The European Physical Journal E最新文献_第10页

MFG-E8: a model of multiple binding modes associated with ps-binding proteins MFG-E8:与ps结合蛋白相关的多种结合模式的模型。

IF 1.8 4区物理与天体物理

The European Physical Journal E Pub Date : 2023-11-24 DOI: 10.1140/epje/s10189-023-00372-w

Tiffany Suwatthee, Daniel Kerr, Sofiya Maltseva, Charles L. Dulberger, Luke Hyeondo Hwang, Benjamin R. Slaw, Wei Bu, Binhua Lin, Erin J. Adams, Ka Yee C. Lee

{"title":"MFG-E8: a model of multiple binding modes associated with ps-binding proteins","authors":"Tiffany Suwatthee, Daniel Kerr, Sofiya Maltseva, Charles L. Dulberger, Luke Hyeondo Hwang, Benjamin R. Slaw, Wei Bu, Binhua Lin, Erin J. Adams, Ka Yee C. Lee","doi":"10.1140/epje/s10189-023-00372-w","DOIUrl":"10.1140/epje/s10189-023-00372-w","url":null,"abstract":"<div><p>Membrane-binding proteins often associate with lipid membranes through a singular binding interface which is generally modeled as a two-state system: bound or unbound. However, even a single interface can engage with more than one mode of binding since a variety of interactions can contribute to the binding event. Unfortunately, the ability to clearly delineate the different binding modes of a singular binding interface has been elusive with existing models. Here, we present a study on milk fat globule EGF factor 8 (MFG-E8), which belongs to a class of proteins that identifies and binds phosphatidylserine (PS). These proteins detect membrane dysregulation implicated in exposed PS in apoptosis and malignant cells. In order to elucidate the factors affecting the binding of MFG-E8, we used a model system consisting of a series of lipid vesicles with varying PS mole fraction to identify the sensitivity of MFG-E8’s binding affinity to changes in electrostatics using a tryptophan fluorescence spectral shift assay. Using a newly developed model, we experimentally identified three binding modes, each associated with a different number of PS lipids, with its cooperativity for binding being enhanced by the availability of negatively charged lipids. X-ray reflectivity experiments additionally suggest that MFG-E8’s binding modes are influenced by membrane packing. The protocols established for elucidating MFG-E8’s interaction with lipid membranes under different membrane conditions can be applied to the study of other membrane-binding proteins that target specific membrane attributes, such as fluidity and electrostatics, and help elucidate these membrane targeting mechanisms and their subsequent binding events.</p><h3>Graphical abstract</h3><div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></div>","PeriodicalId":790,"journal":{"name":"The European Physical Journal E","volume":"46 11","pages":""},"PeriodicalIF":1.8,"publicationDate":"2023-11-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138298060","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}

引用次数: 0

Drying behaviour of nanofluid sessile droplets on self-affine vis-à-vis corrugated nanorough surfaces 纳米流体固结液滴在自仿射可见-à-vis波纹纳米表面上的干燥行为。

IF 1.8 4区物理与天体物理

The European Physical Journal E Pub Date : 2023-11-24 DOI: 10.1140/epje/s10189-023-00374-8

Deeksha Rani, Subhendu Sarkar

{"title":"Drying behaviour of nanofluid sessile droplets on self-affine vis-à-vis corrugated nanorough surfaces","authors":"Deeksha Rani, Subhendu Sarkar","doi":"10.1140/epje/s10189-023-00374-8","DOIUrl":"10.1140/epje/s10189-023-00374-8","url":null,"abstract":"<p>In recent years, evaporative self-assembly of sessile droplets has gained considerable attention owing to its wide applicability in many areas. While the phenomenon is well studied for smooth and isotropically rough (self-affine) surfaces, investigations comparing the outcomes on self-affine vis-à-vis corrugated surfaces remains to be done. In this experimental work, we compare the wetting and evaporation dynamics of nano-colloidal microlitre droplets on self-affine and corrugated nanorough surfaces having identical roughnesses and interface properties. The coupled influence of particle size, concentration, and surface structuring has been explored. Differences in wettability and evaporation dynamics are observed, which are explained via the interaction between wetting fluid and anisotropic surface roughness. Our findings exhibit different temporal behaviour of contact radius and angle in the evaporation process of the droplets. Further, the corrugated surface exhibits anisotropic wettability with a monotonic change in droplet shape as evaporation proceeds, finally giving rise to irregular dried patterns. The scaled rim width and crack spacing of the particulate deposits are examined. Our results can inspire fabrication of surfaces that can facilitate direction-dependent droplet motion for specific applications.</p>","PeriodicalId":790,"journal":{"name":"The European Physical Journal E","volume":"46 11","pages":""},"PeriodicalIF":1.8,"publicationDate":"2023-11-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138298059","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}

