Biofilms are bacterial aggregates that grow on moist surfaces. Thin homogeneous biofilms naturally formed on the walls of conducts may serve as biosensors, providing information on the status of microsystems (MEMS) without disrupting them. However, uncontrolled biofilm growth may largely disturb the environment they develop in, increasing the drag and clogging the tubes. To ensure controlled biofilm expansion we need to understand the effect of external variables on their structure. We formulate a hybrid model for the computational study of biofilms growing in laminar microflows. Biomass evolves according to stochastic rules for adhesion, erosion and motion, informed by numerical approximations of the flow fields at each stage. The model is tested studying the formation of streamers in three dimensional corner flows, gaining some insight on the effect of external variables on their structure.
{"title":"Dynamics of bacterial aggregates in microflows","authors":"Ana Carpio, Baldvin Einarsson, David R. Espeso","doi":"arxiv-2401.07138","DOIUrl":"https://doi.org/arxiv-2401.07138","url":null,"abstract":"Biofilms are bacterial aggregates that grow on moist surfaces. Thin\u0000homogeneous biofilms naturally formed on the walls of conducts may serve as\u0000biosensors, providing information on the status of microsystems (MEMS) without\u0000disrupting them. However, uncontrolled biofilm growth may largely disturb the\u0000environment they develop in, increasing the drag and clogging the tubes. To\u0000ensure controlled biofilm expansion we need to understand the effect of\u0000external variables on their structure. We formulate a hybrid model for the\u0000computational study of biofilms growing in laminar microflows. Biomass evolves\u0000according to stochastic rules for adhesion, erosion and motion, informed by\u0000numerical approximations of the flow fields at each stage. The model is tested\u0000studying the formation of streamers in three dimensional corner flows, gaining\u0000some insight on the effect of external variables on their structure.","PeriodicalId":501321,"journal":{"name":"arXiv - QuanBio - Cell Behavior","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139481742","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}
Biofilms are bacterial aggregates encased in a self-produced polymeric matrix which attach to moist surfaces and are extremely resistant to chemicals and antibiotics. Recent experiments show that their structure is defined by the interplay of elastic deformations and liquid transport within the biofilm, in response to the cellular activity and the interaction with the surrounding environment. We propose a poroelastic model for elastic deformation and liquid transport in three dimensional biofilms spreading on agar surfaces. The motion of the boundaries can be described by the combined use of Von Karman type approximations for the agar/biofilm interface and thin film approximations for the biofilm/air interface. Bacterial activity informs the macroscopic continuous model through source terms and residual stresses, either phenomenological or derived from microscopic models. We present a procedure to estimate the structure of such residual stresses, based on a simple cellular automata description of bacterial activity. Inspired by image processing, we show that a filtering strategy effectively smooths out the rough tensors provided by the stochastic cellular automata rules, allowing us to insert them in the macroscopic model without numerical instability.
{"title":"Biofilms as poroelastic materials","authors":"Ana Carpio, Elena Cebrian, Perfecto Vidal","doi":"arxiv-2401.07060","DOIUrl":"https://doi.org/arxiv-2401.07060","url":null,"abstract":"Biofilms are bacterial aggregates encased in a self-produced polymeric matrix\u0000which attach to moist surfaces and are extremely resistant to chemicals and\u0000antibiotics. Recent experiments show that their structure is defined by the\u0000interplay of elastic deformations and liquid transport within the biofilm, in\u0000response to the cellular activity and the interaction with the surrounding\u0000environment. We propose a poroelastic model for elastic deformation and liquid\u0000transport in three dimensional biofilms spreading on agar surfaces. The motion\u0000of the boundaries can be described by the combined use of Von Karman type\u0000approximations for the agar/biofilm interface and thin film approximations for\u0000the biofilm/air interface. Bacterial activity informs the macroscopic\u0000continuous model through source terms and residual stresses, either\u0000phenomenological or derived from microscopic models. We present a procedure to\u0000estimate the structure of such residual stresses, based on a simple cellular\u0000automata description of bacterial activity. Inspired by image processing, we\u0000show that a filtering strategy effectively smooths out the rough tensors\u0000provided by the stochastic cellular automata rules, allowing us to insert them\u0000in the macroscopic model without numerical instability.","PeriodicalId":501321,"journal":{"name":"arXiv - QuanBio - Cell Behavior","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139481330","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}
Ana Carpio, Elena Cebrian, David R. Espeso, Perfecto Vidal
From multicellular tissues to bacterial colonies, three dimensional cellular structures arise through the interaction of cellular activities and mechanical forces. Simple bacterial communities provide model systems for analyzing such interaction. Biofilms are bacterial aggregates attached to wet surfaces and encased in a self-produced polymeric matrix. Biofilms in flows form filamentary structures that contrast with the wrinkled layers observed on air/solid interfaces. We are able to reproduce both types of shapes through elastic rod and plate models that incorporate information from the biomass production and differentiations process, such as growth rates, growth tensors or inner stresses, as well as constraints imposed by the interaction with environment. A more precise study of biofilm dynamics requires tackling water absorption from its surroundings and fluid transport within the biological system. This process alters the material properties of the biofilm and the overall stresses. We analyze whether poroelastic approaches can provide a suitable combined description of fluid-like and solid-like biofilm behavior.
