Castellini S, Brizioli M, Giraudet C
… +4 more, Carpineti M, Croccolo F, Giavazzi F, Vailati A
Eur Phys J E Soft Matter
· 2024 Apr · PMID 38587607
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The study of phoretic transport phenomena under non-stationary conditions presents several challenges, mostly related to the stability of the experimental apparatus. This is particularly true when investigating with opti...The study of phoretic transport phenomena under non-stationary conditions presents several challenges, mostly related to the stability of the experimental apparatus. This is particularly true when investigating with optical means the subtle temperature and concentration fluctuations that arise during diffusion processes, superimposed to the macroscopic state of the system. Under these conditions, the tenuous signal from fluctuations is easily altered by the presence of artifacts. Here, we address an experimental issue frequently reported in the investigation by means of dynamic shadowgraphy of the non-equilibrium fluctuations arising in liquid mixtures under non-stationary conditions, such as those arising after the imposition or removal of a thermal stress, where experiments show systematically the presence of a spurious contribution in the reconstructed structure function of the fluctuations, which depends quadratically from the time delay. We clarify the mechanisms responsible for this artifact, showing that it is caused by the imperfect alignment of the sample cell with respect to gravity, which couples the temporal evolution of the concentration profile within the sample with the optical signal collected by the shadowgraph diagnostics. We propose a data analysis protocol that enables disentangling the spurious contributions and the genuine dynamics of the fluctuations, which can be thus reliably reconstructed.
Fuchsine acid serves as a supramolecular dye in Masson's trichrome stain, finding extensive applications in histology. It is also utilized with picric acid in Van Gieson's method to reveal red collagen fibers and in Mass...Fuchsine acid serves as a supramolecular dye in Masson's trichrome stain, finding extensive applications in histology. It is also utilized with picric acid in Van Gieson's method to reveal red collagen fibers and in Masson's trichrome to highlight smooth muscle in contrast to collagen. Beyond these applications, it plays a crucial role in electronic fields and photonic devices as an organic semiconductor. Therefore, investigating and predicting the complex molecular structure of fuchsine acid becomes essential, serving as the foundation for understanding its physicochemical features. This article employs topological modeling, specifically a connection number edge partition, to explore the supramolecular nature of fuchsine acid. Closed formulae for key degree-based molecular descriptors are derived, aiming to illuminate the effectiveness of these descriptors for QSAR and QSPR analyses.
We investigate the translocation of a semiflexible polymer through extended patterned pores using Langevin dynamics simulations, specifically focusing on the influence of a time-dependent driving force. Our findings reve...We investigate the translocation of a semiflexible polymer through extended patterned pores using Langevin dynamics simulations, specifically focusing on the influence of a time-dependent driving force. Our findings reveal that, akin to its flexible counterpart, a rigid chain-like molecule translocates faster when subjected to an oscillating force than a constant force of equivalent average magnitude. The enhanced translocation is strongly correlated with the stiffness of the polymer and the stickiness of the pores. The arrangement of the pores plays a pivotal role in translocation dynamics, deeply influenced by the interplay between polymer stiffness and pore-polymer interactions. For heterogeneous polymers with periodically varying stiffness, the oscillating force introduces significant variations in the translocation time distributions based on segment sizes and orientations. On the basis of these insights, we propose a sequencing approach that harnesses distinct pore surface properties that are capable of accurately predicting sequences in heteropolymers with diverse bending rigidities.
Eur Phys J E Soft Matter
· 2024 Apr · PMID 38563859
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We compare three different setups for measuring cell-cell adhesion. We show that the measured strength depends on the type of setup that is used. For identical cells different assays measure different detachment forces....We compare three different setups for measuring cell-cell adhesion. We show that the measured strength depends on the type of setup that is used. For identical cells different assays measure different detachment forces. This can be understood from the fact that cell-cell detachment is a global property of the system. We also analyse the role of external force and line tension on contact angle and cell-cell detachment. Comparison with the experiments suggest that viscous forces play an important role in the process. We dedicate this article to Fyl Pincus who for many of us is an example to be followed not only for outstanding science but also for a marvelous human behavior.
