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EPJ E - Soft Matter and Biological Physics
Journal Prestige (SJR): 0.489 Citation Impact (citeScore): 1 Number of Followers: 1 Hybrid journal (It can contain Open Access articles) ISSN (Print) 1292-8941 - ISSN (Online) 1292-895X Published by Springer-Verlag [2573 journals] |
- Activated complex theory of nucleation
- Abstract: . A new nucleation theory is presented. This theory is based on the assumption that a critical nucleus of the new phase can be regarded as an activated complex that passes through the top of the energy barrier. In the framework of the proposed approach, an equation in a general form for the nucleation rate is obtained. This equation is used to obtain the calculated data in the case of homogeneous nucleation at the vapor-liquid, liquid-vapor, and liquid-solid phase transitions. A comparison of the calculated data with the available experimental data as well as with the calculated data obtained in the framework of the classical nucleation theory is carried out. From a comparison between the calculated data obtained in the framework of the presented theory and the experimental data for the supercooled water-ice phase transition, the dependence on temperature of the surface tension coefficient between supercooled water and ice is determined. Graphical abstract
PubDate: 2019-03-26
- Abstract: . A new nucleation theory is presented. This theory is based on the assumption that a critical nucleus of the new phase can be regarded as an activated complex that passes through the top of the energy barrier. In the framework of the proposed approach, an equation in a general form for the nucleation rate is obtained. This equation is used to obtain the calculated data in the case of homogeneous nucleation at the vapor-liquid, liquid-vapor, and liquid-solid phase transitions. A comparison of the calculated data with the available experimental data as well as with the calculated data obtained in the framework of the classical nucleation theory is carried out. From a comparison between the calculated data obtained in the framework of the presented theory and the experimental data for the supercooled water-ice phase transition, the dependence on temperature of the surface tension coefficient between supercooled water and ice is determined. Graphical abstract
- Tonks-Frenkel instability in electrolyte under high-frequency AC electric
fields- Abstract: . The instability of an electrolyte surface to a high-frequency, 10 to 200kHz, electric field, normal to the interface is investigated theoretically. From a practical viewpoint, such a high frequency leads to the absence of undesired electrochemical reactions and provides an additional control parameter. The theory of unsteady electric double layer by Barrero and Ramos is exploited. At such a high frequency, which is much larger than the eigenfrequency of the mechanical system, the nonlinear mechanical term does not “feel” the fast part of the Coulomb force, but it feels its slower component. In fact, the system behaves as if the electric field were a DC field. The observed instability is qualitatively close to the Tonks-Frenkel instability. The problem of the linear stability of the 1D quiescent stationary solution is solved analytically. For the important limiting cases, simple analytical formulas are derived. The linear stability analysis is complemented by the DNS of the full nonlinear system of equations with broadband low-amplitude white-noise initial conditions. After a transition period, the linear instability mechanism filters out the broad spectrum except for a narrow band near the maximum growth rate in rather good agreement with the linear stability analysis. If the external field is large enough, the nonlinear evolution results in coherent structures with sharp tips resembling to a Taylor cone. An evaluation of the cone angle for different conditions gives its value of about 30° to 60° , which is smaller than the angle of 98.6° for DC field and qualitatively corresponds to the experiments (L.Y. Yeo et al., Phys. Rev. Lett. 92, 133902 (2004)) for the high-frequency AC field and to the theoretical evaluation of the AC Taylor cones in E.A. Demekhin et al., Phys. Rev. E 84, 035301(R) (2011). Graphical abstract
PubDate: 2019-03-26
- Abstract: . The instability of an electrolyte surface to a high-frequency, 10 to 200kHz, electric field, normal to the interface is investigated theoretically. From a practical viewpoint, such a high frequency leads to the absence of undesired electrochemical reactions and provides an additional control parameter. The theory of unsteady electric double layer by Barrero and Ramos is exploited. At such a high frequency, which is much larger than the eigenfrequency of the mechanical system, the nonlinear mechanical term does not “feel” the fast part of the Coulomb force, but it feels its slower component. In fact, the system behaves as if the electric field were a DC field. The observed instability is qualitatively close to the Tonks-Frenkel instability. The problem of the linear stability of the 1D quiescent stationary solution is solved analytically. For the important limiting cases, simple analytical formulas are derived. The linear stability analysis is complemented by the DNS of the full nonlinear system of equations with broadband low-amplitude white-noise initial conditions. After a transition period, the linear instability mechanism filters out the broad spectrum except for a narrow band near the maximum growth rate in rather good agreement with the linear stability analysis. If the external field is large enough, the nonlinear evolution results in coherent structures with sharp tips resembling to a Taylor cone. An evaluation of the cone angle for different conditions gives its value of about 30° to 60° , which is smaller than the angle of 98.6° for DC field and qualitatively corresponds to the experiments (L.Y. Yeo et al., Phys. Rev. Lett. 92, 133902 (2004)) for the high-frequency AC field and to the theoretical evaluation of the AC Taylor cones in E.A. Demekhin et al., Phys. Rev. E 84, 035301(R) (2011). Graphical abstract
- Influence of tetrahedral order on ferromagnetic gel phases
