Biomembranes wrapping cells and organelles are not only the partitions that separate the insides but also dynamic fields for biological functions accompanied by membrane shape changes. In this review, we discuss the spatiotemporal patterns and fluctuations of membranes under nonequilibrium conditions. In particular, we focus on theoretical analyses and simulations. Protein active forces enhance or suppress the membrane fluctuations; the membrane height spectra are deviated from the thermal spectra. Protein binding or unbinding to the membrane is activated or inhibited by other proteins and chemical reactions, such as ATP hydrolysis. Such active binding processes can induce traveling waves, Turing patterns, and membrane morphological changes. They can be represented by the continuum reaction-diffusion equations and discrete lattice/particle models with state flips. The effects of structural changes in amphiphilic molecules on the molecular-assembly structures are also discussed.
包裹细胞和细胞器的生物膜不仅是分隔内部的隔板，也是伴随膜形状变化的生物功能动态场。在这篇综述中，我们将讨论非平衡条件下膜的时空模式和波动。蛋白质活性力增强或抑制膜波动；膜高度谱偏离热谱。蛋白质与膜的结合或解除结合会被其他蛋白质和化学反应（如 ATP 水解）激活或抑制。这种活跃的结合过程可引发行波、图灵模式和膜形态变化，可用连续反应-扩散方程和具有状态翻转的离散晶格/粒子模型来表示。此外，还讨论了两亲分子结构变化对分子组装结构的影响。
{"title":"Nonequilibrium Membrane Dynamics Induced by Active Protein Interactions and Chemical Reactions: A Review","authors":"Hiroshi Noguchi","doi":"arxiv-2407.15371","DOIUrl":"https://doi.org/arxiv-2407.15371","url":null,"abstract":"Biomembranes wrapping cells and organelles are not only the partitions that\u0000separate the insides but also dynamic fields for biological functions\u0000accompanied by membrane shape changes. In this review, we discuss the\u0000spatiotemporal patterns and fluctuations of membranes under nonequilibrium\u0000conditions. In particular, we focus on theoretical analyses and simulations.\u0000Protein active forces enhance or suppress the membrane fluctuations; the\u0000membrane height spectra are deviated from the thermal spectra. Protein binding\u0000or unbinding to the membrane is activated or inhibited by other proteins and\u0000chemical reactions, such as ATP hydrolysis. Such active binding processes can\u0000induce traveling waves, Turing patterns, and membrane morphological changes.\u0000They can be represented by the continuum reaction-diffusion equations and\u0000discrete lattice/particle models with state flips. The effects of structural\u0000changes in amphiphilic molecules on the molecular-assembly structures are also\u0000discussed.","PeriodicalId":501040,"journal":{"name":"arXiv - PHYS - Biological Physics","volume":"06 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141782916","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Biological cells exhibit a hierarchical spatial organization, where various compartments harbor condensates that form by phase separation. Cells can control the emergence of these condensates by affecting compartment size, the amount of the involved molecules, and their physical interactions. While physical interactions directly affect compartment binding and phase separation, they can also cause oligomerization, which has been suggested as a control mechanism. Analyzing an equilibrium model, we illustrate that oligomerization amplifies compartment binding and phase separation, which reinforce each other. This nonlinear interplay can also induce multistability, which provides additional potential for control. Our work forms the basis for deriving thermodynamically consistent kinetic models to understand how biological cells can regulate phase separation in their compartments.
