Biomedical subjects
Robert J Silbey
Publications and source records attributed to Robert J Silbey.
Utilizing the information content in two-state trajectories.
The signal from many single-molecule experiments monitoring molecular processes, such as enzyme turnover by means of fluorescence and opening and closing of ion channel through the flux of ions, consists of a time series of stochastic "on" and "off" (or open and closed) periods, termed a two-state trajectory. This signal reflects the dynamics in the underlying multisubstate on-off kinetic scheme (KS) of the process. The determination of the underlying KS is difficult and sometimes even impossible because of the loss of information in the mapping of the multidimensional KS onto two dimensions. Here we introduce a previously undescribed procedure that efficiently and optimally relates the signal to all equivalent underlying KS. This procedure partitions the space of KS into canonical (unique) forms that can handle any KS and obtains the topology and other details of the canonical form from the data without the need for fitting. Also established are relationships between the data and the topology of the canonical form to the on-off connectivity of a KS. The suggested canonical forms constitute a powerful tool in discriminating between KS. Based on our approach, the upper bound on the information content in two-state trajectories is determined.
Quantitative relationship between analyte concentration and amplified signal intensity of a molecular wire sensor.
The molecular wire approach has recently been proposed as a method to enhance the sensitivity of traditional chemosensors. In this paper, we present the exact quantitative relationship between analyte concentration and the signal for the ideal molecular wire sensor (MWS). The signal profile of a MWS differs from that of traditional chemosensors in that its Stern-Volmer curve has a positive curvature that increases with the number kappa of receptor units in each molecular wire composing the MWS. We find that the sensitivity of the MWS to the change of analyte concentration increases with kappa if kappa is less than a critical value kappa*; otherwise, it becomes a decreasing function of kappa. We also briefly comment on aspects of nonideal sensors.
Interrupted escape and the emergence of exponential relaxation.
A simple statistical theory of irreversible processes in a subsystem coupled to (or "interrupted" by) a stochastic bath is formulated. The theory does not explicitly invoke time scale separation that underlies the standard description of nonequilibrium phenomena and is intrinsic to the concept of quasiequilibrium in the canonical ensemble. Arbitrary statistics and speed of bath fluctuations are straightforwardly treated by the theory. Except in the case of an extremely slow, nonequilibrium bath, the ultimate statistics of interrupted escape are shown to be Poisson, which is solely a consequence of the stationary nature of interactions in a sufficiently dense system. In the limit of a fast bath, the corresponding relaxation rate is shown to equal the initial rate of decay, thus validating a wide class of Golden Rate type expressions at long times. This true exponentiality thus appears when the time scale separation takes place. The theory also applies to a number of specific phenomena including transport in a fluctuating or disordered medium, gated reactions, the line shape theory, and the quantum Zeno effect. The general nature of motional narrowing phenomena is demonstrated and related to the bath mediated slowing down of a decay process with a nearly deterministic uninterrupted escape probability. The corresponding survival probability is shown also to exhibit discernible oscillations around the exponential background. Mathematical tools necessary for using the theory in specific applications are exposed in some detail.
Multichromophoric Förster resonance energy transfer.
The theory of Förster resonance energy transfer is generalized for multichromophoric (MC) and nonequilibrium situations. For the first time, it is clarified that the far-field linear spectroscopic information is insufficient for the determination of the reaction rate and that distance dependence of the rate can vary with the disorder and temperature. Application to a light harvesting complex LH2 reveals the important consequences of a MC structure.
Exact dynamics of a continuous time random walker in the presence of a boundary: beyond the intuitive boundary condition approach.
We derive the exact dynamics of a random walker with arbitrary non-Markovian transport and reaction rate distribution at a boundary, and present exact solutions in the continuum limit. We find that the ultimate escape probability of the particle is independent of the transport mechanism in contradiction to the long-standing belief based on the conventional approach. We also find a phase transition in the relaxation kinetics associated with the heterogeneity of the transport media.