The European Physical Journal E最新文献

{"title":"On the fluid drag reduction in scallop surface","authors":"Botong Li,&nbsp;Zitian Zhao,&nbsp;Linyu Meng,&nbsp;Liangliang Zhu","doi":"10.1140/epje/s10189-024-00434-7","DOIUrl":"10.1140/epje/s10189-024-00434-7","url":null,"abstract":"<div><p>In the field of biomimetics, the tiny riblet structures inspired by shark skin have been extensively studied for their drag reduction properties in turbulent flows. Here, we show that the ridged surface texture of another swimming creature in the ocean, i.e., the scallops, also has some friction drag reduction effect. In this study, we investigated the potential drag reduction effects of scallop shell textures using computational fluid dynamics simulations. Specifically, we constructed a conceptual model featuring an undulating surface pattern on a conical shell geometry that mimics scallop. Simulations modeled turbulent fluid flows over the model inserted at different orientations relative to the flow direction. The results demonstrate appreciable friction drag reduction generated by the ribbed hierarchical structures encasing the scallop, while partial pressure drag reduction exhibits dependence on alignment of scallop to the predominant flow direction. Theoretical mechanisms based on classic drag reduction theory in turbulence was established to explain the drag reduction phenomena. Given the analogous working environments of scallops and seafaring vessels, these findings may shed light on the biomimetic design of surface textures to enhance maritime engineering applications. Besides, this work elucidates an additional evolutionary example of fluid drag reduction, expanding the biological repertoire of swimming species.</p><h3>Graphical abstract</h3><p>Lines used for shear stress data extraction of the shell model and the normalized wall shear of these lines on both models.</p><div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></div>","PeriodicalId":790,"journal":{"name":"The European Physical Journal E","volume":"47 6","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141199221","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integrating machine learning with (alpha )-SAS for enhanced structural analysis in small-angle scattering: applications in biological and artificial macromolecular complexes","authors":"Eugen Mircea Anitas","doi":"10.1140/epje/s10189-024-00435-6","DOIUrl":"10.1140/epje/s10189-024-00435-6","url":null,"abstract":"<p>Small-Angle Scattering (SAS), encompassing both X-ray (SAXS) and Neutron (SANS) techniques, is a crucial tool for structural analysis at the nanoscale, particularly in the realm of biological macromolecules. This paper explores the intricacies of SAS, emphasizing its application in studying complex biological systems and the challenges associated with sample preparation and data analysis. We highlight the use of neutron-scattering properties of hydrogen isotopes and isotopic labeling in SANS for probing structures within multi-subunit complexes, employing techniques like contrast variation (CV) for detailed structural analysis. However, traditional SAS analysis methods, such as Guinier and Kratky plots, are limited by their partial use of available data and inability to operate without substantial <i>a priori</i> knowledge of the sample’s chemical composition. To overcome these limitations, we introduce a novel approach integrating <span>(alpha )</span>-SAS, a computational method for simulating SANS with CV, with machine learning (ML). This approach enables the accurate prediction of scattering contrast in multicomponent macromolecular complexes, reducing the need for extensive sample preparation and computational resources. <span>(alpha )</span>-SAS, utilizing Monte Carlo methods, generates comprehensive datasets from which structural invariants can be extracted, enhancing our understanding of the macromolecular form factor in dilute systems. The paper demonstrates the effectiveness of this integrated approach through its application to two case studies: Janus particles, an artificial structure with a known SAS intensity and contrast, and a biological system involving RNA polymerase II in complex with Rtt103. These examples illustrate the method’s capability to provide detailed structural insights, showcasing its potential as a powerful tool for advanced SAS analysis in structural biology.