{"title":"Binding and dimerization control phase separation in a compartment","authors":"Riccardo Rossetto, Gerrit Wellecke, David Zwicker","doi":"arxiv-2407.15179","DOIUrl":"https://doi.org/arxiv-2407.15179","url":null,"abstract":"Biological cells exhibit a hierarchical spatial organization, where various\u0000compartments harbor condensates that form by phase separation. Cells can\u0000control the emergence of these condensates by affecting compartment size, the\u0000amount of the involved molecules, and their physical interactions. While\u0000physical interactions directly affect compartment binding and phase separation,\u0000they can also cause oligomerization, which has been suggested as a control\u0000mechanism. Analyzing an equilibrium model, we illustrate that oligomerization\u0000amplifies compartment binding and phase separation, which reinforce each other.\u0000This nonlinear interplay can also induce multistability, which provides\u0000additional potential for control. Our work forms the basis for deriving\u0000thermodynamically consistent kinetic models to understand how biological cells\u0000can regulate phase separation in their compartments.","PeriodicalId":501040,"journal":{"name":"arXiv - PHYS - Biological Physics","volume":"38 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141782980","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
In this study, we present a comprehensive analysis of the motion of a tagged monomer within a Gaussian semiflexible polymer model. We carefully derived the generalized Langevin Equation (GLE) that governs the motion of a tagged central monomer. This derivation involves integrating out all the other degrees of freedom within the polymer chain, thereby yielding an effective description of the viscoelastic motion of the tagged monomer. A critical component of our analysis is the memory kernel that appears in the GLE. By examining this kernel, we characterized the impact of bending rigidity on the non-Markovian diffusion dynamics of the tagged monomer. Furthermore, we calculated the mean-squared displacement of the tagged monomer using the derived GLE. Our results not only show remarkable agreement with previously known results in certain limiting cases but also provide dynamic features over the entire timescale.
{"title":"Generalized Langevin equation for a tagged monomer in a Gaussian semiflexible polymer","authors":"Xavier Durang, Jae-Hyung Jeon","doi":"arxiv-2407.14886","DOIUrl":"https://doi.org/arxiv-2407.14886","url":null,"abstract":"In this study, we present a comprehensive analysis of the motion of a tagged\u0000monomer within a Gaussian semiflexible polymer model. We carefully derived the\u0000generalized Langevin Equation (GLE) that governs the motion of a tagged central\u0000monomer. This derivation involves integrating out all the other degrees of\u0000freedom within the polymer chain, thereby yielding an effective description of\u0000the viscoelastic motion of the tagged monomer. A critical component of our\u0000analysis is the memory kernel that appears in the GLE. By examining this\u0000kernel, we characterized the impact of bending rigidity on the non-Markovian\u0000diffusion dynamics of the tagged monomer. Furthermore, we calculated the\u0000mean-squared displacement of the tagged monomer using the derived GLE. Our\u0000results not only show remarkable agreement with previously known results in\u0000certain limiting cases but also provide dynamic features over the entire\u0000timescale.","PeriodicalId":501040,"journal":{"name":"arXiv - PHYS - Biological Physics","volume":"72 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141782986","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Many tissues take the form of thin sheets, being only a single cell thick, but millions of cells wide. These tissue sheets can bend and buckle in the third dimension. In this work, we investigated the growth of suspended and supported tissue sheets using particle-based simulations. We combine particle-based tissue growth and meshless membrane models to simulate the growth of tissue sheets with mechanical feedback. Free suspended growing tissues exhibit wrinkling when growth is sufficiently fast. Conversely, tissues on a substrate form buds when the adhesion to the substrate is weak and/or when the friction with the substrate is strong. These buds undergo a membrane-mediated attraction and subsequently fuse. The complete detachment of tissues from the substrate and straight buckled bump formation are also obtained at very weak adhesion and/or fast growth rates. Tissue pores grow via Ostwald ripening and coalescence. The reported dynamics can also be applied in research on the detachment dynamics of different tissues with weakened adhesion.
