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) 12928941  ISSN (Online) 1292895X Published by SpringerVerlag [2469 journals] 
 Actomyosin contractility requirements and reciprocal cellâ€“tissue
mechanics for cancer cell invasion through collagenbased channels
Free preprint version: Loading...Rate this result: What is this?Please help us test our new preprint finding feature by giving the preprint link a rating.
A 5 star rating indicates the linked preprint has the exact same content as the published article.
Abstract: The interstitial tumor microenvironment is composed of heterogeneously organized collagenrich porous networks as well as channellike structures and interfaces which provide both barriers and guidance for invading cells. Tumor cells invading 3D random porous collagen networks depend upon actomyosin contractility to deform and translocate the nucleus, whereas Rho/Rhoassociated kinasedependent contractility is largely dispensable for migration in stiff capillarylike confining microtracks. To investigate whether this dichotomy of actomyosin contractility dependence also applies to physiological, deformable linear collagen environments, we developed nearly barrierfree collagenscaffold microtracks of varying cross section using twophoton laser ablation. Both very narrow and wide tracks supported singlecell migration by either outward pushing of collagen up to four times when tracks were narrow, or cell pulling on collagen walls down to 50% of the original diameter by traction forces of up to 40 nN when tracks were wide, resulting in track widths optimized to singlecell diameter. Targeting actomyosin contractility by synthetic inhibitors increased cell elongation and nuclear shape change in narrow tracks and abolished cellmediated deformation of both wide and narrow tracks. Accordingly, migration speeds in all channel widths reduced, with migration rates of around 4565% of the original speed persisting. Together, the data suggest that cells engage actomyosin contraction to reciprocally adjust both own morphology and linear track width to optimal size for effective cellular locomotion. Graphic abstract
PubDate: 20220516

 Translationâ€“deformation coupling effects on the Rayleigh instability of
an electrodynamically levitated charged droplet
Free preprint version: Loading...Rate this result: What is this?Please help us test our new preprint finding feature by giving the preprint link a rating.
A 5 star rating indicates the linked preprint has the exact same content as the published article.
Abstract: The breakup pathway of the Rayleigh fission process observed in the past experiments carried out using highspeed imaging of a charged drop levitated in an AC quadrupole trap has shown to exhibit several cycles of shape and centerofmass oscillations followed by asymmetric breakup by ejecting a jet in the upward direction (i.e., opposite to the direction of gravity). We recently attempted to explain this using boundary integral simulations in the Stokes flow limit, wherein the position of the droplet and the polarity of the end cap electrodes were assigned using physical arguments, and the centerofmass motion was not estimated consistently invoking quasistatic conditions. In this work, we explain the experimental observation of upward breakup of charged droplets in a quadrupolar field, using numerical calculations based on the boundary element method considering inviscid droplets levitated electrodynamically using quadrupole electric fields. The centerofmass motion and the end cap are consistently calculated in the numerical scheme. The simulations show that the gravityinduced downward shift in the equilibrium position of the drop in the trap causes significant, largeamplitude shape oscillations superimposed over the centerofmass oscillations of the drop. An important observation here is that the shape oscillations due to the applied quadrupole fields result in sufficient deformations that act as triggers for the onset of the instability below the Rayleigh limit, thereby admitting a subcritical instability. The centerofmass oscillations of the droplet within the trap, which follow the applied frequency, are out of phase with the applied AC signal. Thus the combined effect of shape deformations and dynamic position of the drop leads to an asymmetric breakup such that the Rayleigh fission occurs upward via the ejection of a jet at the north pole of the deformed drop. Graphical abstract
PubDate: 20220513

 Correction to: A biaxial tensional model for early vertebrate
morphogenesis
Free preprint version: Loading...Rate this result: What is this?Please help us test our new preprint finding feature by giving the preprint link a rating.
A 5 star rating indicates the linked preprint has the exact same content as the published article.
Abstract: A Correction to this paper has been published: 10.1140/epje/s10189022001844
PubDate: 20220512