- Abstract: . We investigate the macroscopic dynamics of gels with tetrahedral/octupolar symmetry, which possess in addition a spontaneous permanent magnetization. We derive the corresponding static and dynamic macroscopic equations for a phase, where the magnetization is parallel to one of the improper fourfold tetrahedral symmetry axes. Apart from elastic strains, we take into account relative rotations between the magnetization and the elastic network. The influence of tetrahedral order on these degrees of freedom is investigated and some experiments are proposed that are specific for such a material and allow to indirectly detect tetrahedral order. We also consider the case of a transient network and predict that stationary elastic shear stresses arise when a temperature gradient is applied. Graphical abstract
PubDate: 2019-03-25
- Abstract: . We investigate the macroscopic dynamics of gels with tetrahedral/octupolar symmetry, which possess in addition a spontaneous permanent magnetization. We derive the corresponding static and dynamic macroscopic equations for a phase, where the magnetization is parallel to one of the improper fourfold tetrahedral symmetry axes. Apart from elastic strains, we take into account relative rotations between the magnetization and the elastic network. The influence of tetrahedral order on these degrees of freedom is investigated and some experiments are proposed that are specific for such a material and allow to indirectly detect tetrahedral order. We also consider the case of a transient network and predict that stationary elastic shear stresses arise when a temperature gradient is applied. Graphical abstract
- Transport of dynamic biochemical signals in a microfluidic single cell
trapping channel with varying cross-sections- Abstract: . Dynamic biochemical signal control in vitro is important in the study of cellular responses to dynamic biochemical stimuli in microenvironment in vivo. To this end, we designed a microfluidic single cell trapping channel with varying cross-sections. In this work, we analyzed the transport of dynamic biochemical signals in steady and non-reversing pulsatile flows in such a microchannel. By numerically solving the 2D time-dependent Taylor-Aris dispersion equation, we studied the transport mechanism of different signals with varying parameters. The amplitude spectrum in steady flow shows that the trapping microchannel acts as a low-pass filter due to the longitudinal dispersion. The input signal can be modulated nonlinearly by the pulsatile flow. In addition, the nonlinear modulation effects are affected by the pulsatile flow frequency, the pulsatile flow amplitude and the average flow rate. When the flow frequency is much smaller or larger than that of the biochemical signal, the signal can be transmitted more efficiently. Besides, smaller pulsatile flow amplitude and larger average flow rate can decrease the nonlinear modulation and promote the signal transmission. These results demonstrate that in order to accurately load a desired dynamic biochemical signal to the trapped cell to probe the cellular dynamic response to the dynamic biochemical stimulus, the transport mechanism of the signals in the microchannel should be carefully considered. Graphical abstract
PubDate: 2019-03-21
- Abstract: . Dynamic biochemical signal control in vitro is important in the study of cellular responses to dynamic biochemical stimuli in microenvironment in vivo. To this end, we designed a microfluidic single cell trapping channel with varying cross-sections. In this work, we analyzed the transport of dynamic biochemical signals in steady and non-reversing pulsatile flows in such a microchannel. By numerically solving the 2D time-dependent Taylor-Aris dispersion equation, we studied the transport mechanism of different signals with varying parameters. The amplitude spectrum in steady flow shows that the trapping microchannel acts as a low-pass filter due to the longitudinal dispersion. The input signal can be modulated nonlinearly by the pulsatile flow. In addition, the nonlinear modulation effects are affected by the pulsatile flow frequency, the pulsatile flow amplitude and the average flow rate. When the flow frequency is much smaller or larger than that of the biochemical signal, the signal can be transmitted more efficiently. Besides, smaller pulsatile flow amplitude and larger average flow rate can decrease the nonlinear modulation and promote the signal transmission. These results demonstrate that in order to accurately load a desired dynamic biochemical signal to the trapped cell to probe the cellular dynamic response to the dynamic biochemical stimulus, the transport mechanism of the signals in the microchannel should be carefully considered. Graphical abstract
- The influences of “gas” viscosity on water entry of
hydrophobic spheres- Abstract: . An extremely thin gas film was found between a sphere and a free surface when the sphere impacted onto a water pool. That might influence the generation and evolution of water entry cavity. However, it is quite difficult to be captured through normal numerical and experimental tests. In this work, by using a finite element method we investigate the water entry of a hydrophobic sphere with gas viscosity artificially increased. The air film rupture in the early stage, contact line dynamics on a curved solid surface, and air pocket formation are investigated. The numerical results reveal that the lifetime of the gas film can be predicted by a viscous squeezing flow model qualitatively well. That relates to the fact that the gas film is much thinner than the diameter of the sphere, even when the gas viscosity is 100 times as large as the liquid one. However, inviscid flow can be found in the most part of the liquid bulk. The free surface profile (or the gas film profile) is then determined by the impact speed, namely the Weber number. More importantly, after the “gas” film ruptures at the bottom of the sphere, a contact line is generated. The contact line retracts along the sphere's surface, and the retracting speed fulfils \( U_{MCL}\propto T^{-1/2}\) law generally. This implies that the retracting process of the gas film is dominated by the inertia-capillary balance, rather than simply by the visco-capillary. Graphical abstract
PubDate: 2019-03-21