{"title":"Growing tissue sheets on substrates: buds, buckles, and pores","authors":"Hiroshi Noguchi, Jens Elgeti","doi":"arxiv-2407.13187","DOIUrl":"https://doi.org/arxiv-2407.13187","url":null,"abstract":"Many tissues take the form of thin sheets, being only a single cell thick,\u0000but millions of cells wide. These tissue sheets can bend and buckle in the\u0000third dimension. In this work, we investigated the growth of suspended and\u0000supported tissue sheets using particle-based simulations. We combine\u0000particle-based tissue growth and meshless membrane models to simulate the\u0000growth of tissue sheets with mechanical feedback. Free suspended growing\u0000tissues exhibit wrinkling when growth is sufficiently fast. Conversely, tissues\u0000on a substrate form buds when the adhesion to the substrate is weak and/or when\u0000the friction with the substrate is strong. These buds undergo a\u0000membrane-mediated attraction and subsequently fuse. The complete detachment of\u0000tissues from the substrate and straight buckled bump formation are also\u0000obtained at very weak adhesion and/or fast growth rates. Tissue pores grow via\u0000Ostwald ripening and coalescence. The reported dynamics can also be applied in\u0000research on the detachment dynamics of different tissues with weakened\u0000adhesion.","PeriodicalId":501040,"journal":{"name":"arXiv - PHYS - Biological Physics","volume":"40 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141745037","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nonequilibrium systems, in particular living organisms, are maintained by irreversible transformations of energy that drive diverse functions. Quantifying their irreversibility, as measured by energy dissipation, is essential for understanding the underlying mechanisms. However, existing techniques usually overlook experimental limitations, either by assuming full information or by employing a coarse-graining method that requires knowledge of the structure behind hidden degrees of freedom. Here, we study the inference of dissipation from finite-resolution measurements by employing a recently developed model-free estimator that considers both the sequence of coarse-grained transitions and the waiting time distributions: $sigma_2=sigma_2^ell + sigma_2^t$. The dominant term $sigma_2^ell$ originates from the sequence of observed transitions; we find that it scales with resolution following a power law. Comparing the scaling exponent with a previous estimator highlights the importance of accounting for flux correlations at lower resolutions. $sigma_2^t$ comes from asymmetries in waiting time distributions, with its peak revealing characteristic scales of the underlying dissipative process. Alternatively, the characteristic scale can be detected in a crossover of the scaling of $sigma_2^ell$. This provides a novel perspective for extracting otherwise hidden characteristic dissipative scales directly from dissipation measurements. We illustrate these results in biochemical models as well as complex networks. Overall, this study highlights the significance of resolution considerations in nonequilibrium systems, providing insights into the interplay between experimental resolution, entropy production, and underlying complexity.
{"title":"Dissipation at limited resolutions: Power law and detection of hidden dissipative scales","authors":"Qiwei Yu, Pedro E. Harunari","doi":"arxiv-2407.13707","DOIUrl":"https://doi.org/arxiv-2407.13707","url":null,"abstract":"Nonequilibrium systems, in particular living organisms, are maintained by\u0000irreversible transformations of energy that drive diverse functions.\u0000Quantifying their irreversibility, as measured by energy dissipation, is\u0000essential for understanding the underlying mechanisms. However, existing\u0000techniques usually overlook experimental limitations, either by assuming full\u0000information or by employing a coarse-graining method that requires knowledge of\u0000the structure behind hidden degrees of freedom. Here, we study the inference of\u0000dissipation from finite-resolution measurements by employing a recently\u0000developed model-free estimator that considers both the sequence of\u0000coarse-grained transitions and the waiting time distributions:\u0000$sigma_2=sigma_2^ell + sigma_2^t$. The dominant term $sigma_2^ell$\u0000originates from the sequence of observed transitions; we find that it scales\u0000with resolution following a power law. Comparing the scaling exponent with a\u0000previous estimator highlights the importance of accounting for flux\u0000correlations at lower resolutions. $sigma_2^t$ comes from asymmetries in\u0000waiting time distributions, with its peak revealing characteristic scales of\u0000the underlying dissipative process. Alternatively, the characteristic scale can\u0000be detected in a crossover of the scaling of $sigma_2^ell$. This provides a\u0000novel perspective for extracting otherwise hidden characteristic dissipative\u0000scales directly from dissipation measurements. We illustrate these results in\u0000biochemical models as well as complex networks. Overall, this study highlights\u0000the significance of resolution considerations in nonequilibrium systems,\u0000providing insights into the interplay between experimental resolution, entropy\u0000production, and underlying complexity.","PeriodicalId":501040,"journal":{"name":"arXiv - PHYS - Biological Physics","volume":"25 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141745038","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
A remarkable variety of organisms use metachronal coordination (i.e., numerous neighboring appendages beating sequentially with a fixed phase lag) to swim or pump fluid. This coordination strategy is used by microorganisms to break symmetry at small scales where viscous effects dominate and flow is time-reversible. Some larger organisms use this swimming strategy at intermediate scales, where viscosity and inertia both play important roles. However, the role of individual propulsor kinematics - especially across hydrodynamic scales - is not well-understood, though the details of propulsor motion can be crucial for the efficient generation of flow. To investigate this behavior, we developed a new soft robotic platform using magnetoactive silicone elastomers to mimic the metachronally coordinated propulsors found in swimming organisms. Furthermore, we present a method to passively encode spatially asymmetric beating patterns in our artificial propulsors. We investigated the kinematics and hydrodynamics of three propulsor types, with varying degrees of asymmetry, using Particle Image Velocimetry and high-speed videography. We find that asymmetric beating patterns can move considerably more fluid relative to symmetric beating at the same frequency and phase lag, and that asymmetry can be passively encoded into propulsors via the interplay between elastic and magnetic torques. Our results demonstrate that nuanced differences in propulsor kinematics can substantially impact fluid pumping performance. Our soft robotic platform also provides an avenue to explore metachronal coordination at the meso-scale, which in turn can inform the design of future bioinspired pumping devices and swimming robots.
