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Book ; Online: Viscoelastic active diffusion governed by nonequilibrium fractional Langevin equations

Joo, Sungmin / Jeon, Jae-Hyung

underdamped dynamics and ergodicity breaking

2023

Abstract: In this work, we investigate the active dynamics and ergodicity breaking of a nonequilibrium fractional Langevin equation (FLE) with a power-law memory kernel of the form $K(t)\sim t^{-(2-2H)}$, where $1/2

Abstract	In this work, we investigate the active dynamics and ergodicity breaking of a nonequilibrium fractional Langevin equation (FLE) with a power-law memory kernel of the form $K(t)\sim t^{-(2-2H)}$, where $1/2<H<1$ represents the Hurst exponent. The system is subjected to two distinct noises: a thermal noise satisfying the fluctuation-dissipation theorem and an active noise characterized by an active Ornstein-Uhlenbeck process with a propulsion memory time $\tau_\mathrm{A}$. We provide analytic solutions for the underdamped active fractional Langevin equation, performing both analytical and computational investigations of dynamic observables such as velocity autocorrelation, the two-time position correlation, ensemble- and time-averaged mean-squared displacements (MSDs), and ergodicity-breaking parameters. Our results reveal that the interplay between the active noise and long-time viscoelastic memory effect leads to unusual and complex nonequilibrium dynamics in the active FLE systems. Furthermore, the active FLE displays a new type of discrepancy between ensemble- and time-averaged observables. The active component of the system exhibits ultraweak ergodicity breaking where both ensemble- and time-averaged MSDs have the same functional form with unequal amplitudes. However, the combined dynamics of the active and thermal components of the active FLE system are eventually ergodic in the infinite-time limit. Intriguingly, the system has a long-standing ergodicity-breaking state before recovering the ergodicity. This apparent ergodicity-breaking state becomes exceptionally long-lived as $H\to1$, making it difficult to observe ergodicity within practical measurement times. Our findings provide insight into related problems, such as the transport dynamics for self-propelled particles in crowded or polymeric media.<br />
Keywords	Condensed Matter - Statistical Mechanics ; Condensed Matter - Soft Condensed Matter
Subject code	612
Publishing date	2023-08-27
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Book ; Online: Active Diffusion of Self-Propelled Particles in Semi-Flexible Polymer Networks

Kim, Yeongjin / Kim, Won Kyu / Jeon, Jae-Hyung

2024

Abstract: 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 ... ...

Abstract	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, P\'eclet 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.
Keywords	Condensed Matter - Soft Condensed Matter
Subject code	612
Publishing date	2024-01-08
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: A machine learning approach to discover migration modes and transition dynamics of heterogeneous dendritic cells.

Song, Taegeun / Choi, Yongjun / Jeon, Jae-Hyung / Cho, Yoon-Kyoung

Frontiers in immunology

2023 Volume 14, Page(s) 1129600

Abstract: Dendritic cell (DC) migration is crucial for mounting immune responses. Immature DCs (imDCs) reportedly sense infections, while mature DCs (mDCs) move quickly to lymph nodes to deliver antigens to T cells. However, their highly heterogeneous and complex ... ...

Abstract	Dendritic cell (DC) migration is crucial for mounting immune responses. Immature DCs (imDCs) reportedly sense infections, while mature DCs (mDCs) move quickly to lymph nodes to deliver antigens to T cells. However, their highly heterogeneous and complex innate motility remains elusive. Here, we used an unsupervised machine learning (ML) approach to analyze long-term, two-dimensional migration trajectories of Granulocyte-macrophage colony-stimulating factor (GMCSF)-derived bone marrow-derived DCs (BMDCs). We discovered three migratory modes independent of the cell state: slow-diffusive (SD), slow-persistent (SP), and fast-persistent (FP). Remarkably, imDCs more frequently changed their modes, predominantly following a unicyclic SD→FP→SP→SD transition, whereas mDCs showed no transition directionality. We report that DC migration exhibits a history-dependent mode transition and maturation-dependent motility changes are emergent properties of the dynamic switching of the three migratory modes. Our ML-based investigation provides new insights into studying complex cellular migratory behavior.
MeSH term(s)	Cell Differentiation ; T-Lymphocytes ; Dendritic Cells ; Machine Learning
Language	English
Publishing date	2023-04-04
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2606827-8
ISSN	1664-3224 ; 1664-3224
ISSN (online)	1664-3224
ISSN	1664-3224
DOI	10.3389/fimmu.2023.1129600
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Article ; Online: Nonequilibrium diffusion of active particles bound to a semiflexible polymer network: Simulations and fractional Langevin equation.

