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EPJ E - Soft Matter and Biological Physics
Journal Prestige (SJR): 0.489  Citation Impact (citeScore): 1 Number of Followers: 3  Hybrid journal (It can contain Open Access articles)ISSN (Print) 1292-8941 - ISSN (Online) 1292-895X Published by Springer-Verlag  [2468 journals]
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- Mathematical modeling for prediction of physicochemical characteristics of
cardiovascular drugs via modified reverse degree topological indices-
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Abstract: Global health concerns persist due to the multifaceted nature of heart diseases, which include lifestyle choices, genetic predispositions, and emerging post-COVID complications like myocarditis and pericarditis. This broadens the spectrum of cardiovascular ailments to encompass conditions such as coronary artery disease, heart failure, arrhythmias, and valvular disorders. Timely interventions, including lifestyle modifications and regular medications such as antiplatelets, beta-blockers, angiotensin-converting enzyme inhibitors, antiarrhythmics, and vasodilators, are pivotal in managing these conditions. In drug development, topological indices play a critical role, offering cost-effective computational and predictive tools. This study explores modified reverse degree topological indices, highlighting their adjustable parameters that actively shape the degree sequences of molecular drugs. This feature makes the approach suitable for datasets with unique physicochemical properties, distinguishing it from traditional methods that rely on fixed degree approaches. In our investigation, we examine a dataset of 30 drug compounds, including sotagliflozin, dapagliflozin, dobutamine, etc., which are used in the treatment of cardiovascular diseases. Through the structural analysis, we utilize modified reverse degree indices to develop quantitative structure–property relationship (QSPR) models, aiming to unveil essential understandings of their characteristics for drug development. Furthermore, we compare our QSPR models against the degree-based models, clearly demonstrating the superior effectiveness inherent in our proposed method. Graphical
PubDate: 2024-08-04
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- On pressure-driven Poiseuille flow with non-monotonic rheology
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Abstract: Shear thickening fluids are liquids that stiffen as the applied stress increases. If many of these types of fluids follow a monotonic rheological curve, some experimental and numerical studies suggest that certain fluids, like cornstarch, may exhibit a non-monotonic, S-shaped rheology. Such non-monotonic behavior has however proved very difficult to observe experimentally in classical rheometer. To explain such difficulties, the possible presence of vorticity banding in the rheometer has been considered. To prevent such instabilities, we use a capillary rheometer, which is a cylindrical tube, measuring the flow rate versus the applied pressure drop. With this setup, we indeed observe a non-monotonic behavior: the flow rate increases monotonically at low pressure drops up to a maximum, after which it abruptly decreases to an almost constant flow rate regardless of further increases in pressure drop. This maximum-jump–plateau behavior occurs over a wide range of concentrations and is reproducible without hysteresis, which is in agreement with an S-shaped rheology. However, the obtained flow versus pressure difference function \(Q(\Delta P)\) does not agree with the classical Wyart–Cates rheological model, which predicts an S-shaped non-monotonic function, but with neither a jump nor a plateau. To understand this jump–plateau behavior, we remark that any rheological model would establish a relationship between the flow rate and the local pressure gradient, but not the total pressure drop. We thus discuss and analyze the implications of having an S-shaped non-monotonic flow rate-pressure gradient in Poiseuille flow. In particular, we discuss the possibility of a non-uniform pressure gradient in the direction of the flow, i.e., a kind of streamwise banding. The key issue is then the selection of the gradient pressure distribution along the tube. One solution could arise from an analogy of this problem with the spinodal decomposition. It, however, leads to an increase in flow rate with \(\partial _xP\) up to a plateau between two values of \(\partial _xP\) as determined by the Maxwell construction. To account for the bump–jump behavior, we have implemented a simple dynamical stochastic version of the Wyart–Cates model, where the thickening occurs with a characteristic time. As a result, with increasing the total pressure drop, the flow rate increases monotonically up to a maximum value. Beyond this point, the flow rate drops abruptly to a lower value, forming a slowly decreasing plateau. This behavior is likely to account for the maximum-jump–plateau observed in the experiments. We also show that in such a system, the final state is quite sensitive to the initial state of the fluid, especially its homogeneity. Our results then demonstrate that the mere presence of a non-monotonic rheological curve is sufficient to predict the occurrence of stress banding in the streamwise direction and a plateau flow rate, even if the suspension remains homogeneous. Graphical
PubDate: 2024-08-04
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- Effect of bottom bumpiness of vibrated closed container on granular
dissipation behavior-
