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1.
Sci Rep ; 14(1): 13104, 2024 06 07.
Artigo em Inglês | MEDLINE | ID: mdl-38849458

RESUMO

Bacteria employ quorum sensing as a remarkable mechanism for coordinating behaviors and communicating within their communities. In this study, we introduce a MATLAB Graphical User Interface (GUI) that offers a versatile platform for exploring the dynamics of quorum sensing. Our computational framework allows for the assessment of quorum sensing, the investigation of parameter dependencies, and the prediction of minimum biofilm thickness required for its initiation. A pivotal observation from our simulations underscores the pivotal role of the diffusion coefficient in quorum sensing, surpassing the influence of bacterial cell dimensions. Varying the diffusion coefficient reveals significant fluctuations in autoinducer concentration, highlighting its centrality in shaping bacterial communication. Additionally, our GUI facilitates the prediction of the minimum biofilm thickness necessary to trigger quorum sensing, a parameter contingent on the diffusion coefficient. This feature provides valuable insights into spatial constraints governing quorum sensing initiation. The interplay between production rates and cell concentrations emerges as another critical facet of our study. We observe that higher production rates or cell concentrations expedite quorum sensing, underscoring the intricate relationship between cell communication and population dynamics in bacterial communities. While our simulations align with mathematical models reported in the literature, we acknowledge the complexity of living organisms, emphasizing the value of our GUI for standardizing results and facilitating early assessments of quorum sensing. This computational approach offers a window into the environmental conditions conducive to quorum sensing initiation, encompassing parameters such as the diffusion coefficient, cell concentration, and biofilm thickness. In conclusion, our MATLAB GUI serves as a versatile tool for understanding the diverse aspects of quorum sensing especially for non-biologists. The insights gained from this computational framework advance our understanding of bacterial communication, providing researchers with the means to explore diverse ecological contexts where quorum sensing plays a pivotal role.


Assuntos
Biofilmes , Percepção de Quorum , Biofilmes/crescimento & desenvolvimento , Modelos Biológicos , Bactérias/metabolismo , Fenômenos Fisiológicos Bacterianos , Difusão , Interface Usuário-Computador , Simulação por Computador
2.
Nat Commun ; 15(1): 4896, 2024 Jun 08.
Artigo em Inglês | MEDLINE | ID: mdl-38851790

RESUMO

Biological computing is a promising field with potential applications in biosafety, environmental monitoring, and personalized medicine. Here we present work on the design of bacterial computers using spatial patterning to process information in the form of diffusible morphogen-like signals. We demonstrate, mathematically and experimentally, that single, modular, colonies can perform simple digital logic, and that complex functions can be built by combining multiple colonies, removing the need for further genetic engineering. We extend our experimental system to incorporate sender colonies as morphogen sources, demonstrating how one might integrate different biochemical inputs. Our approach will open up ways to perform biological computation, with applications in bioengineering, biomaterials and biosensing. Ultimately, these computational bacterial communities will help us explore information processing in natural biological systems.


Assuntos
Escherichia coli , Escherichia coli/metabolismo , Escherichia coli/genética , Bactérias/metabolismo , Bactérias/genética , Engenharia Genética/métodos , Difusão , Modelos Biológicos , Bioengenharia/métodos
3.
J Phys Chem B ; 128(23): 5576-5589, 2024 Jun 13.
Artigo em Inglês | MEDLINE | ID: mdl-38833567