Gauquelin E, Kuromiya K, Namba T
… +4 more, Ikawa K, Fujita Y, Ishihara S, Sugimura K
Eur Phys J E Soft Matter
· 2024 Mar · PMID 38538808
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Tissues consist of cells with different molecular and/or mechanical properties. Measuring the forces and stresses in mixed-cell populations is essential for understanding the mechanisms by which tissue development, homeo...Tissues consist of cells with different molecular and/or mechanical properties. Measuring the forces and stresses in mixed-cell populations is essential for understanding the mechanisms by which tissue development, homeostasis, and disease emerge from the cooperation of distinct cell types. However, many previous studies have primarily focused their mechanical measurements on dissociated cells or aggregates of a single-cell type, leaving the mechanics of mixed-cell populations largely unexplored. In the present study, we aimed to elucidate the influence of interactions between different cell types on cell mechanics by conducting in situ mechanical measurements on a monolayer of mammalian epithelial cells. Our findings revealed that while individual cell types displayed varying magnitudes of traction and intercellular stress before mixing, these mechanical values shifted in the mixed monolayer, becoming nearly indistinguishable between the cell types. Moreover, by analyzing a mixed-phase model of active tissues, we identified physical conditions under which such mechanical convergence is induced. Overall, the present study underscores the importance of in situ mechanical measurements in mixed-cell populations to deepen our understanding of the mechanics of multicellular systems.
Eur Phys J E Soft Matter
· 2024 Mar · PMID 38499904
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The equation of state for an ideal gas is simple, which is . In the case of imperfect gases where mutual interactions among the constituents are important, pressure P can be expressed as the series expansion of density...The equation of state for an ideal gas is simple, which is . In the case of imperfect gases where mutual interactions among the constituents are important, pressure P can be expressed as the series expansion of density n with appropriate coefficients, known as virial coefficients . In this paper, we have obtained the first four virial coefficients for a model interaction potential using multidimensional Monte-Carlo integration and importance sampling methods. Next, we perform molecular dynamics simulations with the same for a many-particle system to obtain P as a function of T and n. We compare our numerical data with the virial equation of state.
Eur Phys J E Soft Matter
· 2024 Mar · PMID 38472476
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The vibrational spectrum of granular packings can be used as a signature of the jamming transition, with the density of states at zero frequency becoming nonzero at the transition. It has been proposed previously that th...The vibrational spectrum of granular packings can be used as a signature of the jamming transition, with the density of states at zero frequency becoming nonzero at the transition. It has been proposed previously that the vibrational spectrum of granular packings can be approximately obtained from random matrix theory. Here, we show that the autocorrelation function of the density of states shows good agreement between dynamical numerical simulations of frictionless bead packs near the jamming point and the analytic predictions of the Laguerre orthogonal ensemble of random matrices; there is clear disagreement with the Gaussian orthogonal ensemble, establishing that the Laguerre ensemble correctly reproduces the universal statistical properties of jammed granular matter and excluding the Gaussian orthogonal ensemble. We also present a random lattice model which is a physically motivated variant of the random matrix ensemble. Numerical calculations reveal that this model reproduces the known features of the vibrational density of states of frictionless granular matter, while also retaining the correlation structure seen in the Laguerre random matrix theory.