Han, Hyeong-Tark / Joo, Sungmin / Sakaue, Takahiro / Jeon, Jae-Hyung

The Journal of chemical physics

2023 Volume 159, Issue 2

Abstract: In a viscoelastic environment, the diffusion of a particle becomes non-Markovian due to the memory effect. An open question concerns quantitatively explaining how self-propulsion particles with directional memory diffuse in such a medium. Based on ... ...

Abstract	In a viscoelastic environment, the diffusion of a particle becomes non-Markovian due to the memory effect. An open question concerns quantitatively explaining how self-propulsion particles with directional memory diffuse in such a medium. Based on simulations and analytic theory, we address this issue with active viscoelastic systems where an active particle is connected with multiple semiflexible filaments. Our Langevin dynamics simulations show that the active cross-linker displays superdiffusive and subdiffusive athermal motion with a time-dependent anomalous exponent α. In such viscoelastic feedback, the active particle always exhibits superdiffusion with α = 3/2 at times shorter than the self-propulsion time (τA). At times greater than τA, the subdiffusive motion emerges with α bounded between 1/2 and 3/4. Remarkably, active subdiffusion is reinforced as the active propulsion (Pe) is more vigorous. In the high Pe limit, athermal fluctuation in the stiff filament eventually leads to α = 1/2, which can be misinterpreted with the thermal Rouse motion in a flexible chain. We demonstrate that the motion of active particles cross-linking a network of semiflexible filaments can be governed by a fractional Langevin equation combined with fractional Gaussian noise and an Ornstein-Uhlenbeck noise. We analytically derive the velocity autocorrelation function and mean-squared displacement of the model, explaining their scaling relations as well as the prefactors. We find that there exist the threshold Pe (Pe∗) and crossover times (τ∗ and τ†) above which active viscoelastic dynamics emerge on timescales of τ∗≲ t ≲ τ†. Our study may provide theoretical insight into various nonequilibrium active dynamics in intracellular viscoelastic environments.
Language	English
Publishing date	2023-07-10
Publishing country	United States
Document type	Journal Article
ZDB-ID	3113-6
ISSN	1089-7690 ; 0021-9606
ISSN (online)	1089-7690
ISSN	0021-9606
DOI	10.1063/5.0150224
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Article ; Online: Fractal and Knot-Free Chromosomes Facilitate Nucleoplasmic Transport.

Kim, Yeonghoon / Lizana, Ludvig / Jeon, Jae-Hyung

Physical review letters

2022 Volume 128, Issue 3, Page(s) 38101

Abstract: Chromosomes in the nucleus assemble into hierarchies of 3D domains that, during interphase, share essential features with a knot-free condensed polymer known as the fractal globule (FG). The FG-like chromosome likely affects macromolecular transport, yet ...