- Abstract: . An extremely thin gas film was found between a sphere and a free surface when the sphere impacted onto a water pool. That might influence the generation and evolution of water entry cavity. However, it is quite difficult to be captured through normal numerical and experimental tests. In this work, by using a finite element method we investigate the water entry of a hydrophobic sphere with gas viscosity artificially increased. The air film rupture in the early stage, contact line dynamics on a curved solid surface, and air pocket formation are investigated. The numerical results reveal that the lifetime of the gas film can be predicted by a viscous squeezing flow model qualitatively well. That relates to the fact that the gas film is much thinner than the diameter of the sphere, even when the gas viscosity is 100 times as large as the liquid one. However, inviscid flow can be found in the most part of the liquid bulk. The free surface profile (or the gas film profile) is then determined by the impact speed, namely the Weber number. More importantly, after the “gas” film ruptures at the bottom of the sphere, a contact line is generated. The contact line retracts along the sphere's surface, and the retracting speed fulfils \( U_{MCL}\propto T^{-1/2}\) law generally. This implies that the retracting process of the gas film is dominated by the inertia-capillary balance, rather than simply by the visco-capillary. Graphical abstract
- Gyrotactic phytoplankton in laminar and turbulent flows: A dynamical
systems approach- Abstract: . Gyrotactic algae are bottom heavy, motile cells whose swimming direction is determined by a balance between a buoyancy torque directing them upwards and fluid velocity gradients. Gyrotaxis has, in recent years, become a paradigmatic model for phytoplankton motility in flows. The essential attractiveness of this peculiar form of motility is the availability of a mechanistic description which, despite its simplicity, revealed predictive, rich in phenomenology, easily complemented to include the effects of shape, feedback on the fluid and stochasticity (e.g., in cell orientation). In this review we consider recent theoretical, numerical and experimental results to discuss how, depending on flow properties, gyrotaxis can produce inhomogeneous phytoplankton distributions on a wide range of scales, from millimeters to kilometers, in both laminar and turbulent flows. In particular, we focus on the phenomenon of gyrotactic trapping in nonlinear shear flows and in fractal clustering in turbulent flows. We shall demonstrate the usefulness of ideas and tools borrowed from dynamical systems theory in explaining and interpreting these phenomena. Graphical abstract
PubDate: 2019-03-20
- Abstract: . Gyrotactic algae are bottom heavy, motile cells whose swimming direction is determined by a balance between a buoyancy torque directing them upwards and fluid velocity gradients. Gyrotaxis has, in recent years, become a paradigmatic model for phytoplankton motility in flows. The essential attractiveness of this peculiar form of motility is the availability of a mechanistic description which, despite its simplicity, revealed predictive, rich in phenomenology, easily complemented to include the effects of shape, feedback on the fluid and stochasticity (e.g., in cell orientation). In this review we consider recent theoretical, numerical and experimental results to discuss how, depending on flow properties, gyrotaxis can produce inhomogeneous phytoplankton distributions on a wide range of scales, from millimeters to kilometers, in both laminar and turbulent flows. In particular, we focus on the phenomenon of gyrotactic trapping in nonlinear shear flows and in fractal clustering in turbulent flows. We shall demonstrate the usefulness of ideas and tools borrowed from dynamical systems theory in explaining and interpreting these phenomena. Graphical abstract
- The E. coli transcriptional regulatory network and its spatial embedding
- Abstract: . Usually complex networks are studied as graphs consisting of nodes whose spatial arrangement is of no significance. Several real biological networks are, however, embedded in space. In this paper we study the transcription regulatory network (TRN) of E. coli as a spatially embedded network. The embedding space of this network is the circular E. coli chromosome, i.e. it is practically one dimensional. However, the TRN itself is a high-dimensional network due to the existence of an adequate number of long-range connections. We find that nodes in short topological distance l = 1, 2 tend, on average, to be in shorter spatial distances r indicating an abundance of short-range connections as well. Community analysis of the TRN reveals the interesting fact that highly interconnected subnets consist of nodes that tend to be in spatial proximity on the circular chromosome. We also find indications that for certain transcriptional aspects of the E. coli it is advantageous to treat the circular genome as two line segments starting from the OriC and ending to Ter. Graphical abstract
PubDate: 2019-03-20
- Abstract: . Usually complex networks are studied as graphs consisting of nodes whose spatial arrangement is of no significance. Several real biological networks are, however, embedded in space. In this paper we study the transcription regulatory network (TRN) of E. coli as a spatially embedded network. The embedding space of this network is the circular E. coli chromosome, i.e. it is practically one dimensional. However, the TRN itself is a high-dimensional network due to the existence of an adequate number of long-range connections. We find that nodes in short topological distance l = 1, 2 tend, on average, to be in shorter spatial distances r indicating an abundance of short-range connections as well. Community analysis of the TRN reveals the interesting fact that highly interconnected subnets consist of nodes that tend to be in spatial proximity on the circular chromosome. We also find indications that for certain transcriptional aspects of the E. coli it is advantageous to treat the circular genome as two line segments starting from the OriC and ending to Ter. Graphical abstract
- Settling slip velocity of a spherical particle in an unbounded micropolar
