The European Physical Journal E最新文献

{"title":"Convective mixing in porous media: a review of Darcy, pore-scale and Hele-Shaw studies","authors":"Marco De Paoli","doi":"10.1140/epje/s10189-023-00390-8","DOIUrl":"10.1140/epje/s10189-023-00390-8","url":null,"abstract":"<p>Convection-driven porous media flows are common in industrial processes and in nature. The multiscale and multiphase character of these systems and the inherent nonlinear flow dynamics make convection in porous media a complex phenomenon. As a result, a combination of different complementary approaches, namely theory, simulations and experiments, have been deployed to elucidate the intricate physics of convection in porous media. In this work, we review recent findings on mixing in fluid-saturated porous media convection. We focus on the dissolution of a heavy fluid layer into a lighter one, and we consider different flow configurations. We present Darcy, pore-scale and Hele-Shaw investigations inspired by geophysical processes. While the results obtained for Darcy flows match the dissolution behaviour predicted theoretically, Hele-Shaw and pore-scale investigations reveal a different and tangled scenario in which finite-size effects play a key role. Finally, we present recent numerical and experimental developments and we highlight possible future research directions. The findings reviewed in this work will be crucial to make reliable predictions about the long-term behaviour of dissolution and mixing in engineering and natural processes, which are required to tackle societal challenges such as climate change mitigation and energy transition.</p>","PeriodicalId":790,"journal":{"name":"The European Physical Journal E","volume":"46 12","pages":""},"PeriodicalIF":1.8,"publicationDate":"2023-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1140/epje/s10189-023-00390-8.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138687179","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":"Lipids with negative spontaneous curvature decrease the solubility of the cancer drug paclitaxel in liposomes","authors":"Victoria Steffes,&nbsp;Scott MacDonald,&nbsp;John Crowe,&nbsp;Meena Murali,&nbsp;Kai K. Ewert,&nbsp;Youli Li,&nbsp;Cyrus R. Safinya","doi":"10.1140/epje/s10189-023-00388-2","DOIUrl":"10.1140/epje/s10189-023-00388-2","url":null,"abstract":"<div><p>Paclitaxel (PTX) is a hydrophobic small-molecule cancer drug that loads into the membrane (tail) region of lipid carriers such as liposomes and micelles. The development of improved lipid-based carriers of PTX is an important objective to generate chemotherapeutics with fewer side effects. The lipids 1,2-dioleoyl-<i>sn</i>-glycero-3-phosphoethanolamine (DOPE) and glyceryl monooleate (GMO) show propensity for fusion with other lipid membranes, which has led to their use in lipid vectors of nucleic acids. We hypothesized that DOPE and GMO could enhance PTX delivery to cells through a similar membrane fusion mechanism. As an important measure of drug carrier performance, we evaluated PTX solubility in cationic liposomes containing GMO or DOPE. Solubility was determined by time-dependent kinetic phase diagrams generated from direct observations of PTX crystal formation using differential-interference-contrast optical microscopy. Remarkably, PTX was much less soluble in these liposomes than in control cationic liposomes containing univalent cationic lipid 1,2-dioleoyl-3-trimethylammonium-propane (DOTAP) and 1,2-dioleoyl-<i>sn</i>-glycero-3-phosphatidylcholine (DOPC), which are not fusogenic. In particular, PTX was not substantially soluble in GMO-based cationic liposomes. The fusogenicity of DOPE and GMO is related to the negative spontaneous curvature of membranes containing these lipids, which drives formation of nonlamellar self-assembled phases (inverted hexagonal or gyroid cubic). To determine whether PTX solubility is governed by lipid membrane structure or by local intermolecular interactions, we used synchrotron small-angle X-ray scattering. To increase the signal/noise ratio, we used DNA to condense the lipid formulations into lipoplex pellets. The results suggest that local intermolecular interactions are of greater importance and that the negative spontaneous curvature-inducing lipids DOPE and GMO are not suitable components of liposomal carriers for PTX delivery.