The European Physical Journal E最新文献

{"title":"Local electroneutrality breakdown for electrolytes within varying-section nanopores","authors":"Paolo Malgaretti,&nbsp;Ignacio Pagonabarraga,&nbsp;Jens Harting","doi":"10.1140/epje/s10189-024-00408-9","DOIUrl":"10.1140/epje/s10189-024-00408-9","url":null,"abstract":"<p>We determine the local charge dynamics of a <span>(z-z)</span> electrolyte embedded in a varying-section channel. By means of an expansion based on the length scale separation between the axial and transverse direction of the channel, we derive closed formulas for the local excess charge for both, dielectric and conducting walls, in 2<i>D</i> (planar geometry) as well as in 3<i>D</i> (cylindrical geometry). Our results show that, even at equilibrium, the local charge electroneutrality is broken whenever the section of the channel is not homogeneous for both dielectric and conducting walls as well as for 2<i>D</i> and 3<i>D</i> channels. Interestingly, even within our expansion, the local excess charge in the fluid can be comparable to the net charge on the walls. We critically discuss the onset of such local electroneutrality breakdown in particular with respect to the correction that it induces on the effective free energy profile experienced by tracer ions.\u0000</p>","PeriodicalId":790,"journal":{"name":"The European Physical Journal E","volume":"47 2","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11222217/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139899175","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":"From isolated polyelectrolytes to star-like assemblies: the role of sequence heterogeneity on the statistical structure of the intrinsically disordered neurofilament-low tail domain","authors":"Mathar Kravikass,&nbsp;Gil Koren,&nbsp;Omar A. Saleh,&nbsp;Roy Beck","doi":"10.1140/epje/s10189-024-00409-8","DOIUrl":"10.1140/epje/s10189-024-00409-8","url":null,"abstract":"<p>Intrinsically disordered proteins (IDPs) are a subset of proteins that lack stable secondary structure. Given their polymeric nature, previous mean-field approximations have been used to describe the statistical structure of IDPs. However, the amino-acid sequence heterogeneity and complex intermolecular interaction network have significantly impeded the ability to get proper approximations. One such case is the intrinsically disordered tail domain of neurofilament low (NFLt), which comprises a 50 residue-long uncharged domain followed by a 96 residue-long negatively charged domain. Here, we measure two NFLt variants to identify the impact of the NFLt two main subdomains on its complex interactions and statistical structure. Using synchrotron small-angle x-ray scattering, we find that the uncharged domain of the NFLt induces attractive interactions that cause it to self-assemble into star-like polymer brushes. On the other hand, when the uncharged domain is truncated, the remaining charged N-terminal domains remain isolated in solution with typical polyelectrolyte characteristics. We further discuss how competing long- and short-ranged interactions within the polymer brushes dominate their ensemble structure and, in turn, their implications on previously observed phenomena in NFL native and diseased states.</p><p>Visual schematic of the SAXS measurement results of the Neurofilament-low tail domain IDP (NFLt). NFLts assemble into star-like brushes through their hydrophobic N-terminal domains (marked in blue). In increasing salinity, brush height (h) is initially increased following a decrease while gaining additional tails to their assembly. Isolating the charged sub-domain of the NFLt (marked in red) results in isolated polyelectrolytes</p>","PeriodicalId":790,"journal":{"name":"The European Physical Journal E","volume":"47 2","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10869404/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139734105","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":"Dynamic structure factor of undulating vesicles: finite-size and spherical geometry effects with application to neutron spin echo experiments","authors":"Rony Granek,&nbsp;Ingo Hoffmann,&nbsp;Elizabeth G. Kelley,&nbsp;Michihiro Nagao,&nbsp;Petia M. Vlahovska,&nbsp;Anton Zilman","doi":"10.1140/epje/s10189-023-00400-9","DOIUrl":"10.1140/epje/s10189-023-00400-9","url":null,"abstract":"<p>We consider the dynamic structure factor (DSF) of quasi-spherical vesicles and present a generalization of an expression that was originally formulated by Zilman and Granek (ZG) for scattering from isotropically oriented quasi-flat membrane plaquettes. The expression is obtained in the form of a multi-dimensional integral over the undulating membrane surface. The new expression reduces to the original stretched exponential form in the limit of sufficiently large vesicles, i.e., in the micron range or larger. For much smaller unilamellar vesicles, deviations from the asymptotic, stretched exponential equation are noticeable even if one assumes that the Seifert-Langer leaflet density mode is completely relaxed and membrane viscosity is neglected. To avoid the need for an exhaustive numerical integration while fitting to neutron spin echo (NSE) data, we provide a useful approximation for polydisperse systems that tests well against the numerical integration of the complete expression. To validate the new expression, we performed NSE experiments on variable-size vesicles made of a POPC/POPS lipid mixture and demonstrate an advantage over the original stretched exponential form or other manipulations of the original ZG expression that have been deployed over the years to fit the NSE data. In particular, values of the membrane bending rigidity extracted from the NSE data using the new approximations were insensitive to the vesicle radii and scattering wavenumber and compared very well with expected values of the effective bending modulus (<span>(tilde{kappa })</span>) calculated from results in the literature. Moreover, the <i>generalized scattering theory</i> presented here for an undulating quasi-spherical shell can be easily extended to other models for the membrane undulation dynamics beyond the Helfrich Hamiltonian and thereby provides the foundation for the study of the nanoscale dynamics in more complex and biologically relevant model membrane systems.