fluid- Abstract: . The gravitational settling of small spherical particles in an unbounded micropolar fluid with slip surfaces is considered. The motion is studied under the assumption of low Reynolds number. The slip boundary conditions on velocity and microrotation at the surface of the spherical particle is used. The solution for the stream function of the fluid flow is obtained analytically. The settling velocity is obtained and is plotted against the Knudsen number for various values of the micropolarity parameter and constants depending on the material of the solid surface. The problem of rotational motion of a particle with slip surface is also solved and the torque coefficient acting on the spherical particle is obtained and is plotted against Knudsen number for different values of micropolarity parameter, spin parameter, and the material constants. The correction to the Basset equation for settling velocity under gravity for slip particle in micropolar fluids is discussed with the range of Knudsen number which has been proven with known results available in the literature. Graphical abstract
PubDate: 2019-03-20
- Abstract: . The gravitational settling of small spherical particles in an unbounded micropolar fluid with slip surfaces is considered. The motion is studied under the assumption of low Reynolds number. The slip boundary conditions on velocity and microrotation at the surface of the spherical particle is used. The solution for the stream function of the fluid flow is obtained analytically. The settling velocity is obtained and is plotted against the Knudsen number for various values of the micropolarity parameter and constants depending on the material of the solid surface. The problem of rotational motion of a particle with slip surface is also solved and the torque coefficient acting on the spherical particle is obtained and is plotted against Knudsen number for different values of micropolarity parameter, spin parameter, and the material constants. The correction to the Basset equation for settling velocity under gravity for slip particle in micropolar fluids is discussed with the range of Knudsen number which has been proven with known results available in the literature. Graphical abstract
- Confined flow behaviour of droplets in microcapillary flow
- Abstract: . The problem of droplets flowing in a micritions is relevant in several applications including flow in porous media. When the flow in the capillary is laminar with negligible gravity effects, droplet velocity and deformation depend upon three independent parameters: the droplet size relative to the capillary radius \(\alpha\) \((=a/R)\) , which is a measure of confinement, the viscosity ratio \(\lambda\) between the droplet and the continuous phase and the capillary number Ca which measures the ratio of viscous to capillary forces. Although droplet microconfined flow behaviour in capillaries has been widely investigated by theoretical models, experimental results are still scarce. Here, an experimental campaign focused on the flow behaviour of axisymmetric confined droplets flowing in a microcapillary is carried out. Our experimental results were obtained by using a water in soybean oil emulsion with a low viscosity ratio and the effect of the aforementioned three parameters, \(\alpha\) , \(\lambda\) and Ca, on droplet motion was investigated. Moreover, our experimental results are compared with numerical solutions available in the literature. Graphical abstract
PubDate: 2019-03-18
- Abstract: . The problem of droplets flowing in a micritions is relevant in several applications including flow in porous media. When the flow in the capillary is laminar with negligible gravity effects, droplet velocity and deformation depend upon three independent parameters: the droplet size relative to the capillary radius \(\alpha\) \((=a/R)\) , which is a measure of confinement, the viscosity ratio \(\lambda\) between the droplet and the continuous phase and the capillary number Ca which measures the ratio of viscous to capillary forces. Although droplet microconfined flow behaviour in capillaries has been widely investigated by theoretical models, experimental results are still scarce. Here, an experimental campaign focused on the flow behaviour of axisymmetric confined droplets flowing in a microcapillary is carried out. Our experimental results were obtained by using a water in soybean oil emulsion with a low viscosity ratio and the effect of the aforementioned three parameters, \(\alpha\) , \(\lambda\) and Ca, on droplet motion was investigated. Moreover, our experimental results are compared with numerical solutions available in the literature. Graphical abstract
- Topical Issue on Fluids and Structures: Multi-scale coupling and modeling
- PubDate: 2019-03-12
- PubDate: 2019-03-12
- The Soret effect in ternary mixtures of water+ethanol+triethylene glycol
of equal mass fractions: Ground and microgravity experiments- Abstract: . Measurements of the Soret and thermodiffusion coefficients of a symmetric ternary mixture with equal mass fractions of water, ethanol, and triethylene glycol have been performed by two-color optical beam deflection (2-OBD) and the thermogravitational column technique (TGC) in the laboratory and under microgravity conditions in the Selectable Optical Diagnostics Instrument (SODI) aboard the International Space Station. The results from all three experimental techniques agree within the experimental error bars, which result mainly from the inversion of the contrast factor matrices. TGC shows by far the lowest, 2-OBD the highest error amplification. The microgravity measurements are in between. The agreement with the microgravity results shows that thermosolutal convection could be well controlled in the 2-OBD experiments by a proper orientation of the temperature gradient. Despite the different condition numbers, the results are invariant under the choice of the independent compositions. Based on the orientation of the confidence ellipsoid in the ternary composition diagram, not all coefficients are equally affected by experimental errors. Although there are appreciable uncertainties for water and ethanol, the Soret and the thermodiffusion coefficients of triethylene glycol could be obtained with a good accuracy due to the favorable orientation of the confidence ellipsoid. We have found that water behaves thermophobic, corresponding to a positive Soret coefficient, whereas both ethanol and triethylene glycol are thermophilic with negative Soret coefficients. This resembles the behaviour of the binary system ethanol/water above the ethanol concentration of the sign change. Graphical abstract
