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Gounaris G, Katifori E. Braess's Paradox Analog in Physical Networks of Optimal Exploration. PHYSICAL REVIEW LETTERS 2024; 133:067401. [PMID: 39178443 DOI: 10.1103/physrevlett.133.067401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 01/31/2024] [Accepted: 07/02/2024] [Indexed: 08/25/2024]
Abstract
In stochastic exploration of geometrically embedded graphs, intuition suggests that providing a shortcut between a pair of nodes reduces the mean first passage time of the entire graph. Counterintuitively, we find a Braess's paradox analog. For regular diffusion, shortcuts can worsen the overall search efficiency of the network, although they bridge topologically distant nodes. We propose an optimization scheme under which each edge adapts its conductivity to minimize the graph's search time. The optimization reveals a relationship between the structure and diffusion exponent and a crossover from dense to sparse graphs as the exponent increases.
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Singh P, Mittal A. Pleomorphism in Biological Units of Life: Morphological Heterogeneity in Cells Does Not Translate Uniformly to Subcellular Components. ACS OMEGA 2024; 9:23377-23389. [PMID: 38854505 PMCID: PMC11154962 DOI: 10.1021/acsomega.3c10062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 04/13/2024] [Accepted: 05/14/2024] [Indexed: 06/11/2024]
Abstract
The interplay of the three-dimensional (3D) distribution of various subcellular components and their interactions are expected to control overall cellular morphology in biology. In this study, we aimed to determine whether the pleomorphy observed at the whole-cell level is being reflected by the components constituting the cells by focusing on the 3D distribution of pixel intensities at the single-cell level of the whole (cell) and its parts (the seven subcellular components of the cells-self-assemblies of smaller units). We rigorously acquired and analyzed the image data of RAW264.7 cells at the single-cell level. We report asymmetries in the spatial distribution of pixel intensities at the whole-cell and subcellular component levels along with the occurrence of alterations when pleomorphism is reduced by synchronization of the cell cycle. From our repertoire of seven subcellular components, we report ER, mitochondria, and tubulin to be independent of whole-cell apico-basal heterogeneity of optical density while nuclear, plasma membrane, lysosomal, and actin fluorescence distributions are found to contribute to the apico-basal polarity of the whole cell. While doing so, we have also developed an image analysis algorithm utilizing 2D segmentation to analyze the single cells in 3D using confocal microscopy, a technique that allows us to analyze cellular states in their native hydrated state.
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Affiliation(s)
- Pragya Singh
- Kusuma School of Biological
Sciences, Indian Institute of Technology-Delhi, Hauz Khas, Delhi 110016, India
| | - Aditya Mittal
- Kusuma School of Biological
Sciences, Indian Institute of Technology-Delhi, Hauz Khas, Delhi 110016, India
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Liang Y, Wang W, Metzler R. Aging and confinement in subordinated fractional Brownian motion. Phys Rev E 2024; 109:064144. [PMID: 39020934 DOI: 10.1103/physreve.109.064144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 05/29/2024] [Indexed: 07/20/2024]
Abstract
We study the effects of aging properties of subordinated fractional Brownian motion (FBM) with drift and in harmonic confinement, when the measurement of the stochastic process starts a time t_{a}>0 after its original initiation at t=0. Specifically, we consider the aged versions of the ensemble mean-squared displacement (MSD) and the time-averaged MSD (TAMSD), along with the aging factor. Our results are favorably compared with simulations results. The aging subordinated FBM exhibits a disparity between MSD and TAMSD and is thus weakly nonergodic, while strong aging is shown to effect a convergence of the MSD and TAMSD. The information on the aging factor with respect to the lag time exhibits an identical form to the aging behavior of subdiffusive continuous-time random walks (CTRW). The statistical properties of the MSD and TAMSD for the confined subordinated FBM are also derived. At long times, the MSD in the harmonic potential has a stationary value, that depends on the Hurst index of the parental (nonequilibrium) FBM. The TAMSD of confined subordinated FBM does not relax to a stationary value but increases sublinearly with lag time, analogously to confined CTRW. Specifically, short aging times t_{a} in confined subordinated FBM do not affect the aged MSD, while for long aging times the aged MSD has a power-law increase and is identical to the aged TAMSD.