 Thermogravitational separation in porous vertical and horizontal
cylindrical annular cells saturated by a binary mixture
Free preprint version: Loading...Rate this result: What is this?Please help us test our new preprint finding feature by giving the preprint link a rating.
A 5 star rating indicates the linked preprint has the exact same content as the published article.
Abstract: In this paper, analytical and numerical studies of species separation in vertical and horizontal porous, cylindrical annular cells were presented. The binary fluid, saturating the porous medium, is a water–ethanol mixture. The thickness e of the horizontal and vertical columns is equal to \(R_oR_i\) , where \(R_i\) and \(R_o\) are, respectively, the internal and the external radii. H is the height of the vertical cell, and the length of the horizontal cell. Constant temperatures, \(T_{\mathrm{hot}}\) and \(T_{\mathrm{cold}}\) , were imposed on the inner and outer cylinders. Since an important species separation, in thermogravitational column (TGC), is obtained for \(e<<H\) , the same assumption was made for the two configurations. The analytical solution was obtained using the parallel flow approximation for both configurations. The governing equations were solved numerically for 2D and 3D configurations using two different software (Comsol Multiphysics and a spectral collocation method with Gauss–Lobatto–Chebyshev points). Velocity, temperature, mass fraction fields and time to reach steady state were compared for the two configurations. The amount of species separated at the top or the bottom of each cell was also compared for each configuration. Graphical abstract
PubDate: 20220512

 Measuring the average cell size and width of its distribution in cellular
tissues using Fourier transform
Free preprint version: Loading...Rate this result: What is this?Please help us test our new preprint finding feature by giving the preprint link a rating.
A 5 star rating indicates the linked preprint has the exact same content as the published article.
Abstract: We present an indepth investigation of a fully automated Fourierbased analysis to determine the cell size and the width of its distribution in 3D biological tissues. The results are thoroughly tested using generated images, and we offer valuable criteria for image acquisition settings to optimize accuracy. We demonstrate that the most important parameter is the number of cells in the field of view, and we show that accurate measurements can already be made on volume only containing \(3\times 3\times 3\) cells. The resolution in z is also not so important, and a reduced number of indepth images, of order of one per cell, already provides a measure of the mean cell size with less than 5% error. The technique thus appears to be a very promising tool for very fast live local volume cell measurement in 3D tissues in vivo while strongly limiting photobleaching and phototoxicity issues. Graphic abstract
PubDate: 20220509

 Effect of an excess of surfactant on thermophoresis, mass diffusion and
viscosity in an oily surfactantstabilized ferrofluid
Free preprint version: Loading...Rate this result: What is this?Please help us test our new preprint finding feature by giving the preprint link a rating.
A 5 star rating indicates the linked preprint has the exact same content as the published article.
Abstract: The effect of an excess of surfactant on the thermophoresis of a sterically stabilized ferrofluid is investigated experimentally by forced Rayleigh scattering (FRS). The experiments are performed with a stable magnetic fluid sample to which controlled amounts of surfactant are added. A decrease in the thermally induced transport of magnetic nanoparticles is observed while increasing the temperature T. The positive Soret coefficient \(S_{\mathrm{T}}\) decreases by adding 2 vol% of surfactant at room temperature. As shown by FRS relaxation, this decreasing is mainly associated with a reduction of the interaction between the carrier fluid and individual nanoparticles. No significant effect of extra surfactant on the sign of \(S_{\mathrm{T}}\) is observed at higher T’s (up to \(\sim \,85\,^{\circ }\) C). Dynamic light scattering at room temperature reveals the presence of a small amount of clusters/aggregates in the samples, which are hardly detectable by FRS relaxation. The presence of these small clusters/aggregates is confirmed by a rheological probing of the fluid properties. Whatever T, a small amount of added surfactant first causes a decrease of the ferrofluid viscosity, associated with a 10% decreasing of the flow activation energy. Further on, viscosity and activation energy both recover at higher excess surfactant concentrations. These results are analyzed in terms of saturation of the surfactant layer, concentration of free surfactant chains and heat of transport of the nanoparticles. Graphic abstract
PubDate: 20220505