RESUMO

Single-molecule free diffusion experiments enable accurate quantification of coexisting species or states. However, unequal brightness and diffusivity introduce a burst selection bias and affect the interpretation of experimental results. We address this issue with a photon-by-photon maximum likelihood method, burstML, which explicitly considers burst selection criteria. BurstML accurately estimates parameters, including photon count rates, diffusion times, Förster resonance energy transfer (FRET) efficiencies, and population, even in cases where species are poorly distinguished in FRET efficiency histograms. We develop a quantitative theory that determines the fraction of photon bursts corresponding to each species and thus obtain accurate species populations from the measured burst fractions. In addition, we provide a simple approximate formula for burst fractions and establish the range of parameters where unequal brightness and diffusivity can significantly affect the results obtained by conventional methods. The performance of the burstML method is compared with that of a maximum likelihood method that assumes equal species brightness and diffusivity, as well as standard Gaussian fitting of FRET efficiency histograms, using both simulated and real single-molecule data for cold-shock protein, protein L, and protein G. The burstML method enhances the accuracy of parameter estimation in single-molecule fluorescence studies.


Assuntos
Transferência Ressonante de Energia de Fluorescência , Difusão , Fótons , Funções Verossimilhança , Imagem Individual de Molécula/métodos
4.
Philos Trans R Soc Lond B Biol Sci ; 379(1906): 20230220, 2024 Jul 29.
Artigo em Inglês | MEDLINE | ID: mdl-38853553

RESUMO

This review focuses on the activity-dependent diffusion trapping of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors (AMPARs) as a crucial mechanism for the expression of early long-term potentiation (LTP), a process central to learning and memory. Despite decades of research, the precise mechanisms by which LTP induction leads to an increase in AMPAR responses at synapses have been elusive. We review the different hypotheses that have been put forward to explain the increased AMPAR responsiveness during LTP. We discuss the dynamic nature of AMPAR complexes, including their constant turnover and activity-dependent modifications that affect their synaptic accumulation. We highlight a hypothesis suggesting that AMPARs are diffusively trapped at synapses through activity-dependent interactions with protein-based binding slots in the post-synaptic density (PSD), offering a potential explanation for the increased synaptic strength during LTP. Furthermore, we outline the challenges still to be addressed before we fully understand the functional roles and molecular mechanisms of AMPAR dynamic nanoscale organization in LTP. This article is part of a discussion meeting issue 'Long-term potentiation: 50 years on'.


Assuntos
Potenciação de Longa Duração , Receptores de AMPA , Potenciação de Longa Duração/fisiologia , Receptores de AMPA/metabolismo , Animais , Sinapses/fisiologia , Sinapses/metabolismo , Difusão , Humanos , Densidade Pós-Sináptica/metabolismo
5.
Math Biosci Eng ; 21(4): 5826-5837, 2024 Apr 28.
Artigo em Inglês | MEDLINE | ID: mdl-38872560

RESUMO

In the present work, both direct and inverse problems are considered for a Fisher-type fractional diffusion equation, which is proposed to describe the phenomenon of cell migration. For the direct problem, a solution is given via the Fourier method and the Laplace transform. On the other hand, we solved the inverse problem from a Bayesian statistical framework using a set of data that are the result of a cell migration experiment on a wound closure assay. We estimated the parameters of the mathematical model via Markov Chain Monte Carlo methods.


Assuntos
Teorema de Bayes , Movimento Celular , Cadeias de Markov , Modelos Biológicos , Método de Monte Carlo , Humanos , Simulação por Computador , Algoritmos , Difusão , Análise de Fourier , Animais
6.
J Phys Chem Lett ; 15(20): 5476-5487, 2024 May 23.
Artigo em Inglês | MEDLINE | ID: mdl-38748082

RESUMO

Proteins, genetic material, and membranes are fundamental to all known organisms, yet these components alone do not constitute life. Life emerges from the dynamic processes of self-organization, assembly, and active motion, suggesting the existence of similar artificial systems. Against this backdrop, our Perspective explores a variety of chemical phenomena illustrating how nonequilibrium self-organization and micromotors contribute to life-like behavior and functionalities. After explaining key terms, we discuss specific examples including enzymatic motion, diffusiophoretic and bubble-driven self-propulsion, pattern-forming reaction-diffusion systems, self-assembling inorganic aggregates, and hierarchically emergent phenomena. We also provide a roadmap for combining self-organization and active motion and discuss possible outcomes through biological analogs. We suggest that this research direction, deeply rooted in physical chemistry, offers opportunities for further development with broad impacts on related sciences and technologies.


