Unraveling the similarity of the photoabsorption of deprotonated p-coumaric acid in the gas phase and within the photoactive yellow protein

Using advanced QM/MM methods, the surprisingly negligible shift of the lowest-lying bright electronic excitation of the deprotonated p-coumaric acid (pCA(-)) within the photoactive yellow protein (PYP) is shown to stem from a subtle balance between hypsochromic and bathochromic effects. More specifically, it is found that the change in the excitation energy as a consequence of the disruption of the planarity of pCA(-) inside PYP is nearly canceled out by the shift induced by the intermolecular interactions of the chromophore and the protein as a whole. These results provide important insights about the primary absorption and the tuning of the chromophore by the protein environment in PYP.     

Runge–Kutta Lawson schemes for stochastic differential equations

In this paper, we present a framework to construct general stochastic Runge–Kutta Lawson schemes. We prove that the schemes inherit the consistency and convergence properties of the underlying Runge–Kutta scheme, and confirm this in some numerical experiments. We also investigate the stability properties of the methods and show for some examples, that the new schemes have improved stability properties compared to the underlying schemes.

     

Femtosecond laser excitation of dielectric materials: experiments and modeling of optical properties and ablation depths

Modeling of the interaction between a dielectric material and ultrashort laser pulses provides the temporal evolution of the electronic excitation and the optical properties of the dielectric. Experimentally determined reflectances and ablation depths for sapphire are compared to the calculations. A decrease in reflectance at high fluences is observed experimentally, which demonstrates the necessity of a temperature-dependent electron scattering rate in the model. The comparison thus provides new constraints on the optical parameters of the model.     

A Dynamic Two-Phase Pore-Scale Model of Imbibition

We present a dynamic pore-scale network model of imbibition, capable of calculating residual oil saturation for any given capillary number, viscosity ratio, contact angle, and aspect ratio. Our goal is not to predict the outcome of core floods, but rather to perform a sensitivity analysis of the above-mentioned parameters, except from the viscosity ratio. We find that contact angle, aspect ratio, and capillary number all have a significant influence on the competition between piston-like advance, leading to high recovery, and snap-off, causing oil entrapment. Due to significant CPU-time requirements we did not incorporate long-range correlations among pore and throat sizes in our network, but were limited to small-range correlations. Consequently, the gradual suppression of snap-off occurs within one order of magnitude of the capillary number. At capillary numbers around 10⁸ - 10⁷ snap-off has been entirely inhibited, in agreement with results obtained by Blunt (1997) who used a quasi-static model. For higher aspect ratios, the effect of rate and contact angle is more pronounced.     

An instability of the Godunov scheme

We construct a solution to a 2 × 2 strictly hyperbolic system of conservation laws, showing that the Godunov scheme [13] can produce an arbitrarily large amount of oscillations. This happens when the speed of a shock is close to rational, inducing a resonance with the grid. Differently from the Glimm scheme or the vanishing‐viscosity method, for systems of conservation laws our counterexample indicates that no a priori BV bounds or L¹‐stability estimates can in general be valid for finite difference schemes. © 2006 Wiley Periodicals, Inc.     

A uniqueness result related to the stability of explicit Runge-Kutta methods

The polynomial associated with the largest disk of stability of anm-stage explict Runge-Kutta method of orderp is unique.     

Measurement of spin alignment for the 15N32 (6.33 MeV) state from the (16O, 15N) reaction using γ-recoil in flight

High resolution for the ²⁷Al(¹⁶O, ¹⁵N)²⁸Si reaction were measured with a Q3D magnetic spectrometer. The broadened line shape of the ${}^{15}\text{N}{}_{\mathrm{<mtext>3</mtext><mtext>2</mtext>}}$ (6.33 MeV) state after γ-decay in flight was analysed. The m-state population of this state was deduced taking the E2/M1 mixing ratio of δ = +0.1 into account. The connection between spin alignment and the dynamics of the transfer process is discussed.     

Dilaton as the Higgs boson

We propose a model where the role of the electroweak Higgs field is played by the dilaton. The model contains terms which explicitly violate gauge invariance; however, it is shown that this violation is fictitious, so that the model is a consistent low-energy effective theory. In the simplest version of the idea the resulting low-energy effective theory is the same as the top mode standard model.     

First-principles modelling of scanning tunneling microscopy using non-equilibrium Green’s functions

The investigation of electron transport processes in nano-scale architectures plays a crucial role in the development of surface chemistry and nano-technology. Experimentally, an important driving force within this research area has been the concurrent refinements of scanning tunneling microscopy (STM) techniques. The theoretical treatment of the STM operation has traditionally been based on the Bardeen and Tersoff-Hamann methods which take as input the single-particle wave functions and eigenvalues obtained from finite cluster or slabs models of the surface-tip interface. Here, we present a novel STM simulation scheme based on non-equilibrium Green’s functions (NEGF) and Wannier functions which is both accurate and very efficient. The main novelty of the scheme compared to the Bardeen and Tersoff-Hamann approaches is that the coupling to the infinite (macroscopic) electrodes is taken into account. As an illustrating example we apply the NEGF-STM method to the Si(001)-(2×1):H surface with sub-surface P doping and discuss the results in comparison to the Bardeen and Tersoff-Hamann methods.     

Powered partial least squares discriminant analysis

From the fundamental parts of PLS‐DA, Fisher's canonical discriminant analysis (FCDA) and Powered PLS (PPLS), we develop the concept of powered PLS for classification problems (PPLS‐DA). By taking advantage of a sequence of data reducing linear transformations (consistent with the computation of ordinary PLS‐DA components), PPLS‐DA computes each component from the transformed data by maximization of a parameterized Rayleigh quotient associated with FCDA. Models found by the powered PLS methodology can contribute to reveal the relevance of particular predictors and often requires fewer and simpler components than their ordinary PLS counterparts. From the possibility of imposing restrictions on the powers available for optimization we obtain an explorative approach to predictive modeling not available to the traditional PLS methods. Copyright © 2008 John Wiley & Sons, Ltd.