 Predicting thermodiffusion in simple binary fluid mixtures

Free preprint version: Loading...Rate this result: What is this?Please help us test our new preprint finding feature by giving the preprint link a rating.
A 5 star rating indicates the linked preprint has the exact same content as the published article.
Abstract: The predictive capabilities of some existing theoretical models to quantify thermodiffusion have been investigated in this work. To do so, the tests have been performed on two model fluids, the hardsphere and the LennardJones (including spheres and dimers) ones, exploring different mixtures and thermodynamic conditions thanks to extensive molecular simulations. It has been confirmed that the thermal diffusion factor should be expressed as the sum of one term related to the isotope effect and one term related to the “chemical” effects and that a kinetic term is required to quantify thermodiffusion from the gas state to the liquid state. In addition, regarding the isotope effects, it has been obtained that none of the available theoretical models are able to yield a reasonable prediction relatively to the molecular simulations results and that the moment of inertia contribution is one order of magnitude smaller than the mass contribution in the liquid state. Finally, concerning the chemical effects, it has been shown the Shukla and Firoozabadi model, complemented with a kinetic term, is probably the most reasonable option to estimate the chemical contribution to the thermal diffusion factor, even if it fails in capturing the effect of the asymmetry in size and in shape between the species. Overall, this works confirms that there is still a lack of a generic model able to predict accurately thermal diffusion factors, or equivalently Soret coefficient, in simple binary mixtures from the gas state to the liquid state. Graphical abstract
PubDate: 20220504

 Soret separation and thermoosmosis in porous media

Free preprint version: Loading...Rate this result: What is this?Please help us test our new preprint finding feature by giving the preprint link a rating.
A 5 star rating indicates the linked preprint has the exact same content as the published article.
Abstract: When a temperature difference is applied over a porous medium soaked with a fluid mixture, two effects may be observed, a component separation (the Ludwig–Soret effect, thermodiffusion) and a pressure difference due to thermoosmosis. In this work, we have studied both effects using nonequilibrium thermodynamics and molecular dynamics. We have derived expressions for the two characteristic parameters, the Soret coefficient and the thermoosmotic coefficient in terms of phenomenological transport coefficients, and we show how they are related. Numerical values for these coefficients were obtained for a twocomponent fluid in a solid matrix where both fluid and solid are Lennard–Jones/spline particles. We found that both effects depend strongly on the porosity of the medium and weakly on the interactions between the fluid components and the matrix. The Soret coefficient depends strongly on whether the fluid is sampled from inside the porous medium or from bulk phases outside, which must be considered in experimental measurements using packed columns. If we use a methane/decane mixture in bulk as an example, our results for the Soret coefficient give that a temperature difference of 10 K will separate the mixture to about 49.5/50.5 and give no pressure difference. In a reservoir with 30% porosity, the separation will be 49.8/50.2, whereas the pressure difference will be about 15 bar. Thermoosmotic pressures with this order or magnitude have been observed in frostheave experiments. Graphic abstract
PubDate: 20220503

 Nonlinearities in shadowgraphy experiments on nonequilibrium fluctuations
in polymer solutions
Free preprint version: Loading...Rate this result: What is this?Please help us test our new preprint finding feature by giving the preprint link a rating.
A 5 star rating indicates the linked preprint has the exact same content as the published article.
Abstract: Giant thermal and solutal nonequilibrium fluctuations are observed in shadowgraphy experiments on liquid mixtures subjected to a temperature gradient. For large temperature differences, both the temperature and the composition dependence of the relevant thermophysical parameters and the nonlinear terms in the diffusion equation need to be taken into account, leading to a nonlinear concentration profile. For temperature differences exceeding the inverse of the Soret coefficient, in our example approximately 10 K, the usual data evaluation yields increasingly wrong diffusion and Soret coefficients that are off by almost a factor of two for a temperature difference of 50 K. A local model that treats the measured shadowgraph signal as a superposition of the contributions from every layer of the sample is able to capture the essential trend and yields a good agreement with experimental data. The results are important for the application of shadowgraphy as a tool for the measurement of Soret and diffusion coefficients, where large temperature gradients promise a good signaltonoise ratio. Graphical abstract
PubDate: 20220426

