Incorporation of inhomogeneous ion diffusion coefficients into kinetic lattice grand canonical monte carlo simulations and application to ion current calculations in a simple model ion channel

To deal with inhomogeneous diffusion coefficients of ions without altering the lattice spacing in the kinetic lattice grand canonical Monte Carlo (KLGCMC) simulation, an algorithm that incorporates diffusion coefficient variation into move probabilities is proposed and implemented into KLGCMC calculations. Using this algorithm, the KLGCMC simulation method is applied to the calculation of ion currents in a simple model ion channel system. Comparisons of ion currents and ion concentrations from these simulations with Poisson-Nernst-Planck (PNP) results show good agreement between the two methods for parameters where the latter method is expected to be accurate.     

A rod model for three dimensional deformations of single-walled carbon nanotubes

A continuum model for single-walled carbon nanotubes (SWCNT) is presented which is based on an extension to the special Cosserat theory of rods (Kumar and Mukherjee, 2011). The model allows deformation of a nanotube’s lateral surface in a one dimensional framework and hence is an efficient substitute to the commonly used two dimensional shell models for nanotubes. The model predicts a new coupling mode in chiral nanotubes – coupling between twist and cross-sectional shrinkage implying that the three deformation modes (extension, twist and cross-sectional shrinkage) are all coupled to each other. Atomistic simulations based on the density functional based tight binding method (DFTB) are performed on a (9, 6) SWCNT and the simulation data is used to estimate material parameters of this rod model. A peculiar behavior of the nanotube is observed when it is axially stretched – induced rotation of each cross-section is equal in magnitude but opposite to that of its two neighboring cross-sections. This is shown to be an effect of relative shift/inner-displacement between the two SWCNT sub-lattices.     

The electronic absorption and magnetic circular dichroism spectra of IrBr6 2- in several host crystals

The absorption and magnetic circular dichroism (M.C.D.) spectrum of the IrBr₆ ^2- ion at room and liquid helium temperature has been studied in the host crystals (NH₄)₂SnBr₆, K₂SnBr₆ and (C₂H₅NH₃)₂SnBr₆ in the region ～11 000–21 000 cm^-1. An interpretation of the spectrum is presented which differs significantly from those suggested previously. In order of increasing energy the allowed bands are assigned to the following ligand-to-metal charge-transfer transitions: E_g ″(² T _2g )→ U_u ′(² T _1u ) (13–14 000 cm^-1), E_g ″(² T _2g )→ E_u ″(² T _2u ) (16 800 cm^-1), and E_g ″(² T _2g )→ U_u ′(² T _2u ) (～ 18 300 cm^-1). Both our absorption and M.C.D. data strongly suggest a Jahn-Teller splitting of the U_u ′(² T _1u ) state but contradict a previous suggestion of such a splitting of the U_u ′(² T _2u ) state. Consideration of σ—π mixing in the t _1u (π + σ) molecular orbital suggests that the ～17 300 cm^-1 band arises from the orbitally-forbidden E_g ″(² T _2g )→ E_u ′(² T _1u ) transition. Bands in the 11 000–13 000 cm^-1 region are assigned to parity-forbidden charge-transfer transitions to states generated by the t _1g (π)→ t _2g excitation. The fine structure seen at liquid helium temperature in K₂SnBr₆ : Ir⁴⁺ both in the 14 500 cm^-1 band and overlying the E_g ″→ U_u ′(² T _2u ) band appears to be associated with parity-forbidden transitions.     

A discrete action principle for electrodynamics and the construction of explicit symplectic integrators for linear,non-dispersive media

In this work, we derive a discrete action principle for electrodynamics that can be used to construct explicit symplectic integrators for Maxwell’s equations. Different integrators are constructed depending on the choice of discrete Lagrangian used to approximate the action. By combining discrete Lagrangians in an explicit symplectic partitioned Runge–Kutta method, an integrator capable of achieving any order of accuracy is obtained. Using the von Neumann stability analysis, we show that the integrators greatly increase the numerical stability and reduce the numerical dispersion compared to other methods. For practical purposes, we demonstrate how to implement the integrators using many features of the finite-difference time-domain method. However, our approach is also applicable to other spatial discretizations, such as those used in finite element methods. Using this implementation, numerical examples are presented that demonstrate the ability of the integrators to efficiently reduce and maintain a minimal amount of numerical dispersion, particularly when the time-step is less than the stability limit. The integrators are therefore advantageous for modeling large, inhomogeneous computational domains.     

