A Transition State Theory for Calculating Hopping Times and Diffusion in Highly Confined Fluids

Monte Carlo simulation is used to study the dynamical crossover from single file diffusion to normal diffusion in fluids confined to narrow channels. We show that the long time diffusion coefficients for a series of systems involving hard and soft interaction potentials can be described in terms of a hopping time that measures the time it takes for a particle to escape the cage formed by its neighbors in the pore. Free energy barriers for the particle hopping process are calculated and used to show that transition state theory effectively describes the hopping time for all the systems studied, over a range of pore diameters. Our work suggests that the combination of hopping times and transition state theory offers a useful and general framework to describe the dynamics of these highly confined fluids.Comment: 6 figure

Practical 3-splitting beyond Strang

Operator splitting is a popular divide-and-conquer strategy for solving differential equations. Typically, the right-hand side of the differential equation is split into a number of parts that can then be integrated separately. Many methods are known that split the right-hand side into two parts. This approach is limiting, however, and there are situations when 3-splitting is more natural and ultimately more advantageous. The second-order Strang operator-splitting method readily generalizes to a right-hand side splitting into any number of operators. It is arguably the most popular method for 3-splitting because of its efficiency, ease of implementation, and intuitive nature. Other 3-splitting methods exist, but they are less well-known, and evaluations of their performance in practice are scarce. We demonstrate the effectiveness of some alternative 3-split, second-order methods to Strang splitting on two problems: the reaction-diffusion Brusselator, which can be split into three parts that each have closed-form solutions, and the kinetic Vlasov--Poisson equations that is used in semi-Lagrangian plasma simulations. We find alternative second-order 3-operator-splitting methods that realize efficiency gains of 10\%--20\% over traditional Strang splitting

Physiological accuracy in simulating refractory cardiac tissue: the volume-averaged bidomain model vs. the cell-based EMI model

The refractory period of cardiac tissue can be quantitatively described using strength-interval (SI) curves. The information captured in SI curves is pertinent to the design of anti-arrhythmic devices including pacemakers and implantable cardioverter defibrillators. As computational cardiac modelling becomes more prevalent, it is feasible to consider the generation of computationally derived SI curves as a supplement or precursor to curves that are experimentally derived. It is beneficial, therefore, to examine the profiles of the SI curves produced by different cardiac tissue models to determine whether some models capture the refractory period more accurately than others. In this study, we compare the unipolar SI curves of two tissue models: the current state-of-the-art bidomain model and the recently developed extracellular-membrane-intracellular (EMI) model. The EMI model's resolution of individual cell structure makes it a more detailed model than the bidomain model, which forgoes the structure of individual cardiac cells in favour of treating them homogeneously as a continuum. We find that the resulting SI curves elucidate differences between the models, including that the behaviour of the EMI model is noticeably closer to the refractory behaviour of experimental data compared to that of the bidomain model. These results hold implications for future computational pacemaker simulations and shed light on the predicted refractory properties of cardiac tissue from each model.Comment: 30 pages, 12 figures, 3 table

Beyond domain alignment: Revealing the effect of intrinsic magnetic order on electrochemical water splitting

To reach a long term viable green hydrogen economy, rational design of active oxygen evolution reaction (OER) catalysts is critical. An important hurdle in this reaction originates from the fact that the reactants are singlet molecules, whereas the oxygen molecule has a triplet ground state with parallel spin alignment, implying that magnetic order in the catalyst is essential. Accordingly, multiple experimentalists reported a positive effect of external magnetic fields on OER activity of ferromagnetic catalysts. However, it remains a challenge to investigate the influence of the intrinsic magnetic order on catalytic activity. Here, we tuned the intrinsic magnetic order of epitaxial La$_{0.67}$Sr$_{0.33}$MnO$_{3}$ thin film model catalysts from ferro- to paramagnetic by changing the temperature in-situ during water electrolysis. Using this strategy, we show that ferromagnetic ordering below the Curie temperature enhances OER activity. Moreover, we show a slight current density enhancement upon application of an external magnetic field and find that the dependence of magnetic field direction correlates with the magnetic anisotropy in the catalyst film. Our work thus suggests that both the intrinsic magnetic order in La$_{0.67}$Sr$_{0.33}$MnO$_{3}$ films and magnetic domain alignment increase their catalytic activity. We observe no long-range magnetic order at the catalytic surface, implying that the OER enhancement is connected to the magnetic order of the bulk catalyst. Combining the effects found with existing literature, we propose a unifying picture for the spin-polarized enhancement in magnetic oxide catalysts.Comment: The following article will be submitted to Applied Physics Reviews. Main text (incl. references) 19 pages, 8 figures. Supplementary text 9 pages, 13 figure

Chaste : Cancer, Heart and Soft Tissue Environment

Funding: UK Engineering and Physical Sciences Research Council [grant number EP/N509711/1 (J.K.)].Chaste (Cancer, Heart And Soft Tissue Environment) is an open source simulation package for the numerical solution of mathematical models arising in physiology and biology. To date, Chaste development has been driven primarily by applications that include continuum modelling of cardiac electrophysiology (‘Cardiac Chaste’), discrete cell-based modelling of soft tissues (‘Cell-based Chaste’), and modelling of ventilation in lungs (‘Lung Chaste’). Cardiac Chaste addresses the need for a high-performance, generic, and verified simulation framewor kfor cardiac electrophysiology that is freely available to the scientific community. Cardiac chaste provides a software package capable of realistic heart simulations that is efficient, rigorously tested, and runs on HPC platforms. Cell-based Chaste addresses the need for efficient and verified implementations of cell-based modelling frameworks, providing a set of extensible tools for simulating biological tissues. Computational modelling, along with live imaging techniques, plays an important role in understanding the processes of tissue growth and repair. A wide range of cell-based modelling frameworks have been developed that have each been successfully applied in a range of biological applications. Cell-based Chaste includes implementations of the cellular automaton model, the cellular Potts model, cell-centre models with cell representations as overlapping spheres or Voronoi tessellations, and the vertex model. Lung Chaste addresses the need for a novel, generic and efficient lung modelling software package that is both tested and verified. It aims to couple biophysically-detailed models of airway mechanics with organ-scale ventilation models in a package that is freely available to the scientific community.Publisher PDFPeer reviewe

Measurement of the cross-section and charge asymmetry of WW bosons produced in proton-proton collisions at s=8\sqrt{s}=8 TeV with the ATLAS detector

This paper presents measurements of the $W^+ \rightarrow \mu^+\nu$ and $W^- \rightarrow \mu^-\nu$ cross-sections and the associated charge asymmetry as a function of the absolute pseudorapidity of the decay muon. The data were collected in proton--proton collisions at a centre-of-mass energy of 8 TeV with the ATLAS experiment at the LHC and correspond to a total integrated luminosity of 20.2~\mbox{fb^{-1}}. The precision of the cross-section measurements varies between 0.8% to 1.5% as a function of the pseudorapidity, excluding the 1.9% uncertainty on the integrated luminosity. The charge asymmetry is measured with an uncertainty between 0.002 and 0.003. The results are compared with predictions based on next-to-next-to-leading-order calculations with various parton distribution functions and have the sensitivity to discriminate between them.Comment: 38 pages in total, author list starting page 22, 5 figures, 4 tables, submitted to EPJC. All figures including auxiliary figures are available at https://atlas.web.cern.ch/Atlas/GROUPS/PHYSICS/PAPERS/STDM-2017-13