The European Physical Journal E最新文献

{"title":"The role of epistasis in evolutionary rescue","authors":"Osmar Freitas,&nbsp;Paulo R. A. Campos","doi":"10.1140/epje/s10189-024-00445-4","DOIUrl":"10.1140/epje/s10189-024-00445-4","url":null,"abstract":"<p>The process by which adaptive evolution preserves a population threatened with extinction due to environmental changes is known as evolutionary rescue. Several factors determine the fate of those populations, including demography and genetic factors, such as standing genetic variation, gene flow, availability of <i>de novo mutations</i>, and so on. Despite the extensive debate about evolutionary rescue in the current literature, a study about the role of epistasis and the topography of the fitness landscape on the fate of dwindling populations is missing. In the current work, we aim to fill this gap and study the influence of epistasis on the probability of extinction of populations. We present simulation results, and analytical approximations are derived. Counterintuitively, we show that the likelihood of extinction is smaller when the degree of epistasis is higher. The reason underneath is twofold: first, higher epistasis can promote mutations of more significant phenotypic effects, but also, the incongruence between the maps genotype–phenotype and phenotype–fitness turns the fitness landscape at low epistasis more rugged, thus curbing some of its advantages.</p>","PeriodicalId":790,"journal":{"name":"The European Physical Journal E","volume":"47 7","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141775894","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":"Molecular structure of DNA via Zagreb connection descriptors","authors":"Muhammad Mudassar Hassan,&nbsp;Xiang-Feng Pan","doi":"10.1140/epje/s10189-024-00442-7","DOIUrl":"10.1140/epje/s10189-024-00442-7","url":null,"abstract":"<p>Topological indices quantify the connectivity and structural properties of chemical compounds. We use the topological indices for predicting and evaluating the numerous properties of molecules, such as boiling temperatures, toxicity, and biological activity. Zagreb connection indices are a useful tool for studying the structural characteristics of the DNA backbone network. These indices provide important information on the arrangement and connections between nucleotide bases inside the DNA molecule. These indices show compactness, complexity, and topological properties in order to predict DNA bending propensity, DNA-protein interaction, and DNA stability. DNA folding patterns and the impact of mutations on DNA networks are areas of further research for these topological indices. In this study, we calculate Zagreb connection indices and modified Zagreb connection indices for backbone DNA network and subdivided backbone DNA network. Furthermore, we compute the hyper-Zagreb connection index, the inverse sum connection index, and the harmonic connection index.</p>","PeriodicalId":790,"journal":{"name":"The European Physical Journal E","volume":"47 7","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141776026","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":"Nematodynamics with odd and rotational viscosities","authors":"L. M. Pismen","doi":"10.1140/epje/s10189-024-00441-8","DOIUrl":"10.1140/epje/s10189-024-00441-8","url":null,"abstract":"<div><p>We explore a novel mechanism of interactions between nematic order and flow including odd and rotational viscosities, and investigate activity-induced instabilities in the framework of this model. We show how these modes of viscous dissipation can be incorporated in the Ericksen–Leslie formalism, but it does not eliminate deficiencies of the approach based on Onsager’s reciprocal relations that lead to spurious instabilities. The suggested way of deriving nematodynamic equations, based on a specific mechanism applicable to rigid rods, is not universal, but it avoids referring to Onsager’s relations and avoids spurious instabilities in the absence of an active inputs. The model is further applied to the analysis of instabilities in active media</p></div>","PeriodicalId":790,"journal":{"name":"The European Physical Journal E","volume":"47 7","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1140/epje/s10189-024-00441-8.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141775895","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":"Modelling intracellular transport in crowded environments: effects of motor association to cargos","authors":"Sutapa Mukherji,&nbsp;Dhruvi K. Patel","doi":"10.1140/epje/s10189-024-00440-9","DOIUrl":"10.1140/epje/s10189-024-00440-9","url":null,"abstract":"<p>In intracellular transports, motor proteins transport macromolecules as cargos to desired locations by moving on biopolymers such as microtubules. Recent experiments suggest that, while moving in crowded environments, cargos that can associate motor proteins during their translocation have larger run-length and association time compared to free motors. Here, we model the dynamics of a cargo that can associate at the most <i>m</i> free motors present on the microtubule track as obstacles to its motion. The proposed models display competing effects of association and crowding, leading to a peak in the run-length with the free-motor density. For <span>(m=2)</span> and 3, we show that this feature is governed by the largest eigenvalue of the transition matrix describing the cargo dynamics. In all the above cases, free motors are assumed to be present on the microtubule as stalled obstacles. We finally compare simulation results for the run-length for general scenarios where the free motors undergo processive motion in addition to binding and unbinding to or from the microtubule.