{"title":"Biofilm mechanics and patterns","authors":"Ana Carpio, Elena Cebrian, David R. Espeso, Perfecto Vidal","doi":"arxiv-2401.05323","DOIUrl":"https://doi.org/arxiv-2401.05323","url":null,"abstract":"From multicellular tissues to bacterial colonies, three dimensional cellular\u0000structures arise through the interaction of cellular activities and mechanical\u0000forces. Simple bacterial communities provide model systems for analyzing such\u0000interaction. Biofilms are bacterial aggregates attached to wet surfaces and\u0000encased in a self-produced polymeric matrix. Biofilms in flows form filamentary\u0000structures that contrast with the wrinkled layers observed on air/solid\u0000interfaces. We are able to reproduce both types of shapes through elastic rod\u0000and plate models that incorporate information from the biomass production and\u0000differentiations process, such as growth rates, growth tensors or inner\u0000stresses, as well as constraints imposed by the interaction with environment. A\u0000more precise study of biofilm dynamics requires tackling water absorption from\u0000its surroundings and fluid transport within the biological system. This process\u0000alters the material properties of the biofilm and the overall stresses. We\u0000analyze whether poroelastic approaches can provide a suitable combined\u0000description of fluid-like and solid-like biofilm behavior.","PeriodicalId":501321,"journal":{"name":"arXiv - QuanBio - Cell Behavior","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139422389","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}
Alan Givré, Alejandro Colman-Lerner, Silvina Ponce Dawson
Cells continuously sense their surroundings to detect modifications and generate responses. Very often changes in extracellular concentrations initiate signaling cascades that eventually result in changes in gene expression. Increasing stimulus strengths can be encoded in increasing concentration amplitudes or increasing activation frequencies of intermediaries of the pathway. In this Letter we show how the different way in which amplitude and frequency encoding map environmental changes impact on the cell's information transmission capabilities. While amplitude encoding is optimal for a limited range of stimuli strengths around a finite value, frequency encoding information transmission can improve or remain relatively flat as the stimulus strength increases. The apparently redundant combination of both mechanisms in some cell types may then serve the purpose of expanding the range over which stimulus strengths can be reliably discriminated. In this Letter we also discuss a possible example of this mechanism.
{"title":"Amplitude and Frequency encodings give cells a different lens to sense the environment","authors":"Alan Givré, Alejandro Colman-Lerner, Silvina Ponce Dawson","doi":"arxiv-2401.04089","DOIUrl":"https://doi.org/arxiv-2401.04089","url":null,"abstract":"Cells continuously sense their surroundings to detect modifications and\u0000generate responses. Very often changes in extracellular concentrations initiate\u0000signaling cascades that eventually result in changes in gene expression.\u0000Increasing stimulus strengths can be encoded in increasing concentration\u0000amplitudes or increasing activation frequencies of intermediaries of the\u0000pathway. In this Letter we show how the different way in which amplitude and\u0000frequency encoding map environmental changes impact on the cell's information\u0000transmission capabilities. While amplitude encoding is optimal for a limited\u0000range of stimuli strengths around a finite value, frequency encoding\u0000information transmission can improve or remain relatively flat as the stimulus\u0000strength increases. The apparently redundant combination of both mechanisms in\u0000some cell types may then serve the purpose of expanding the range over which\u0000stimulus strengths can be reliably discriminated. In this Letter we also\u0000discuss a possible example of this mechanism.","PeriodicalId":501321,"journal":{"name":"arXiv - QuanBio - Cell Behavior","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139408764","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}
T cells undergo large shape changes (morphodynamics) when migrating. While progress has been made elucidating the molecular basis of cell migration, statistical characterization of morphodynamics and migration has been limited, particularly in physiologically realistic 3D environments. A previous study (H. Cavanagh et al., J. R. Soc. Interface 19: 20220081) found discrete states of dynamics as well as periodic oscillations of shape. However, we show that these results are due to artifacts of the analysis methods. Here, we present a revised analysis of the data, applying a method based on an underdamped Langevin equation. We find that different shape modes have different correlation times. We also find novel non-Gaussian effects. This study provides a framework in which quantitative comparisons of cell morphodynamics and migration can be made, e.g. between different biological conditions or mechanistic models.