</p>","PeriodicalId":790,"journal":{"name":"The European Physical Journal E","volume":"47 6","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141236262","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A microfluidic platform for the synthesis of polymer and polymer-protein-based protocells","authors":"Jessica Ann O’Callaghan,&nbsp;Neha P. Kamat,&nbsp;Kevin B. Vargo,&nbsp;Rajarshi Chattaraj,&nbsp;Daeyeon Lee,&nbsp;Daniel A. Hammer","doi":"10.1140/epje/s10189-024-00428-5","DOIUrl":"10.1140/epje/s10189-024-00428-5","url":null,"abstract":"<p>In this study, we demonstrate the fabrication of polymersomes, protein-blended polymersomes, and polymeric microcapsules using droplet microfluidics. Polymersomes with uniform, single bilayers and controlled diameters are assembled from water-in-oil-in-water double-emulsion droplets. This technique relies on adjusting the interfacial energies of the droplet to completely separate the polymer-stabilized inner core from the oil shell. Protein-blended polymersomes are prepared by dissolving protein in the inner and outer phases of polymer-stabilized droplets. Cell-sized polymeric microcapsules are assembled by size reduction in the inner core through osmosis followed by evaporation of the middle phase. All methods are developed and validated using the same glass-capillary microfluidic apparatus. This integrative approach not only demonstrates the versatility of our setup, but also holds significant promise for standardizing and customizing the production of polymer-based artificial cells.</p>","PeriodicalId":790,"journal":{"name":"The European Physical Journal E","volume":"47 6","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11147907/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141199220","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effects of local incompressibility on the rheology of composite biopolymer networks","authors":"Anupama Gannavarapu,&nbsp;Sadjad Arzash,&nbsp;Iain Muntz,&nbsp;Jordan L. Shivers,&nbsp;Anna-Maria Klianeva,&nbsp;Gijsje H. Koenderink,&nbsp;Fred C. MacKintosh","doi":"10.1140/epje/s10189-024-00422-x","DOIUrl":"10.1140/epje/s10189-024-00422-x","url":null,"abstract":"<p>Fibrous networks such as collagen are common in biological systems. Recent theoretical and experimental efforts have shed light on the mechanics of single component networks. Most real biopolymer networks, however, are composites made of elements with different rigidity. For instance, the extracellular matrix in mammalian tissues consists of stiff collagen fibers in a background matrix of flexible polymers such as hyaluronic acid (HA). The interplay between different biopolymer components in such composite networks remains unclear. In this work, we use 2D coarse-grained models to study the nonlinear strain-stiffening behavior of composites. We introduce a local volume constraint to model the incompressibility of HA. We also perform rheology experiments on composites of collagen with HA. Theoretically and experimentally, we demonstrate that the linear shear modulus of composite networks can be increased by approximately an order of magnitude above the corresponding moduli of the pure components. Our model shows that this synergistic effect can be understood in terms of the local incompressibility of HA, which acts to suppress density fluctuations of the collagen matrix with which it is entangled.</p><p>A snapshot of a composite network on a triangular lattice. Collagen fibers (black) interact with a hyaluronic acid matrix, represented by both dashed lines and gray hexagons that resist volume change. </p>","PeriodicalId":790,"journal":{"name":"The European Physical Journal E","volume":"47 5","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141157349","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Texture identification in liquid crystal-protein droplets using evaporative drying, generalized additive modeling, and K-means Clustering","authors":"Anusuya Pal,&nbsp;Amalesh Gope","doi":"10.1140/epje/s10189-024-00429-4","DOIUrl":"10.1140/epje/s10189-024-00429-4","url":null,"abstract":"<p>Sessile drying droplets manifest distinct morphological patterns, encompassing diverse systems, viz., DNA, proteins, blood, and protein-liquid crystal (LC) complexes. This study employs an integrated methodology that combines drying droplet, image texture analysis (features from First Order Statistics, Gray Level Co-occurrence Matrix, Gray Level Run Length Matrix, Gray Level Size Zone Matrix, and Gray Level Dependence Matrix), and statistical data analysis (Generalized Additive Modeling and K-means clustering). It provides a comprehensive qualitative and quantitative exploration by examining LC-protein droplets at varying initial phosphate buffered concentrations (0x, 0.25x, 