Optimal target search on a fast folding polymer chain with volume exchange

We study the search process of a target on a rapidly folding polymer (`DNA') by an ensemble of particles (`proteins'), whose search combines 1D diffusion along the chain, Levy type diffusion mediated by chain looping, and volume exchange. A rich behavior of the search process is obtained with respect to the physical parameters, in particular, for the optimal search.Comment: 4 pages, 3 figures, REVTe

Towards deterministic equations for Levy walks: the fractional material derivative

Levy walks are random processes with an underlying spatiotemporal coupling. This coupling penalizes long jumps, and therefore Levy walks give a proper stochastic description for a particle's motion with broad jump length distribution. We derive a generalized dynamical formulation for Levy walks in which the fractional equivalent of the material derivative occurs. Our approach will be useful for the dynamical formulation of Levy walks in an external force field or in phase space for which the description in terms of the continuous time random walk or its corresponding generalized master equation are less well suited

Helix untwisting and bubble formation in circular DNA

The base pair fluctuations and helix untwisting are examined for a circular molecule. A realistic mesoscopic model including twisting degrees of freedom and bending of the molecular axis is proposed. The computational method, based on path integral techniques, simulates a distribution of topoisomers with various twist numbers and finds the energetically most favorable molecular conformation as a function of temperature. The method can predict helical repeat, openings loci and bubble sizes for specific sequences in a broad temperature range. Some results are presented for a short DNA circle recently identified in mammalian cells.Comment: The Journal of Chemical Physics, vol. 138 (2013), in pres

Development, implementation and evaluation of satellite-aided agricultural monitoring systems

Research activities in support of AgRISTARS Inventory Technology Development Project in the use of aerospace remote sensing for agricultural inventory described include: (1) corn and soybean crop spectral temporal signature characterization; (2) efficient area estimation techniques development; and (3) advanced satellite and sensor system definition. Studies include a statistical evaluation of the impact of cultural and environmental factors on crop spectral profiles, the development and evaluation of an automatic crop area estimation procedure, and the joint use of SEASAT-SAR and LANDSAT MSS for crop inventory

Understanding and utilization of Thematic Mapper and other remotely sensed data for vegetation monitoring

The TM Tasseled Cap transformation, which provides both a 50% reduction in data volume with little or no loss of important information and spectral features with direct physical association, is presented and discussed. Using both simulated and actual TM data, some important characteristics of vegetation and soils in this feature space are described, as are the effects of solar elevation angle and atmospheric haze. A preliminary spectral haze diagnostic feature, based on only simulated data, is also examined. The characteristics of the TM thermal band are discussed, as is a demonstration of the use of TM data in energy balance studies. Some characteristics of AVHRR data are described, as are the sensitivities to scene content of several LANDSAT-MSS preprocessing techniques

Theoretical characterization of a model of aragonite crystal orientation in red abalone nacre

Nacre, commonly known as mother-of-pearl, is a remarkable biomineral that in red abalone consists of layers of 400-nm thick aragonite crystalline tablets confined by organic matrix sheets, with the $(001)$ crystal axes of the aragonite tablets oriented to within $\pm$ 12 degrees from the normal to the layer planes. Recent experiments demonstrate that this orientational order develops over a distance of tens of layers from the prismatic boundary at which nacre formation begins. Our previous simulations of a model in which the order develops because of differential tablet growth rates (oriented tablets growing faster than misoriented ones) yield patterns of tablets that agree qualitatively and quantitatively with the experimental measurements. This paper presents an analytical treatment of this model, focusing on how the dynamical development and eventual degree of order depend on model parameters. Dynamical equations for the probability distributions governing tablet orientations are introduced whose form can be determined from symmetry considerations and for which substantial analytic progress can be made. Numerical simulations are performed to relate the parameters used in the analytic theory to those in the microscopic growth model. The analytic theory demonstrates that the dynamical mechanism is able to achieve a much higher degree of order than naive estimates would indicate.Comment: 20 pages, 3 figure

Intelligent systems in the context of surrounding environment

We investigate the behavioral patterns of a population of agents, each controlled by a simple biologically motivated neural network model, when they are set in competition against each other in the Minority Model of Challet and Zhang. We explore the effects of changing agent characteristics, demonstrating that crowding behavior takes place among agents of similar memory, and show how this allows unique `rogue' agents with higher memory values to take advantage of a majority population. We also show that agents' analytic capability is largely determined by the size of the intermediary layer of neurons. In the context of these results, we discuss the general nature of natural and artificial intelligence systems, and suggest intelligence only exists in the context of the surrounding environment (embodiment). Source code for the programs used can be found at http://neuro.webdrake.net/

Finding the optimum activation energy in DNA breathing dynamics: A Simulated Annealing approach

We demonstrate how the stochastic global optimization scheme of Simulated Annealing can be used to evaluate optimum parameters in the problem of DNA breathing dynamics. The breathing dynamics is followed in accordance with the stochastic Gillespie scheme with the denaturation zones in double stranded DNA studied as a single molecule time series. Simulated Annealing is used to find the optimum value of the activation energy for which the equilibrium bubble size distribution matches with a given value. It is demonstrated that the method overcomes even large noise in the input surrogate data.Comment: 9 pages, 4 figures, iop article package include

Average shape of fluctuations for subdiffusive walks

We study the average shape of fluctuations for subdiffusive processes, i.e., processes with uncorrelated increments but where the waiting time distribution has a broad power-law tail. This shape is obtained analytically by means of a fractional diffusion approach. We find that, in contrast with processes where the waiting time between increments has finite variance, the fluctuation shape is no longer a semicircle: it tends to adopt a table-like form as the subdiffusive character of the process increases. The theoretical predictions are compared with numerical simulation results.Comment: 4 pages, 6 figures. Accepted for publication Phys. Rev. E (Replaced for the latest version, in press.) Section II rewritte

Diffusion on random site percolation clusters. Theory and NMR microscopy experiments with model objects

Quasi two-dimensional random site percolation model objects were fabricate based on computer generated templates. Samples consisting of two compartments, a reservoir of H$_2$O gel attached to a percolation model object which was initially filled with D$_2$O, were examined with NMR (nuclear magnetic resonance) microscopy for rendering proton spin density maps. The propagating proton/deuteron inter-diffusion profiles were recorded and evaluated with respect to anomalous diffusion parameters. The deviation of the concentration profiles from those expected for unobstructed diffusion directly reflects the anomaly of the propagator for diffusion on a percolation cluster. The fractal dimension of the random walk, $d_w$, evaluated from the diffusion measurements on the one hand and the fractal dimension, $d_f$, deduced from the spin density map of the percolation object on the other permits one to experimentally compare dynamical and static exponents. Approximate calculations of the propagator are given on the basis of the fractional diffusion equation. Furthermore, the ordinary diffusion equation was solved numerically for the corresponding initial and boundary conditions for comparison. The anomalous diffusion constant was evaluated and is compared to the Brownian case. Some ad hoc correction of the propagator is shown to pay tribute to the finiteness of the system. In this way, anomalous solutions of the fractional diffusion equation could experimentally be verified for the first time.Comment: REVTeX, 12 figures in GIF forma