{"title":"Encoding spatiotemporal asymmetry in artificial cilia with a ctenophore-inspired soft-robotic platform","authors":"David J. Peterman, Margaret L. Byron","doi":"arxiv-2407.13894","DOIUrl":"https://doi.org/arxiv-2407.13894","url":null,"abstract":"A remarkable variety of organisms use metachronal coordination (i.e.,\u0000numerous neighboring appendages beating sequentially with a fixed phase lag) to\u0000swim or pump fluid. This coordination strategy is used by microorganisms to\u0000break symmetry at small scales where viscous effects dominate and flow is\u0000time-reversible. Some larger organisms use this swimming strategy at\u0000intermediate scales, where viscosity and inertia both play important roles.\u0000However, the role of individual propulsor kinematics - especially across\u0000hydrodynamic scales - is not well-understood, though the details of propulsor\u0000motion can be crucial for the efficient generation of flow. To investigate this\u0000behavior, we developed a new soft robotic platform using magnetoactive silicone\u0000elastomers to mimic the metachronally coordinated propulsors found in swimming\u0000organisms. Furthermore, we present a method to passively encode spatially\u0000asymmetric beating patterns in our artificial propulsors. We investigated the\u0000kinematics and hydrodynamics of three propulsor types, with varying degrees of\u0000asymmetry, using Particle Image Velocimetry and high-speed videography. We find\u0000that asymmetric beating patterns can move considerably more fluid relative to\u0000symmetric beating at the same frequency and phase lag, and that asymmetry can\u0000be passively encoded into propulsors via the interplay between elastic and\u0000magnetic torques. Our results demonstrate that nuanced differences in propulsor\u0000kinematics can substantially impact fluid pumping performance. Our soft robotic\u0000platform also provides an avenue to explore metachronal coordination at the\u0000meso-scale, which in turn can inform the design of future bioinspired pumping\u0000devices and swimming robots.","PeriodicalId":501040,"journal":{"name":"arXiv - PHYS - Biological Physics","volume":"40 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141745174","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nicole Luchetti, Keith M. Smith, Margherita A. G. Matarrese, Alessandro Loppini, Simonetta Filippi, Letizia Chiodo
Living systems rely on coordinated molecular interactions, especially those related to gene expression and protein activity. The Unfolded Protein Response is a crucial mechanism in eukaryotic cells, activated when unfolded proteins exceed a critical threshold. It maintains cell homeostasis by enhancing protein folding, initiating quality control, and activating degradation pathways when damage is irreversible. This response functions as a dynamic signaling network, with proteins as nodes and their interactions as edges. We analyze these protein-protein networks across different organisms to understand their intricate intra-cellular interactions and behaviors. In this work, analyzing twelve organisms, we assess how fundamental measures in network theory can individuate seed-proteins and specific pathways across organisms. We employ network robustness to evaluate and compare the strength of the investigated PPI networks, and the structural controllability of complex networks to find and compare the sets of driver nodes necessary to control the overall networks. We find that network measures are related to phylogenetics, and advanced network methods can identify main pathways of significance in the complete Unfolded Protein Response mechanism.