</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 12","pages":""},"PeriodicalIF":1.8,"publicationDate":"2023-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138686843","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":"Computational approaches to lipid-based nucleic acid delivery systems","authors":"Giovanni Settanni","doi":"10.1140/epje/s10189-023-00385-5","DOIUrl":"10.1140/epje/s10189-023-00385-5","url":null,"abstract":"<div><p>Nucleic acid-based therapies have shown enormous effectiveness as vaccines against the recent COVID19 pandemics and hold great promises in the fight of a broad spectrum of diseases ranging from viral infections to cancer up to genetically transmitted pathologies. Due to their highly degradable polyanionic nature, nucleic acids need to be packed in sophisticate delivery vehicles which compact them up, protect them from early degradation and help delivery them to the right tissue/cells. Lipid-based nanoparticles (LNP) represent, at present, the main solution for nucleic acid delivery. They are made of a mixture of lipids whose key ingredient is an ionizable cationic lipid. Indeed, the interactions between the polyanionic nucleic acids and the ionizable cationic lipids, and their pH-dependent regulation in the life cycle of the nanoparticle, from production to cargo delivery, mostly determine the effectiveness of the therapeutic approach. Notwithstanding the large improvements in the delivery efficiency of LNPs in the last two decades, it is estimated that only a small fraction of the cargo is actually delivered, stimulating further research for the design of more effective LNP formulations. A rationally driven design would profit from the knowledge of the precise molecular structure of these materials, which is however still either missing or characterized by poor spatial resolution. Computational approaches have often been used as a molecular microscope either to enrich the available experimental data and provide a molecular-level picture of the LNPs or even simulate specific processes involving the formation and/or the molecular mechanisms of action of the LNP. Here, I review the recent literature in the field.</p></div>","PeriodicalId":790,"journal":{"name":"The European Physical Journal E","volume":"46 12","pages":""},"PeriodicalIF":1.8,"publicationDate":"2023-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1140/epje/s10189-023-00385-5.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138630010","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":"Mosquito swarms shear harden","authors":"Andy M. Reynolds","doi":"10.1140/epje/s10189-023-00379-3","DOIUrl":"10.1140/epje/s10189-023-00379-3","url":null,"abstract":"<div><p>Recently Cavagna et al. (Sci Rep 13(1): 8745, 2023) documented the swarming behaviors of laboratory-based <i>Anopheles gambiae</i> mosquitoes. Here key observations from this 3D-video tracking study are reproduced by a minimally structured (maximum entropy) stochastic trajectory model. The modelling shows that in contrast with midge swarms which are a form of collective behavior, unperturbed mosquito swarms are more like collections of individuals that independently circulate around a fixed location. The modelling predicts the observed response <i>Anopheles gambiae</i> mosquitoes in wild swarms to varying wind speeds (Butail et al. in J Med Entomol 50(3): 552–559, 2013). It is shown that this response can be attributed to shear hardening. This is because mosquitoes are found to be attracted to the centre of the swarm by an effective force that increases with increasing flight speed. Mosquitoes can therefore better resist the influence of environmental disturbances by increasing their flight speeds. This contrasts with other emergent mechanical-like properties of swarming which arise accidentally without a change in an individual’s behavior. The new results add to the growing realization that perturbations can drive swarms into more robust states.</p></div>","PeriodicalId":790,"journal":{"name":"The European Physical Journal E","volume":"46 12","pages":""},"PeriodicalIF":1.8,"publicationDate":"2023-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1140/epje/s10189-023-00379-3.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138553097","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":"Correction to: Pincus blob elasticity in an intrinsically disordered protein","authors":"Hoang P. Truong,&nbsp;Ian L. Morgan,&nbsp;Gil Koren,&nbsp;Ram Avinery,&nbsp;Roy Beck,&nbsp;Omar A. Saleh","doi":"10.1140/epje/s10189-023-00382-8","DOIUrl":"10.1140/epje/s10189-023-00382-8","url":null,"abstract":"","PeriodicalId":790,"journal":{"name":"The European Physical Journal E","volume":"46 12","pages":""},"PeriodicalIF":1.8,"publicationDate":"2023-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138558106","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":"The Soret coefficient of human low-density lipoprotein in solution: a thermophilic behavior","authors":"Luciene Oliveira Machado,&nbsp;Dennys Reis,&nbsp;Antônio Martins