Assuntos
Movimento (Física) , Difusão
7.
J Phys Chem Lett ; 15(20): 5428-5435, 2024 May 23.
Artigo em Inglês | MEDLINE | ID: mdl-38743920

RESUMO

Nanoplastic-lipid interaction is vital to understanding the nanoscale mechanism of plastic adsorption and aggregation on a lipid membrane surface. However, a single-particle mechanistic picture of the nanoplastic transport process on a lipid surface remains unclear. Here, we report a salt-dependent non-Gaussian transport mechanism of polystyrene particles on a supported 1-palmitoyl-2-oleoyl-glycero-3-phosphocholine (POPC) lipid bilayer surface. Particle stickiness on the POPC surface increases with salt concentration, where the particles stay longer at the surface and diffuse to shorter distances. Additionally, a non-Gaussian diffusion state dominates the transport process at high salt concentrations. Our current study provides insight into the transport mechanism of polystyrene (PS) particles on supported lipid membranes, which is essential to understanding fundamental questions regarding the adsorption mechanisms of nanoplastics on lipid surfaces.


Assuntos
Bicamadas Lipídicas , Fosfatidilcolinas , Poliestirenos , Cloreto de Sódio , Bicamadas Lipídicas/química , Fosfatidilcolinas/química , Poliestirenos/química , Cloreto de Sódio/química , Propriedades de Superfície , Adsorção , Difusão
8.
Zhongguo Zhong Yao Za Zhi ; 49(8): 2158-2168, 2024 Apr.
Artigo em Chinês | MEDLINE | ID: mdl-38812231

RESUMO

This study systematically explored the transdermal diffusion law of functional substances of Jingu Zhitong Gel(JGZTG). The transdermal diffusion research methods of JGZTG were investigated by single factor trial with the automated transdermal(dry-heat) sampling system. High performance liquid chromatography(HPLC) content determination method was established to determine the contents of ferulic acid, senkyunolide I, cinnamic acid, hydroxy-ε-xanthoxylin, hydroxy-α-xanthoxylin, and hydroxy-ß-xanthoxylin in the transdermal diffusion solution of JGZTG. The transdermal diffusion law of the components within 16 h was investigated. The results showed that the optimal transdermal diffusion method of JGZTG was as follows: Rat skin was used as the transdermal barrier; normal saline was used as the receiving medium; the dosage of JGZTG was 0.3 g, and the receiving solution was extracted by ethyl acetate. The results of transdermal diffusion showed that the release of ferulic acid, cinnamic acid, and senkyunolide I increased significantly at 0-8 h and slowed down at 8-16 h. The drug release was a synergic process of diffusion and dissolution, in which ferulic acid and cinnamic acid followed Higuchi and Ritger-Peppas equations, and liguolactone I followed Higuchi equation. The transdermal diffusion curves of hydroxy-ε-zanthoxylin, hydroxy-α-zanthoxylin, and hydroxy-ß-zanthoxylin showed continuous release within 16 h, and the drug release was skeleton dissolution. The diffusion law followed zero-order equation, first-order equation, and Ritger-Peppas equation. In clonclusion, it is a controlled release of ferulic acid, ligustrone I, cinnamic acid, hydroxy-ε-pyrroxylin, hydroxy-α-pyrroxylin, and hydroxy-ß-pyrroxylin in JGZTG, which can maintain stable blood drug concentration with 16 h, and the cumulative transmittance of each component with 12 h can reach 80% of cumulative transmittance with 24 h, which is in line with the clinical drug use law of bis in die.


