The European Physical Journal E最新文献

{"title":"Non-specific cargo–filament interactions slow down motor-driven transport","authors":"Joelle A. Labastide,&nbsp;David A. Quint,&nbsp;Reilly K. Cullen,&nbsp;Bryan Maelfeyt,&nbsp;Jennifer L. Ross,&nbsp;Ajay Gopinathan","doi":"10.1140/epje/s10189-023-00394-4","DOIUrl":"10.1140/epje/s10189-023-00394-4","url":null,"abstract":"<div><p>Active, motor-based cargo transport is important for many cellular functions and cellular development. However, the cell interior is complex and crowded and could have many weak, non-specific interactions with the cargo being transported. To understand how cargo-environment interactions will affect single motor cargo transport and multi-motor cargo transport, we use an artificial quantum dot cargo bound with few (~ 1) to many (~ 5–10) motors allowed to move in a dense microtubule network. We find that kinesin-driven quantum dot cargo is slower than single kinesin-1 motors. Excitingly, there is some recovery of the speed when multiple motors are attached to the cargo. To determine the possible mechanisms of both the slow down and recovery of speed, we have developed a computational model that explicitly incorporates multi-motor cargos interacting non-specifically with nearby microtubules, including, and predominantly with the microtubule on which the cargo is being transported. Our model has recovered the experimentally measured average cargo speed distribution for cargo-motor configurations with few and many motors, implying that numerous, weak, non-specific interactions can slow down cargo transport and multiple motors can reduce these interactions thereby increasing velocity.</p><h3>Graphic abstract</h3>\u0000<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":"2023-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138823997","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":"Instanton-based importance sampling for extreme fluctuations in a shell model for turbulent energy cascade","authors":"Guilherme Tegoni Goedert,&nbsp;Luca Biferale","doi":"10.1140/epje/s10189-023-00392-6","DOIUrl":"10.1140/epje/s10189-023-00392-6","url":null,"abstract":"<p>Many out-of-equilibrium flows present non-Gaussian fluctuations in physically relevant observables, such as energy dissipation rate. This implies extreme fluctuations that, although rarely observed, have a significant phenomenology. Recently, path integral methods for importance sampling have emerged from formalism initially devised for quantum field theory and are being successfully applied to the Burgers equation and other fluid models. We proposed exploring the domain of application of these methods using a shell model, a dynamical system for turbulent energy cascade which can be numerically sampled for extreme events in an efficient manner and presents many interesting properties. We start from a validation of the instanton-based importance sampling methodology in the heat equation limit. We explored the limits of the method as nonlinearity grows stronger, finding good qualitative results for small values of the leading nonlinear coefficient. A worst agreement between numerical simulations of the whole systems and instanton results for estimation of the distribution’s flatness is observed when increasing the nonlinear intensities.\u0000</p>","PeriodicalId":790,"journal":{"name":"The European Physical Journal E","volume":"46 12","pages":""},"PeriodicalIF":1.8,"publicationDate":"2023-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138827608","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":"Electrostatics and hydrophobicity in the dynamics of intrinsically disordered proteins","authors":"Renee Vancraenenbroeck,&nbsp;Hagen Hofmann","doi":"10.1140/epje/s10189-023-00383-7","DOIUrl":"10.1140/epje/s10189-023-00383-7","url":null,"abstract":"<div><p>Internal friction is a major contribution to the dynamics of intrinsically disordered proteins (IDPs). Yet, the molecular origin of internal friction has so far been elusive. Here, we investigate whether attractive electrostatic interactions in IDPs modulate internal friction differently than the hydrophobic effect. To this end, we used nanosecond fluorescence correlation spectroscopy (nsFCS) and single-molecule Förster resonance energy transfer (FRET) to quantify the conformation and dynamics of the disordered DNA-binding domains Myc, Max and Mad at different salt concentrations. We find that internal friction effects are stronger when the chain is compacted by electrostatic attractions compared to the hydrophobic effect. Although the effect is moderate, the results show that the heteropolymeric nature of IDPs is reflected in their dynamics.</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":"2023-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1140/epje/s10189-023-00383-7.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138823889","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":"Hopf bifurcation control of macroscopic traffic flow model considering vehicle braking effect","authors":"WenHuan Ai,&nbsp;MingMing Wang,&nbsp;DaWei Liu","doi":"10.1140/epje/s10189-023-00393-5","DOIUrl":"10.1140/epje/s10189-023-00393-5","url":null,"abstract":"<div><p>Traffic congestion not only has a great impact on people's travel, but also increases energy consumption and air pollution. The control analysis of the macroscopic traffic flow model considering the vehicle braking effect is particularly important, reflecting the impact on the actual traffic flow density wave, so as to better solve the actual traffic problems. In this paper, based on a speed difference optimization speed model, the micro–macro-variables are transformed into a high-order continuous traffic flow model. Then, a random function considering the physical correlation of random components is added to the high-order continuous traffic flow model to establish a random traffic flow model that can reflect the uncertain behavior of traffic flow acceleration or deceleration. Based on this stochastic traffic model, the existence of Hopf bifurcation and bifurcation control of the traffic flow system model considering stochastic characteristics are derived by using Hopf bifurcation theorem. By Chebyshev polynomial approximation method, the stochastic problem of the system is transformed into the bifurcation control problem of its equivalent deterministic system. A feedback controller is designed to delay the occurrence of Hopf bifurcation and control the amplitude of the limit cycle. Without changing the equilibrium point of the system, the complete elimination of Hopf bifurcation can be achieved by controlling the amplitude of the limit cycle. That is, the feedback controller is used to modify the bifurcation characteristics of the system, such as the bifurcation appearing at the equilibrium point in the control system moves forward, moves backward or disappears, so as to achieve the effect of preventing or alleviating traffic congestion.</p><h3>Graphical abstract</h3>\u0000<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":"2023-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138796221","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":"Observation of non-equilibrium fluctuation in the shear-stress-driven hemoglobin aggregates","authors":"A. Kabiraj,&nbsp;G. Mallik,&nbsp;P. P. Dash,&nbsp;P. Kumari,&nbsp;M. Bandyopadhyay,&nbsp;S. Rath","doi":"10.1140/epje/s10189-023-00389-1","DOIUrl":"10.1140/epje/s10189-023-00389-1","url":null,"abstract":"<div><p>Non-equilibrium fluctuations caused by the rearrangement of hemoglobin molecules into an aggregate state under shear stress have been investigated experimentally. The flow response under the shear stress (<i>σ</i>) corroborates the presence of contrasting aggregate and rejuvenation states governed by entropy production and consumption events. From the time-dependent shear rate fluctuation studies of aggregate states, the probability distribution function (PDF) of the rate of work done is observed to be spread from negative to positive values with a net positive mean. The PDFs follow the steady-state fluctuation theorem, even at a smaller timescale than that desired by the theorem. The behavior of the effective temperature (<i>T</i>_eff) that emerges from a non-equilibrium fluctuation and interconnects with the structural restrictions of the aggregate state of our driven system is observed to be within the boundary of the thermodynamic uncertainty. The increase in <i>T</i>_eff with the applied <i>σ</i> illustrates a phenomenal nonlinear power flux-dependent aggregating behavior in a classic bio-molecular-driven system.</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":"2023-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138816573","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":"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}