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Lin S, Feng D, Han X, Li L, Lin Y, Gao H. Microfluidic platform for omics analysis on single cells with diverse morphology and size: A review. Anal Chim Acta 2024; 1294:342217. [PMID: 38336406 DOI: 10.1016/j.aca.2024.342217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 01/04/2024] [Accepted: 01/04/2024] [Indexed: 02/12/2024]
Abstract
BACKGROUND Microfluidic techniques have emerged as powerful tools in single-cell research, facilitating the exploration of omics information from individual cells. Cell morphology is crucial for gene expression and physiological processes. However, there is currently a lack of integrated analysis of morphology and single-cell omics information. A critical challenge remains: what platform technologies are the best option to decode omics data of cells that are complex in morphology and size? RESULTS This review highlights achievements in microfluidic-based single-cell omics and isolation of cells based on morphology, along with other cell sorting methods based on physical characteristics. Various microfluidic platforms for single-cell isolation are systematically presented, showcasing their diversity and adaptability. The discussion focuses on microfluidic devices tailored to the distinct single-cell isolation requirements in plants and animals, emphasizing the significance of considering cell morphology and cell size in optimizing single-cell omics strategies. Simultaneously, it explores the application of microfluidic single-cell sorting technologies to single-cell sequencing, aiming to effectively integrate information about cell shape and size. SIGNIFICANCE AND NOVELTY The novelty lies in presenting a comprehensive overview of recent accomplishments in microfluidic-based single-cell omics, emphasizing the integration of different microfluidic platforms and their implications for cell morphology-based isolation. By underscoring the pivotal role of the specialized morphology of different cells in single-cell research, this review provides robust support for delving deeper into the exploration of single-cell omics data.
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Affiliation(s)
- Shujin Lin
- Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, 350025, China; Central Laboratory at the Second Affiliated Hospital of Fujian University of Traditional Chinese Medicine, Fujian-Macao Science and Technology Cooperation Base of Traditional Chinese Medicine-Oriented Chronic Disease Prevention and Treatment, Innovation and Transformation Center, Fujian University of Traditional Chinese Medicine, China
| | - Dan Feng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiao Han
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, 350108, China.
| | - Ling Li
- Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, 350025, China; The First Clinical Medical College of Fujian Medical University, Fuzhou, 350004, China; Hepatopancreatobiliary Surgery Department, The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350004, China.
| | - Yao Lin
- Central Laboratory at the Second Affiliated Hospital of Fujian University of Traditional Chinese Medicine, Fujian-Macao Science and Technology Cooperation Base of Traditional Chinese Medicine-Oriented Chronic Disease Prevention and Treatment, Innovation and Transformation Center, Fujian University of Traditional Chinese Medicine, China; Collaborative Innovation Center for Rehabilitation Technology, Fujian University of Traditional Chinese Medicine, China.
| | - Haibing Gao
- Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, 350025, China.