Chang SY, Vora SR, Young CD
… +2 more, Shetty A, Ma AWK
Eur Phys J E Soft Matter
· 2024 Mar · PMID 38457022
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The viscoelasticity of a carbon nanotube (CNT)-laden air-water interface was characterized using two different experimental methods. The first experimental method used a Langmuir-Pockels (LP) trough coupled with a pair o...The viscoelasticity of a carbon nanotube (CNT)-laden air-water interface was characterized using two different experimental methods. The first experimental method used a Langmuir-Pockels (LP) trough coupled with a pair of oscillating barriers. The second method is termed the Bicone-Trough (BT) method, where a LP trough was custom-built and fit onto a rheometer equipped with a bicone fixture to standardize the preparation and conditioning of a particle-laden interface especially at high particle coverages. The performance of both methods was evaluated by performing Fast Fourier Transform (FFT) analysis to calculate the signal-to-noise ratios (SNR). Overall, the rheometer-based BT method offered better strain control and considerably higher SNRs compared to the Oscillatory Barriers (OB) method that oscillated barriers with relatively limited positional and speed control. For a CNT surface coverage of 165 mg/m and a frequency of 100 mHz, the interfacial shear modulus obtained from the OB method increased from 39 to 57 mN/m as the normal strain amplitude increased from 1 to 3%. No linear viscoelastic regime was experimentally observed for a normal strain as small as 0.5%. In the BT method, a linear regime was observed below a shear strain of 0.1%. The interfacial shear modulus decreased significantly from 96 to 2 mN/m as the shear strain amplitude increased from 0.025 to 10%.
Eur Phys J E Soft Matter
· 2024 Mar · PMID 38427109
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The rheology of particle suspensions has been extensively explored in the case of a simple shear flow, but less in other flow configurations which are also important in practice. Here we investigate the behavior of a sus...The rheology of particle suspensions has been extensively explored in the case of a simple shear flow, but less in other flow configurations which are also important in practice. Here we investigate the behavior of a suspension in a squeeze flow, which we revisit using local pressure measurements to deduce the effective viscosity. The flow is generated by approaching a moving disk to a fixed wall at constant velocity in the low Reynolds number limit. We measure the evolution of the pressure field at the wall and deduce the effective viscosity from the radial pressure drop. After validation of our device using a Newtonian fluid, we measure the effective viscosity of a suspension for different squeezing speeds and volume fractions of particles. We find results in agreement with the Maron-Pierce law, an empirical expression for the viscosity of suspensions that was established for simple shear flows. We prove that this method to determine viscosity remains valid in the limit of large gap width. This makes it possible to study the rheology of suspensions within this limit and therefore suspensions composed of large particles, in contrast to Couette flow cells which require small gaps.
Eur Phys J E Soft Matter
· 2024 Feb · PMID 38376695
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Liquid-liquid phase separation (LLPS) in binary or multi-component solutions is a well-studied subject in soft matter with extensive applications in biological systems. In recent years, several experimental studies focus...Liquid-liquid phase separation (LLPS) in binary or multi-component solutions is a well-studied subject in soft matter with extensive applications in biological systems. In recent years, several experimental studies focused on LLPS of solutes in hydrated gels, where the formation of coexisting domains induces elastic deformations within the gel. While the experimental studies report unique physical characteristics of these systems, such as sensitivity to mechanical forces and stabilization of multiple, periodic phase-separated domains, the theoretical understanding of such systems and the role of long-range interactions have not emphasized the nonlinear nature of the equilibrium binodal for strong segregation of the solute. In this paper, we formulate a generic, mean-field theory of a hydrated gel in the presence of an additional solute which changes the elastic properties of the gel. We derive equations for the equilibrium binodal of the phase separation of the solvent and solute and show that the deformations induced by the solute can result in effective long-range interactions between phase-separating solutes that can either enhance or, in the case of externally applied pressure, suppress phase separation of the solute relative to the case where there is no gel. This causes the coexisting concentrations at the binodal to depend on the system-wide average concentration, in contrast to the situation for phase separation in the absence of the gel.