引用次数: 0

Foam drainage equation in fractal dimensions: breaking and instabilities 分形维数的泡沫排水方程:破碎与不稳定。

IF 1.8 4区物理与天体物理

The European Physical Journal E Pub Date : 2023-11-13 DOI: 10.1140/epje/s10189-023-00368-6

Rami Ahmad El-Nabulsi, Waranont Anukool

引用次数: 2

Lift at low Reynolds number 低雷诺数时的升力。

IF 1.8 4区物理与天体物理

The European Physical Journal E Pub Date : 2023-11-13 DOI: 10.1140/epje/s10189-023-00369-5

Lionel Bureau, Gwennou Coupier, Thomas Salez

引用次数: 1

D11 and small angle neutron scattering: a paradigm of ILL D11和小角中子散射:一种惯性散射模式。

IF 1.8 4区物理与天体物理

The European Physical Journal E Pub Date : 2023-11-13 DOI: 10.1140/epje/s10189-023-00362-y

John White

引用次数: 0

Effects of cytoskeletal network mesh size on cargo transport 细胞骨架网络网格大小对货物运输的影响。

IF 1.8 4区物理与天体物理

The European Physical Journal E Pub Date : 2023-11-10 DOI: 10.1140/epje/s10189-023-00358-8

Nimisha Krishnan, Niranjan Sarpangala, Maria Gamez, Ajay Gopinathan, Jennifer L. Ross

引用次数: 0

Detecting a periodic signal by a population of spiking neurons in the weakly nonlinear response regime 在弱非线性反应状态下，由一群尖峰神经元检测周期性信号。

IF 1.8 4区物理与天体物理

The European Physical Journal E Pub Date : 2023-11-06 DOI: 10.1140/epje/s10189-023-00371-x

Maria Schlungbaum, Benjamin Lindner

{"title":"Detecting a periodic signal by a population of spiking neurons in the weakly nonlinear response regime","authors":"Maria Schlungbaum, Benjamin Lindner","doi":"10.1140/epje/s10189-023-00371-x","DOIUrl":"10.1140/epje/s10189-023-00371-x","url":null,"abstract":"<p>Motivated by experimental observations, we investigate a variant of the cocktail party problem: the detection of a weak periodic stimulus in the presence of fluctuations and another periodic stimulus which is stronger than the periodic signal to be detected. Specifically, we study the response of a population of stochastic leaky integrate-and-fire (LIF) neurons to two periodic signals and focus in particular on the question, whether the presence of one of the stimuli can be detected from the population activity. As a detection criterion, we use a simple threshold-crossing of the population activity over a certain time window. We show by means of the receiver operating characteristics (ROC) that the detectability depends only weakly on the time window of observation but rather strongly on the stimulus amplitude. Counterintuitively, the detection of the weak periodic signal can be facilitated by the presence of a strong periodic input current depending on the frequencies of the two signals and on the dynamical regime in which the neurons operate. Beside numerical simulations of the model, we present an analytical approximation for the ROC curve that is based on the weakly nonlinear response theory for a stochastic LIF neuron.</p>","PeriodicalId":790,"journal":{"name":"The European Physical Journal E","volume":"46 11","pages":""},"PeriodicalIF":1.8,"publicationDate":"2023-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71476818","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}

引用次数: 0

Anomalous diffusion of lithium-anion clusters in ionic liquids 锂阴离子团簇在离子液体中的异常扩散。

IF 1.8 4区物理与天体物理

The European Physical Journal E Pub Date : 2023-11-02 DOI: 10.1140/epje/s10189-023-00365-9