{"title":"A statistical mechanics investigation of Unfolded Protein Response across organisms","authors":"Nicole Luchetti, Keith M. Smith, Margherita A. G. Matarrese, Alessandro Loppini, Simonetta Filippi, Letizia Chiodo","doi":"arxiv-2407.12464","DOIUrl":"https://doi.org/arxiv-2407.12464","url":null,"abstract":"Living systems rely on coordinated molecular interactions, especially those\u0000related to gene expression and protein activity. The Unfolded Protein Response\u0000is a crucial mechanism in eukaryotic cells, activated when unfolded proteins\u0000exceed a critical threshold. It maintains cell homeostasis by enhancing protein\u0000folding, initiating quality control, and activating degradation pathways when\u0000damage is irreversible. This response functions as a dynamic signaling network,\u0000with proteins as nodes and their interactions as edges. We analyze these\u0000protein-protein networks across different organisms to understand their\u0000intricate intra-cellular interactions and behaviors. In this work, analyzing\u0000twelve organisms, we assess how fundamental measures in network theory can\u0000individuate seed-proteins and specific pathways across organisms. We employ\u0000network robustness to evaluate and compare the strength of the investigated PPI\u0000networks, and the structural controllability of complex networks to find and\u0000compare the sets of driver nodes necessary to control the overall networks. We\u0000find that network measures are related to phylogenetics, and advanced network\u0000methods can identify main pathways of significance in the complete Unfolded\u0000Protein Response mechanism.","PeriodicalId":501040,"journal":{"name":"arXiv - PHYS - Biological Physics","volume":"39 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141745172","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Alexandros A. Fragkopoulos, Florian Böhme, Nicole Drewes, Oliver Bäumchen
Photosynthetic microbes have evolved and successfully adapted to the ever-changing environmental conditions in complex microhabitats throughout almost all ecosystems on Earth. In the absence of light, they can sustain their biological functionalities through aerobic respiration, and even in anoxic conditions through anaerobic metabolic activity. For a suspension of photosynthetic microbes in an anaerobic environment, individual cellular motility is directly controlled by its photosynthetic activity, i.e. the intensity of the incident light absorbed by chlorophyll. The effects of the metabolic activity on the collective motility on the population level, however, remain elusive so far. Here, we demonstrate that at high light intensities, a suspension of photosynthetically active microbes exhibits a stable reverse sedimentation profile of the cell density due to the microbes' natural bias to move against gravity. With decreasing photosynthetic activity, and therefore suppressed individual motility, the living suspension becomes unstable giving rise to coherent bioconvective flows. The collective motility is fully reversible and manifests as regular, three-dimensional plume structures, in which flow rates and cell distributions are directly controlled via the light intensity. The coherent flows emerge in the highly unfavourable condition of lacking both light and oxygen and, thus, might help the microbial collective to expand the exploration of their natural habitat in search for better survival conditions.
{"title":"Metabolic activity controls the emergence of coherent flows in microbial suspensions","authors":"Alexandros A. Fragkopoulos, Florian Böhme, Nicole Drewes, Oliver Bäumchen","doi":"arxiv-2407.09884","DOIUrl":"https://doi.org/arxiv-2407.09884","url":null,"abstract":"Photosynthetic microbes have evolved and successfully adapted to the\u0000ever-changing environmental conditions in complex microhabitats throughout\u0000almost all ecosystems on Earth. In the absence of light, they can sustain their\u0000biological functionalities through aerobic respiration, and even in anoxic\u0000conditions through anaerobic metabolic activity. For a suspension of\u0000photosynthetic microbes in an anaerobic environment, individual cellular\u0000motility is directly controlled by its photosynthetic activity, i.e. the\u0000intensity of the incident light absorbed by chlorophyll. The effects of the\u0000metabolic activity on the collective motility on the population level, however,\u0000remain elusive so far. Here, we demonstrate that at high light intensities, a\u0000suspension of photosynthetically active microbes exhibits a stable reverse\u0000sedimentation profile of the cell density due to the microbes' natural bias to\u0000move against gravity. With decreasing photosynthetic activity, and therefore\u0000suppressed individual motility, the living suspension becomes unstable giving\u0000rise to coherent bioconvective flows. The collective motility is fully\u0000reversible and manifests as regular, three-dimensional plume structures, in\u0000which flow rates and cell distributions are directly controlled via the light\u0000intensity. The coherent flows emerge in the highly unfavourable condition of\u0000lacking both light and oxygen and, thus, might help the microbial collective to\u0000expand the exploration of their natural habitat in search for better survival\u0000conditions.","PeriodicalId":501040,"journal":{"name":"arXiv - PHYS - Biological Physics","volume":"34 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141720957","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
William J Ceely, Marina Chugunova, Ali Nadim, James D Sterling
Polyelectrolyte brushes consist of a set of charged linear macromolecules each tethered at one end to a surface. An example is the glycocalyx which refers to hair-like negatively charged sugar molecules that coat the outside membrane of all cells. We consider the transport and equilibrium distribution of ions, and the resulting electrical potential, when such a brush is immersed in a salt buffer containing monovalent cations (sodium and/or potassium). The Gouy-Chapman model for ion screening at a charged surface captures the effects of the Coulombic force that drives ion electrophoresis and diffusion, but neglects non-Coulombic forces and ion pairing. By including the distinct binding affinities of these counter-ions with the brush, and their so-called Born radii, which account for Born forces acting on them when the permittivity is non-uniform, we propose modified Poisson-Nernst-Planck continuum models that show the distinct profiles that may result depending on those ion-specific properties.
