Biomedical subjects

James B Witkoskie

Publications and source records attributed to James B Witkoskie.

8 recordsLinked to original sources

PubMed2006

Aging correlation functions of the interrupted fractional Fokker-Planck propagator.

The authors explore aging in a general semi-Markov process with arbitrary waiting time distributions and discuss the role of trapping phenomenon in glasses in determining the waiting time distributions. In certain limits, they obtain a two-time propagator for the fractional Fokker-Planck equation through coordination, but one can generalize the construction to incorporate cutoffs in the aging of the system, i.e., the interrupted aging. The construction allows the incorporation of cutoffs in the aging of the system, and the exploration of signatures of aging effects in systems that eventually achieve equilibrium. Cutoffs in aging effects are illustrated for interrupted fractional diffusion in a harmonic potential and for the on-time probability of a quantum dot system.

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PubMed2006

Testing for renewal and detailed balance violations in single-molecule blinking processes.

This paper examines methods to test one- and two-dimensional histograms for several features including the renewal properties, detailed balance violations, and experimental condition dependences. The tests are simple to implement and allow rigorous statistical determination of the existence of these kinetic features. The tests are used to determine the lower bound on the number of measurements necessary to differentiate underlying kinetic models.

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PubMed2006

Description of the fluorescence intensity time trace of collections of CdSe nanocrystal quantum dots based on single quantum dot fluorescence blinking statistics.

This paper analyzes the observed phenomenology of the fluorescence time trace of collections of quantum dots (QDs) in terms of the model parameters that characterize the fluorescence blinking statistics of single QDs. We demonstrate that the non-universal dynamics that appear in fluorescence time traces of collections of QDs at short time scales are related to the universal dynamics that appear at longer time scales. We explore how the extent of time separation between the short and long dynamics affects the transition region and the dynamics at longer time scales. We suggest a methodology to extract single QD statistical model parameters from experimental fluorescence time traces of collections of QDs. We explore theoretical time traces and their experimental analogs for three different cases that span the diverse nonuniversal dynamics that appear at short time scales.

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PubMed2004

Single molecule kinetics. I. Theoretical analysis of indicators.

Single molecule experiments reveal intriguing phenomenon in chemical and biological systems. Several indicators of complex dynamics, including "intensity" correlations, "event" correlations, and characteristic functions have been proposed, but extraction of information from these indicators can be difficult since these indicators only observe certain characteristics of the system. Generally, for systems that follow Poisson kinetics, all of these indicators contain similar information about the relaxation times of the system and the connections between different relaxation times, but the information is convoluted in different ways so the strength of various indicators is system specific. The paper discusses the theoretical implications and information content of various data analysis methods for single molecule experiments and demonstrates the relationships between indicators. Under certain conditions, common indicators contain all available information about systems with Poisson kinetics between degenerate states, but extraction of this information is generally not numerically feasible. The paper also discusses practical issues associated with these analyses, which motivates a numerical study based on Bayes' formula in the companion paper [J. Witkoskie and J. S. Cao, J. Chem. Phys. 121, 6373 (2004), following paper].

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PubMed2004

Single molecule kinetics. II. Numerical Bayesian approach.

As discussed in the companion paper [J. B. Witkoskie and J. S. Cao, J. Chem. Phys. 121, 6361 (2004), preceding paper], quantitative extraction of information from single molecule experiments by several proposed indicators is difficult since the experiments only observe certain characteristics of the system, even though the indicators can contain all available information. This paper shows how one can circumvent the shortcomings of these indicators by combining information extracted from indicators with a numerical Bayesian statistical approach. The Bayesian approach determines the relative probability of various models reproducing the entire sequence of the single molecules trajectory, instead of binning and averaging over the data, which removes much of this information.

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PubMed2004

Scaling and universality of inherent structure simulations.

In this paper we explore the inherent structures (IS) approach to the dynamics of the East constrained kinetic Ising model. The inherent structures do not capture the nature of the dynamics of many quantities, including the spin autocorrelation function. Simply monitoring the quenched energy fluctuations, i.e., IS energy, results in an oversimplified single order-parameter description of the system's dynamics, but examining other features, such as domain dynamics or normal modes, may give a more complete and useful picture of the dynamics. The universality in the behavior of the IS energy of this model does not reveal nonuniversal features of the kinetics that determine long-time relaxation of the system. As a result, popular functional forms, such as the stretched exponential relaxation or Gaussian distribution of energies, may be a numerical fit to data with little physical justification. Filtering data can be shown to erase features of the system and the resulting quantities resemble more universal functional forms that lack physical insight. These results for the East model have implications for IS simulations of realistic systems and suggest careful analysis including the examination of other potential order parameters is necessary to evaluate the validity of applications of universal and scaling arguments to IS simulations.

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PubMed2004

Basis set study of classical rotor lattice dynamics.

The reorientational relaxation of molecular systems is important in many phenomenon and applications. In this paper, we explore the reorientational relaxation of a model Brownian rotor lattice system with short range interactions in both the high and low temperature regimes. In this study, we use a basis set expansion to capture collective motions of the system. The single particle basis set is used in the high temperature regime, while the spin wave basis is used in the low temperature regime. The equations of motion derived in this approach are analogous to the generalized Langevin equation, but the equations render flexibility by allowing nonequilibrium initial conditions. This calculation shows that the choice of projection operators in the generalized Langevin equation (GLE) approach corresponds to defining a specific inner-product space, and this inner-product space should be chosen to reveal the important physics of the problem. The basis set approach corresponds to an inner-product and projection operator that maintain the orthogonality of the spherical harmonics and provide a convenient platform for analyzing GLE expansions. The results compare favorably with numerical simulations, and the formalism is easily extended to more complex systems.

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PubMed2002

Brownian motion in dynamically disordered media.

The motion of Brownian test particles in a model random potential with time dependent correlations is investigated using four methods: renormalized perturbation, perturbation using Martin, Siggia, and Rose functional formalism (MSR), the Edwards variational method on the MSR functional, and renormalization group with the MSR function. The disorder averaged one-particle propagators determined by the renormalized perturbation expansion and MSR perturbation expansion are identical to the second and possibly higher order, and the two-particle propagators determined by these perturbation methods are identical at the first and possibly higher order. The one-particle propagator determined by the Edwards method is identical to the perturbation expansions at the first order, but the second-order analogue of the Edwards method has a more complex expression, which reduces to the second-order perturbation expression with additional higher-order terms. The diffusion constant and two-particle correlations are calculated from these propagators and are used to determine the effects of the random potential on the Brownian particles. Generally, the diffusion rate decreases with the disorder strength and increases with the temporal decay rate. The two competing mechanisms result in an enhancement of the diffusion constant for weak potentials with fast temporal fluctuations. The system exhibits two-particle correlations that are inherently non-Gaussian and indicate clustering behavior. The diffusion constant is also determined from a simple one-loop renormalization group calculation. In the static limit, the diffusion constant calculated by the renormalization group recovers the results of Deem and Chandler [M.W. Deem and D. Chandler, J. Stat. Phys. 76, 911 (1994)].

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