Eur Phys J E Soft Matter
· 2024 Feb · PMID 38372943
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We determine the local charge dynamics of a [Formula: see text] electrolyte embedded in a varying-section channel. By means of an expansion based on the length scale separation between the axial and transverse direction...We determine the local charge dynamics of a [Formula: see text] electrolyte embedded in a varying-section channel. By means of an expansion based on the length scale separation between the axial and transverse direction of the channel, we derive closed formulas for the local excess charge for both, dielectric and conducting walls, in 2D (planar geometry) as well as in 3D (cylindrical geometry). Our results show that, even at equilibrium, the local charge electroneutrality is broken whenever the section of the channel is not homogeneous for both dielectric and conducting walls as well as for 2D and 3D channels. Interestingly, even within our expansion, the local excess charge in the fluid can be comparable to the net charge on the walls. We critically discuss the onset of such local electroneutrality breakdown in particular with respect to the correction that it induces on the effective free energy profile experienced by tracer ions.
Eur Phys J E Soft Matter
· 2024 Feb · PMID 38372851
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The organization of live cells into tissues and their subsequent biological function involves inter-cell mechanical interactions, which are mediated by their elastic environment. To model this interaction, we consider ce...The organization of live cells into tissues and their subsequent biological function involves inter-cell mechanical interactions, which are mediated by their elastic environment. To model this interaction, we consider cells as spherical active force dipoles surrounded by an unbounded elastic matrix. Even though we assume that this elastic medium responds linearly, each cell's regulation of its mechanical activity leads to nonlinearities in the emergent interactions between cells. We study the many-body nature of these interactions by considering several geometries that include three or more cells. We show that for different regulatory behaviors of the cells' activity, the total elastic energy stored in the medium differs from the superposition of all two-body interactions between pairs of cells within the system. Specifically, we find that the many-body interaction energy between cells that regulate their position is smaller than the sum of interactions between all pairs of cells in the system, while for cells that do not regulate their position, the many-body interaction is larger than the superposition prediction. Thus, such higher-order interactions should be considered when studying the mechanics of multiple cells in proximity.
Eur Phys J E Soft Matter
· 2024 Feb · PMID 38358563
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Intrinsically disordered proteins (IDPs) are a subset of proteins that lack stable secondary structure. Given their polymeric nature, previous mean-field approximations have been used to describe the statistical structur...Intrinsically disordered proteins (IDPs) are a subset of proteins that lack stable secondary structure. Given their polymeric nature, previous mean-field approximations have been used to describe the statistical structure of IDPs. However, the amino-acid sequence heterogeneity and complex intermolecular interaction network have significantly impeded the ability to get proper approximations. One such case is the intrinsically disordered tail domain of neurofilament low (NFLt), which comprises a 50 residue-long uncharged domain followed by a 96 residue-long negatively charged domain. Here, we measure two NFLt variants to identify the impact of the NFLt two main subdomains on its complex interactions and statistical structure. Using synchrotron small-angle x-ray scattering, we find that the uncharged domain of the NFLt induces attractive interactions that cause it to self-assemble into star-like polymer brushes. On the other hand, when the uncharged domain is truncated, the remaining charged N-terminal domains remain isolated in solution with typical polyelectrolyte characteristics. We further discuss how competing long- and short-ranged interactions within the polymer brushes dominate their ensemble structure and, in turn, their implications on previously observed phenomena in NFL native and diseased states.
Granek R, Hoffmann I, Kelley EG
… +3 more, Nagao M, Vlahovska PM, Zilman A
Eur Phys J E Soft Matter
· 2024 Feb · PMID 38355850
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We consider the dynamic structure factor (DSF) of quasi-spherical vesicles and present a generalization of an expression that was originally formulated by Zilman and Granek (ZG) for scattering from isotropically oriented...We consider the dynamic structure factor (DSF) of quasi-spherical vesicles and present a generalization of an expression that was originally formulated by Zilman and Granek (ZG) for scattering from isotropically oriented quasi-flat membrane plaquettes. The expression is obtained in the form of a multi-dimensional integral over the undulating membrane surface. The new expression reduces to the original stretched exponential form in the limit of sufficiently large vesicles, i.e., in the micron range or larger. For much smaller unilamellar vesicles, deviations from the asymptotic, stretched exponential equation are noticeable even if one assumes that the Seifert-Langer leaflet density mode is completely relaxed and membrane viscosity is neglected. To avoid the need for an exhaustive numerical integration while fitting to neutron spin echo (NSE) data, we provide a useful approximation for polydisperse systems that tests well against the numerical integration of the complete expression. To validate the new expression, we performed NSE experiments on variable-size vesicles made of a POPC/POPS lipid mixture and demonstrate an advantage over the original stretched exponential form or other manipulations of the original ZG expression that have been deployed over the years to fit the NSE data. In particular, values of the membrane bending rigidity extracted from the NSE data using the new approximations were insensitive to the vesicle radii and scattering wavenumber and compared very well with expected values of the effective bending modulus ([Formula: see text]) calculated from results in the literature. Moreover, the generalized scattering theory presented here for an undulating quasi-spherical shell can be easily extended to other models for the membrane undulation dynamics beyond the Helfrich Hamiltonian and thereby provides the foundation for the study of the nanoscale dynamics in more complex and biologically relevant model membrane systems.