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Jiang C, Luo HY, Xu X, Dou SX, Li W, Guan D, Ye F, Chen X, Guo M, Wang PY, Li H. Switch of cell migration modes orchestrated by changes of three-dimensional lamellipodium structure and intracellular diffusion. Nat Commun 2023; 14:5166. [PMID: 37620390 PMCID: PMC10449835 DOI: 10.1038/s41467-023-40858-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 08/14/2023] [Indexed: 08/26/2023] Open
Abstract
Cell migration plays important roles in many biological processes, but how migrating cells orchestrate intracellular molecules and subcellular structures to regulate their speed and direction is still not clear. Here, by characterizing the intracellular diffusion and the three-dimensional lamellipodium structures of fish keratocyte cells, we observe a strong positive correlation between the intracellular diffusion and cell migration speed and, more importantly, discover a switching of cell migration modes with reversible intracellular diffusion variation and lamellipodium structure deformation. Distinct from the normal fast mode, cells migrating in the newly-found slow mode have a deformed lamellipodium with swollen-up front and thinned-down rear, reduced intracellular diffusion and compartmentalized macromolecule distribution in the lamellipodium. Furthermore, in turning cells, both lamellipodium structure and intracellular diffusion dynamics are also changed, with left-right symmetry breaking. We propose a mechanism involving the front-localized actin polymerization and increased molecular crowding in the lamellipodium to explain how cells spatiotemporally coordinate the intracellular diffusion dynamics and the lamellipodium structure in regulating their migrations.
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Affiliation(s)
- Chao Jiang
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
- School of Systems Science and Institute of Nonequilibrium Systems, Beijing Normal University, Beijing, 100875, China
- School of Physical Sciences and School of Engineering Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hong-Yu Luo
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
- School of Physical Sciences and School of Engineering Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xinpeng Xu
- Physics Program, Guangdong Technion-Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong, 515063, China
- Technion-Israel Institute of Technology, Haifa, 32000, Israel
| | - Shuo-Xing Dou
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
- School of Physical Sciences and School of Engineering Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wei Li
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong, 523808, China
| | - Dongshi Guan
- School of Physical Sciences and School of Engineering Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Nonlinear Mechanics, Institute of Mechanics, Chinese Academy of Sciences, Beijing, 100190, China
| | - Fangfu Ye
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
- School of Physical Sciences and School of Engineering Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong, 523808, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325001, China
| | - Xiaosong Chen
- School of Systems Science and Institute of Nonequilibrium Systems, Beijing Normal University, Beijing, 100875, China
| | - Ming Guo
- Department of Mechanical Engineering, MIT, 77 Massachusetts Ave, Cambridge, MA, 02139, USA
| | - Peng-Ye Wang
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China.
- School of Physical Sciences and School of Engineering Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
- Songshan Lake Materials Laboratory, Dongguan, Guangdong, 523808, China.
| | - Hui Li
- School of Systems Science and Institute of Nonequilibrium Systems, Beijing Normal University, Beijing, 100875, China.
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Scott ZC, Koning K, Vanderwerp M, Cohen L, Westrate LM, Koslover EF. Endoplasmic reticulum network heterogeneity guides diffusive transport and kinetics. Biophys J 2023; 122:3191-3205. [PMID: 37401053 PMCID: PMC10432226 DOI: 10.1016/j.bpj.2023.06.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 05/17/2023] [Accepted: 06/28/2023] [Indexed: 07/05/2023] Open
Abstract
The endoplasmic reticulum (ER) is a dynamic network of interconnected sheets and tubules that orchestrates the distribution of lipids, ions, and proteins throughout the cell. The impact of its complex, dynamic morphology on its function as an intracellular transport hub remains poorly understood. To elucidate the functional consequences of ER network structure and dynamics, we quantify how the heterogeneity of the peripheral ER in COS7 cells affects diffusive protein transport. In vivo imaging of photoactivated ER membrane proteins demonstrates their nonuniform spreading to adjacent regions, in a manner consistent with simulations of diffusing particles on extracted network structures. Using a minimal network model to represent tubule rearrangements, we demonstrate that ER network dynamics are sufficiently slow to have little effect on diffusive protein transport. Furthermore, stochastic simulations reveal a novel consequence of ER network heterogeneity: the existence of "hot spots" where sparse diffusive reactants are more likely to find one another. ER exit sites, specialized domains regulating cargo export from the ER, are shown to be disproportionately located in highly accessible regions, further from the outer boundary of the cell. Combining in vivo experiments with analytic calculations, quantitative image analysis, and computational modeling, we demonstrate how structure guides diffusive protein transport and reactions in the ER.