T 细胞在迁移时会发生巨大的形状变化（形态动力学）。虽然在阐明细胞迁移的分子基础方面取得了进展，但对形态动力学和迁移的统计描述还很有限，尤其是在生理上逼真的三维环境中。之前的一项研究（H.Cavanagh 等人，J. R. Soc. Interface 19: 20220081）发现了动力学的离散状态以及形状的周期性振荡。然而，我们的研究表明，这些结果是由于分析方法的误差造成的。在此，我们采用基于欠阻尼朗温方程的方法，对数据进行了详细分析。我们发现，不同的形状模式具有不同的相关时间。我们还发现了新的非高斯效应。这项研究提供了一个可以对细胞形态动力学和迁移进行定量比较的框架，例如在不同生物条件或力学模型之间进行比较。
{"title":"Quantifying T cell morphodynamics and migration in 3D collagen matrices","authors":"Yeeren I. Low","doi":"arxiv-2401.03595","DOIUrl":"https://doi.org/arxiv-2401.03595","url":null,"abstract":"T cells undergo large shape changes (morphodynamics) when migrating. While\u0000progress has been made elucidating the molecular basis of cell migration,\u0000statistical characterization of morphodynamics and migration has been limited,\u0000particularly in physiologically realistic 3D environments. A previous study (H.\u0000Cavanagh et al., J. R. Soc. Interface 19: 20220081) found discrete states of\u0000dynamics as well as periodic oscillations of shape. However, we show that these\u0000results are due to artifacts of the analysis methods. Here, we present a\u0000revised analysis of the data, applying a method based on an underdamped\u0000Langevin equation. We find that different shape modes have different\u0000correlation times. We also find novel non-Gaussian effects. This study provides\u0000a framework in which quantitative comparisons of cell morphodynamics and\u0000migration can be made, e.g. between different biological conditions or\u0000mechanistic models.","PeriodicalId":501321,"journal":{"name":"arXiv - QuanBio - Cell Behavior","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139412445","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}
Cells continuously interact with their environment and respond to changes accordingly. Very often changes in the concentration of extracellular substances occur which, through receptor binding, give rise to a sequence of intracellular changes in what is called a signaling cascade. Increasing intensities of the external stimulus can result in increasing concentrations or increasing activation of the internal messengers or can induce a pulsatile behavior of increasing frequency with stimulus strength. This last behavior has been observed in intracellular Ca$^{2+}$ signals in which Ca$^{2+}$ is released from the endoplasmic reticulum through Inositol Trisphosphate Receptors (IP$_3$Rs), an ubiquitous signaling mechanism involved in many processes of physiological relevance. A statistical analysis of the time intervals between subsequent IP$_3$R-mediated Ca$^{2+}$ pulses observed experimentally has revealed an exponential dependence with the external stimulus strength in several cell types. This type of dependence, which is reminiscent of Kramers' law for thermally activated barrier crossing, has also been derived for certain excitable systems. Excitable systems have a stable stationary solution and, upon perturbations that surpass a threshold, perform a long excursion in phase space before returning to equilibrium. In this paper we use a very simple mathematical model of IP$_3$R-mediated Ca$^{2+}$ signals and published experimental results to derive the scaling law between the interpulse time and the external stimulus strength.
