Correction: Convective heat transfer in a measurement cell for scanning electrochemical microscopy.

Correction for 'Convective heat transfer in a measurement cell for scanning electrochemical microscopy' by Javor K. Novev et al., Phys. Chem. Chem. Phys., 2016, 18, 29836-29846.

A thermostated cell for electrochemistry: minimising natural convection and investigating the role of evaporation and radiation.

An optimised thermostated electrochemical cell is designed and implemented. This is informed by experimental and computational studies characterizing the extent to which the thermostating of an electrochemical cell via a heated bath can be realised, both with the cell closed and open to the environment. The heat transfer in the system is simulated and probed experimentally; special emphasis is put on heat loss due to radiation and evaporation. Experiments and simulations demonstrate that these two mechanisms of heat transfer lead to a steady temperature in the cell that differs from that of the thermostat by ∼0.1 K. Simulations indicate that spatial inhomogeneities in the stationary temperature drive natural convective flows with a significant velocity. These new physical insights inform the optimization of a new electrochemical cell and its application in measurements of the impact frequency of silver nanoparticles as a function of temperature.

Thermal convection in electrochemical cells. Boundaries with heterogeneous thermal conductivity and implications for scanning electrochemical microscopy.

We investigate the heat transfer in a cylinder-shaped electrochemical cell with solid, thermally insulating walls. The cell is filled with a liquid and a solid substrate that is thermostated from below is situated at its base. The initial temperature of the liquid is different from that of the substrate so as to mimic imperfect thermostating in an electrochemical experiment; as heat transfer acts to diminish the temperature difference between the two, natural convection ensues. The influence of inhomogeneities in the thermal conductivity of the solid is studied - numerical simulations of the heat transfer in the system are conducted for substrates that are comprised of a thermally conductive material, an insulating one or a combination thereof. It is shown that the substrate structure strongly influences the structure and intensity of the natural convective flows emerging in the system. The present work demonstrates that under the idealized conditions under consideration, depending on the substrate structure, natural convection due to imperfect solution thermostating may give rise to flows whose local velocity can reach values as high as 10-3 m s-1. Moreover, as comparison between cells of two different radii shows, both the intensity and the temporal evolution of the flows arising in this system are highly sensitive to the precise geometry of the experimental cell. These results can have far-reaching consequences for the interpretation of results from experimental techniques such as scanning electrochemical microscopy.

Convective heat transfer in a measurement cell for scanning electrochemical microscopy.

Electrochemical experiments, especially those performed with scanning electrochemical microscopy (SECM), are often carried out without taking special care to thermostat the solution; it is usually assumed that its temperature is homogeneous and equal to the ambient. The present study aims to test this assumption via numerical simulations of the heat transfer in a particular system - the typical measurement cell for SECM. It is assumed that the temperature of the solution is initially homogeneous but different from that of its surroundings; convective heat transfer in the solution and the surrounding air is taken into account within the framework of the Boussinesq approximation. The hereby presented theoretical treatment indicates that an initial temperature difference of the order of 1 K dissipates with a characteristic time scale of ∼1000 s; the thermal equilibration is accompanied by convective flows with a maximum velocity of ∼10-4 m s-1; furthermore, the temporal evolution of the temperature profile is influenced by the sign of the initial difference. These results suggest that, unless the temperature of the solution is rigorously controlled, convection may significantly compromise the interpretation of data from SECM and other electrochemical techniques, which is usually done on the basis of diffusion-only models.

Predicting phenotype transition probabilities via conditional algorithmic probability approximations.

Unravelling the structure of genotype-phenotype (GP) maps is an important problem in biology. Recently, arguments inspired by algorithmic information theory (AIT) and Kolmogorov complexity have been invoked to uncover simplicity bias in GP maps, an exponentially decaying upper bound in phenotype probability with the increasing phenotype descriptional complexity. This means that phenotypes with many genotypes assigned via the GP map must be simple, while complex phenotypes must have few genotypes assigned. Here, we use similar arguments to bound the probability P(x → y) that phenotype x, upon random genetic mutation, transitions to phenotype y. The bound is [Formula: see text], where [Formula: see text] is the estimated conditional complexity of y given x, quantifying how much extra information is required to make y given access to x. This upper bound is related to the conditional form of algorithmic probability from AIT. We demonstrate the practical applicability of our derived bound by predicting phenotype transition probabilities (and other related quantities) in simulations of RNA and protein secondary structures. Our work contributes to a general mathematical understanding of GP maps and may facilitate the prediction of transition probabilities directly from examining phenotype themselves, without utilizing detailed knowledge of the GP map.

Spatiotemporal model of cellular mechanotransduction via Rho and YAP.