</p>","PeriodicalId":790,"journal":{"name":"The European Physical Journal E","volume":"47 7","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141603108","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":"Effect of internal structure and resin deformability on drying rate and stress in convective drying of silica–latex coatings","authors":"Hiroaki Tanaka,&nbsp;Yoshiyuki Komoda,&nbsp;Takafumi Horie,&nbsp;Naoto Ohmura","doi":"10.1140/epje/s10189-024-00432-9","DOIUrl":"10.1140/epje/s10189-024-00432-9","url":null,"abstract":"<div><p>Latex paint is an aqueous dispersion of nano-sized polymer particles that can form a thin film by itself or mixed with rigid particles. We have developed an apparatus that can simultaneously measure drying rate and stress generation and have investigated the film formation process of a latex-only coating layer under convection drying. In the present study, we adopted the same method to investigate the film formation process of the silica–latex coating layer. As a result, we were able to systematically correlate the drying rate change by the equivalent thickness of latex particles accumulated with silica particles at the drying surface. Furthermore, it is unveiled that the drying rate in the former stage depends on drying temperature, while the drying rate changed to be dominated by silica content after the particle-packing layer was formed over the entire coating layer. On the other hand, the model we proposed for stress generation, considering the temperature effect on latex deformability, was found to be applicable to the present experimental system by replacing a portion of deformable particles with rigid particles.</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":"47 7","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11224093/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141533307","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":"Calorimetric, optical and dielectric measurements on two Schiff’s based liquid crystalline materials exhibiting multiple phase transitions","authors":"Prabir Sarkar,&nbsp;Barnali Barman,&nbsp;Parameswara Rao Alapati,&nbsp;Malay Kumar Das","doi":"10.1140/epje/s10189-024-00436-5","DOIUrl":"10.1140/epje/s10189-024-00436-5","url":null,"abstract":"<div><p>We report high-resolution calorimetric, optical and dielectric studies on two Schiff’s based liquid crystalline materials, 4O.5 and 5O.5, which exhibit multiple phase transitions. The study goes beyond the commonly studied isotropic-to-nematic (I–N) and nematic-to-smectic A (N–SmA) phase transitions and explores higher-order smectic phase transitions. The critical exponent, <i>α</i> values, for different phase transitions has been explored. For the I–N, N–SmA, SmA–SmC, SmC–SmF, SmF–CrG and SmB–CrG transitions, <i>α</i> values close to 0.5 and amplitude ratios <i>A</i>⁻/<i>A</i>⁺ ~ 1.6 and <i>D</i>⁻/<i>D</i>⁺ ~ 1 indicate a first-order nature. Notably, for the SmA–SmB transition, although <i>α</i> (≈ 0.64) is larger than the tricritical value of 0.5, <i>A</i>⁻/<i>A</i>⁺ ~ 1.2 and <i>D</i>⁻/<i>D</i>⁺ ~ 1, and the study reports an order parameter critical exponent (<i>β</i>) of 0.26 ± 0.002, which supports a tricritical nature for this transition. Importantly, the ratios of <i>A</i>⁻/<i>A</i>⁺ and <i>D</i>⁻/<i>D</i>⁺ are found to have similar values across all three-measurement methods, indicating consistency and agreement among these methods.</p><h3>Graphical abstract</h3><div><figure><div><div><picture><source><img></source></picture></div><div><p>Optical textures of the SmF and CrG phases. Temperature dependence of birefringence for compounds 4O.5 and 5O.5</p></div></div></figure></div></div>","PeriodicalId":790,"journal":{"name":"The European Physical Journal E","volume":"47 6","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141441945","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":"Analysis of the number of topological defects in active nematic fluids under applied shear flow","authors":"Zhenna Li,&nbsp;Hao Ye,&nbsp;Jianzhong Lin,&nbsp;Zhenyu Ouyang","doi":"10.1140/epje/s10189-024-00437-4","DOIUrl":"10.1140/epje/s10189-024-00437-4","url":null,"abstract":"<div><p>The number of topological defects in the shear flow of active nematic fluids is numerically investigated in this study. The evolution of the flow state of extensile active nematic fluids is explored by increasing the activity of active nematic fluids. Evidently, medium-activity active nematic fluids exhibit a highly ordered vortex lattice fluid state. However, high-activity active nematic fluids exhibit a meso-scale turbulent flow accompanied by topological defects. The number of topological defects (<i>N</i>_def) increases with increasing shear Reynolds number (<i>R</i>e_s). Fluid viscosity strongly influences <i>N</i>_def, while the influence of fluid density is relatively weak. <i>N</i>_def decreases with increasing activity length scale (<i>l</i>_<i>ζ</i>) value. A small <i>Re</i>_s value strongly influences <i>N</i>_def, whereas a large <i>l</i>_<i>ζ</i> value only weakly influences <i>N</i>_def. As the activity increases, <i>N</i>_def in contractile active nematic fluids becomes larger than that of extensile active nematic fluids.