Figueiredo Neto","doi":"10.1140/epje/s10189-023-00377-5","DOIUrl":"10.1140/epje/s10189-023-00377-5","url":null,"abstract":"<div><p>Thermodiffusion, or Soret effect, is the physical phenomenon of matter gradients originated by the migration of chemical species induced by thermal gradients. Thermodiffusion has been widely applied in the study of colloidal suspensions. In this study, we investigate the termodiffusion behavior of low-density lipoprotein (LDL) particles, by the Soret coefficient measurement. It is a new approach to studies of plasma lipoproteins. The experimental work was based on thermal- and Soret-lens effects. These effects were induced by laser irradiation of the samples, at two different time scales, in a Z-scan setup. LDL samples were analyzed under physiological conditions, notedly, ionic strength and pH, and at different temperatures. Temperature dependence of Soret coefficient showed a slight decrease in the absolute value of this coefficient, as a function of temperature increasing. However, its sign does not change at the temperatures investigated (15, 22.5 and 37.5 °C). The results show that LDL particles exhibit thermophilic behavior. The origin of this thermophilic behavior is not yet completely understood. We discuss some aspects that can be related with the Soret effect in LDL samples.</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 12","pages":""},"PeriodicalIF":1.8,"publicationDate":"2023-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138497467","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":"Statics and dynamics of point boojums, line and modified Saturn ring topological defects in nematic confined geometry","authors":"P. V. Dolganov,&nbsp;N. A. Spiridenko,&nbsp;V. K. Dolganov","doi":"10.1140/epje/s10189-023-00387-3","DOIUrl":"10.1140/epje/s10189-023-00387-3","url":null,"abstract":"<div><p>In this paper we study the static structure and the dynamics of topological defects associated with isotropic droplets in nematic environment. Investigations were made in confined geometry of optical cells when the droplet size was of the order of or larger than the gap of the cell. We observed the coexistence of point boojums and Saturn ring or modified Saturn ring defects. We found transformation of the Saturn ring defect to two localized broad defects at increasing the droplet size. At droplet coalescence antipodes of point and localized broad defects were born and the dynamics of their annihilation with existing defects was investigated. We found strong difference in the process of annihilation of point and localized broad defects.</p><h3>Graphical Abstract</h3><div><figure><div><div><picture><source><img></source></picture></div><div><p>Microscope images of isotropic droplets in nematic environment in a planar cell. The director orientation far from the droplets is in horizontal direction. The photographs were taken with crossed vertical and horizontal polarizers (<b>a</b>) and with a single horizontal polarizer (<b>b</b>). The cell thickness is 100 μm. Droplet diameter is less than the cell thickness. 1 and 2 are point boojums, L is the Saturn ring defect</p></div></div></figure></div></div>","PeriodicalId":790,"journal":{"name":"The European Physical Journal E","volume":"46 12","pages":""},"PeriodicalIF":1.8,"publicationDate":"2023-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1140/epje/s10189-023-00387-3.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138497466","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":"Induced phase transformation in ionizable colloidal nanoparticles","authors":"Leticia López-Flores,&nbsp;Monica Olvera de la Cruz","doi":"10.1140/epje/s10189-023-00386-4","DOIUrl":"10.1140/epje/s10189-023-00386-4","url":null,"abstract":"<p>Acid–base equilibria directly influence the functionality and behavior of particles in a system. Due to the ionizing effects of acid–base functional groups, particles will undergo charge exchange. The degree of ionization and their intermolecular and electrostatic interactions are controlled by varying the pH and salt concentration of the solution in a system. Although the pH can be tuned in experiments, it is hard to model this effect using simulations or theoretical approaches. This is due to the difficulty in treating charge regulation and capturing the cooperative effects in a colloidal suspension with Coulombic interaction. In this work, we analyze a suspension of ionizable colloidal particles via molecular dynamics (MD) simulations, along with Monte Carlo simulations for charge regulation (MC-CR) and derive a phase diagram of the system as a function of pH. It is observed that as pH increases, particles functionalized with acid groups change their arrangement from face-centered cubic (FCC) packing to a disordered state. We attribute these transitions to an increase in the degree of charge polydispersity arising from an increase in pH. Our work shows that charge regulation leads to amorphous solids in colloids when the mean nanoparticle charge is sufficiently high.