{"title":"Cell information processing via frequency encoding and excitability","authors":"Alan Givré, Silvina Ponce Dawson","doi":"arxiv-2312.17629","DOIUrl":"https://doi.org/arxiv-2312.17629","url":null,"abstract":"Cells continuously interact with their environment and respond to changes\u0000accordingly. Very often changes in the concentration of extracellular\u0000substances occur which, through receptor binding, give rise to a sequence of\u0000intracellular changes in what is called a signaling cascade. Increasing\u0000intensities of the external stimulus can result in increasing concentrations or\u0000increasing activation of the internal messengers or can induce a pulsatile\u0000behavior of increasing frequency with stimulus strength. This last behavior has\u0000been observed in intracellular Ca$^{2+}$ signals in which Ca$^{2+}$ is released\u0000from the endoplasmic reticulum through Inositol Trisphosphate Receptors\u0000(IP$_3$Rs), an ubiquitous signaling mechanism involved in many processes of\u0000physiological relevance. A statistical analysis of the time intervals between\u0000subsequent IP$_3$R-mediated Ca$^{2+}$ pulses observed experimentally has\u0000revealed an exponential dependence with the external stimulus strength in\u0000several cell types. This type of dependence, which is reminiscent of Kramers'\u0000law for thermally activated barrier crossing, has also been derived for certain\u0000excitable systems. Excitable systems have a stable stationary solution and,\u0000upon perturbations that surpass a threshold, perform a long excursion in phase\u0000space before returning to equilibrium. In this paper we use a very simple\u0000mathematical model of IP$_3$R-mediated Ca$^{2+}$ signals and published\u0000experimental results to derive the scaling law between the interpulse time and\u0000the external stimulus strength.","PeriodicalId":501321,"journal":{"name":"arXiv - QuanBio - Cell Behavior","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-12-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139066950","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}
Indrajit Tah, Daniel Haertter, Janice M. Crawford, Daniel P. Kiehart, Christoph F. Schmidt, Andrea J. Liu
Dorsal closure is a process that occurs during embryogenesis of Drosophila melanogaster. During dorsal closure, the amnioserosa (AS), a one-cell thick epithelial tissue that fills the dorsal opening, shrinks as the lateral epidermis sheets converge and eventually merge. During this process, the aspect ratio of amnioserosa cells increases markedly. The standard 2-dimensional vertex model, which successfully describes tissue sheet mechanics in multiple contexts, would in this case predict that the tissue should fluidize via cell neighbor changes. Surprisingly, however, the amnioserosa remains an elastic solid with no such events. We here present a minimal extension to the vertex model that explains how the amnioserosa can achieve this unexpected behavior. We show that continuous shrinkage of the preferred cell perimeter and cell perimeter polydispersity lead to the retention of the solid state of the amnioserosa. Our model accurately captures measured cell shape and orientation changes and predicts non-monotonic junction tension that we confirm with laser ablation experiments.
{"title":"Minimal vertex model explains how the amnioserosa avoids fluidization during Drosophila dorsal closure","authors":"Indrajit Tah, Daniel Haertter, Janice M. Crawford, Daniel P. Kiehart, Christoph F. Schmidt, Andrea J. Liu","doi":"arxiv-2312.12926","DOIUrl":"https://doi.org/arxiv-2312.12926","url":null,"abstract":"Dorsal closure is a process that occurs during embryogenesis of Drosophila\u0000melanogaster. During dorsal closure, the amnioserosa (AS), a one-cell thick\u0000epithelial tissue that fills the dorsal opening, shrinks as the lateral\u0000epidermis sheets converge and eventually merge. During this process, the aspect\u0000ratio of amnioserosa cells increases markedly. The standard 2-dimensional\u0000vertex model, which successfully describes tissue sheet mechanics in multiple\u0000contexts, would in this case predict that the tissue should fluidize via cell\u0000neighbor changes. Surprisingly, however, the amnioserosa remains an elastic\u0000solid with no such events. We here present a minimal extension to the vertex\u0000model that explains how the amnioserosa can achieve this unexpected behavior.\u0000We show that continuous shrinkage of the preferred cell perimeter and cell\u0000perimeter polydispersity lead to the retention of the solid state of the\u0000amnioserosa. Our model accurately captures measured cell shape and orientation\u0000changes and predicts non-monotonic junction tension that we confirm with laser\u0000ablation experiments.","PeriodicalId":501321,"journal":{"name":"arXiv - QuanBio - Cell Behavior","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138823412","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}
Sirine Amiri, Yirui Zhang, Andonis Gerardos, Cécile Sykes, Pierre Ronceray
The ability of eukaryotic cells to squeeze through constrictions is limited by the stiffness of their large and rigid nucleus. However, migrating cells are often able to overcome this limitation and pass through constrictions much smaller than their nucleus, a mechanism that is not yet understood. This is what we address here through a data-driven approach using microfluidic devices where cells migrate through controlled narrow spaces of sizes comparable to the ones encountered in physiological situations. Stochastic Force Inference is applied to experimental nuclear trajectories and nuclear shape descriptors, resulting in equations that effectively describe this phenomenon of nuclear translocation. By employing a model where the channel geometry is an explicit parameter and by training it over experimental data with different sizes of constrictions, we ensure that the resulting equations are predictive to other geometries. Altogether, the approach developed here paves the way for a mechanistic and quantitative description of dynamical cell complexity during its motility.