</p><h3>Graphical abstract</h3>\u0000<div><figure><div><div><picture><source><img></source></picture></div><div><p>Graphical abstract represents the flow state of meso-scale turbulent accompanied by topological defects. For the two dimensional case, two types of topological defects, namely comet-like + 1/2 and trefoil-like − 1/2 topological defects</p></div></div></figure></div></div>","PeriodicalId":790,"journal":{"name":"The European Physical Journal E","volume":"47 6","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141425944","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":"Structure-property modeling of physicochemical properties of fractal trigonal triphenylenoids by means of novel degree-based topological indices","authors":"K. Jyothish,&nbsp;Roy Santiago,&nbsp;S. Govardhan,&nbsp;Sakander Hayat","doi":"10.1140/epje/s10189-024-00438-3","DOIUrl":"10.1140/epje/s10189-024-00438-3","url":null,"abstract":"<p>Trigonal triphenylenoids (TTPs) are a fascinating class of organic molecules with unique structural and electronic properties. Their diverse applications, ranging from organic electronics to nonlinear optics, have spurred significant research interest in understanding their physicochemical behavior. Topological indices, mathematical descriptors derived from the molecular graph, offer valuable insights into the structural complexity and potential properties of TTPs. This work focuses on exploring the utility of degree-based topological indices in characterizing and predicting the properties of trigonal triphenylenoids. We systematically calculate various degree-based topological indices, for a diverse set of TTPs with varying substituents and topologies. The relationships between these indices and key physicochemical properties, such as HOMO-LUMO energy gap, thermodynamic stability, and reactivity are investigated using statistical and machine learning approaches. We identify significant correlations between specific degree-based indices and different properties, allowing for potential prediction of these properties based solely on the topological information.</p>","PeriodicalId":790,"journal":{"name":"The European Physical Journal E","volume":"47 6","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141417119","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":"Bifurcation analysis and control of improved traffic flow model considering the effect of strong winds","authors":"Wenhuan Ai,&nbsp;Zhengqing Lei,&nbsp;Danyang Li,&nbsp;Jingming Zeng,&nbsp;Dawei Liu","doi":"10.1140/epje/s10189-024-00433-8","DOIUrl":"10.1140/epje/s10189-024-00433-8","url":null,"abstract":"<div><p>In recent years, the problem of traffic congestion has become increasingly serious, and research on traffic system control has become a new hotspot. Studying the bifurcation characteristics of traffic flow systems and designing control schemes for unstable support points can alleviate traffic congestion from a new perspective. This article improves the full speed differential model considering strong wind models from the perspective of bifurcation control to adjust traffic flow. This article theoretically proves the existence conditions of Hopf bifurcation and saddle node bifurcation in the model and finds the stability mutation point of the transportation system stability. A nonlinear system feedback controller was designed for unstable bifurcation points using Chebyshev polynomial approximation and random feedback control methods. Without changing the system equilibrium point, the advance, delay, and elimination of Hopf bifurcation were achieved, and the abrupt behavior of the transportation system was controlled, thereby alleviating traffic congestion. This article explains the changes in the stability of complex transportation systems from the perspective of bifurcation analysis, which can better capture the characteristics of traffic flow. By adjusting the control parameters in the feedback controller, the influence of boundary conditions on the stability of the transportation system is fully described, and the influence of unstable focal points and saddle points on the system is suppressed, thereby slowing down the traffic flow. In addition, unstable bifurcation points can be eliminated, and the Hopf bifurcation can be controlled to advance, delay, and disappear, thereby achieving control over the stable behavior of the transportation system. This helps alleviate traffic congestion and also helps describe actual traffic phenomena.</p><h3>Graphical abstract</h3><div><figure><div><div><picture><source><img></source></picture></div><div><p>Schematic diagram of the force situation of vehicles under wind force</p></div></div></figure></div></div>","PeriodicalId":790,"journal":{"name":"The European Physical Journal E","volume":"47 6","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141330082","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":"Phase separation, edge currents, and Hall effect for active matter with Magnus dynamics","authors":"B. Adorjáni,&nbsp;A. Libál,&nbsp;C. Reichhardt,&nbsp;C. J. O. Reichhardt","doi":"10.1140/epje/s10189-024-00431-w","DOIUrl":"10.1140/epje/s10189-024-00431-w","url":null,"abstract":"<p>We examine run-and-tumble disks in two-dimensional systems where the particles also have a Magnus component to their dynamics. For increased activity, we find that the system forms a motility-induced phase-separated (MIPS) state with chiral edge flow around the clusters, where the direction of the current is correlated with the sign of the Magnus term. The stability of the MIPS state is non-monotonic as a function of increasing Magnus term amplitude, with the MIPS region first extending down to lower activities followed by a break up of MIPS at large Magnus amplitudes into a gel-like state. We examine the dynamics in the presence of quenched disorder and a uniform drive and find that the bulk flow exhibits a drive-dependent Hall angle. This is a result of the side jump effect produced by scattering from the pinning sites and is similar to the behavior found for skyrmions in chiral magnets with quenched disorder.</p><p>Active Magnus particles without pinning or drift force in the presence of gradually increasing Magnus terms showing <b>a</b> a rotating cluster mode, <b>b</b> a rotating cluster with clear shear banding at its edge, <b>c</b> a sheared band spanning the system, and <b>d</b> a disordered state where neither clusters nor shear bands can form. The colors indicate the net displacement of the particles, while the arrows show the rotation or shear directions</p>","PeriodicalId":790,"journal":{"name":"The European Physical Journal E","volume":"47 6","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141282662","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}