Assuntos
Medicamentos de Ervas Chinesas , Absorção Cutânea , Medicamentos de Ervas Chinesas/química , Medicamentos de Ervas Chinesas/farmacocinética , Medicamentos de Ervas Chinesas/administração & dosagem , Ratos , Animais , Difusão , Administração Cutânea , Pele/metabolismo , Pele/química , Géis/química , Masculino , Ratos Sprague-Dawley , Cromatografia Líquida de Alta Pressão , Cinamatos/farmacocinética , Cinamatos/análise , Cinamatos/química , Ácidos Cumáricos/farmacocinética , Ácidos Cumáricos/análise
9.
PLoS Comput Biol ; 20(5): e1012158, 2024 May.
Artigo em Inglês | MEDLINE | ID: mdl-38768214

RESUMO

The self-organization of cells relies on the profound complexity of protein-protein interactions. Challenges in directly observing these events have hindered progress toward understanding their diverse behaviors. One notable example is the interaction between molecular motors and cytoskeletal systems that combine to perform a variety of cellular functions. In this work, we leverage theory and experiments to identify and quantify the rate-limiting mechanism of the initial association between a cargo-bound kinesin motor and a microtubule track. Recent advances in optical tweezers provide binding times for several lengths of kinesin motors trapped at varying distances from a microtubule, empowering the investigation of competing models. We first explore a diffusion-limited model of binding. Through Brownian dynamics simulations and simulation-based inference, we find this simple diffusion model fails to explain the experimental binding times, but an extended model that accounts for the ADP state of the molecular motor agrees closely with the data, even under the scrutiny of penalizing for additional model complexity. We provide quantification of both kinetic rates and biophysical parameters underlying the proposed binding process. Our model suggests that a typical binding event is limited by ADP state rather than physical search. Lastly, we predict how these association rates can be modulated in distinct ways through variation of environmental concentrations and physical properties.


Assuntos
Cinesinas , Microtúbulos , Ligação Proteica , Cinesinas/metabolismo , Cinesinas/química , Cinética , Microtúbulos/metabolismo , Microtúbulos/química , Biologia Computacional , Difosfato de Adenosina/metabolismo , Difosfato de Adenosina/química , Simulação por Computador , Modelos Biológicos , Difusão
10.
J Phys Chem B ; 128(22): 5293-5309, 2024 Jun 06.
Artigo em Inglês | MEDLINE | ID: mdl-38808573

RESUMO

Given the fact that the cellular interior is crowded by many different kinds of macromolecules, it is important that in vitro studies be carried out in the presence of mixed crowder systems. In this regard, we have used binary crowders formed by the combination of some of the commonly used crowding agents, namely, Ficoll 70, Dextran 70, Dextran 40, and PEG 8000 (PEG 8), to study how these affect enzyme activity, dynamics, and crowder diffusion. The enzyme chosen is AK3L1, an isoform of adenylate kinase. To investigate its dynamics, we have carried out three single point mutations (A74C, A132C, and A209C) with the cysteine residues being labeled with a coumarin-based solvatochromic probe [CPM: (7-diethylamino-3-(4-maleimido-phenyl)-4-methylcoumarin)]. Both enzyme activity and dynamics decreased in the binary mixtures as compared with the sum of the individual crowders, suggesting a reduction in excluded volume (in the mixture). To gain deeper insights into the binary mixtures, fluorescence correlation spectroscopy studies were carried out using fluorescein isothiocyanate-labeled Dextran 70 and tetramethylrhodamine-labeled AK3L1 as the diffusion probes. Diffusion in binary mixtures was observed to be much more constrained (relative to the sum of the individual crowders) for the labeled enzyme as compared to the labeled crowder showing different environments being faced by the two species. This was further confirmed during imaging of the phase-separated droplets formed in the binary mixtures having PEG as one of the crowding agents. The interior of these droplets was found to be rich in crowders and densely packed, as shown by confocal and digital holographic microscopy images, with the enzymes predominantly residing outside these droplets, that is, in the relatively less crowded regions. Taken together, our data provide important insights into various aspects of the simplest form of mixed crowding, that is, composed of just two components, and also hint at the enhanced complexity that the cellular interior presents toward having a detailed and comprehensive understanding of the same.