0.5x, 0.75x, and 1x) during the drying process under optical microscopy with crossed polarizing configuration. Notably, it unveils distinct LC-protein textures across three drying stages: initial, middle, and final. The Generalized Additive Modeling (GAM) reveals that all the features significantly contribute to differentiating LC-protein droplets. Integrating the K-means clustering method with GAM analysis elucidates how textures evolve through the three drying stages compared to the entire drying process. Notably, the final drying stage stands out with well-defined, non-overlapping clusters, supporting the visual observations of unique LC textures. Furthermore, this paper contributes valuable insights, showcasing the efficacy of drying droplets as a rapid and straightforward tool for characterizing and classifying dynamic LC textures.</p>","PeriodicalId":790,"journal":{"name":"The European Physical Journal E","volume":"47 5","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11126455/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141086434","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Programming tunable active dynamics in a self-propelled robot","authors":"Somnath Paramanick,&nbsp;Arnab Pal,&nbsp;Harsh Soni,&nbsp;Nitin Kumar","doi":"10.1140/epje/s10189-024-00430-x","DOIUrl":"10.1140/epje/s10189-024-00430-x","url":null,"abstract":"<p>We present a scheme for producing tunable active dynamics in a self-propelled robotic device. The robot moves using the differential drive mechanism where two wheels can vary their instantaneous velocities independently. These velocities are calculated by equating robot’s equations of motion in two dimensions with well-established active particle models and encoded into the robot’s microcontroller. We demonstrate that the robot can depict active Brownian, run and tumble, and Brownian dynamics with a wide range of parameters. The resulting motion analyzed using particle tracking shows excellent agreement with the theoretically predicted trajectories. Later, we show that its motion can be switched between different dynamics using light intensity as an external parameter. Intriguingly, we demonstrate that the robot can efficiently navigate through many obstacles by performing stochastic reorientations driven by the gradient in light intensity towards a desired location, namely the target. This work opens an avenue for designing tunable active systems with the potential of revealing the physics of active matter and its application for bio- and nature-inspired robotics.</p>","PeriodicalId":790,"journal":{"name":"The European Physical Journal E","volume":"47 5","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141086409","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Inertial active harmonic particle with memory induced spreading by viscoelastic suspension","authors":"F. Adersh,&nbsp;M. Muhsin,&nbsp;M. Sahoo","doi":"10.1140/epje/s10189-024-00424-9","DOIUrl":"10.1140/epje/s10189-024-00424-9","url":null,"abstract":"<p>We investigate the self-propulsion of an inertial active particle confined in a two-dimensional harmonic trap. The particle is suspended in a non-Newtonian or viscoelastic suspension with a friction kernel that decays exponentially with a time constant characterizing the memory timescale or transient elasticity of the medium. By solving the associated non-Markovian dynamics, we identify two regimes in parameter space distinguishing the oscillatory and non-oscillatory behavior of the particle motion. By simulating the particle trajectories and exactly calculating the steady-state probability distribution functions and mean square displacement; interestingly, we observe that with an increase in the memory time scale, the effective temperature of the environment increases. As a consequence, the particle becomes energetic and spread away from the center, covering larger space inside the confinement. On the other hand, with an increase in the duration of the activity, the particle becomes trapped by the harmonic confinement.