PubDate: 2019-03-07
- Abstract: . Measurements of the Soret and thermodiffusion coefficients of a symmetric ternary mixture with equal mass fractions of water, ethanol, and triethylene glycol have been performed by two-color optical beam deflection (2-OBD) and the thermogravitational column technique (TGC) in the laboratory and under microgravity conditions in the Selectable Optical Diagnostics Instrument (SODI) aboard the International Space Station. The results from all three experimental techniques agree within the experimental error bars, which result mainly from the inversion of the contrast factor matrices. TGC shows by far the lowest, 2-OBD the highest error amplification. The microgravity measurements are in between. The agreement with the microgravity results shows that thermosolutal convection could be well controlled in the 2-OBD experiments by a proper orientation of the temperature gradient. Despite the different condition numbers, the results are invariant under the choice of the independent compositions. Based on the orientation of the confidence ellipsoid in the ternary composition diagram, not all coefficients are equally affected by experimental errors. Although there are appreciable uncertainties for water and ethanol, the Soret and the thermodiffusion coefficients of triethylene glycol could be obtained with a good accuracy due to the favorable orientation of the confidence ellipsoid. We have found that water behaves thermophobic, corresponding to a positive Soret coefficient, whereas both ethanol and triethylene glycol are thermophilic with negative Soret coefficients. This resembles the behaviour of the binary system ethanol/water above the ethanol concentration of the sign change. Graphical abstract
- Motility and cell shape roles in the rheology of growing bacteria cultures
- Abstract: . Cell shape, size and self-motility appear as determinant intrinsic cell factors in the rheological behavior of living bacterial cultures during the growth process. In this work three different species were considered due to their differences on these intrinsic characteristics: two different strains of Staphylococcus aureus - strain COL and its isogenic cell wall autolysis mutant, RUSAL9 - both non-motile and Escherichia coli and Bacillus subtilis - both presenting intrinsic motility. In situ real-time rheology, was used to characterize the activity of growing bacteria, under steady-shear conditions, in particular the viscosity growth curve was measured, for a constant shear flow rate, presenting for all studied cultures, different and rich flow curves. These complex rheological behaviors are a consequence of two coupled effects: the cell density continuous increase and its changing interacting properties, where cell size and shape and intrinsic motility are major players. Graphical abstract
PubDate: 2019-03-01
- Abstract: . Cell shape, size and self-motility appear as determinant intrinsic cell factors in the rheological behavior of living bacterial cultures during the growth process. In this work three different species were considered due to their differences on these intrinsic characteristics: two different strains of Staphylococcus aureus - strain COL and its isogenic cell wall autolysis mutant, RUSAL9 - both non-motile and Escherichia coli and Bacillus subtilis - both presenting intrinsic motility. In situ real-time rheology, was used to characterize the activity of growing bacteria, under steady-shear conditions, in particular the viscosity growth curve was measured, for a constant shear flow rate, presenting for all studied cultures, different and rich flow curves. These complex rheological behaviors are a consequence of two coupled effects: the cell density continuous increase and its changing interacting properties, where cell size and shape and intrinsic motility are major players. Graphical abstract
- Kinetics of growth of non-equilibrium fluctuations during thermodiffusion
in a polymer solution- Abstract: . A thermal diffusion process occurring in a binary liquid mixture is accompanied by long ranged non-equilibrium concentration fluctuations. The amplitude of these fluctuations at large length scales can be orders of magnitude larger than that of equilibrium ones. So far non-equilibrium fluctuations have been mainly investigated under stationary or quasi-stationary conditions, a situation that allows to achieve a detailed statistical characterization of their static and dynamic properties. In this work we investigate the kinetics of growth of non-equilibrium concentration fluctuations during a transient thermodiffusion process, starting from a configuration where the concentration of the sample is uniform. The use of a large molecular weight polymer solution allows to attain a slow dynamics of growth of the macroscopic concentration profile. We focus on the development of fluctuations at small wave vectors, where their amplitude is strongly limited by the presence of gravity. We show that the growth rate of non-equilibrium fluctuations follows a power law \( R_f(q,t)\propto \frac{1}{t}\) as a function of time, without any typical time scale and independently of the wave vector. We formulate a phenomenological model that allows to relate the rate of growth of non-equilibrium fluctuations to the growth of the macroscopic concentration profile in the absence of arbitrary parameters. Graphical abstract
PubDate: 2019-02-27