Assuntos
Adenilato Quinase , Polietilenoglicóis , Difusão , Adenilato Quinase/metabolismo , Adenilato Quinase/química , Adenilato Quinase/genética , Polietilenoglicóis/química , Ficoll/química , Dextranos/química , Dextranos/metabolismo , Espectrometria de Fluorescência , Mutação Puntual , Cumarínicos/química , Cumarínicos/metabolismo
11.
Environ Sci Pollut Res Int ; 31(23): 33848-33866, 2024 May.
Artigo em Inglês | MEDLINE | ID: mdl-38691288

RESUMO

Deep-sea mining inevitably produces plumes, which will pose a serious threat to the marine environment with the continuous movement and diffusion of plumes along with ocean currents. The terminal settling velocity (wt) of irregular particles is one of the crucial factors for determining the plumes' diffusion range. It is generally calculated by drag coefficient (CD), while most existing CD models only consider single shape characteristic parameter or have a smaller range of Reynolds number (Re). In this study, a new shape factor (γ) of irregular particles is proposed by considering the thickness (one-dimension), the projected area (two-dimension), and the surface area (three-dimension) of irregular particles as well as their coupling effect to establish a modified CD model for calculating the wt. A modified Gaussian plume model is proposed to predict the horizontal diffusion distance of the plume particles by considering the settling velocity and diffusion effect of irregular particles. Research results show that the wt increases nearly linearly, with a gradually decreased slope and slightly then greatly with the increasing of γ, dp (diameter) and ρp (density), respectively. The modified CD model is verified to be more valid with a wider application range (Re < 3×105) than five existing CD models by the test results. The larger the ρp or dp, the larger the wt and thus the smaller the Sh. This study could provide a theoretical basis for calculating the plume diffusion range to further study the impact of deep-sea mining on the ocean environment.


Assuntos
Mineração , Modelos Teóricos , Oceanos e Mares , Difusão
12.
Nature ; 629(8014): 1062-1068, 2024 May.
Artigo em Inglês | MEDLINE | ID: mdl-38720082

RESUMO

Most chemistry and biology occurs in solution, in which conformational dynamics and complexation underlie behaviour and function. Single-molecule techniques1 are uniquely suited to resolving molecular diversity and new label-free approaches are reshaping the power of single-molecule measurements. A label-free single-molecule method2-16 capable of revealing details of molecular conformation in solution17,18 would allow a new microscopic perspective of unprecedented detail. Here we use the enhanced light-molecule interactions in high-finesse fibre-based Fabry-Pérot microcavities19-21 to detect individual biomolecules as small as 1.2 kDa, a ten-amino-acid peptide, with signal-to-noise ratios (SNRs) >100, even as the molecules are unlabelled and freely diffusing in solution. Our method delivers 2D intensity and temporal profiles, enabling the distinction of subpopulations in mixed samples. Notably, we observe a linear relationship between passage time and molecular radius, unlocking the potential to gather crucial information about diffusion and solution-phase conformation. Furthermore, mixtures of biomolecule isomers of the same molecular weight and composition but different conformation can also be resolved. Detection is based on the creation of a new molecular velocity filter window and a dynamic thermal priming mechanism that make use of the interplay between optical and thermal dynamics22,23 and Pound-Drever-Hall (PDH) cavity locking24 to reveal molecular motion even while suppressing environmental noise. New in vitro ways of revealing molecular conformation, diversity and dynamics can find broad potential for applications in the life and chemical sciences.