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Abstract: The dissipation behavior of granular balls inside quasi-two-dimensional closed containers with different levels of bottom bumpiness under vibration is examined in this article using the discrete element method. The quasi-two-dimensional closed granular system used in this paper has dimensions of \(L_{x} \times L_{y} \times L_{z} = 60\,{\text{mm}} \times 5\,{\text{mm}} \times 120\,{\text{mm}}\) , and the diameters of the 279 filled granular balls are 4 mm. First, the dynamic behavior and damping effects of granular balls within a flat-bottomed closed container are explored across the range of relevant excitation parameters, identifying four high damping granular phases. Second, this study investigated the impact of the container's bottom surface bumpiness, convex height, and number of bumps on the dissipative behavior of internal granular balls. The findings reveal that a single 2 mm bump on the container's bottom surface maximally enhances the damping effect on the granular balls. Finally, by comparing the optimal damping behavior of granular balls inside a flat-bottomed container with that of a container featuring a single 2 mm bump at the bottom, this study revealed how the protruding bottom surface enhances the damping effect on the granular balls inside the container. This provides theoretical support for optimizing the performance of granular dampers in engineering practice by controlling the morphology of the cavity bottom surface. Graphical abstract
PubDate: 2024-07-29
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- Nematodynamics with odd and rotational viscosities
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Abstract: Abstract 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
PubDate: 2024-07-27
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- Molecular structure of DNA via Zagreb connection descriptors
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Abstract: 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. Graphical abstract
PubDate: 2024-07-27
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- The role of epistasis in evolutionary rescue
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Abstract: 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 de novo mutations, 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. Graphic abstract
PubDate: 2024-07-27
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- Modelling intracellular transport in crowded environments: effects of
motor association to cargos-
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Abstract: 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 m 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 \(m=2\) 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. Graphical abstract
PubDate: 2024-07-13
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- Effect of internal structure and resin deformability on drying rate and
stress in convective drying of silica–latex coatings-
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Abstract: 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. Graphical abstract
PubDate: 2024-07-04
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- Editorial
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PubDate: 2024-06-26
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- Calorimetric, optical and dielectric measurements on two Schiff’s based
liquid crystalline materials exhibiting multiple phase transitions-
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Abstract: 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, α values, for different phase transitions has been explored. For the I–N, N–SmA, SmA–SmC, SmC–SmF, SmF–CrG and SmB–CrG transitions, α values close to 0.5 and amplitude ratios A−/A+ ~ 1.6 and D−/D+ ~ 1 indicate a first-order nature. Notably, for the SmA–SmB transition, although α (≈ 0.64) is larger than the tricritical value of 0.5, A−/A+ ~ 1.2 and D−/D+ ~ 1, and the study reports an order parameter critical exponent (β) of 0.26 ± 0.002, which supports a tricritical nature for this transition. Importantly, the ratios of A−/A+ and D−/D+ are found to have similar values across all three-measurement methods, indicating consistency and agreement among these methods. Graphical abstract Optical textures of the SmF and CrG phases. Temperature dependence of birefringence for compounds 4O.5 and 5O.5
PubDate: 2024-06-24
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- Analysis of the number of topological defects in active nematic fluids
under applied shear flow-
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Abstract: 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 (Ndef) increases with increasing shear Reynolds number (Res). Fluid viscosity strongly influences Ndef, while the influence of fluid density is relatively weak. Ndef decreases with increasing activity length scale (lζ) value. A small Res value strongly influences Ndef, whereas a large lζ value only weakly influences Ndef. As the activity increases, Ndef in contractile active nematic fluids becomes larger than that of extensile active nematic fluids. Graphical abstract 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
PubDate: 2024-06-20
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- Structure-property modeling of physicochemical properties of fractal
trigonal triphenylenoids by means of novel degree-based topological
indices-
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Abstract: 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. Graphic abstract
PubDate: 2024-06-18
