A temperature behavior of the frustrated translational mode of adsorbate and the nature of the "adsorbate-substrate" interaction

A temperature behavior of the frustrated translational mode (T-mode) of a light particle, coupled by different regimes of ohmicity to the surface, is studied within a formalism of the generalized diffusion coefficients. The memory effects of the adsorbate motion are considered to be the main reason of the T-mode origin. Numerical calculations yield a thermally induced shift and broadening of the T-mode, which is found to be linear in temperature for Ohmic and super-Ohmic systems and nonlinear for strongly sub-Ohmic ones. We obtain analytical expressions for the T-mode shift and width at weak coupling for the systems with integer "ohmicity" indexes n=0-2 in zero temperature and high temperature limits. We provide an explanation of the experimentally observed blue- or red-shifts of the T-mode on the basis of a comparative analysis of two typical times of the system evolution: a time of decay of the "velocity-velocity" autocorrelation function, and a correlation time of the thermal bath random forces. A relation of the T-mode to the multiple jumps of the adsorbate is discussed, and generalization of conditions of the multiple hopping to the case of quantum surface diffusion is performed.Comment: 12 pages, 4 figure

The stochastic behavior of a molecular switching circuit with feedback

Background: Using a statistical physics approach, we study the stochastic switching behavior of a model circuit of multisite phosphorylation and dephosphorylation with feedback. The circuit consists of a kinase and phosphatase acting on multiple sites of a substrate that, contingent on its modification state, catalyzes its own phosphorylation and, in a symmetric scenario, dephosphorylation. The symmetric case is viewed as a cartoon of conflicting feedback that could result from antagonistic pathways impinging on the state of a shared component. Results: Multisite phosphorylation is sufficient for bistable behavior under feedback even when catalysis is linear in substrate concentration, which is the case we consider. We compute the phase diagram, fluctuation spectrum and large-deviation properties related to switch memory within a statistical mechanics framework. Bistability occurs as either a first-order or second-order non-equilibrium phase transition, depending on the network symmetries and the ratio of phosphatase to kinase numbers. In the second-order case, the circuit never leaves the bistable regime upon increasing the number of substrate molecules at constant kinase to phosphatase ratio. Conclusions: The number of substrate molecules is a key parameter controlling both the onset of the bistable regime, fluctuation intensity, and the residence time in a switched state. The relevance of the concept of memory depends on the degree of switch symmetry, as memory presupposes information to be remembered, which is highest for equal residence times in the switched states. Reviewers: This article was reviewed by Artem Novozhilov (nominated by Eugene Koonin), Sergei Maslov, and Ned Wingreen.Comment: Version published in Biology Direct including reviewer comments and author responses, 28 pages, 7 figure

Reflectance measurement of two-dimensional photonic crystal nanocavities with embedded quantum dots

The spectra of two-dimensional photonic crystal slab nanocavities with embedded InAs quantum dots are measured by photoluminescence and reflectance. In comparing the spectra taken by these two different methods, consistency with the nanocavities' resonant wavelengths is found. Furthermore, it is shown that the reflectance method can measure both active and passive cavities. Q-factors of nanocavities, whose resonant wavelengths range from 1280 to 1620 nm, are measured by the reflectance method in cross polarization. Experimentally, Q-factors decrease for longer wavelengths and the intensity, reflected by the nanocavities on resonance, becomes minimal around 1370 nm. The trend of the Q-factors is explained by the change of the slab thickness relative to the resonant wavelength, showing a good agreement between theory and experiment. The trend of reflected intensity by the nanocavities on resonance can be understood as effects that originate from the PC slab and the underlying air cladding thickness. In addition to three dimensional finite-difference time-domain calculations, an analytical model is introduced that is able to reproduce the wavelength dependence of the reflected intensity observed in the experiment.Comment: 24 pages, 7 figures, corrected+full versio