- Abstract: . A thermal diffusion process occurring in a binary liquid mixture is accompanied by long ranged non-equilibrium concentration fluctuations. The amplitude of these fluctuations at large length scales can be orders of magnitude larger than that of equilibrium ones. So far non-equilibrium fluctuations have been mainly investigated under stationary or quasi-stationary conditions, a situation that allows to achieve a detailed statistical characterization of their static and dynamic properties. In this work we investigate the kinetics of growth of non-equilibrium concentration fluctuations during a transient thermodiffusion process, starting from a configuration where the concentration of the sample is uniform. The use of a large molecular weight polymer solution allows to attain a slow dynamics of growth of the macroscopic concentration profile. We focus on the development of fluctuations at small wave vectors, where their amplitude is strongly limited by the presence of gravity. We show that the growth rate of non-equilibrium fluctuations follows a power law \( R_f(q,t)\propto \frac{1}{t}\) as a function of time, without any typical time scale and independently of the wave vector. We formulate a phenomenological model that allows to relate the rate of growth of non-equilibrium fluctuations to the growth of the macroscopic concentration profile in the absence of arbitrary parameters. Graphical abstract
- First-passage time statistics of stochastic transcription process for
time-dependent reaction rates- Abstract: . Transcription in gene expression is an intrinsically noisy process which involves production and degradation of mRNAs. An important quantity to describe this stochastic process is the first-passage time (FPT), i.e., the time taken by mRNAs to reach a particular threshold. The process of transcription can be modelled as a simple birth-death process, assuming that the promoter is always in an active state and to encode the stochastic environment we consider the transcription rate to be time dependent. This generalization is suitable to capture bursty mRNA dynamics usually modelled as an ON-Off model and simplifies the calculation of FPT statistics for a cell population. We study the role of periodic modulation of the transcription rate on different moments of FPT distribution of a population of cells. Our calculation shows that for sinusoidal modulation there exists an extremal value of mean FPT as a function of the time period and phase of the transcription signal. However, for the square wave modulation of transcription rates simulation results show that the extremal value of the MFPT behaves monotonically with the variation of the phase. Graphical abstract
PubDate: 2019-02-25
- Abstract: . Transcription in gene expression is an intrinsically noisy process which involves production and degradation of mRNAs. An important quantity to describe this stochastic process is the first-passage time (FPT), i.e., the time taken by mRNAs to reach a particular threshold. The process of transcription can be modelled as a simple birth-death process, assuming that the promoter is always in an active state and to encode the stochastic environment we consider the transcription rate to be time dependent. This generalization is suitable to capture bursty mRNA dynamics usually modelled as an ON-Off model and simplifies the calculation of FPT statistics for a cell population. We study the role of periodic modulation of the transcription rate on different moments of FPT distribution of a population of cells. Our calculation shows that for sinusoidal modulation there exists an extremal value of mean FPT as a function of the time period and phase of the transcription signal. However, for the square wave modulation of transcription rates simulation results show that the extremal value of the MFPT behaves monotonically with the variation of the phase. Graphical abstract
- Density fields for branching, stiff networks in rigid confining regions
- Abstract: . We develop a formalism to describe the equilibrium distributions for segments of confined branched networks consisting of stiff filaments. This is applicable to certain situations of cytoskeleton in cells, such as for example actin filaments with branching due to the Arp2/3 complex. We develop a grand ensemble formalism that enables the computation of segment density and polarisation profiles within the confines of the cell. This is expressed in terms of the solution to nonlinear integral equations for auxiliary functions. We find three specific classes of behaviour depending on filament length, degree of branching and the ratio of persistence length to the dimensions of the geometry. Our method allows a numerical approach for semi-flexible filaments that are networked. Graphical abstract
PubDate: 2019-02-22
- Abstract: . We develop a formalism to describe the equilibrium distributions for segments of confined branched networks consisting of stiff filaments. This is applicable to certain situations of cytoskeleton in cells, such as for example actin filaments with branching due to the Arp2/3 complex. We develop a grand ensemble formalism that enables the computation of segment density and polarisation profiles within the confines of the cell. This is expressed in terms of the solution to nonlinear integral equations for auxiliary functions. We find three specific classes of behaviour depending on filament length, degree of branching and the ratio of persistence length to the dimensions of the geometry. Our method allows a numerical approach for semi-flexible filaments that are networked. Graphical abstract
- A hydrodynamic-stochastic model of chemotactic ciliated microorganisms
- Abstract: . Biological systems like ciliated microorganisms are capable of responding to the external chemical gradients, a process known as chemotaxis. In this process, the internal signaling network of the microorganism is triggered due to binding of the chemoattractant molecules with the receptors on the surface of the body. This can alter the activity at the surface of the microorganism. We study the chemotaxis of ciliated microorganisms using the chiral squirmer model, a spherical body with a surface slip velocity. In the presence of a chemical gradient, the coefficients of the slip velocity get modified resulting in a change in the path followed by the body. We observe that the strength of the gradient is not the only parameter which controls the dynamics of the body but also the adaptation time plays a very significant role in the success of chemotaxis. The trajectory of the body is smooth if we ignore the discreteness in the ligand-receptor binding which is stochastic in nature. In the presence of the latter, the path is not only irregular but the whole dynamics of the body changes. We calculate the mean first passage time, by varying the strength of the chemical gradient and the adaptation time, to determine the success rate of chemotaxis. Graphical abstract