Interpreting,analysing and modelling COVID-19 mortality data

We present results on the mortality statistics of the COVID-19 epidemic in a number of countries. Our data analysis suggests classifying countries in five groups, (1) Western countries, (2) East Block, (3) developed Southeast Asian countries, (4) Northern Hemisphere developing countries and (5) Southern Hemisphere countries. Comparing the number of deaths per million inhabitants, a pattern emerges in which the Western countries exhibit the largest mortality rate. Furthermore, comparing the running cumulative death tolls as the same level of outbreak progress in different countries reveals several subgroups within the Western countries and further emphasises the difference between the five groups. Analysing the relationship between deaths per million and life expectancy in different countries, taken as a proxy of the preponderance of elderly people in the population, a main reason behind the relatively more severe COVID-19 epidemic in the Western countries is found to be their larger population of elderly people, with exceptions such as Norway and Japan, for which other factors seem to dominate. Our comparison between countries at the same level of outbreak progress allows us to identify and quantify a measure of efficiency of the level of stringency of confinement measures. We find that increasing the stringency from 20 to 60 decreases the death count by about 50 lives per million in a time window of 20  days. Finally, we perform logistic equation analyses of deaths as a means of tracking the dynamics of outbreaks in the “first wave” and estimating the associated ultimate mortality, using four different models to identify model error and robustness of results. This quantitative analysis allows us to assess the outbreak progress in different countries, differentiating between those that are at a quite advanced stage and close to the end of the epidemic from those that are still in the middle of it. This raises many questions in terms of organisation, preparedness, governance structure and so on.

     

Electrodynamics of Noble Metal Nanoparticles and Nanoparticle Clusters

In this paper we examine the electrodynamics of silver nanoparticles and of clusters of nanoparticles, with an emphasis on extinction spectra and of electric fields near the particle surfaces that are important in determining surface-enhanced Raman (SER) intensities. The particles and clusters are chosen to be representative of what has been studied in recent work on colloids and with lithographically prepared particles. These include spheres, spheroids, truncated tetrahedrons, and clusters of two or three of these particles, with sizes that are too large to be described with simple electrostatic approximations but small compared to the wavelength of light. The electrodynamics calculations are mostly based on the discrete dipole approximation (DDA), which is a coupled-finite element approach which produces exact or nearly exact results for particles of arbitrary size and shape if fully converged. Mie theory results are used to study the validity of the DDA for spherical particles, and we also study the validity of the modified long wavelength approximation (MLWA), which is based on perturbative corrections to the electrostatic limit, and of the single dipole per particle approximation (SDA). The results show how the dipole plasmon resonance properties and the electric field contours around the particle vary with particle shape and size for isolated particles. For clusters of particles, we study the effect of interparticle spacing on plasmon resonance characteristics. We also show that the quadrupole resonance is much less sensitive to particle shape and interparticle interactions than the dipole plasmon resonance. These results provide benchmarks that will be used in future comparisons with experiment.     

A numerical method of analyzing beta decay measurements and its application to the 1− → 0+ transitions of170Tm,186Re and210Bi

A numerical method is proposed for determining nuclear matrix elements from beta decay measurements. The method is based on the least squares principle, and its main application is the analysis of beta ray spectra. Its main result is to show that a spectrum shape measurement usually determines only a second order polynomial of the matrix elements to a high precision whereas each of the matrix elements can vary within wide limits. The method is applied to the first forbidden non unique transitions (1^?→ 0⁺) of¹⁷⁰Tm,¹⁸⁶Re and²¹⁰Bi (RaE). The 3 contributing matrix elements and their ranges of error are determined from recent measurements.