</p>","PeriodicalId":790,"journal":{"name":"The European Physical Journal E","volume":"47 2","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139734104","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":"Collective motion of chiral particles in complex noise environments","authors":"Jun Huang,&nbsp;Zhi-Gang Shao","doi":"10.1140/epje/s10189-023-00403-6","DOIUrl":"10.1140/epje/s10189-023-00403-6","url":null,"abstract":"<p>Collective motion of chiral particles in complex noise environments is investigated based on the Vicsek model. In the model, we added chirality, along with complex noise, affecting particles clustering motion. Particles can only avoid noise interference in a specific channel, and this consideration is more realistic due to the complexity of the environment. Via simulations, we find that the channel proportion, <i>p</i>, critically influences chiral particle synchronization. Specifically, we observe a disorder-order transition at critical <span>(p_textrm{c})</span>, only when <span>(p&gt;p_textrm{c})</span>, the system can achieve global synchronization. Combined with our definition of spatial distribution parameter and observation of the model, the reason is that particles begin to escape from the noise region under the influence of complex noise. In addition, the value of <span>(p_textrm{c})</span> increases linearly with velocity, while it decreases monotonically with the increase in chirality and interaction radius. Interestingly, an appropriate noise amplitude minimizes <span>(p_textrm{c})</span>. Our findings may inspire novel strategies to manipulate self-propelled particles of distinct chirality to achieve desired spatial migration and global synchronization.\u0000</p>","PeriodicalId":790,"journal":{"name":"The European Physical Journal E","volume":"47 2","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139690937","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":"Macroscopic dynamics of the ferroelectric smectic (A_F) phase with (C_{infty v} ) symmetry","authors":"Helmut R. Brand,&nbsp;Harald Pleiner","doi":"10.1140/epje/s10189-024-00406-x","DOIUrl":"10.1140/epje/s10189-024-00406-x","url":null,"abstract":"<p>We present the macroscopic dynamics of ferroelectric smectic <i>A</i>, smectic <span>(A_F)</span>, liquid crystals reported recently experimentally by three groups. In this fluid and orthogonal smectic phase, the macroscopic polarization, <span>({textbf{P}})</span>, is parallel to the layer normal thus giving rise to <span>(C_{infty v})</span> overall symmetry for this phase in the spatially homogeneous limit. A combination of linear irreversible thermodynamics and symmetry arguments is used to derive the resulting dynamic equations applicable at sufficiently low frequencies and sufficiently long wavelengths. Compared to non-polar smectic <i>A</i> phases, we find a static cross-coupling between compression of the layering and bending of the layers, which does not lead to elastic forces, but to elastic stresses. In addition, it turns out that a reversible cross-coupling between flow and the magnitude of the polarization modifies the velocities of both, first and second sound. At the same time, the relaxation of the polarization gives rise to dissipative effects for second sound at the same order of the wavevector as for the sound velocity. We also analyze reversible cross-coupling terms between elongational flow and electric fields as well as temperature and concentration gradients, which lend themselves to experimental detection. Apparently this type of terms has never been considered before for smectic phases. The question how the linear <span>({{textbf{P}} cdot textbf{E}})</span> coupling in the energy alters the macroscopic response behavior when compared to usual non-polar smectic <i>A</i> phases is also addressed.</p>","PeriodicalId":790,"journal":{"name":"The European Physical Journal E","volume":"47 2","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1140/epje/s10189-024-00406-x.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139666896","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":"Optimal escapes in active matter","authors":"Luca Angelani","doi":"10.1140/epje/s10189-023-00402-7","DOIUrl":"10.1140/epje/s10189-023-00402-7","url":null,"abstract":"<p>The out-of-equilibrium character of active particles, responsible for accumulation at boundaries in confining domains, determines not-trivial effects when considering escape processes. Non-monotonous behavior of exit times with respect to tumbling rate (inverse of mean persistent time) appears, as a consequence of the competing processes of exploring the bulk and accumulate at boundaries. By using both 1D analytical results and 2D numerical simulations of run-and-tumble particles with different behaviours at boundaries, we scrutinize this very general phenomenon of active matter, evidencing the role of accumulation at walls for the existence of optimal tumbling rates for fast escapes.