Strong geometric frustration in model glassformers

We consider three popular model glassformers, the Kob-Andersen and Wahnstr\"om binary Lennard-Jones models and weakly polydisperse hard spheres. Although these systems exhibit a range of fragilities, all feature a rather similar behaviour in their local structure approaching dynamic arrest. In particular we use the dynamic topological cluster classification to extract a locally favoured structure which is particular to each system. These structures form percolating networks, however in all cases there is a strong decoupling between structural and dynamic lengthscales. We suggest that the lack of growth of the structural lengthscale may be related to strong geometric frustration.Comment: 14 pages, Accepted by J. Non-Crystalline Solids, 7th International Discussion Meeting on Relaxation in Complex Systems Proceeding

Structure in sheared supercooled liquids:Dynamical rearrangements of an effective system of icosahedra

We consider a binary Lennard-Jones glassformer whose super-Arrhenius dynamics are correlated with the formation of particles organized into icosahedra under simple steady state shear. We recast this glassformer as an effective system of icosahedra [Pinney et al. J. Chem. Phys. 143 244507 (2015)]. From the observed population of icosahedra in each steady state, we obtain an effective temperature which is linearly dependent on the shear rate in the range considered. Upon shear banding, the system separates into a region of high shear rate and a region of low shear rate. The effective temperatures obtained in each case show that the low shear regions correspond to a significantly lower temperature than the high shear regions. Taking a weighted average of the effective temperature of these regions (weight determined by region size) yields an estimate of the effective temperature which compares well with an effective temperature based on the global mesocluster population of the whole system.Comment: accepted by J. Chehm. Phy

Solvable two-dimensional time-dependent non-Hermitian quantum systems with infinite dimensional Hilbert space in the broken PT-regime

We provide exact analytical solutions for a two-dimensional explicitly time-dependent non-Hermitian quantum system. While the time-independent variant of the model studied is in the broken PT-symmetric phase for the entire range of the model parameters, and has therefore a partially complex energy eigenspectrum, its time-dependent version has real energy expectation values at all times. In our solution procedure we compare the two equivalent approaches of directly solving the time-dependent Dyson equation with one employing the Lewis–Riesenfeld method of invariants. We conclude that the latter approach simplifies the solution procedure due to the fact that the invariants of the non-Hermitian and Hermitian system are related to each other in a pseudo-Hermitian fashion, which in turn does not hold for their corresponding time-dependent Hamiltonians. Thus constructing invariants and subsequently using the pseudo-Hermiticity relation between them allows to compute the Dyson map and to solve the Dyson equation indirectly. In this way one can bypass to solve nonlinear differential equations, such as the dissipative Ermakov–Pinney equation emerging in our and many other systems

Recasting a model atomistic glassformer as a system of icosahedra

We consider a binary Lennard-Jones glassformer whose super-Arrhenius dynamics are correlated with the formation of icosahedral structures. Upon cooling these icosahedra organize into mesoclusters. We recast this glassformer as an effective system of icosahedra which we describe with a population dynamics model. This model we parameterize with data from the temperature regime accessible to molecular dynamics simulations. We then use the model to determine the population of icosahedra in mesoclusters at arbitrary temperature. Using simulation data to incorporate dynamics into the model we predict relaxation behavior at temperatures inaccessible to conventional approaches. Our model predicts super-Arrhenius dynamics whose relaxation time remains finite for non-zero temperature.Comment: 10 pages, 9 figure

Analysis of signalling pathways using continuous time Markov chains

We describe a quantitative modelling and analysis approach for signal transduction networks. We illustrate the approach with an example, the RKIP inhibited ERK pathway [CSK+03]. Our models are high level descriptions of continuous time Markov chains: proteins are modelled by synchronous processes and reactions by transitions. Concentrations are modelled by discrete, abstract quantities. The main advantage of our approach is that using a (continuous time) stochastic logic and the PRISM model checker, we can perform quantitative analysis such as what is the probability that if a concentration reaches a certain level, it will remain at that level thereafter? or how does varying a given reaction rate affect that probability? We also perform standard simulations and compare our results with a traditional ordinary differential equation model. An interesting result is that for the example pathway, only a small number of discrete data values is required to render the simulations practically indistinguishable

Nonlinearity Management in Higher Dimensions

In the present short communication, we revisit nonlinearity management of the time-periodic nonlinear Schrodinger equation and the related averaging procedure. We prove that the averaged nonlinear Schrodinger equation does not support the blow-up of solutions in higher dimensions, independently of the strength in the nonlinearity coefficient variance. This conclusion agrees with earlier works in the case of strong nonlinearity management but contradicts those in the case of weak nonlinearity management. The apparent discrepancy is explained by the divergence of the averaging procedure in the limit of weak nonlinearity management.Comment: 9 pages, 1 figure

Solutions to Maxwell's Equations using Spheroidal Coordinates

Analytical solutions to the wave equation in spheroidal coordinates in the short wavelength limit are considered. The asymptotic solutions for the radial function are significantly simplified, allowing scalar spheroidal wave functions to be defined in a form which is directly reminiscent of the Laguerre-Gaussian solutions to the paraxial wave equation in optics. Expressions for the Cartesian derivatives of the scalar spheroidal wave functions are derived, leading to a new set of vector solutions to Maxwell's equations. The results are an ideal starting point for calculations of corrections to the paraxial approximation

An exploration of alternative visualisations of the basic helix-loop-helix protein interaction network

Background: Alternative representations of biochemical networks emphasise different aspects of the data and contribute to the understanding of complex biological systems. In this study we present a variety of automated methods for visualisation of a protein-protein interaction network, using the basic helix-loop-helix ( bHLH) family of transcription factors as an example. Results: Network representations that arrange nodes ( proteins) according to either continuous or discrete information are investigated, revealing the existence of protein sub-families and the retention of interactions following gene duplication events. Methods of network visualisation in conjunction with a phylogenetic tree are presented, highlighting the evolutionary relationships between proteins, and clarifying the context of network hubs and interaction clusters. Finally, an optimisation technique is used to create a three-dimensional layout of the phylogenetic tree upon which the protein-protein interactions may be projected. Conclusion: We show that by incorporating secondary genomic, functional or phylogenetic information into network visualisation, it is possible to move beyond simple layout algorithms based on network topology towards more biologically meaningful representations. These new visualisations can give structure to complex networks and will greatly help in interpreting their evolutionary origins and functional implications. Three open source software packages (InterView, TVi and OptiMage) implementing our methods are available

Unified Treatment of Heterodyne Detection: the Shapiro-Wagner and Caves Frameworks

A comparative study is performed on two heterodyne systems of photon detectors expressed in terms of a signal annihilation operator and an image band creation operator called Shapiro-Wagner and Caves' frame, respectively. This approach is based on the introduction of a convenient operator $\hat \psi$ which allows a unified formulation of both cases. For the Shapiro-Wagner scheme, where $[\hat \psi, \hat \psi^{\dag}] =0$, quantum phase and amplitude are exactly defined in the context of relative number state (RNS) representation, while a procedure is devised to handle suitably and in a consistent way Caves' framework, characterized by $[\hat \psi, \hat \psi^{\dag}] \neq 0$, within the approximate simultaneous measurements of noncommuting variables. In such a case RNS phase and amplitude make sense only approximately.Comment: 25 pages. Just very minor editorial cosmetic change