{"title":"Inferring geometrical dynamics of cell nucleus translocation","authors":"Sirine Amiri, Yirui Zhang, Andonis Gerardos, Cécile Sykes, Pierre Ronceray","doi":"arxiv-2312.12402","DOIUrl":"https://doi.org/arxiv-2312.12402","url":null,"abstract":"The ability of eukaryotic cells to squeeze through constrictions is limited\u0000by the stiffness of their large and rigid nucleus. However, migrating cells are\u0000often able to overcome this limitation and pass through constrictions much\u0000smaller than their nucleus, a mechanism that is not yet understood. This is\u0000what we address here through a data-driven approach using microfluidic devices\u0000where cells migrate through controlled narrow spaces of sizes comparable to the\u0000ones encountered in physiological situations. Stochastic Force Inference is\u0000applied to experimental nuclear trajectories and nuclear shape descriptors,\u0000resulting in equations that effectively describe this phenomenon of nuclear\u0000translocation. By employing a model where the channel geometry is an explicit\u0000parameter and by training it over experimental data with different sizes of\u0000constrictions, we ensure that the resulting equations are predictive to other\u0000geometries. Altogether, the approach developed here paves the way for a\u0000mechanistic and quantitative description of dynamical cell complexity during\u0000its motility.","PeriodicalId":501321,"journal":{"name":"arXiv - QuanBio - Cell Behavior","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138819896","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}
Jacob Knight, Paula García-Galindo, Johannes Pausch, Gunnar Pruessner
A wide array of biological systems can navigate in shallow gradients of chemoattractant with remarkable precision. Whilst previous approaches model such systems using coarse-grained chemical density profiles, we construct a dynamical model consisting of a chemotactic cell responding to discrete cue particles. For a cell without internal memory, we derive an effective velocity with which the cell approaches a point source of cue particles. We find that the effective velocity becomes negative beyond some homing radius, which represents an upper bound on the distance within which chemotaxis can be reliably performed. This work lays the foundation for the analytical characterisation of more detailed models of chemotaxis.
{"title":"Memoryless Chemotaxis with Discrete Cues","authors":"Jacob Knight, Paula García-Galindo, Johannes Pausch, Gunnar Pruessner","doi":"arxiv-2312.11346","DOIUrl":"https://doi.org/arxiv-2312.11346","url":null,"abstract":"A wide array of biological systems can navigate in shallow gradients of\u0000chemoattractant with remarkable precision. Whilst previous approaches model\u0000such systems using coarse-grained chemical density profiles, we construct a\u0000dynamical model consisting of a chemotactic cell responding to discrete cue\u0000particles. For a cell without internal memory, we derive an effective velocity\u0000with which the cell approaches a point source of cue particles. We find that\u0000the effective velocity becomes negative beyond some homing radius, which\u0000represents an upper bound on the distance within which chemotaxis can be\u0000reliably performed. This work lays the foundation for the analytical\u0000characterisation of more detailed models of chemotaxis.","PeriodicalId":501321,"journal":{"name":"arXiv - QuanBio - Cell Behavior","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138745585","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}
Mitra Rezaei, Hamidreza Arjmandi, Mohammad Zoofaghari, Kajsa Kanebratt, Liisa Vilen, David Janzen, Peter Gennemark, Adam Noel
Recent molecular communication (MC) research has integrated more detailed computational models to capture the dynamics of practical biophysical systems. This research focuses on developing realistic models for MC transceivers inspired by spheroids - three-dimensional cell aggregates commonly used in organ-on-chip experimental systems. Potential applications that can be used or modeled with spheroids include nutrient transport in an organ-on-chip system, the release of biomarkers or reception of drug molecules by a cancerous tumor site, or transceiver nanomachines participating in information exchange. In this paper, a simple diffusive MC system is considered where a spheroidal transmitter and receiver are in an unbounded fluid environment. These spheroidal antennas are modeled as porous media for diffusive signaling molecules, then their boundary conditions and effective diffusion coefficients are characterized. Further, for either a point source or spheroidal transmitter, Green's function for concentration (GFC) outside and inside the receiving spheroid is analytically derived and formulated in terms of an infinite series and confirmed by a particle-based simulator (PBS). The provided GFCs enable computation of the transmitted and received signals in the spheroidal communication system. This study shows that the porous structure of the receiving spheroid amplifies diffusion signals but also disperses them, thus there is a trade-off between porosity and information transmission rate. Also, the results reveal that the porous arrangement of the transmitting spheroid not only disperses the received signal but also attenuates it. System performance is also evaluated in terms of bit error rate (BER). Decreasing the porosity of the receiving spheroid is shown to enhance system performance. Conversely, reducing the porosity of the transmitting spheroid can adversely affect system performance.