</p>","PeriodicalId":790,"journal":{"name":"The European Physical Journal E","volume":"47 1","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11222286/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139569456","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":"Vesicle condensation induced by synapsin: condensate size, geometry, and vesicle shape deformations","authors":"Jette Alfken,&nbsp;Charlotte Neuhaus,&nbsp;András Major,&nbsp;Alyona Taskina,&nbsp;Christian Hoffmann,&nbsp;Marcelo Ganzella,&nbsp;Arsen Petrovic,&nbsp;David Zwicker,&nbsp;Rubén Fernández-Busnadiego,&nbsp;Reinhard Jahn,&nbsp;Dragomir Milovanovic,&nbsp;Tim Salditt","doi":"10.1140/epje/s10189-023-00404-5","DOIUrl":"10.1140/epje/s10189-023-00404-5","url":null,"abstract":"<p>We study the formation of vesicle condensates induced by the protein synapsin, as a cell-free model system mimicking vesicle pool formation in the synapse. The system can be considered as an example of liquid–liquid phase separation (LLPS) in biomolecular fluids, where one phase is a complex fluid itself consisting of vesicles and a protein network. We address the pertinent question why the LLPS is self-limiting and stops at a certain size, i.e., why macroscopic phase separation is prevented. Using fluorescence light microscopy, we observe different morphologies of the condensates (aggregates) depending on the protein-to-lipid ratio. Cryogenic electron microscopy then allows us to resolve individual vesicle positions and shapes in a condensate and notably the size and geometry of adhesion zones between vesicles. We hypothesize that the membrane tension induced by already formed adhesion zones then in turn limits the capability of vesicles to bind additional vesicles, resulting in a finite condensate size. In a simple numerical toy model we show that this effect can be accounted for by redistribution of effective binding particles on the vesicle surface, accounting for the synapsin-induced adhesion zone.</p>","PeriodicalId":790,"journal":{"name":"The European Physical Journal E","volume":"47 1","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-01-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11233366/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139545048","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":"Detachment forces during parallel-plate gap separation mediated by a simple yield-stress fluid","authors":"Vítor Hugo de Oliveira Pereira,&nbsp;Wilson Barros Jr.","doi":"10.1140/epje/s10189-023-00397-1","DOIUrl":"10.1140/epje/s10189-023-00397-1","url":null,"abstract":"<p>In this work we have monitored the multiple stages of the normal traction force response of a yield-stress fluid confined between two circular parallel plates that are separated at constant velocity. At narrow initial gaps, the air–fluid interface suffers from the Saffman–Taylor instability, confirmed by visual inspection of fingering patterns imprinted on the fluid. At larger initial gaps, the fluid preserves the initially imposed circular symmetry of the confining plates, indicating the absence of instability. Due to the system characteristics and experimental environment, the multiple traction force contributions occurred in cascade, permitting us to isolate the adhesion responses associated with viscosity, capillarity, and yield stress. Employing a standard Herschel–Bulkley model, we assessed the scaling of the traction force in multiple regimes—specifically, evaluating the dependencies of the fingering to yield-stress transitions.</p>","PeriodicalId":790,"journal":{"name":"The European Physical Journal E","volume":"47 1","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139519198","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":"Scaling regimes for wormlike chains confined to cylindrical surfaces under tension","authors":"Greg Morrison,&nbsp;D. Thirumalai","doi":"10.1140/epje/s10189-023-00384-6","DOIUrl":"10.1140/epje/s10189-023-00384-6","url":null,"abstract":"<div><p>We compute the free energy of confinement <span>(mathcal{{F}})</span> for a wormlike chain (WLC), with persistence length <span>(l_p)</span>, that is confined to the surface of a cylinder of radius <i>R</i> under an external tension <i>f</i> using a mean field variational approach. For long chains, we analytically determine the behavior of the chain in a variety of regimes, which are demarcated by the interplay of <span>(l_p)</span>, the Odijk deflection length (<span>(l_d=(R^2l_p)^{1/3})</span>), and the Pincus length (<span>(l_f = {k_BT}/{f})</span>, with <span>(k_BT)</span> being the thermal energy). The theory accurately reproduces the Odijk scaling for strongly confined chains at <span>(f=0)</span>, with <span>(mathcal{{F}}sim Ll_p^{-1/3}R^{-2/3})</span>. For moderate values of <i>f</i>, the Odijk scaling is discernible only when <span>({l_p}gg R)</span> for strongly confined chains. Confinement does not significantly alter the scaling of the mean extension for sufficiently high tension. The theory is used to estimate unwrapping forces for DNA from nucleosomes.</p></div>","PeriodicalId":790,"journal":{"name":"The European Physical Journal E","volume":"47 1","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139511408","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":"Correction: Convective mixing in porous media: a review of Darcy, pore-scale and Hele-Shaw studies","authors":"Marco De Paoli","doi":"10.1140/epje/s10189-023-00401-8","DOIUrl":"10.1140/epje/s10189-023-00401-8","url":null,"abstract":"","PeriodicalId":790,"journal":{"name":"The European Physical Journal E","volume":"47 1","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1140/epje/s10189-023-00401-8.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139416059","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}