Assuntos
Peptídeos , Imagem Individual de Molécula , Difusão , Isomerismo , Luz , Peptídeos/análise , Peptídeos/química , Peptídeos/efeitos da radiação , Razão Sinal-Ruído , Imagem Individual de Molécula/métodos , Soluções , Conformação Proteica , Peso Molecular , Movimento (Física)
13.
Sci Adv ; 10(22): eadl5576, 2024 May 31.
Artigo em Inglês | MEDLINE | ID: mdl-38820163

RESUMO

Despite great progress in the field, chronic Pseudomonas aeruginosa (Pa) infections remain a major cause of mortality in patients with cystic fibrosis (pwCF), necessitating treatment with antibiotics. Pf is a filamentous bacteriophage produced by Pa and acts as a structural element in Pa biofilms. Pf presence has been associated with antibiotic resistance and poor outcomes in pwCF, although the underlying mechanisms are unclear. We have investigated how Pf and sputum biopolymers impede antibiotic diffusion using pwCF sputum and fluorescent recovery after photobleaching. We demonstrate that tobramycin interacts with Pf and sputum polymers through electrostatic interactions. We also developed a set of mathematical models to analyze the complex observations. Our analysis suggests that Pf in sputum reduces the diffusion of charged antibiotics due to a greater binding constant associated with organized liquid crystalline structures formed between Pf and sputum polymers. This study provides insights into antibiotic tolerance mechanisms in chronic Pa infections and may offer potential strategies for novel therapeutic approaches.


Assuntos
Antibacterianos , Pseudomonas aeruginosa , Escarro , Eletricidade Estática , Escarro/microbiologia , Antibacterianos/farmacologia , Pseudomonas aeruginosa/efeitos dos fármacos , Pseudomonas aeruginosa/virologia , Humanos , Fibrose Cística/metabolismo , Infecções por Pseudomonas/tratamento farmacológico , Infecções por Pseudomonas/microbiologia , Tobramicina/farmacologia , Difusão , Biofilmes/efeitos dos fármacos , Bacteriófagos
14.
J Am Chem Soc ; 146(23): 16097-16104, 2024 Jun 12.
Artigo em Inglês | MEDLINE | ID: mdl-38805671

RESUMO

Communication between cells is crucial to the survival of both uni- and multicellular organisms. The primary mode of communication involves chemical cues. There is great current interest in mimicking this behavior in synthetic cells to understand the physical basis of intercellular communication and design collective functional behavior. Using liposomal cell mimics, we demonstrate how a chemical input can elicit a mechanical response (enhanced motility). We employed a single substrate to trigger enzyme cascade-induced control of the diffusion of up to three different liposome populations. Furthermore, substrate competition allows temporal control over enhanced diffusion. The use of enzyme cascades to propagate chemical signals provides a robust and efficient mechanism for diverse populations of protocells to coordinate their motion in response to signals from each other.


Assuntos
Lipossomos , Lipossomos/química , Lipossomos/metabolismo , Difusão
15.
J Contam Hydrol ; 264: 104357, 2024 May.
Artigo em Inglês | MEDLINE | ID: mdl-38729027

RESUMO

Most of the available data on diffusion in natural clayey rocks consider tracer diffusion in the absence of a salinity gradient despite the fact that such gradients are frequently found in natural and engineered subsurface environments. To assess the role of such gradients on the diffusion properties of clayey materials, through-diffusion experiments were carried out in the presence and absence of a salinity gradient using salt-diffusion and radioisotope tracer techniques. The experiments were carried out with vermiculite samples that contained equal proportions of interparticle and interlayer porosities so as to assess also the role played by the two types of porosities on the diffusion of water and ions. Data were interpreted using both a classical Fickian diffusion model and with a reactive transport code, CrunchClay that can handle multi-porosity diffusion processes in the presence of charged surfaces. By combining experimental and simulated data, we demonstrated that (i) the flux of water diffusing through vermiculite interlayer porosity was minor compared to that diffusing through the interparticle porosity, and (ii) a model considering at least three types of porous volumes (interlayer, interparticle diffuse layer, and bulk interparticle) was necessary to reproduce consistently the variations of neutral and charged species diffusion as a function of salinity gradient conditions.


