ranging from non-polar to polar molecules and ions in a matrix of collapsed Poly(N-isopropylacrylamide) (PNIPAM) polymers in water by means of extensive molecular dynamics simulations. We find that the water distributes heterogeneously in fractal-like cluster structures embedded in the nanometer-sized voids of the polymer matrix. The nano-clustered water acts as an important player in the penetrant diffusion, which proceeds via a hopping mechanism through `wet' transition states: the penetrants hop from one void to another via transient water channels opened by rare but decisive polymer fluctuations. The diffusivities of the studied penetrants extend over almost five orders of magnitude and thus enable a formulation of an analytical scaling relation with a clear non-Stokesian, exponential dependence of the diffusion coefficient on the penetrant's radius for the uncharged penetrants. Charged penetrants (ions) behave differently as they get captured in large isolated water clusters. Finally, we find large energetic activation barriers for hopping, which significantly depend on the hydration state and thereby challenge available transport theories.

cond-mat.soft↗