Abstract	Chromosomes in the nucleus assemble into hierarchies of 3D domains that, during interphase, share essential features with a knot-free condensed polymer known as the fractal globule (FG). The FG-like chromosome likely affects macromolecular transport, yet its characteristics remain poorly understood. Using computer simulations and scaling analysis, we show that the 3D folding and macromolecular size of the chromosomes determine their transport characteristics. Large-scale subdiffusion occurs at a critical particle size where the network of accessible volumes is critically connected. Condensed chromosomes have connectivity networks akin to simple Bernoulli bond percolation clusters, regardless of the polymer models. However, even if the network structures are similar, the tracer's walk dimension varies. It turns out that the walk dimension depends on the network topology of the accessible volume and dynamic heterogeneity of the tracer's hopping rate. We find that the FG structure has a smaller walk dimension than other random geometries, suggesting that the FG-like chromosome structure accelerates macromolecular diffusion and target-search.
MeSH term(s)	Cell Nucleus ; Chromosomes ; Fractals ; Interphase ; Models, Genetic ; Polymers
Chemical Substances	Polymers
Language	English
Publishing date	2022-02-04
Publishing country	United States
Document type	Journal Article
ZDB-ID	208853-8
ISSN	1079-7114 ; 0031-9007
ISSN (online)	1079-7114
ISSN	0031-9007
DOI	10.1103/PhysRevLett.128.038101
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Article ; Online: Statistical modeling of mRNP transport in dendrites: A comparative analysis of β-actin and Arc mRNP dynamics.

Ahn, Hyerim / Durang, Xavier / Shim, Jae Youn / Park, Gaeun / Jeon, Jae-Hyung / Park, Hye Yoon

Traffic (Copenhagen, Denmark)

2023 Volume 24, Issue 11, Page(s) 522–532

Abstract: Localization of messenger RNA (mRNA) in dendrites is crucial for regulating gene expression during long-term memory formation. mRNA binds to RNA-binding proteins (RBPs) to form messenger ribonucleoprotein (mRNP) complexes that are transported by motor ... ...

Abstract	Localization of messenger RNA (mRNA) in dendrites is crucial for regulating gene expression during long-term memory formation. mRNA binds to RNA-binding proteins (RBPs) to form messenger ribonucleoprotein (mRNP) complexes that are transported by motor proteins along microtubules to their target synapses. However, the dynamics by which mRNPs find their target locations in the dendrite have not been well understood. Here, we investigated the motion of endogenous β-actin and Arc mRNPs in dissociated mouse hippocampal neurons using the MS2 and PP7 stem-loop systems, respectively. By evaluating the statistical properties of mRNP movement, we found that the aging Lévy walk model effectively describes both β-actin and Arc mRNP transport in proximal dendrites. A critical difference between β-actin and Arc mRNPs was the aging time, the time lag between transport initiation and measurement initiation. The longer mean aging time of β-actin mRNP (~100 s) compared with that of Arc mRNP (~30 s) reflects the longer half-life of constitutively expressed β-actin mRNP. Furthermore, our model also permitted us to estimate the ratio of newly generated and pre-existing β-actin mRNPs in the dendrites. This study offers a robust theoretical framework for mRNP transport, which provides insight into how mRNPs locate their targets in neurons.
MeSH term(s)	Mice ; Animals ; Actins/metabolism ; Ribonucleoproteins/metabolism ; Dendrites/metabolism ; RNA, Messenger/genetics ; RNA, Messenger/metabolism
Chemical Substances	messenger ribonucleoprotein ; Actins ; Ribonucleoproteins ; RNA, Messenger
Language	English
Publishing date	2023-08-06
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1483852-7
ISSN	1600-0854 ; 1398-9219
ISSN (online)	1600-0854
ISSN	1398-9219
DOI	10.1111/tra.12913
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Book ; Online: Nonequilibrium diffusion of active particles bound to a semi-flexible polymer network

Han, HyeongTark / Joo, Sungmin / Sakaue, Takahiro / Jeon, Jae-Hyung

simulations and fractional Langevin equation

2023

Abstract: In a viscoelastic environment, the diffusion of a particle becomes non-Markovian due to the memory effect. An open question is to quantitatively explain how self-propulsion particles with directional memory diffuse in such a medium. Based on simulations ... ...

