Origins of concentration dependence of waiting times for single-molecule fluorescence binding

Binary fluorescence time series obtained from single-molecule imaging experiments can be used to infer protein binding kinetics, in particular, association and dissociation rate constants from waiting time statistics of fluorescence intensity changes. In many cases, rate constants inferred from fluorescence time series exhibit nonintuitive dependence on ligand concentration. Here we examine several possible mechanistic and technical origins that may induce ligand dependence of rate constants. Using aggregated Markov models, we show under the condition of detailed balance that non-fluorescent bindings and missed events due to transient interactions, instead of conformation fluctuations, may underly the dependence of waiting times and thus apparent rate constants on ligand concentrations. In general, waiting times are rational functions of ligand concentration. The shape of concentration dependence is qualitatively affected by the number of binding sites in the single molecule and is quantitatively tuned by model parameters. We also show that ligand dependence can be caused by non-equilibrium conditions which result in violations of detailed balance and require an energy source. As to a different but significant mechanism, we examine the effect of ambient buffers that can substantially reduce the effective concentration of ligands that interact with the single molecules. To demonstrate the effects by these mechanisms, we applied our results to analyze the concentration dependence in a single-molecule experiment EGFR binding to fluorophore-labeled adaptor protein Grb2 by Morimatsu et al. (PNAS,104:18013,2007).Comment: 11 pages, 4 figures; J. Chem. Phys., 137, 201

Oblique Long Waves on Beach and Induced Longshore Current

This study considers the 3D runup of long waves on a uniform beach of constant or variable downward slope that is connected to an open ocean of uniform depth. An inviscid linear long-wave theory is applied to obtain the fundamental solution for a uniform train of sinusoidal waves obliquely incident upon a uniform beach of variable downward slope without wave breaking. For waves at nearly grazing incidence, runup is significant only for the waves in a set of eigenmodes being trapped within the beach at resonance with the exterior ocean waves. Fourier synthesis is employed to analyze a solitary wave and a train of cnoidal waves obliquely incident upon a sloping beach, with the nonlinear and dispersive effects neglected at this stage. Comparison is made between the present theory and the ray theory to ascertain a criterion of validity. The wave-induced longshore current is evaluated by finding the Stokes drift of the fluid particles carried by the momentum of the waves obliquely incident upon a sloping beach. Currents of significant velocities are produced by waves at incidence angles about 45 [degrees] and by grazing waves trapped on the beach. Also explored are the effects of the variable downward slope and curvature of a uniform beach on 3D runup and reflection of long waves

Quantum Spin Chain, Toeplitz Determinants and Fisher-Hartwig Conjecture

We consider one-dimensional quantum spin chain, which is called XX model, XX0 model or isotropic XY model in a transverse magnetic field. We study the model on the infinite lattice at zero temperature. We are interested in the entropy of a subsystem [a block of L neighboring spins]. It describes entanglement of the block with the rest of the ground state. G. Vidal, J.I. Latorre, E. Rico, and A. Kitaev showed that for large blocks the entropy scales logarithmically. We prove the logarithmic formula for the leading term and calculate the next term. We discovered that the dependence on the magnetic field interacting with spins is very simple: the magnetic field effectively reduce the size of the subsystem. We also calculate entropy of a subsystem of a small size. We also evaluated Renyi and Tsallis entropies of the subsystem. We represented the entropy in terms of a Toeplitz determinant and calculated the asymptotic analytically.Comment: LATEX, 17 pages, 1 fi

On locally n×nn \times n grid graphs

We investigate locally $n \times n$ grid graphs, that is, graphs in which the neighbourhood of any vertex is the Cartesian product of two complete graphs on $n$ vertices. We consider the subclass of these graphs for which each pair of vertices at distance two is joined by sufficiently many paths of length $2$. The number of such paths is known to be at most $2n$ by previous work of Blokhuis and Brouwer. We show that if each distance two pair is joined by at least $n-1$ paths of length $2$ then the diameter is bounded by $O(\log(n))$, while if each pair is joined by at least $2(n-1)$ such paths then the diameter is at most $3$ and we give a tight upper bound on the order of the graphs. We show that graphs meeting this upper bound are distance-regular antipodal covers of complete graphs. We exhibit an infinite family of such graphs which are locally $n \times n$ grid for odd prime powers $n$, and apply these results to locally $5 \times 5$ grid graphs to obtain a classification for the case where either all $\mu$-graphs have order at least $8$ or all $\mu$-graphs have order $c$ for some constant $c$