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- Bifurcation analysis and control of improved traffic flow model
considering the effect of strong winds-
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Abstract: 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. Graphical abstract Schematic diagram of the force situation of vehicles under wind force
PubDate: 2024-06-16
DOI: 10.1140/epje/s10189-024-00433-8
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- Phase separation, edge currents, and Hall effect for active matter with
Magnus dynamics-
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Abstract: 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. Graphical abstract Active Magnus particles without pinning or drift force in the presence of gradually increasing Magnus terms showing a a rotating cluster mode, b a rotating cluster with clear shear banding at its edge, c a sheared band spanning the system, and d 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
PubDate: 2024-06-06
DOI: 10.1140/epje/s10189-024-00431-w
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- On the fluid drag reduction in scallop surface
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Abstract: In the field of biomimetics, the tiny riblet structures inspired by shark skin have been extensively studied for their drag reduction properties in turbulent flows. Here, we show that the ridged surface texture of another swimming creature in the ocean, i.e., the scallops, also has some friction drag reduction effect. In this study, we investigated the potential drag reduction effects of scallop shell textures using computational fluid dynamics simulations. Specifically, we constructed a conceptual model featuring an undulating surface pattern on a conical shell geometry that mimics scallop. Simulations modeled turbulent fluid flows over the model inserted at different orientations relative to the flow direction. The results demonstrate appreciable friction drag reduction generated by the ribbed hierarchical structures encasing the scallop, while partial pressure drag reduction exhibits dependence on alignment of scallop to the predominant flow direction. Theoretical mechanisms based on classic drag reduction theory in turbulence was established to explain the drag reduction phenomena. Given the analogous working environments of scallops and seafaring vessels, these findings may shed light on the biomimetic design of surface textures to enhance maritime engineering applications. Besides, this work elucidates an additional evolutionary example of fluid drag reduction, expanding the biological repertoire of swimming species. Graphical abstract Lines used for shear stress data extraction of the shell model and the normalized wall shear of these lines on both models.
PubDate: 2024-06-03
DOI: 10.1140/epje/s10189-024-00434-7
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- A microfluidic platform for the synthesis of polymer and
polymer-protein-based protocells-
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Abstract: In this study, we demonstrate the fabrication of polymersomes, protein-blended polymersomes, and polymeric microcapsules using droplet microfluidics. Polymersomes with uniform, single bilayers and controlled diameters are assembled from water-in-oil-in-water double-emulsion droplets. This technique relies on adjusting the interfacial energies of the droplet to completely separate the polymer-stabilized inner core from the oil shell. Protein-blended polymersomes are prepared by dissolving protein in the inner and outer phases of polymer-stabilized droplets. Cell-sized polymeric microcapsules are assembled by size reduction in the inner core through osmosis followed by evaporation of the middle phase. All methods are developed and validated using the same glass-capillary microfluidic apparatus. This integrative approach not only demonstrates the versatility of our setup, but also holds significant promise for standardizing and customizing the production of polymer-based artificial cells. Graphical
PubDate: 2024-06-03
DOI: 10.1140/epje/s10189-024-00428-5
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- Integrating machine learning with $$\alpha $$ -SAS for enhanced structural
analysis in small-angle scattering: applications in biological and
artificial macromolecular complexes-
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Abstract: Small-Angle Scattering (SAS), encompassing both X-ray (SAXS) and Neutron (SANS) techniques, is a crucial tool for structural analysis at the nanoscale, particularly in the realm of biological macromolecules. This paper explores the intricacies of SAS, emphasizing its application in studying complex biological systems and the challenges associated with sample preparation and data analysis. We highlight the use of neutron-scattering properties of hydrogen isotopes and isotopic labeling in SANS for probing structures within multi-subunit complexes, employing techniques like contrast variation (CV) for detailed structural analysis. However, traditional SAS analysis methods, such as Guinier and Kratky plots, are limited by their partial use of available data and inability to operate without substantial a priori knowledge of the sample’s chemical composition. To overcome these limitations, we introduce a novel approach integrating \(\alpha \) -SAS, a computational method for simulating SANS with CV, with machine learning (ML). This approach enables the accurate prediction of scattering contrast in multicomponent macromolecular complexes, reducing the need for extensive sample preparation and computational resources. \(\alpha \) -SAS, utilizing Monte Carlo methods, generates comprehensive datasets from which structural invariants can be extracted, enhancing our understanding of the macromolecular form factor in dilute systems. The paper demonstrates the effectiveness of this integrated approach through its application to two case studies: Janus particles, an artificial structure with a known SAS intensity and contrast, and a biological system involving RNA polymerase II in complex with Rtt103. These examples illustrate the method’s capability to provide detailed structural insights, showcasing its potential as a powerful tool for advanced SAS analysis in structural biology. Graphic
