Signatures of correlated excitonic dynamics in two-dimensional spectroscopy of the Fenna-Matthew-Olson photosynthetic complex

Long-lived excitonic coherence in photosynthetic proteins has become an exciting area of research because it may provide design principles for enhancing the efficiency of energy transfer in a broad range of materials. In this publication, we provide new evidence that long-lived excitonic coherence in the Fenna-Mathew-Olson pigment-protein (FMO) complex is consistent with the assumption of cross correlation in the site basis, indicating that each site shares bath fluctuations. We analyze the structure and character of the beating crosspeak between the two lowest energy excitons in two-dimensional (2D) electronic spectra of the FMO Complex. To isolate this dynamic signature, we use the two-dimensional linear prediction Z-transform as a platform for filtering coherent beating signatures within 2D spectra. By separating signals into components in frequency and decay rate representations, we are able to improve resolution and isolate specific coherences. This strategy permits analysis of the shape, position, character, and phase of these features. Simulations of the crosspeak between excitons 1 and 2 in FMO under different regimes of cross correlation verify that statistically independent site fluctuations do not account for the elongation and persistence of the dynamic crosspeak. To reproduce the experimental results, we invoke near complete correlation in the fluctuations experienced by the sites associated with excitons 1 and 2. This model contradicts ab initio quantum mechanic∕molecular mechanics simulations that observe no correlation between the energies of individual sites. This contradiction suggests that a new physical model for long-lived coherence may be necessary. The data presented here details experimental results that must be reproduced for a physical model of quantum coherence in photosynthetic energy transfer.     

Conformational effect on small angle neutron scattering behavior of interacting polyelectrolyte solutions: a perspective of integral equation theory

We present small angle neutron scattering (SANS) measurements of deuterium oxide (D(2)O) solutions of linear and star sodium poly(styrene sulfonate) (NaPSS) as a function of polyelectrolyte concentration. Emphasis is on understanding the dependence of their SANS coherent scattering cross section I(Q) on the molecular architecture of single polyelectrolyte. The key finding is that for a given concentration, star polyelectrolytes exhibit more pronounced characteristic peaks in I(Q), and the position of the first peak occurs at a smaller Q compared to their linear counterparts. Based on a model of integral equation theory, we first compare the SANS experimental I(Q) of salt-free polyelectrolyte solutions with that predicted theoretically. Having seen their satisfactory qualitative agreement, the dependence of counterion association behavior on polyelectrolyte geometry and concentration is further explored. Our predictions reveal that the ionic environment of polyelectrolyte exhibits a strong dependence on polyelectrolyte geometry at lower polyelectrolyte concentration. However, when both linear and star polyelectrolytes exceed their overlap concentrations, the spatial distribution of counterion is found to be essentially insensitive to polyelectrolyte geometry due to the steric effect.     

Neutron self-shielding in irradiation channels of small reactors is isotropic

In order to predict the self-shielding effect in neutron activation of non-spherical samples in reactor neutron spectra, it is important to know whether the neutron field is sufficiently anisotropic to cause significant variations between horizontal and vertical sample orientation or with orientation relative to the direction towards the reactor core. Metal wires with significant neutron self-shielding were irradiated in several channels of the SLOWPOKE reactor at Ecole Polytechnique Montreal and the TRIGA reactor at the Jožef Stefan Institute. In all cases, the amount of thermal or epithermal self-shielding was found to be identical, within the experimental uncertainty, regardless of the orientation of the wire, indicating that the neutron field is essentially isotropic. Models used to predict neutron self-shielding need to be adjusted accordingly. In our Monte Carlo model, the tube-shaped neutron source was moved back into the moderator and reflecting materials near the sample location were included, which produced an isotropic neutron field at the sample location.     