 Hydrodynamics of electrocapillarity propelled nonNewtonian droplets
through microconfinements
Free preprint version: Loading...Rate this result: What is this?Please help us test our new preprint finding feature by giving the preprint link a rating.
A 5 star rating indicates the linked preprint has the exact same content as the published article.
Abstract: In this article, we theoretically explore the dynamics of droplet motion and its evolution during electrocapillarity propelled actuation within microfluidic systems. The study covers a wide gamut of fluids, wherein we investigate the dynamics of both pseudoplastic and dilatant fluid droplets. It is observed that change in the fluid rheology of the nonNewtonian fluids leads to significant morphing of the droplet dynamics during the actuation and propulsion event when compared to the Newtonian counterparts. We validate the theory using experimental reports on similar systems employing Newtonian droplets. The influence of governing parameters such as the actuation voltage and its transients, dielectric layer thickness on the electrodes and electrode spacing is probed. We also explore the influence of the interfacial properties of the system, such as channel wall friction, droplet wettability, and capillary friction, and establish that the fluid rheology, in conjunction with the interfacial features regulate the electroactuation and propulsion of the droplets. We further provide theoretical estimates on the optimal design of the electroactuation system in terms of a proposed electrointerfacial tension parameter. The findings may hold significance towards design and development of microfluidics with electroactuation systems. Graphical
PubDate: 20220425

 Traveling waves of a colloidal suspension in a closed cell

Free preprint version: Loading...Rate this result: What is this?Please help us test our new preprint finding feature by giving the preprint link a rating.
A 5 star rating indicates the linked preprint has the exact same content as the published article.
Abstract: Twodimensional oscillatory flows in the convective cell filled with a colloidal suspension are investigated. We consider transient and permanent evolution scenarios of the traveling wave that were found in experimental investigation (Donzelli et al. in Phys Rev Lett 102:104503, 2009). The nanoparticle transport mechanisms (thermodiffusion and gravity settling) are analyzed and elucidated with the help of finitedifference numerical simulations for Hyflon MFA colloidal suspension. The spatiotemporal characteristics of the stable (permanent) traveling waves are determined. The dependence of the Rayleigh number on the Lewis number at the boundary of existence of the stable traveling wave is obtained. Graphic abstract
PubDate: 20220425

 Mass effects for thermodiffusion in dilute aqueous solutions

Free preprint version: Loading...Rate this result: What is this?Please help us test our new preprint finding feature by giving the preprint link a rating.
A 5 star rating indicates the linked preprint has the exact same content as the published article.
Abstract: Thermodiffusion is the phenomenon by which molecules in a mixture present concentration gradients in response to an imposed temperature gradient. Despite decades of investigations, this effect remains poorly understood at a molecular level. A common, phenomenological approach is to individuate the molecular factors that influence the Soret coefficient, the parameter that quantifies the resulting concentrationgradient. Experimental studies, often performed on organic mixtures, as well as simulations of model particle systems have evidenced that the difference in masses between the mixture components has an important effect on the amplitude of the Soret coefficient. Here, we use molecular dynamics simulations of a thermophoretic setting to investigate the mass dependence of the Soret coefficient in dilute aqueous solutions. An advantage of simulation approaches is that they are not limited in the range of explored molecular masses, which is often limited to isotopic substitutions in the experiments. Our simulations reveal that the mass dependence of the Soret coefficient in these solutions is in agreement with previous experimental and simulation work on molecularsize systems. In particular, it is sensitive to the relative mass difference between the solute and the solvent, but not to their absolute mass. Adjusting the mass of the solvent and of the solute can turn a thermophobic solution into a thermophilic one, where solute accumulation is reversed. This demonstrates that the mass effect can indeed compensate for the other contributions to the Soret coefficient. Finally, we find that changing the molecular moments of inertia has a much more limited impact as compared to a change in the total molecular mass. Graphical
PubDate: 20220421