How cells sense and respond to mechanical stimuli remains an open question. Recent advances have identified the translocation of Yes-associated protein (YAP) between nucleus and cytoplasm as a central mechanism for sensing mechanical forces and regulating mechanotransduction. We formulate a spatiotemporal model of the mechanotransduction signalling pathway that includes coupling of YAP with the cell force-generation machinery through the Rho family of GTPases. Considering the active and inactive forms of a single Rho protein (GTP/GDP-bound) and of YAP (non-phosphorylated/phosphorylated), we study the cross-talk between cell polarization due to active Rho and YAP activation through its nuclear localization. For fixed mechanical stimuli, our model predicts stationary nuclear-to-cytoplasmic YAP ratios consistent with experimental data at varying adhesive cell area. We further predict damped and even sustained oscillations in the YAP nuclear-to-cytoplasmic ratio by accounting for recently reported positive and negative YAP-Rho feedback. Extending the framework to time-varying mechanical stimuli that simulate cyclic stretching and compression, we show that the YAP nuclear-to-cytoplasmic ratio's time dependence follows that of the cyclic mechanical stimulus. The model presents one of the first frameworks for understanding spatiotemporal YAP mechanotransduction, providing several predictions of possible YAP localization dynamics, and suggesting new directions for experimental and theoretical studies.

Mesoscale modelling of polymer aggregate digestion.

We use mesoscale simulations to gain insight into the digestion of biopolymers by studying the break-up dynamics of polymer aggregates (boluses) bound by physical cross-links. We investigate aggregate evolution, establishing that the linking bead fraction and the interaction energy are the main parameters controlling stability with respect to diffusion. We show via a simplified model that chemical breakdown of the constituent molecules causes aggregates that would otherwise be stable to disperse. We further investigate breakdown of biopolymer aggregates in the presence of fluid flow. Shear flow in the absence of chemical breakdown induces three different regimes depending on the flow Weissenberg number ( W i ). i) At W i ≪ 1 , shear flow has a negligible effect on the aggregates. ii) At W i ∼ 1 , the aggregates behave approximately as solid bodies and move and rotate with the flow. iii) At W i ≫ 1 , the energy input due to shear overcomes the attractive cross-linking interactions and the boluses are broken up. Finally, we study bolus evolution under the combined action of shear flow and chemical breakdown, demonstrating a synergistic effect between the two at high reaction rates.

Surface tension and surface Δχ-potential of concentrated Z+:Z- electrolyte solutions.

Schmutzer's model for the surface of aqueous electrolyte solutions is generalized to Z+:Z- salts. The thickness of the ion-free layer is calculated from the thickness of the "hydrophobic gap" at the water surface (1.38Å) and the radii of the ionic hydration shells. The overlap between the adsorption and the diffuse double layers is accounted for. The proposed model predicts the dependence of the surface tension σ and the surface Δχ-potential on the electrolyte concentration c(el) in agreement with the available data, without adjustable parameters. The Hofmeister effect on σ for salts of the same valence type is explained with their ion-specific activity coefficients. The negative value (toward air) of the Δχ-potential of most 1:1 electrolytes originates from the dipole moment of the water molecules at the surface. The negative χ-potential due to water dipoles is inversely proportional to the dielectric permittivity ε of the solution. Since ε diminishes as c(el) increases, most 1:1 electrolyte solutions exhibit a more negative χ-potential than pure water (Δχ<0). The Hofmeister series of Δχ of 1:1 salts (Δχ(LiCl) ≈ Δχ(NaCl)<Δχ(KCl)<Δχ(KF)) follows the corresponding series of ε (ε(LiCl) ≈ ε(NaCl)<ε(KCl)<ε(KF)). The theory allows the estimation of the surface potential χ0 of pure water from the experimental data for electrolyte solutions; the result, χ0 ≈ -100 mV, confirms the value currently accepted in the literature.

Surface tension of concentrated electrolyte solutions.

The surface tension σ of inorganic electrolyte aqueous solutions at a given concentration c follows the Hofmeister series. The explanation of this phenomenon was sought in the increased adsorption of certain ions due to specific ion-surface interactions. However, the ion-specific dependence of the activity coefficient γ(±) on c also influences σ, and its contribution to the ion-specificity of σ prevails. Thus, the surface tension of potassium salts follows the order σ(KOH)>σ(KCl)>σ(KNO3), which turns out to be a direct corollary of the corresponding activity coefficients series: γ(KOH)>γ(KCl)>γ(KNO3). In fact, the adsorption of NO(3)(-) at the water surface is lower than that of OH(-) and Cl(-)! If the bulk ion-specific effects are correctly evaluated, Schmutzer's classical model predicts accurately the surface tension of a large number of inorganic salt solutions in a wide concentration range, without adjustable parameters. This model accounts for image and hydration forces. Comparison with tensiometric data shows that other ion-surface interactions play a role only in the adsorption of ions of bare radius larger than a threshold value of about 1.95 Å (e.g. HCOO(-), I(-), SCN(-)).