Verifying agent-based models with steady-state analysis

Agent-based modeling has been well received in the simulation community. Complex systems are simulated by many autonomous agents whose behavior is defined by a conceptual model. However, the model can be improperly implemented or misinterpreted resulting in an implementation that does not reflect the conceptual rules. It is imperative that the implementation’s function be tested against the model’s expected outcome. In this paper, we present certain steady-state techniques that can be used to verify the operation of agent-based simulations. These methods are introduced and then applied to an ecological model which simulates reproductive dynamics of mosquitoes.     

Dynamics of Nodal Points and the Nodal Count on a Family of Quantum Graphs

We investigate the properties of the zeros of the eigenfunctions on quantum graphs (metric graphs with a Schr?dinger-type differential operator). Using tools such as scattering approach and eigenvalue interlacing inequalities we derive several formulas relating the number of the zeros of the n-th eigenfunction to the spectrum of the graph and of some of its subgraphs. In a special case of the so-called dihedral graph we prove an explicit formula that only uses the lengths of the edges, entirely bypassing the information about the graph??s eigenvalues. The results are explained from the point of view of the dynamics of zeros of the solutions to the scattering problem.     

Spectral Stability of Ideal-Gas Shock Layers

Extending recent results in the isentropic case, we use a combination of asymptotic ODE estimates and numerical Evans-function computations to examine the spectral stability of shock-wave solutions of the compressible Navier–Stokes equations with ideal gas equation of state. Our main results are that, in appropriately rescaled coordinates, the Evans function associated with the linearized operator about the wave (i) converges in the large-amplitude limit to the Evans function for a limiting shock profile of the same equations, for which internal energy vanishes at one end state; and (ii) has no unstable (positive real part) zeros outside a uniform ball |λ| ≦ Λ. Thus, the rescaled eigenvalue ODE for the set of all shock waves, augmented with the (nonphysical) limiting case, form a compact family of boundary-value problems that can be conveniently investigated numerically. An extensive numerical Evans-function study yields one-dimensional spectral stability, independent of amplitude, for gas constant γ in [1.2, 3] and ratio ν/μ of heat conduction to viscosity coefficient within [0.2, 5] (γ ≈ 1.4, ν/μ ≈ 1.47 for air). Other values may be treated similarly but were not considered. The method of analysis extends also to the multi-dimensional case, a direction that we shall pursue in a future work.     

Particles for tracing turbulent liquid helium

We address the problem of making quantitative measurements of local flow velocities in turbulent liquid helium, using tracer particles. We survey and evaluate presently available particles and previous work to establish the need to develop new particles for the purpose. We present the first practical solution for visualizing fluid motions using a suspension of solid hydrogen particles with diameters of about 2 μm. The hydrogen particles can be used to study flows with Taylor-microscale Reynolds numbers between 85 and 775. The particles can be used equally well with the PIV, LDV, or particle-tracking techniques.     

Effects of strong anchoring on the dynamic moduli of heterogeneous nematic polymers II: oblique anchoring angles

We extend previous work on the linear viscoelastic moduli of heterogeneous nematic polymers in a small-amplitude oscillatory shear flow, focusing on the role of the orientational anchoring conditions at the plates. When tangential or normal anchoring conditions are applied, the Doi–Marrucci–Greco orientation tensor-flow model effectively reduces to the Leslie–Ericksen director-flow model, predicting that director distortions control the dynamic moduli with negligible contributions from tensor-order parameters. In this paper, we examine oblique anchoring angles. We use a combination of analysis and numerical simulation on the generalized tensor-flow system for arbitrary anchoring conditions to show that any oblique anchoring condition induces a nontrivial order parameter contribution to the dynamic moduli, which vanishes only in the limit of tangential or normal anchoring. Our approach reveals that the storage and loss moduli admit an approximate decomposition in terms of two reduced problems that are exactly solvable: the heterogeneous director–flow response plus the monodomain tensor response to an imposed shear. The importance of this result is that we gain scaling properties of the moduli with respect to material parameters and experimental conditions without having to compute and assimilate across the full parameter space. These results provide insight into the relative importance of the distortional vs bulk nematic elastic stress in determining the viscoelastic moduli, predicting that anchoring conditions tune the relative contributions.