</p>","PeriodicalId":790,"journal":{"name":"The European Physical Journal E","volume":"46 12","pages":""},"PeriodicalIF":1.8,"publicationDate":"2023-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1140/epje/s10189-023-00386-4.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138497464","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":"Lipid vesicle pools studied by passive X-ray microrheology","authors":"Titus Czajka,&nbsp;Charlotte Neuhaus,&nbsp;Jette Alfken,&nbsp;Moritz Stammer,&nbsp;Yuriy Chushkin,&nbsp;Diego Pontoni,&nbsp;Christian Hoffmann,&nbsp;Dragomir Milovanovic,&nbsp;Tim Salditt","doi":"10.1140/epje/s10189-023-00375-7","DOIUrl":"10.1140/epje/s10189-023-00375-7","url":null,"abstract":"<p>Vesicle pools can form by attractive interaction in a solution, mediated by proteins or divalent ions such as calcium. The pools, which are alternatively also denoted as vesicle clusters, form by liquid-liquid phase separation (LLPS) from an initially homogeneous solution. Due to the short range liquid-like order of vesicles in the pool or cluster, the vesicle-rich phase can also be regarded as a condensate, and one would like to better understand not only the structure of these systems, but also their dynamics. The diffusion of vesicles, in particular, is expected to change when vesicles are arrested in a pool. Here we investigate whether passive microrheology based on X-ray photon correlation spectroscopy (XPCS) is a suitable tool to study model systems of artificial lipid vesicles exhibiting LLPS, and more generally also other heterogeneous biomolecular fluids. We show that by adding highly scattering tracer particles to the solution, valuable information on the single vesicle as well as collective dynamics can be inferred. While the correlation functions reveal freely diffusing tracer particles in solutions at low CaCl<span>(_{2})</span> concentrations, the relaxation rate <span>(Gamma (q))</span> shows a nonlinear dependence on <span>(q^2)</span> at a higher concentration of around 8 mM CaCl<span>(_{2})</span>, characterised by two linear regimes with a broad cross-over. We explain this finding based on arrested diffusion in percolating vesicle clusters.</p>","PeriodicalId":790,"journal":{"name":"The European Physical Journal E","volume":"46 12","pages":""},"PeriodicalIF":1.8,"publicationDate":"2023-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1140/epje/s10189-023-00375-7.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138497465","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":"Connection number topological aspect for backbone DNA networks","authors":"Ali Ahmad,&nbsp;Ali N. A. Koam,&nbsp;Ibtisam Masmali,&nbsp;Muhammad Azeem,&nbsp;Haleemah Ghazwani","doi":"10.1140/epje/s10189-023-00381-9","DOIUrl":"10.1140/epje/s10189-023-00381-9","url":null,"abstract":"<p>The present study investigates the complex topological characteristics of DNA networks, with a specific emphasis on the innovative metric known as Connection Number (CN) as a key factor in determining network structure. The Connection Number, represented as <i>CN</i>(<i>v</i>) for a vertex <i>v</i>, measures the count of unique paths that link <i>v</i> to every other vertex in the network. By employing rigorous mathematical modeling and analysis techniques, we are able to reveal the profound implications of CN (complex networks) in characterizing the structural robustness and dynamics of information flow within DNA networks. The study of how the theory of graphs and chemicals interact is known as chemical graph theory. This paper, computing the hyper Zagreb connection index, augmented connection index, inverse sum connection index, harmonic connection index, symmetric division connection index, geometric arithmetic connection index, and atom bond connectivity connection index, of two significant types of backbone DNA and Barycentric subdivision of backbone DNA networks. Direct method computation is used to produce these Connection-based topological descriptors.</p>","PeriodicalId":790,"journal":{"name":"The European Physical Journal E","volume":"46 12","pages":""},"PeriodicalIF":1.8,"publicationDate":"2023-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1140/epje/s10189-023-00381-9.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138486369","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}