{"title":"Modeling Ion-Specific Effects in Polyelectrolyte Brushes: A Modified Poisson-Nernst-Planck Model","authors":"William J Ceely, Marina Chugunova, Ali Nadim, James D Sterling","doi":"arxiv-2407.09633","DOIUrl":"https://doi.org/arxiv-2407.09633","url":null,"abstract":"Polyelectrolyte brushes consist of a set of charged linear macromolecules\u0000each tethered at one end to a surface. An example is the glycocalyx which\u0000refers to hair-like negatively charged sugar molecules that coat the outside\u0000membrane of all cells. We consider the transport and equilibrium distribution\u0000of ions, and the resulting electrical potential, when such a brush is immersed\u0000in a salt buffer containing monovalent cations (sodium and/or potassium). The\u0000Gouy-Chapman model for ion screening at a charged surface captures the effects\u0000of the Coulombic force that drives ion electrophoresis and diffusion, but\u0000neglects non-Coulombic forces and ion pairing. By including the distinct\u0000binding affinities of these counter-ions with the brush, and their so-called\u0000Born radii, which account for Born forces acting on them when the permittivity\u0000is non-uniform, we propose modified Poisson-Nernst-Planck continuum models that\u0000show the distinct profiles that may result depending on those ion-specific\u0000properties.","PeriodicalId":501040,"journal":{"name":"arXiv - PHYS - Biological Physics","volume":"74 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141720958","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
M. Hidalgo-Soria, Y. Haddad, E. Barkai, Y. Garini, S. Burov
Investigating the dynamics of chromatin and the factors that are affecting it, has provided valuable insights into the organization and functionality of the genome in the cell nucleus. We control the expression of Lamin-A, an important organizer protein of the chromatin and nucleus structure. By simultaneously tracking tens of chromosomal loci (telomeres) in each nucleus, we find that the motion of chromosomal loci in Lamin-A depleted cells is both faster and more directed on a scale of a few micrometers, which coincides with the size of chromosome territories. Moreover, in the absence of Lamin-A we reveal the existence of correlations among neighboring telomeres. We show how these pairwise correlations are linked with the intermittent and persistent character of telomere trajectories, underscoring the importance of Lamin-A protein in chromosomal organization.
{"title":"Directed Motion and Spatial Coherence in the Cell Nucleus","authors":"M. Hidalgo-Soria, Y. Haddad, E. Barkai, Y. Garini, S. Burov","doi":"arxiv-2407.08899","DOIUrl":"https://doi.org/arxiv-2407.08899","url":null,"abstract":"Investigating the dynamics of chromatin and the factors that are affecting\u0000it, has provided valuable insights into the organization and functionality of\u0000the genome in the cell nucleus. We control the expression of Lamin-A, an\u0000important organizer protein of the chromatin and nucleus structure. By\u0000simultaneously tracking tens of chromosomal loci (telomeres) in each nucleus,\u0000we find that the motion of chromosomal loci in Lamin-A depleted cells is both\u0000faster and more directed on a scale of a few micrometers, which coincides with\u0000the size of chromosome territories. Moreover, in the absence of Lamin-A we\u0000reveal the existence of correlations among neighboring telomeres. We show how\u0000these pairwise correlations are linked with the intermittent and persistent\u0000character of telomere trajectories, underscoring the importance of Lamin-A\u0000protein in chromosomal organization.","PeriodicalId":501040,"journal":{"name":"arXiv - PHYS - Biological Physics","volume":"51 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141720960","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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