Assuntos
Silicatos de Alumínio , Argila , Salinidade , Porosidade , Difusão , Argila/química , Silicatos de Alumínio/química , Água/química , Íons/química , Modelos Teóricos
16.
Colloids Surf B Biointerfaces ; 239: 113955, 2024 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-38754200

RESUMO

Lipid-based drug delivery systems offer the potential to enhance bioavailability, reduce dosing frequency, and improve patient adherence. In aqueous environment, initially dry lipid depots take up water and form liquid crystalline phases. Variation of lipid composition, depot size and hydration-induced phase transitions will plausibly affect the diffusion in and out of the depot. Lipid depots of soybean phosphatidylcholine (SPC) and glycerol dioleate (GDO) mixtures were hydrated for varying time durations in a phosphate-buffered saline (PBS) buffer and then analyzed with Karl Fischer titration, magnetic resonance imaging (MRI) and gravimetrically. Mathematical modeling of the swelling process using diffusion equations, was used to estimate the parameters of diffusion. Both composition of lipid mixture and depot size affect swelling kinetics… The diffusion parameters obtained in Karl Fischer titration and MRI (with temporal and spatial resolution respectively) are in good agreement. Remarkably, the MRI results show a gradient of water content within the depot even after the end of diffusion process. Apparently contradicting the first Fick's law in its classical form, these results find an explanation using the generalized Fick's law that considers the gradient of chemical potential rather than concentration as the driving force of diffusion.


Assuntos
Glycine max , Fosfatidilcolinas , Fosfatidilcolinas/química , Glycine max/química , Cinética , Difusão , Água/química , Imageamento por Ressonância Magnética , Diglicerídeos/química
17.
Eur Phys J E Soft Matter ; 47(5): 30, 2024 May 08.
Artigo em Inglês | MEDLINE | ID: mdl-38720027

RESUMO

The aggregation or clustering of proteins and other macromolecules plays an important role in the formation of large-scale molecular assemblies within cell membranes. Examples of such assemblies include lipid rafts, and postsynaptic domains (PSDs) at excitatory and inhibitory synapses in neurons. PSDs are rich in scaffolding proteins that can transiently trap transmembrane neurotransmitter receptors, thus localizing them at specific spatial positions. Hence, PSDs play a key role in determining the strength of synaptic connections and their regulation during learning and memory. Recently, a two-dimensional (2D) diffusion-mediated aggregation model of PSD formation has been developed in which the spatial locations of the clusters are determined by a set of fixed anchoring sites. The system is kept out of equilibrium by the recycling of particles between the cell membrane and interior. This results in a stationary distribution consisting of multiple clusters, whose average size can be determined using an effective mean-field description of the particle concentration around each anchored cluster. In this paper, we derive corrections to the mean-field approximation by applying the theory of diffusion in singularly perturbed domains. The latter is a powerful analytical method for solving two-dimensional (2D) and three-dimensional (3D) diffusion problems in domains where small holes or perforations have been removed from the interior. Applications range from modeling intracellular diffusion, where interior holes could represent subcellular structures such as organelles or biological condensates, to tracking the spread of chemical pollutants or heat from localized sources. In this paper, we take the bounded domain to be the cell membrane and the holes to represent anchored clusters. The analysis proceeds by partitioning the membrane into a set of inner regions around each cluster, and an outer region where mean-field interactions occur. Asymptotically matching the inner and outer stationary solutions generates an asymptotic expansion of the particle concentration, which includes higher-order corrections to mean-field theory that depend on the positions of the clusters and the boundary of the domain. Motivated by a recent study of light-activated protein oligomerization in cells, we also develop the analogous theory for cluster formation in a three-dimensional (3D) domain. The details of the asymptotic analysis differ from the 2D case due to the contrasting singularity structure of 2D and 3D Green's functions.