PubDate: 2024-06-03
DOI: 10.1140/epje/s10189-024-00435-6
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- Effects of local incompressibility on the rheology of composite biopolymer
networks-
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Abstract: Fibrous networks such as collagen are common in biological systems. Recent theoretical and experimental efforts have shed light on the mechanics of single component networks. Most real biopolymer networks, however, are composites made of elements with different rigidity. For instance, the extracellular matrix in mammalian tissues consists of stiff collagen fibers in a background matrix of flexible polymers such as hyaluronic acid (HA). The interplay between different biopolymer components in such composite networks remains unclear. In this work, we use 2D coarse-grained models to study the nonlinear strain-stiffening behavior of composites. We introduce a local volume constraint to model the incompressibility of HA. We also perform rheology experiments on composites of collagen with HA. Theoretically and experimentally, we demonstrate that the linear shear modulus of composite networks can be increased by approximately an order of magnitude above the corresponding moduli of the pure components. Our model shows that this synergistic effect can be understood in terms of the local incompressibility of HA, which acts to suppress density fluctuations of the collagen matrix with which it is entangled. Graphical A snapshot of a composite network on a triangular lattice. Collagen fibers (black) interact with a hyaluronic acid matrix, represented by both dashed lines and gray hexagons that resist volume change.
PubDate: 2024-05-27
DOI: 10.1140/epje/s10189-024-00422-x
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- Texture identification in liquid crystal-protein droplets using
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Abstract: Sessile drying droplets manifest distinct morphological patterns, encompassing diverse systems, viz., DNA, proteins, blood, and protein-liquid crystal (LC) complexes. This study employs an integrated methodology that combines drying droplet, image texture analysis (features from First Order Statistics, Gray Level Co-occurrence Matrix, Gray Level Run Length Matrix, Gray Level Size Zone Matrix, and Gray Level Dependence Matrix), and statistical data analysis (Generalized Additive Modeling and K-means clustering). It provides a comprehensive qualitative and quantitative exploration by examining LC-protein droplets at varying initial phosphate buffered concentrations (0x, 0.25x, 0.5x, 0.75x, and 1x) during the drying process under optical microscopy with crossed polarizing configuration. Notably, it unveils distinct LC-protein textures across three drying stages: initial, middle, and final. The Generalized Additive Modeling (GAM) reveals that all the features significantly contribute to differentiating LC-protein droplets. Integrating the K-means clustering method with GAM analysis elucidates how textures evolve through the three drying stages compared to the entire drying process. Notably, the final drying stage stands out with well-defined, non-overlapping clusters, supporting the visual observations of unique LC textures. Furthermore, this paper contributes valuable insights, showcasing the efficacy of drying droplets as a rapid and straightforward tool for characterizing and classifying dynamic LC textures. Graphical
PubDate: 2024-05-24
DOI: 10.1140/epje/s10189-024-00429-4
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- Programming tunable active dynamics in a self-propelled robot
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Abstract: We present a scheme for producing tunable active dynamics in a self-propelled robotic device. The robot moves using the differential drive mechanism where two wheels can vary their instantaneous velocities independently. These velocities are calculated by equating robot’s equations of motion in two dimensions with well-established active particle models and encoded into the robot’s microcontroller. We demonstrate that the robot can depict active Brownian, run and tumble, and Brownian dynamics with a wide range of parameters. The resulting motion analyzed using particle tracking shows excellent agreement with the theoretically predicted trajectories. Later, we show that its motion can be switched between different dynamics using light intensity as an external parameter. Intriguingly, we demonstrate that the robot can efficiently navigate through many obstacles by performing stochastic reorientations driven by the gradient in light intensity towards a desired location, namely the target. This work opens an avenue for designing tunable active systems with the potential of revealing the physics of active matter and its application for bio- and nature-inspired robotics. Graphical abstract
PubDate: 2024-05-23
DOI: 10.1140/epje/s10189-024-00430-x
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