PubDate: 2019-02-21
- Abstract: . Biological systems like ciliated microorganisms are capable of responding to the external chemical gradients, a process known as chemotaxis. In this process, the internal signaling network of the microorganism is triggered due to binding of the chemoattractant molecules with the receptors on the surface of the body. This can alter the activity at the surface of the microorganism. We study the chemotaxis of ciliated microorganisms using the chiral squirmer model, a spherical body with a surface slip velocity. In the presence of a chemical gradient, the coefficients of the slip velocity get modified resulting in a change in the path followed by the body. We observe that the strength of the gradient is not the only parameter which controls the dynamics of the body but also the adaptation time plays a very significant role in the success of chemotaxis. The trajectory of the body is smooth if we ignore the discreteness in the ligand-receptor binding which is stochastic in nature. In the presence of the latter, the path is not only irregular but the whole dynamics of the body changes. We calculate the mean first passage time, by varying the strength of the chemical gradient and the adaptation time, to determine the success rate of chemotaxis. Graphical abstract
- Resolving solution conformations of the model semi-flexible
polyelectrolyte homogalacturonan using molecular dynamics simulations and
small-angle x-ray scattering- Abstract: . The conformation of polyelectrolytes in the solution state has long been of interest in polymer science. Herein we utilize all atom molecular dynamics simulations (MD) and small-angle x-ray scattering experiments (SAXS) to elucidate the molecular structure of the model polyelectrolyte homogalacturonan. Several degrees of polymerization were studied and in addition partial methylesterification of the otherwise charge-carrying carboxyl groups was used in order to generate samples with varying intra-chain charge distributions. It is shown that at length scales above around 1nm the conformation of isolated chains has surprisingly little dependence on the charge distribution or the concentration of attendant monovalent salts, reflective of the intrinsic stiffness of the saccharide rings and the dynamical constraints of the glycosidic linkage. Indeed the conformation of isolated chains over all accessible length scales is well described by the atomic coordinates available from fibre diffraction studies. Furthermore, in more concentrated systems it is shown that, after careful analysis of the SAXS data, the form of the inter-particle effects heralded by the emergence of a so-called polyelectrolyte peak, can be extracted, and that this phenomena can be reproduced by multiple chain MD simulations. Graphical abstract
PubDate: 2019-02-21
- Abstract: . The conformation of polyelectrolytes in the solution state has long been of interest in polymer science. Herein we utilize all atom molecular dynamics simulations (MD) and small-angle x-ray scattering experiments (SAXS) to elucidate the molecular structure of the model polyelectrolyte homogalacturonan. Several degrees of polymerization were studied and in addition partial methylesterification of the otherwise charge-carrying carboxyl groups was used in order to generate samples with varying intra-chain charge distributions. It is shown that at length scales above around 1nm the conformation of isolated chains has surprisingly little dependence on the charge distribution or the concentration of attendant monovalent salts, reflective of the intrinsic stiffness of the saccharide rings and the dynamical constraints of the glycosidic linkage. Indeed the conformation of isolated chains over all accessible length scales is well described by the atomic coordinates available from fibre diffraction studies. Furthermore, in more concentrated systems it is shown that, after careful analysis of the SAXS data, the form of the inter-particle effects heralded by the emergence of a so-called polyelectrolyte peak, can be extracted, and that this phenomena can be reproduced by multiple chain MD simulations. Graphical abstract
- Dielectric properties of wet steam based on a double relaxation time model
- Abstract: . The last stages of most steam turbines operate in wet steam, resulting in water erosion of the rotor blades and the reduction of turbine efficiency. Accurate measurement of steam wetness is the key to ensure an efficient and stable operation of steam turbines. The equivalent complex permittivity model of wet steam was established by Maxwell-Wagner non-homogeneous dielectric theory, and the complex permittivity distribution of frequency and temperature changes of saturated water, dry saturated steam, and wet steam was derived. The measurement experiments verified the above properties of dry saturated steam and wet steam. The complex permittivity of the wet steam is similar to that for the dry saturated steam. The real part increases with increasing frequency and temperature. When the frequency is large or the temperature is low, the real part approaches 1. The imaginary part increases first and then decreases with the increase of frequency. In addition, with the increase of temperature, the imaginary part becomes larger. When the temperature is low, the imaginary part is close to 0, which is independent of the frequency. Graphical abstract
PubDate: 2019-02-21
- Abstract: . The last stages of most steam turbines operate in wet steam, resulting in water erosion of the rotor blades and the reduction of turbine efficiency. Accurate measurement of steam wetness is the key to ensure an efficient and stable operation of steam turbines. The equivalent complex permittivity model of wet steam was established by Maxwell-Wagner non-homogeneous dielectric theory, and the complex permittivity distribution of frequency and temperature changes of saturated water, dry saturated steam, and wet steam was derived. The measurement experiments verified the above properties of dry saturated steam and wet steam. The complex permittivity of the wet steam is similar to that for the dry saturated steam. The real part increases with increasing frequency and temperature. When the frequency is large or the temperature is low, the real part approaches 1. The imaginary part increases first and then decreases with the increase of frequency. In addition, with the increase of temperature, the imaginary part becomes larger. When the temperature is low, the imaginary part is close to 0, which is independent of the frequency. Graphical abstract