Eur Phys J E Soft Matter
· 2024 Feb · PMID 38319445
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Collective motion of chiral particles in complex noise environments is investigated based on the Vicsek model. In the model, we added chirality, along with complex noise, affecting particles clustering motion. Particles...Collective motion of chiral particles in complex noise environments is investigated based on the Vicsek model. In the model, we added chirality, along with complex noise, affecting particles clustering motion. Particles can only avoid noise interference in a specific channel, and this consideration is more realistic due to the complexity of the environment. Via simulations, we find that the channel proportion, p, critically influences chiral particle synchronization. Specifically, we observe a disorder-order transition at critical [Formula: see text], only when [Formula: see text], the system can achieve global synchronization. Combined with our definition of spatial distribution parameter and observation of the model, the reason is that particles begin to escape from the noise region under the influence of complex noise. In addition, the value of [Formula: see text] increases linearly with velocity, while it decreases monotonically with the increase in chirality and interaction radius. Interestingly, an appropriate noise amplitude minimizes [Formula: see text]. Our findings may inspire novel strategies to manipulate self-propelled particles of distinct chirality to achieve desired spatial migration and global synchronization.
Eur Phys J E Soft Matter
· 2024 Feb · PMID 38305841
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We present the macroscopic dynamics of ferroelectric smectic A, smectic , liquid crystals reported recently experimentally by three groups. In this fluid and orthogonal smectic phase, the macroscopic polarization, , is p...We present the macroscopic dynamics of ferroelectric smectic A, smectic , liquid crystals reported recently experimentally by three groups. In this fluid and orthogonal smectic phase, the macroscopic polarization, , is parallel to the layer normal thus giving rise to overall symmetry for this phase in the spatially homogeneous limit. A combination of linear irreversible thermodynamics and symmetry arguments is used to derive the resulting dynamic equations applicable at sufficiently low frequencies and sufficiently long wavelengths. Compared to non-polar smectic A phases, we find a static cross-coupling between compression of the layering and bending of the layers, which does not lead to elastic forces, but to elastic stresses. In addition, it turns out that a reversible cross-coupling between flow and the magnitude of the polarization modifies the velocities of both, first and second sound. At the same time, the relaxation of the polarization gives rise to dissipative effects for second sound at the same order of the wavevector as for the sound velocity. We also analyze reversible cross-coupling terms between elongational flow and electric fields as well as temperature and concentration gradients, which lend themselves to experimental detection. Apparently this type of terms has never been considered before for smectic phases. The question how the linear coupling in the energy alters the macroscopic response behavior when compared to usual non-polar smectic A phases is also addressed.
