Reaction Pathways Based on the Gradient of the Mean First-Passage Time

Finding representative reaction pathways is necessary for understanding mechanisms of molecular processes, but is considered to be extremely challenging. We propose a new method to construct reaction paths based on mean first-passage times. This approach incorporates information of all possible reaction events as well as the effect of temperature. The method is applied to exemplary reactions in a continuous and in a discrete setting. The suggested approach holds great promise for large reaction networks that are completely characterized by the method through a pathway graph.Comment: v2; 4 pages including 5 figure

Noise Dressing of Financial Correlation Matrices

We show that results from the theory of random matrices are potentially of great interest to understand the statistical structure of the empirical correlation matrices appearing in the study of price fluctuations. The central result of the present study is the remarkable agreement between the theoretical prediction (based on the assumption that the correlation matrix is random) and empirical data concerning the density of eigenvalues associated to the time series of the different stocks of the S&P500 (or other major markets). In particular the present study raises serious doubts on the blind use of empirical correlation matrices for risk management.Comment: Latex (Revtex) 3 pp + 2 postscript figures (in-text

Universality for orthogonal and symplectic Laguerre-type ensembles

We give a proof of the Universality Conjecture for orthogonal (beta=1) and symplectic (beta=4) random matrix ensembles of Laguerre-type in the bulk of the spectrum as well as at the hard and soft spectral edges. Our results are stated precisely in the Introduction (Theorems 1.1, 1.4, 1.6 and Corollaries 1.2, 1.5, 1.7). They concern the appropriately rescaled kernels K_{n,beta}, correlation and cluster functions, gap probabilities and the distributions of the largest and smallest eigenvalues. Corresponding results for unitary (beta=2) Laguerre-type ensembles have been proved by the fourth author in [23]. The varying weight case at the hard spectral edge was analyzed in [13] for beta=2: In this paper we do not consider varying weights. Our proof follows closely the work of the first two authors who showed in [7], [8] analogous results for Hermite-type ensembles. As in [7], [8] we use the version of the orthogonal polynomial method presented in [25], [22] to analyze the local eigenvalue statistics. The necessary asymptotic information on the Laguerre-type orthogonal polynomials is taken from [23].Comment: 75 page

Lateral Segregation of Photosystem I in Cyanobacterial Thylakoids

Photosystem I (PSI) is the dominant photosystem in cyanobacteria and it plays a pivotal role in cyanobacterial metabolism. Despite its biological importance, the native organisation of PSI in cyanobacterial thylakoid membranes is poorly understood. Here, we use atomic force microscopy (AFM) to show that ordered, extensive macromolecular arrays of PSI complexes are present in thylakoids from Thermosynechococcus (T.) elongatus, Synechococcus sp. PCC 7002 and Synechocystis sp PCC 6803. Hyperspectral confocal fluorescence microscopy (HCFM) and three-dimensional structured illumination microscopy (3D-SIM) of Synechocystis sp PCC 6803 cells visualise PSI domains within the context of the complete thylakoid system. Crystallographic and AFM data were used to build a structural model of a membrane landscape comprising 96 PSI trimers and 27,648 chlorophyll a molecules. Rather than facilitating inter-trimer energy transfer the close associations between PSI primarily maximise packing efficiency; short-range interactions with Complex I and cytochrome b6f are excluded from these regions of the membrane, so PSI turnover is sustained by long-distance diffusion of the electron donors at the membrane surface. Elsewhere, PSI-photosystem II (PSII) contact zones provide sites for docking phycobilisomes and the formation of megacomplexes. PSI-enriched domains in cyanobacteria might foreshadow the partitioning of PSI into stromal lamellae in plants, similarly sustained by long-distance diffusion of electron carriers

Role of quantum coherence in chromophoric energy transport

The role of quantum coherence and the environment in the dynamics of excitation energy transfer is not fully understood. In this work, we introduce the concept of dynamical contributions of various physical processes to the energy transfer efficiency. We develop two complementary approaches, based on a Green's function method and energy transfer susceptibilities, and quantify the importance of the Hamiltonian evolution, phonon-induced decoherence, and spatial relaxation pathways. We investigate the Fenna-Matthews-Olson protein complex, where we find a contribution of coherent dynamics of about 10% and of relaxation of 80%.Comment: 5 pages, 3 figures, included static disorder, correlated environmen

Distribution of entanglement in light-harvesting complexes and their quantum efficiency

Recent evidence of electronic coherence during energy transfer in photosynthetic antenna complexes has reinvigorated the discussion of whether coherence and/or entanglement has any practical functionality for these molecular systems. Here we investigate quantitative relationships between the quantum yield of a light-harvesting complex and the distribution of entanglement among its components. Our study focusses on the entanglement yield or average entanglement surviving a time scale comparable to the average excitation trapping time. As a prototype system we consider the Fenna-Matthews-Olson (FMO) protein of green sulphur bacteria and show that there is an inverse relationship between the quantum efficiency and the average entanglement between distant donor sites. Our results suggest that longlasting electronic coherence among distant donors might help modulation of the lightharvesting function.Comment: Version accepted for publication in NJ

A Random Matrix Model for Color Superconductivity at Zero Chemical Potential

We discuss random matrix models for the spontaneous breaking of both chiral and color symmetries at zero chemical potential and finite temperature. Exploring different Lorentz and gauge symmetric color structures of the random matrix interactions, we find that spontaneous chiral symmetry breaking is always thermodynamically preferred over diquark condensation. Stable diquark condensates appear only as SU(2) rotated chiral condensates, which do not represent an independent thermodynamic phase. Our analysis is based on general symmetry arguments and hence suggests that no stable and independent diquark phase can form in QCD with two flavors at zero quark chemical potential.Comment: 26 pages, 1 figure, uses ReVTeX and epsf.st

Pseudo-unitary symmetry and the Gaussian pseudo-unitary ensemble of random matrices

Employing the currently discussed notion of pseudo-Hermiticity, we define a pseudo-unitary group. Further, we develop a random matrix theory which is invariant under such a group and call this ensemble of pseudo-Hermitian random matrices as the pseudo-unitary ensemble. We obtain exact results for the nearest-neighbour level spacing distribution for (2 X 2) PT-symmetric Hamiltonian matrices which has a novel form, s log (1/s) near zero spacing. This shows a level repulsion in marked distinction with an algebraic form in the Wigner surmise. We believe that this paves way for a description of varied phenomena in two-dimensional statistical mechanics, quantum chromodynamics, and so on.Comment: 9 pages, 2 figures, LaTeX, submitted to the Physical Review Letters on August 20, 200

Staggered Fermions and Gauge Field Topology

Based on a large number of smearing steps, we classify SU(3) gauge field configurations in different topological sectors. For each sector we compare the exact analytical predictions for the microscopic Dirac operator spectrum of quenched staggered fermions. In all sectors we find perfect agreement with the predictions for the sector of topological charge zero, showing explicitly that the smallest Dirac operator eigenvalues of staggered fermions at presently realistic lattice couplings are insensitive to gauge field topology. On the smeared configurations, $4\nu$ eigenvalues clearly separate out from the rest on configurations of topological charge $\nu$, and move towards zero in agreement with the index theorem.Comment: LaTeX, 10 page