 Finite dimension and particle heterogeneous DLAs

Free preprint version: Loading...Rate this result: What is this?Please help us test our new preprint finding feature by giving the preprint link a rating.
A 5 star rating indicates the linked preprint has the exact same content as the published article.
Abstract: We study heterogeneous Diffusion Limited Aggregates (DLAs) i.e. those formed by a mixture, in different proportions, of 4legged and 2legged particles. We fixed the total number of particles, let the proportions vary, and computed their finite dimension, a recent addition to the list of “fractal” dimensions. At one extreme, when all particles are 4legged, the corresponding DLAs are complex, fractal structures whose appearance resembles very much that of the DLAs that occur in Nature. At the other extreme, when almost all particles are 2legged, the DLAs lose much of their complexity and acquire long rectilinear stretches so that their appearance resembles more and more the structure of the underlying lattice. We expected the complexity in between would decrease monotonically, and this would be reflected in the finite dimension of the corresponding DLAs. However, the finite dimension first increases and then, when the proportion of 4legged to 2legged particles is about 30 to 70, starts decreasing. In the paper, we study and explain the mechanisms behind this unexpected, counterintuitive behaviour. Graphical abstract
PubDate: 20220420

 Forcevelocity relation and loadsharing in the linear polymerization
ratchet revisited: the effects of barrier diffusion
Free preprint version: Loading...Rate this result: What is this?Please help us test our new preprint finding feature by giving the preprint link a rating.
A 5 star rating indicates the linked preprint has the exact same content as the published article.
Abstract: We study the velocityforce (VF) relation for a Brownian ratchet consisting of a linear rigid polymer growing against a diffusing barrier, acted upon by a opposing constant force (F). Using a careful mathematical analysis, we derive the VF relations in the extreme limits of fast and slow barrier diffusion. In the first case, V depends exponentially on the load F, in agreement with the wellknown formula proposed by Peskin, Odell and Oster (1993), while the relationship becomes linear in the second case. For a bundle of two filaments growing against a common barrier, equal sharing of load in the corresponding VF relation is predicted by a meanfield argument in both limits. However, the scaling behaviour of velocity with the number of filaments is different for the two cases. In the limit of large D, the validity of the meanfield approach is tested, and partially supported by a detailed and rigorous analysis. Our principal predictions are also verified in numerical simulations. Graphic abstract
PubDate: 20220413

 Correction to: Efficient eventdriven simulations of hard spheres

Free preprint version: Loading...Rate this result: What is this?Please help us test our new preprint finding feature by giving the preprint link a rating.
A 5 star rating indicates the linked preprint has the exact same content as the published article.
PubDate: 20220411

 Internucleosomal potentials from nucleosomal positioning data

Free preprint version: Loading...Rate this result: What is this?Please help us test our new preprint finding feature by giving the preprint link a rating.
A 5 star rating indicates the linked preprint has the exact same content as the published article.
Abstract: Abstract No systematic method exists to derive internucleosomal potentials between nucleosomes along a chromosome consistently across a given genome. Such potentials can yield information on nucleosomal ordering, thermal as well as mechanical properties of chromosomes. Thus, indirectly, they shed light on a possible mechanical genomic code along a chromosome. To develop a method yielding effective internucleosomal potentials between nucleosomes, a generalized LennardJones potential for the parameterization is developed based on nucleosomal positioning data. This approach eliminates some of the problems that the underlying nucleosomal positioning data have, rendering the extraction difficult on the individual nucleosomal level. Furthermore, patterns on which to base a classification along a chromosome appear on larger domains, such as hetero and euchromatin. An intuitive selection strategy for the noisy optimization problem is employed to derive effective exponents for the generalized potential. The method is tested on the Candida albicans genome. Applying kmeans clustering based on potential parameters and thermodynamic compressibilities, a genomewide clustering of nucleosome sequences is obtained for C. albicans. This clustering shows that a chromosome beyond the classical dichotomic categories of hetero and euchromatin is more featurerich.
PubDate: 20220411