Eur Phys J E Soft Matter
· 2024 Jan · PMID 38281233
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The out-of-equilibrium character of active particles, responsible for accumulation at boundaries in confining domains, determines not-trivial effects when considering escape processes. Non-monotonous behavior of exit tim...The out-of-equilibrium character of active particles, responsible for accumulation at boundaries in confining domains, determines not-trivial effects when considering escape processes. Non-monotonous behavior of exit times with respect to tumbling rate (inverse of mean persistent time) appears, as a consequence of the competing processes of exploring the bulk and accumulate at boundaries. By using both 1D analytical results and 2D numerical simulations of run-and-tumble particles with different behaviours at boundaries, we scrutinize this very general phenomenon of active matter, evidencing the role of accumulation at walls for the existence of optimal tumbling rates for fast escapes.
Alfken J, Neuhaus C, Major A
… +9 more, Taskina A, Hoffmann C, Ganzella M, Petrovic A, Zwicker D, Fernández-Busnadiego R, Jahn R, Milovanovic D, Salditt T
Eur Phys J E Soft Matter
· 2024 Jan · PMID 38270681
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We study the formation of vesicle condensates induced by the protein synapsin, as a cell-free model system mimicking vesicle pool formation in the synapse. The system can be considered as an example of liquid-liquid phas...We study the formation of vesicle condensates induced by the protein synapsin, as a cell-free model system mimicking vesicle pool formation in the synapse. The system can be considered as an example of liquid-liquid phase separation (LLPS) in biomolecular fluids, where one phase is a complex fluid itself consisting of vesicles and a protein network. We address the pertinent question why the LLPS is self-limiting and stops at a certain size, i.e., why macroscopic phase separation is prevented. Using fluorescence light microscopy, we observe different morphologies of the condensates (aggregates) depending on the protein-to-lipid ratio. Cryogenic electron microscopy then allows us to resolve individual vesicle positions and shapes in a condensate and notably the size and geometry of adhesion zones between vesicles. We hypothesize that the membrane tension induced by already formed adhesion zones then in turn limits the capability of vesicles to bind additional vesicles, resulting in a finite condensate size. In a simple numerical toy model we show that this effect can be accounted for by redistribution of effective binding particles on the vesicle surface, accounting for the synapsin-induced adhesion zone.
Eur Phys J E Soft Matter
· 2024 Jan · PMID 38261239
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In this work we have monitored the multiple stages of the normal traction force response of a yield-stress fluid confined between two circular parallel plates that are separated at constant velocity. At narrow initial ga...In this work we have monitored the multiple stages of the normal traction force response of a yield-stress fluid confined between two circular parallel plates that are separated at constant velocity. At narrow initial gaps, the air-fluid interface suffers from the Saffman-Taylor instability, confirmed by visual inspection of fingering patterns imprinted on the fluid. At larger initial gaps, the fluid preserves the initially imposed circular symmetry of the confining plates, indicating the absence of instability. Due to the system characteristics and experimental environment, the multiple traction force contributions occurred in cascade, permitting us to isolate the adhesion responses associated with viscosity, capillarity, and yield stress. Employing a standard Herschel-Bulkley model, we assessed the scaling of the traction force in multiple regimes-specifically, evaluating the dependencies of the fingering to yield-stress transitions.
Eur Phys J E Soft Matter
· 2024 Jan · PMID 38252375
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We compute the free energy of confinement [Formula: see text] for a wormlike chain (WLC), with persistence length [Formula: see text], that is confined to the surface of a cylinder of radius R under an external tension f...We compute the free energy of confinement [Formula: see text] for a wormlike chain (WLC), with persistence length [Formula: see text], that is confined to the surface of a cylinder of radius R under an external tension f using a mean field variational approach. For long chains, we analytically determine the behavior of the chain in a variety of regimes, which are demarcated by the interplay of [Formula: see text], the Odijk deflection length ([Formula: see text]), and the Pincus length ([Formula: see text], with [Formula: see text] being the thermal energy). The theory accurately reproduces the Odijk scaling for strongly confined chains at [Formula: see text], with [Formula: see text]. For moderate values of f, the Odijk scaling is discernible only when [Formula: see text] for strongly confined chains. Confinement does not significantly alter the scaling of the mean extension for sufficiently high tension. The theory is used to estimate unwrapping forces for DNA from nucleosomes.