</p><p>Schematic diagram of the research problem. Self-propulsion of an inertial active particle in a two dimensional harmonic well subjected to a viscoelastic environment</p>","PeriodicalId":790,"journal":{"name":"The European Physical Journal E","volume":"47 5","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140943376","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Droplet motion driven by humidity gradients during evaporation and condensation","authors":"Hernán Barrio-Zhang,&nbsp;Élfego Ruiz-Gutiérrez,&nbsp;Daniel Orejon,&nbsp;Gary G. Wells,&nbsp;Rodrigo Ledesma-Aguilar","doi":"10.1140/epje/s10189-024-00426-7","DOIUrl":"10.1140/epje/s10189-024-00426-7","url":null,"abstract":"<p>The motion of droplets on solid surfaces in response to an external gradient is a fundamental problem with a broad range of applications, including water harvesting, heat exchange, mixing and printing. Here we study the motion of droplets driven by a humidity gradient, i.e. a variation in concentration of their own vapour in the surrounding gas phase. Using lattice-Boltzmann simulations of a diffuse-interface hydrodynamic model to account for the liquid and gas phases, we demonstrate that the droplet migrates towards the region of higher vapour concentration. This effect holds in situations where the ambient gradient drives either the evaporation or the condensation of the droplet, or both simultaneously. We identify two main mechanisms responsible for the observed motion: a difference in surface wettability, which we measure in terms of the Young stress, and a variation in surface tension, which drives a Marangoni flow. Our results are relevant in advancing our knowledge of the interplay between gas and liquid phases out of thermodynamic equilibrium, as well as for applications involving the control of droplet motion.</p>","PeriodicalId":790,"journal":{"name":"The European Physical Journal E","volume":"47 5","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11089009/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140911227","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structure–property modeling of coumarins and coumarin-related compounds in pharmacotherapy of cancer by employing graphical topological indices","authors":"Sujata T. Timmanaikar,&nbsp;Sakander Hayat,&nbsp;Sunilkumar M. Hosamani,&nbsp;Shabana Banu","doi":"10.1140/epje/s10189-024-00427-6","DOIUrl":"10.1140/epje/s10189-024-00427-6","url":null,"abstract":"<p>Coumarins, a subgroup of colorless and crystalline oxygenated heterocyclic compounds originally discovered in the plant Dipteryx odorata, were the subject of a recent study investigating their quantitative structure–activity relationship (QSAR) in cancer pharmacotherapy. This study utilized graph theoretical molecular descriptors, also known as topological indices, as a numerical representation method for the chemical structures embedded in molecular graphs. These descriptors, derived from molecular graphs, play a pivotal role in quantitative structure–property relationship (QSPR) analysis. In this paper, intercorrelation between the Balban index, connective eccentric index, eccentricity connectivity index, harmonic index, hyper Zagreb index, first path Zagreb index, second path Zagreb index, Randic index, sum connectivity index, graph energy and Laplacian energy is studied on the set of molecular graphs of coumarins. It is found that the pairs of degree-based indices are highly intercorrelated. The use of these molecular descriptors in structure–boiling point modeling was analyzed. Finally, the curve-linear regression between considered molecular descriptors with physicochemical properties of coumarins and coumarin-related compounds is obtained.\u0000</p><p>Some of the coumarin-related anti-cancer compounds considered in this study </p>","PeriodicalId":790,"journal":{"name":"The European Physical Journal E","volume":"47 5","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140908034","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Asymptotic analysis of particle cluster formation in the presence of anchoring sites","authors":"Paul C. Bressloff","doi":"10.1140/epje/s10189-024-00425-8","DOIUrl":"10.1140/epje/s10189-024-00425-8","url":null,"abstract":"&lt;p&gt;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.&lt;/p&gt;&lt;p&gt;2D model of diffusion-based protein cluster formation in the presence of anchoring cites and particle recycling. &lt;b&gt;a&lt;/b&gt; A set of &lt;i&gt;N&lt;/i&gt; anchoring sites at positions &lt;span&gt;({textbf{x}}_j)&lt;/span&gt;, &lt;span&gt;(j=1,ldots ,N)&lt;/span&gt;, in a bounded domain &lt;span&gt;(Omega )&lt;/span&gt;. &lt;b&gt;b&lt;/b&gt; Diffusing particles accumulate at the anchoring sites resulting in the formation of particle aggregates or clusters &lt;span&gt;({{mathcal {U}}}_j)&lt;/span&gt;. &lt;b&gt;c&lt;/b&gt; The c","PeriodicalId":790,"journal":{"name":"The European Physical Journal E","volume":"47 5","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11078859/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140890981","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}