Abstract	In a viscoelastic environment, the diffusion of a particle becomes non-Markovian due to the memory effect. An open question is to quantitatively explain how self-propulsion particles with directional memory diffuse in such a medium. Based on simulations and analytic theory, we address this issue with active viscoelastic systems where an active particle is connected with multiple semi-flexible filaments. Our Langevin dynamics simulations show that the active cross-linker displays super- and sub-diffusive athermal motion with a time-dependent anomalous exponent $\alpha$. In such viscoelastic feedback, the active particle always has superdiffusion with $\alpha=3/2$ at times shorter than the self-propulsion time ($\tau_A$). At times greater than $\tau_A$, the subdiffusion emerges with $\alpha$ bounded between $1/2$ and $3/4$. Remarkably, the active subdiffusion is reinforced as the active propulsion (Pe) is more vigorous. In the high-Pe limit, the athermal fluctuation in the stiff filament eventually leads to $\alpha=1/2$, which can be misinterpreted with the thermal Rouse motion in a flexible chain. We demonstrate that the motion of active particles cross-linking a network of semi-flexible filaments can be governed by a fractional Langevin equation combined with fractional Gaussian noise and an Ornstein-Uhlenbeck noise. We analytically derive the velocity autocorrelation function and mean-squared displacement of the model, explaining their scaling relations as well as the prefactors. We find that there exist the threshold Pe ($\mathrm{Pe}^$) and cross-over times ($\tau^$ and $\tau^\dagger$) above which the active viscoelastic dynamics emerge on the timescales of $\tau^* \lesssim t \lesssim \tau^\dagger$. Our study may provide a theoretical insight into various nonequilibrium active dynamics in intracellular viscoelastic environments.
Keywords	Condensed Matter - Soft Condensed Matter ; Physics - Biological Physics
Subject code	612
Publishing date	2023-03-10
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Active Diffusion of Self-Propelled Particles in Flexible Polymer Networks

Kim, Yeongjin / Joo, Sungmin / Kim, Won Kyu / Jeon, Jae-Hyung

Macromolecules. 2022 Aug. 02, v. 55, no. 16

2022

Abstract: Biopolymer networks having a meshwork topology, e.g., extracellular matrices and mucus gels, are ubiquitous. Understanding the diffusion mechanism of self-propelled agents, including Janus colloidal particles, through such biopolymer networks is thus of ... ...

Abstract	Biopolymer networks having a meshwork topology, e.g., extracellular matrices and mucus gels, are ubiquitous. Understanding the diffusion mechanism of self-propelled agents, including Janus colloidal particles, through such biopolymer networks is thus of paramount importance. Here, for the first time, we computationally explore this issue in depth by explicitly modeling three-dimensional biopolymer networks and performing Langevin dynamics simulations of the active diffusion of the self-propelled tracers therein. We demonstrate that the diffusion dynamics of the active tracers feature rich, distinct physics depending on the mesh-to-particle size and Péclet number (Pe). When the particle is smaller than the mesh size ratio, it moves as if in free space with 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 via the trapping-and-hopping mechanism. 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. We study the trapped time distribution, flight-length distribution, mean-squared displacement, and long-time diffusivity on varying the Pe number and the tracer size. Finally, we discuss the scaling behavior of the long-time diffusivity with Pe, where we find a Pe range that yields a nontrivial power law. The latter turns out to originate from a large fluctuation of the trapped, activated tracers in conjugation with responsive polymer networks.
Keywords	biopolymers ; diffusivity ; mucus ; particle size ; topology ; viscoelasticity
Language	English
Dates of publication	2022-0802
Size	p. 7136-7147.
Publishing place	American Chemical Society
Document type	Article
ZDB-ID	1491942-4
ISSN	1520-5835 ; 0024-9297
ISSN (online)	1520-5835
ISSN	0024-9297
DOI	10.1021/acs.macromol.2c00610
Database	NAL-Catalogue (AGRICOLA)

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Article: Enhanced Sensing Behavior of Three-Dimensional Microfluidic Paper-Based Analytical Devices (3D-μPADs) with Evaporation-Free Enclosed Channels for Point-of-Care Testing.