YeongKyu Lee, JunBeom Cho, Junseong Kim, Won Bo Lee, YongSeok Jho

{"title":"Anomalous diffusion of lithium-anion clusters in ionic liquids","authors":"YeongKyu Lee, JunBeom Cho, Junseong Kim, Won Bo Lee, YongSeok Jho","doi":"10.1140/epje/s10189-023-00365-9","DOIUrl":"10.1140/epje/s10189-023-00365-9","url":null,"abstract":"<p>Lithium-ion transport is significantly retarded in ionic liquids (ILs). In this work, we performed extensive molecular dynamics simulations to mimic the kinetics of lithium ions in ILs using [<i>N</i>-methyl-<i>N</i>-propylpyrrolidium (pyr<span>(_{13})</span>)][bis(trifluoromethanesulfonyl)imide (Ntf<span>(_{2})</span>)] with added LiNtf<span>(_{2})</span> salt. And we analyzed their transport, developing a two-state model and comparing it to the machine learning-identified states. The transport of lithium ions involves local shell exchanges of the Ntf<span>(_{2})</span> in the medium. We calculated train size distributions over various time scales. The train size distribution decays as a power law, representing non-Poissonian bursty shell exchanges. We analyzed the non-Poissonian processes of lithium ions transport as a two-state (soft and hard) model. We analytically calculated the transition probability of the two-state model, which fits well to the lifetime autocorrelation functions of LiNtf<span>(_{2})</span> shells. To identify two states, we introduced the graph neutral network incorporating local molecular structure. The results reveal that the shell-soft state mainly contributes to the transport of the lithium ions, and their contribution is more important in low temperatures. Hence, it is the key for enhanced lithium ion transport to increase the fraction of the shell-soft state.</p>","PeriodicalId":790,"journal":{"name":"The European Physical Journal E","volume":"46 11","pages":""},"PeriodicalIF":1.8,"publicationDate":"2023-11-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71419489","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}

引用次数: 0

Effect of ionic strength on the assembly of simian vacuolating virus capsid protein around poly(styrene sulfonate) 离子强度对猿猴空泡化病毒衣壳蛋白在聚（苯乙烯磺酸盐）周围组装的影响。

IF 1.8 4区物理与天体物理

The European Physical Journal E Pub Date : 2023-11-02 DOI: 10.1140/epje/s10189-023-00363-x

Roi Asor, Surendra W. Singaram, Yael Levi-Kalisman, Michael F. Hagan, Uri Raviv

{"title":"Effect of ionic strength on the assembly of simian vacuolating virus capsid protein around poly(styrene sulfonate)","authors":"Roi Asor, Surendra W. Singaram, Yael Levi-Kalisman, Michael F. Hagan, Uri Raviv","doi":"10.1140/epje/s10189-023-00363-x","DOIUrl":"10.1140/epje/s10189-023-00363-x","url":null,"abstract":"<p>Virus-like particles (VLPs) are noninfectious nanocapsules that can be used for drug delivery or vaccine applications. VLPs can be assembled from virus capsid proteins around a condensing agent, such as RNA, DNA, or a charged polymer. Electrostatic interactions play an important role in the assembly reaction. VLPs assemble from many copies of capsid protein, with a combinatorial number of intermediates. Hence, the mechanism of the reaction is poorly understood. In this paper, we combined solution small-angle X-ray scattering (SAXS), cryo-transmission electron microscopy (TEM), and computational modeling to determine the effect of ionic strength on the assembly of Simian Vacuolating Virus 40 (SV40)-like particles. We mixed poly(styrene sulfonate) with SV40 capsid protein pentamers at different ionic strengths. We then characterized the assembly product by SAXS and cryo-TEM. To analyze the data, we performed Langevin dynamics simulations using a coarse-grained model that revealed incomplete, asymmetric VLP structures consistent with the experimental data. We found that close to physiological ionic strength, <span>(T=1)</span> VLPs coexisted with VP1 pentamers. At lower or higher ionic strengths, incomplete particles coexisted with pentamers and <span>(T=1)</span> particles. Including the simulated structures was essential to explain the SAXS data in a manner that is consistent with the cryo-TEM images.</p>","PeriodicalId":790,"journal":{"name":"The European Physical Journal E","volume":"46 11","pages":""},"PeriodicalIF":1.8,"publicationDate":"2023-11-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71419490","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}

引用次数: 2

Permanent shear localization in dense disordered materials due to microscopic inertia 由于微观惯性，致密无序材料中的永久剪切局部化。

IF 1.8 4区物理与天体物理

The European Physical Journal E Pub Date : 2023-11-02 DOI: 10.1140/epje/s10189-023-00367-7

Vishwas V. Vasisht, Magali Le Goff, Kirsten Martens, Jean-Louis Barrat

引用次数: 3