 A physical mechanism underlying the torque generation of the bacterial
flagellar motor
Free preprint version: Loading...Rate this result: What is this?Please help us test our new preprint finding feature by giving the preprint link a rating.
A 5 star rating indicates the linked preprint has the exact same content as the published article.
Abstract: This study proposes a physical mechanism underlying the torque generation of a bacterial flagellar motor (BFM), in which the torque for the rotation of the rotor can be generated from impulsive forces resulting from collisions between the randomly moving stator and rotor. The torque required for the rotation of the rotor may be generated through two coexisting mechanisms: mechanism (A), in which the stator collides with the rotor, whose rotation axis fluctuates asymmetrically, generating a torque in the direction of the rod, and mechanism (B), in which physical collisions between the stator and the asymmetric \(\hbox {FliG}_{{\mathrm{N}}\, }\) and \(\hbox {FliG}_{{\mathrm{M}}}\) generate the torque in the direction of the rod. Mechanism (A) might be related the bidirectional rotation and the tumbling of the motion of the cell. Mechanism (B) might be related to occurrence of the steps in the time traces of the rotational angle, backward stepping or switching of the rotational direction, and the kneeshaped \(\uptau _{{\mathrm{ext}}}\) – \(\upomega \) relation. The abovementioned characteristics of the rotation of BFM are reproduced in a model device designed to confirm the applicability of the proposed concept to real BFM. Moreover, a prediction of the disappearance of the kneeshaped \(\uptau _{\mathrm{ext}}\) – \(\upomega \) relation of the actual BFM at a high temperature is proposed. Graphic abstract
PubDate: 20220411

 A biaxial tensional model for early vertebrate morphogenesis

Free preprint version: Loading...Rate this result: What is this?Please help us test our new preprint finding feature by giving the preprint link a rating.
A 5 star rating indicates the linked preprint has the exact same content as the published article.
Abstract: We propose a simple biaxial tensional model which is able to reproduce at a qualitative level several aspects of early stages of vertebrate morphogenesis. The model is based on subsequent excitable contractions of an orthoradial and periclinal (radial) set of contracting lines, which generate first the basic embryonic pattern (a motile tube), and second the lateral orifices such as ears, eyes, mouth, gills, etc. An important aspect of the model is the selfarresting character of the process, akin to wound healing. At later stages, the biaxial lines may also work in extension, and this generates a developmental feedback which is quadratic with respect to curvature. Graphic abstract
PubDate: 20220408

 Spontaneous flow created by active topological defects

Free preprint version: Loading...Rate this result: What is this?Please help us test our new preprint finding feature by giving the preprint link a rating.
A 5 star rating indicates the linked preprint has the exact same content as the published article.
Abstract: Topological defects are at the root of the largescale organization of liquid crystals. In twodimensional active nematics, two classes of topological defects of charges \(\pm 1/2\) are known to play a major role due to active stresses. Despite this importance, few analytical results have been obtained on the flowfield and activestress patterns around active topological defects. Using the generic hydrodynamic theory of active systems, we investigate the flow and stress patterns around these topological defects in unbounded, twodimensional active nematics. Under generic assumptions, we derive analytically the spontaneous velocity and stall force of selfadvected defects in the presence of both shear and rotational viscosities. Applying our formalism to the dynamics of monolayers of elongated cells at confluence, we show that the nonconservation of cell number generically increases the selfadvection velocity and could provide an explanation for their observed role in cellular extrusion and multilayering. We finally investigate numerically the influence of the Ericksen stress. Our work paves the way to a generic study of the role of topological defects in active nematics, and in particular in monolayers of elongated cells. Graphical abstract
PubDate: 20220407

 Effect of varying load in moving period of a step on dynamics of molecular
motors
Free preprint version: Loading...Rate this result: What is this?Please help us test our new preprint finding feature by giving the preprint link a rating.
A 5 star rating indicates the linked preprint has the exact same content as the published article.
Abstract: During the processive stepping of a molecular motor on its polar track, a step consists of a long dwell period and a very short moving period. In single molecule optical trapping experiments to determine the load dependence of the motor dynamics, although the motor experiences a constant load during the dwell period, it experiences a varying load during the moving period. However, in previous theoretical studies to explain the single molecule optical trapping data, it was simply assumed that the motor experiences a constant load during both the dwell period and the following moving period. Thus, an important but unclear issue is whether the assumption is appropriate in the theoretical studies. Here, we take kinesin and myosinV as examples to study theoretically the motor dynamics with the consideration of the varying load during the moving period and compare with that with the assumption of the constant load. The studies show that in the optical trapping experiments employed in the literature, for the kinesin with a small step size of about 8 nm it is a good approximation to make the theoretical studies by assuming that the motor experiences the constant load during the moving period. For the myosinV with a large step size of about 36 nm, there are small but noticeable deviations of the results obtained by considering that the motor experiences the varying load during the moving period from those by assuming that the motor experiences the constant load. Graphical abstract .
PubDate: 20220323