- Latex films with gradients in crosslink density created by
small-molecule-based auto-stratification- Abstract: . A suitable balance of convective and diffusive transport of small molecules contained in the liquid phase of a drying latex film leads to auto-stratification and to functionally graded films. Differing from blends of latex particles, which may also experience drying-induced segregation, small molecules retain their mobility after the particles have touched and have formed an elastically coupled network. The use of a thickener, which turns the dispersion into a weak gel and prevents the free flow of particles, is compatible with this approach (and even advantageous). A problem with small molecules is fast diffusive equilibration of concentration differences. For this reason, composition gradients along the lateral direction, where the characteristic length scale is centimeters, are more easily achieved than gradients along the vertical. Addition of a thickener slows down the diffusion, which aids the development of gradients along the vertical. The application example chosen was the crosslinking agent adipic dihydrazide, ADH, which takes part in keto-hydrazide coupling. Its heterogeneous distribution produces a spatially variable crosslink-density in the dry film as evidenced by Raman microscopy. A side aspect of the work is an inward flow of serum, which is observed for high-Tg films. An explanation for this “anti-coffee-ring effect” --based on pore collapse driven by the polymer-water interfacial energy combined with finite polymer elasticity-- is proposed. Graphical abstract
PubDate: 2019-02-21
- Abstract: . A suitable balance of convective and diffusive transport of small molecules contained in the liquid phase of a drying latex film leads to auto-stratification and to functionally graded films. Differing from blends of latex particles, which may also experience drying-induced segregation, small molecules retain their mobility after the particles have touched and have formed an elastically coupled network. The use of a thickener, which turns the dispersion into a weak gel and prevents the free flow of particles, is compatible with this approach (and even advantageous). A problem with small molecules is fast diffusive equilibration of concentration differences. For this reason, composition gradients along the lateral direction, where the characteristic length scale is centimeters, are more easily achieved than gradients along the vertical. Addition of a thickener slows down the diffusion, which aids the development of gradients along the vertical. The application example chosen was the crosslinking agent adipic dihydrazide, ADH, which takes part in keto-hydrazide coupling. Its heterogeneous distribution produces a spatially variable crosslink-density in the dry film as evidenced by Raman microscopy. A side aspect of the work is an inward flow of serum, which is observed for high-Tg films. An explanation for this “anti-coffee-ring effect” --based on pore collapse driven by the polymer-water interfacial energy combined with finite polymer elasticity-- is proposed. Graphical abstract
- Influence of anisotropic nanoparticles on the deposition pattern of an
evaporating droplet- Abstract: . The suppression or enhancement of the “coffee ring” effect depends on whether nanoparticles easily adhere to the gas-liquid interface and particle shape. To obtain deposition patterns of suspensions of nanoparticles strongly deviating from spheres, which is less studied in the literature, prolate ellipsoidal and cylindrical rod-shaped particles with a minimum aspect ratio of 4 are selected. Dynamic viscosity, which is a function of particle shape and volume fraction, is introduced into the evolution equations for film thickness and particle concentration. The nanoparticle deposition features and the contact line dynamics are examined numerically, and the effect of particle shape on the drying process is analysed. The results show that the contact line is in the depinning state during the droplet shrinkage, while the concentration and effective layer thickness of nanoparticles in the ring-formation region decrease with time, and the deposition band widens. The deposition ring height increases, and the recession of the contact line slows down with increasing aspect ratio. This means that for nanoparticles deviating strongly from spheres and not easily adhering to the gas-liquid interface, the “coffee ring” effect is enhanced when the suspension dries. A larger aspect ratio leads to a more obvious “coffee ring” feature. Graphical abstract
PubDate: 2019-02-20
- Abstract: . The suppression or enhancement of the “coffee ring” effect depends on whether nanoparticles easily adhere to the gas-liquid interface and particle shape. To obtain deposition patterns of suspensions of nanoparticles strongly deviating from spheres, which is less studied in the literature, prolate ellipsoidal and cylindrical rod-shaped particles with a minimum aspect ratio of 4 are selected. Dynamic viscosity, which is a function of particle shape and volume fraction, is introduced into the evolution equations for film thickness and particle concentration. The nanoparticle deposition features and the contact line dynamics are examined numerically, and the effect of particle shape on the drying process is analysed. The results show that the contact line is in the depinning state during the droplet shrinkage, while the concentration and effective layer thickness of nanoparticles in the ring-formation region decrease with time, and the deposition band widens. The deposition ring height increases, and the recession of the contact line slows down with increasing aspect ratio. This means that for nanoparticles deviating strongly from spheres and not easily adhering to the gas-liquid interface, the “coffee ring” effect is enhanced when the suspension dries. A larger aspect ratio leads to a more obvious “coffee ring” feature. Graphical abstract