最近的分子通讯（MC）研究整合了更详细的计算模型，以捕捉实际生物物理系统的动态。这项研究的重点是受球形体（常用于片上器官实验系统的三维细胞聚集体）的启发，开发MC收发器的现实模型。受球体启发而建立的 MC 收发器的现实模型--球体是有机芯片实验系统中常用的三维细胞聚集体。球体的潜在应用或模型可用于器官芯片系统中的营养物质运输、生物标记物的释放或癌症肿瘤部位对药物分子的接收，或参与信息交换的收发器纳米机械。本文考虑了一个简单的扩散 MC 系统，在该系统中，球形发射器和接收器处于无界流体环境中。这些球形天线被模拟为扩散信号分子的多孔介质，然后对它们的边界条件和有效扩散系数进行表征。此外，对于点源或球面发射器，接收球面内外的浓度格林函数（GFC）都是通过分析推导出来的，并以无穷级数表示，由基于粒子的模拟器（PBS）进行确认。根据所提供的 GFC，可以计算球形通信系统中的发射和接收信号。研究表明，接收球面的多孔结构会放大扩散信号，但同时也会分散信号，因此在多孔性和信息传输速率之间存在权衡。系统性能还通过误码率（BER）进行了评估。相反，降低发射球面的多孔性会对系统性能产生不利影响。
{"title":"Spheroidal Molecular Communication via Diffusion: Signaling Between Homogeneous Cell Aggregates","authors":"Mitra Rezaei, Hamidreza Arjmandi, Mohammad Zoofaghari, Kajsa Kanebratt, Liisa Vilen, David Janzen, Peter Gennemark, Adam Noel","doi":"arxiv-2312.04427","DOIUrl":"https://doi.org/arxiv-2312.04427","url":null,"abstract":"Recent molecular communication (MC) research has integrated more detailed\u0000computational models to capture the dynamics of practical biophysical systems.\u0000This research focuses on developing realistic models for MC transceivers\u0000inspired by spheroids - three-dimensional cell aggregates commonly used in\u0000organ-on-chip experimental systems. Potential applications that can be used or\u0000modeled with spheroids include nutrient transport in an organ-on-chip system,\u0000the release of biomarkers or reception of drug molecules by a cancerous tumor\u0000site, or transceiver nanomachines participating in information exchange. In\u0000this paper, a simple diffusive MC system is considered where a spheroidal\u0000transmitter and receiver are in an unbounded fluid environment. These\u0000spheroidal antennas are modeled as porous media for diffusive signaling\u0000molecules, then their boundary conditions and effective diffusion coefficients\u0000are characterized. Further, for either a point source or spheroidal\u0000transmitter, Green's function for concentration (GFC) outside and inside the\u0000receiving spheroid is analytically derived and formulated in terms of an\u0000infinite series and confirmed by a particle-based simulator (PBS). The provided\u0000GFCs enable computation of the transmitted and received signals in the\u0000spheroidal communication system. This study shows that the porous structure of\u0000the receiving spheroid amplifies diffusion signals but also disperses them,\u0000thus there is a trade-off between porosity and information transmission rate.\u0000Also, the results reveal that the porous arrangement of the transmitting\u0000spheroid not only disperses the received signal but also attenuates it. System\u0000performance is also evaluated in terms of bit error rate (BER). Decreasing the\u0000porosity of the receiving spheroid is shown to enhance system performance.\u0000Conversely, reducing the porosity of the transmitting spheroid can adversely\u0000affect system performance.","PeriodicalId":501321,"journal":{"name":"arXiv - QuanBio - Cell Behavior","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138554108","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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