Assuntos
Membrana Celular , Difusão , Membrana Celular/metabolismo , Membrana Celular/química , Microdomínios da Membrana/química , Microdomínios da Membrana/metabolismo , Modelos Biológicos
18.
Phys Rev E ; 109(4-1): 044405, 2024 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-38755868

RESUMO

Active propulsion, as performed by bacteria and Janus particles, in combination with hydrodynamic interaction results in the accumulation of bacteria at a flat wall. However, in microfluidic devices with cylindrical pillars of sufficiently small radius, self-propelled particles can slide along and scatter off the surface of a pillar, without becoming trapped over long times. This nonequilibrium scattering process has been predicted to result in large diffusivities, even at high obstacle density, unlike particles that undergo classical specular reflection. Here, we test this prediction by experimentally studying the nonequilibrium scattering of pusherlike swimmers in microfluidic obstacle lattices. To explore the role of tumbles in the scattering process, we microscopically tracked wild-type (run and tumble) and smooth-swimming (run only) mutants of the bacterium Escherichia coli scattering off microfluidic pillars. We quantified key scattering parameters and related them to previously proposed models that included a prediction for the diffusivity, discussing their relevance. Finally, we discuss potential interpretations of the role of tumbles in the scattering process and connect our work to the broader study of swimmers in porous media.


Assuntos
Escherichia coli , Modelos Biológicos , Escherichia coli/citologia , Movimento , Difusão , Mutação , Hidrodinâmica
19.
Food Res Int ; 183: 114185, 2024 May.
Artigo em Inglês | MEDLINE | ID: mdl-38760122

RESUMO

Low- and no-calorie sweeteners reduce the amount of carbohydrates in foods and beverages. However, concerns about taste perception surrounding the role of non-nutritive sweeteners in the oral cavity remain unanswered. One of the parameters that influences taste perception is the diffusion coefficient of the sweetener molecules inside the mucin layer lining the mouth. This study investigated the impact of diffusion coefficients of common high-intensity sweeteners on taste perception focusing on the sweeteners' diffusion through mucin. Transwell Permeable Support well plates were used to measure diffusion coefficients of samples that were collected at specific intervals to estimate the coefficients based on concentration measurements. The diffusion coefficients of acesulfame-K, aspartame, rebaudioside M, sucralose, and sucrose with and without NaCl were compared. We found that different sweeteners show different diffusion behavior through mucin and that the presence of salt enhances the diffusion. These findings contribute insights into the diffusion of high-intensity sweeteners, offer a way to evaluate diffusion coefficients in real-time, and inform the development of products with improved taste profiles.


Assuntos
Mucinas , Sacarose , Edulcorantes , Difusão , Mucinas/metabolismo , Sacarose/análogos & derivados , Percepção Gustatória , Humanos , Tiazinas
20.
Commun Biol ; 7(1): 573, 2024 May 15.
Artigo em Inglês | MEDLINE | ID: mdl-38750123

RESUMO

Vesicles carry out many essential functions within cells through the processes of endocytosis, exocytosis, and passive and active transport. This includes transporting and delivering molecules between different parts of the cell, and storing and releasing neurotransmitters in neurons. To date, computational simulation of these key biological players has been rather limited and has not advanced at the same pace as other aspects of cell modeling, restricting the realism of computational models. We describe a general vesicle modeling tool that has been designed for wide application to a variety of cell models, implemented within our software STochastic Engine for Pathway Simulation (STEPS), a stochastic reaction-diffusion simulator that supports realistic reconstructions of cell tissue in tetrahedral meshes. The implementation is validated in an extensive test suite, parallel performance is demonstrated in a realistic synaptic bouton model, and example models are visualized in a Blender extension module.


Assuntos
Simulação por Computador , Difusão , Modelos Biológicos , Software , Vesículas Sinápticas/metabolismo , Exocitose/fisiologia , Animais , Humanos , Endocitose/fisiologia , Neurônios/fisiologia , Neurônios/metabolismo , Processos Estocásticos
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