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Affiliation(s)
| | - Katherine Koning
- Department of Chemistry and Biochemistry, Calvin University, Grand Rapids, Michigan
| | - Molly Vanderwerp
- Department of Chemistry and Biochemistry, Calvin University, Grand Rapids, Michigan
| | | | - Laura M Westrate
- Department of Chemistry and Biochemistry, Calvin University, Grand Rapids, Michigan
| | - Elena F Koslover
- Department of Physics, University of California, San Diego, La Jolla, California.
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Akenuwa OH, Abel SM. Organization and dynamics of cross-linked actin filaments in confined environments. Biophys J 2023; 122:30-42. [PMID: 36461638 PMCID: PMC9822838 DOI: 10.1016/j.bpj.2022.11.2944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 11/02/2022] [Accepted: 11/28/2022] [Indexed: 12/03/2022] Open
Abstract
The organization of the actin cytoskeleton is impacted by the interplay between physical confinement, features of cross-linking proteins, and deformations of semiflexible actin filaments. Some cross-linking proteins preferentially bind filaments in parallel, although others bind more indiscriminately. However, a quantitative understanding of how the mode of binding influences the assembly of actin networks in confined environments is lacking. Here we employ coarse-grained computer simulations to study the dynamics and organization of semiflexible actin filaments in confined regions upon the addition of cross-linkers. We characterize how the emergent behavior is influenced by the system shape, the number and type of cross-linking proteins, and the length of filaments. Structures include isolated clusters of filaments, highly connected filament bundles, and networks of interconnected bundles and loops. Elongation of one dimension of the system promotes the formation of long bundles that align with the elongated axis. Dynamics are governed by rapid cross-linking into aggregates, followed by a slower change in their shape and connectivity. Cross-linking decreases the average bending energy of short or sparsely connected filaments by suppressing shape fluctuations. However, it increases the average bending energy in highly connected networks because filament bundles become deformed, and small numbers of filaments exhibit long-lived, highly unfavorable configurations. Indiscriminate cross-linking promotes the formation of high-energy configurations due to the increased likelihood of unfavorable, difficult-to-relax configurations at early times. Taken together, this work demonstrates physical mechanisms by which cross-linker binding and physical confinement impact the emergent behavior of actin networks, which is relevant both in cells and in synthetic environments.
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Affiliation(s)
- Oghosa H Akenuwa
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee
| | - Steven M Abel
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee.
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Zhu Q, Zhou Y, Marchesoni F, Zhang HP. Colloidal Stochastic Resonance in Confined Geometries. PHYSICAL REVIEW LETTERS 2022; 129:098001. [PMID: 36083679 DOI: 10.1103/physrevlett.129.098001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 04/01/2022] [Accepted: 08/04/2022] [Indexed: 06/15/2023]
Abstract
We investigate the dynamical properties of a colloidal particle in a double cavity. Without external driving, the particle hops between two free-energy minima with transition mean time depending on the system's entropic and energetic barriers. We then drive the particle with a periodic force. When the forcing period is set at twice the transition mean time, a statistical synchronization between particle motion and forcing phase marks the onset of a stochastic resonance mechanism. Comparisons between experimental results and predictions from the Fick-Jacobs theory and Brownian dynamics simulation reveal significant hydrodynamic effects, which change both resonant amplification and noise level. We further show that hydrodynamic effects can be incorporated into existing theory and simulation by using an experimentally measured particle diffusivity.
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Affiliation(s)
- Qian Zhu
- School of Physics and Astronomy and Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yang Zhou
- School of Physics and Astronomy and Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Fabio Marchesoni
- Center for Phononics and Thermal Energy Science, School of Physics Science and Engineering, Tongji University, Shanghai 200092, China
- Dipartimento di Fisica, Universitá di Camerino, I-62032 Camerino, Italy
| | - H P Zhang
- School of Physics and Astronomy and Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
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