Jeon, Jaehyung / Park, Chanyong / Ponnuvelu, Dinesh Veeran / Park, Sungsu

Diagnostics (Basel, Switzerland)

2021 Volume 11, Issue 6

Abstract: Despite the potential in fabrication of microfluidic paper-based analytical devices (μPADs) for point-of-care testing (POCT) kits, the development of simple, accurate, and rapid devices with higher sensitivity remains challenging. Here, we report a novel ...

Abstract	Despite the potential in fabrication of microfluidic paper-based analytical devices (μPADs) for point-of-care testing (POCT) kits, the development of simple, accurate, and rapid devices with higher sensitivity remains challenging. Here, we report a novel method for 3D-μPAD fabrication with enclosed channels using vat photopolymerization to avoid fluid evaporation. In detail, height of the enclosed channels was adjusted from 0.3 to 0.17 mm by varying the UV exposure time from 1 to 4 s for the top barrier, whereas the exposure time for the bottom and side barriers was fixed. As a result, sample flow in the enclosed channels of 3D-μPADs showed lesser wicking speed with very scant evaporation compared to that in the hemi channels in the 3D-μPADs. The stoppage of evaporation in the enclosed channels significantly improved the gray intensity and uniformity in the detection zone of the 3D-μPADs, resulting in as low as 0.3 mM glucose detection. Thus 3D-μPADs with enclosed channels showed enhanced sensitivity compared to the 3D-μPADs with hemi channels when dealing with a small volume sample. Our work provides a new insight into 3D-μPAD design with enclosed channels, which redefines the methodology in 3D printing.
Language	English
Publishing date	2021-05-28
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2662336-5
ISSN	2075-4418
ISSN	2075-4418
DOI	10.3390/diagnostics11060977
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Article ; Online: 3D printed fluidic swab for COVID-19 testing with improved diagnostic yield and user comfort.

Kim, Joochan / Jeon, Jaehyung / Jang, Hyowon / Moon, Youngkwang / Abafogi, Abdurhaman Teyib / van Noort, Danny / Lee, Jinkee / Kang, Taejoon / Park, Sungsu

Nano convergence

2023 Volume 10, Issue 1, Page(s) 45

Abstract: The current standard method of diagnosing coronavirus disease 2019 (COVID-19) involves uncomfortable and invasive nasopharyngeal (NP) sampling using cotton swabs (CS), which can be unsuitable for self-testing. Although mid-turbinate sampling is an ... ...

Abstract	The current standard method of diagnosing coronavirus disease 2019 (COVID-19) involves uncomfortable and invasive nasopharyngeal (NP) sampling using cotton swabs (CS), which can be unsuitable for self-testing. Although mid-turbinate sampling is an alternative, it has a lower diagnostic yield than NP sampling. Nasal wash (NW) has a similar diagnostic yield to NP sampling, but is cumbersome to perform. In this study, we introduce a 3D printed fluidic swab (3DPFS) that enables easy NW sampling for COVID-19 testing with improved diagnostic yield. The 3DPFS comprises a swab head, microchannel, and socket that can be connected to a syringe containing 250 µL of NW solution. The 3DPFS efficiently collects nasal fluid from the surface of the nasal cavity, resulting in higher sensitivity than CS for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This was confirmed by both reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and lateral flow assays (LFA) in virus-spiked nasal samples and clinical samples. Additionally, users reported greater comfort when using the 3DPFS compared to CS. These findings suggest that the 3DPFS can improve the performance of COVID-19 testing by facilitating efficient and less painful nasal sample collection.
Language	English
Publishing date	2023-09-16
Publishing country	England
Document type	Journal Article
ZDB-ID	2760386-6
ISSN	2196-5404 ; 2196-5404
ISSN (online)	2196-5404
ISSN	2196-5404
DOI	10.1186/s40580-023-00393-3
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