Iterative Linearized Density Matrix Propagation for Modeling Coherent Energy Transfer in Photosynthetic Light Harvesting

We present results of calculations [1] that employ a new mixed quantum classical iterative density matrix propagation approach (ILDM , or so called Is‐Landmap) [2] to explore the survival of coherence in different photo synthetic models. Our model studies confirm the long lived quantum coherence , while conventional theoretical tools (such as Redfield equation) fail to describe these phenomenon [3,4]. Our ILDM method is a numerical exactly propagation scheme and can be served as a bench mark calculation tools[2]. Result get from ILDM and from other recent methods have been compared and show agreement with each other[4,5]. Long lived coherence plateau has been attribute to the shift of harmonic potential due to the system bath interaction, and the harvesting efficiency is a balance between the coherence and dissipation[1]. We use this approach to investigate the excitation energy transfer dynamics in various light harvesting complex include Fenna‐Matthews‐Olsen light harvesting complex[1] and Cryptophyte Phycocyanin 645 [6]. [1] P.Huo and D.F.Coker ,J. Chem. Phys. 133, 184108 (2010) . [2] E.R. Dunkel, S. Bonella, and D.F. Coker, J. Chem. Phys. 129, 114106 (2008). [3] A. Ishizaki and G.R. Fleming, J. Chem. Phys. 130, 234111 (2009). [4] A. Ishizaki and G.R. Fleming, Proc. Natl. Acad. Sci. 106, 17255 (2009). [5] G. Tao and W.H. Miller, J. Phys. Chem. Lett. 1, 891 (2010). [6] P.Huo and D.F.Coker in preparation

SOUND PROPAGATION AND SCATTERING IN BUBBLY LIQUIDS

In the ocean, natural and artificial processes generate clouds of bubbles which scatter and attenuate sound. Measurements have shown that at the individual bubble resonance frequency, sound propagation in this medium is highly attenuated and dispersive. Theory to explain this behavior exists in the literature, and is adequate away from resonance. However, due to excessive attenuation near resonance, little experimental data exists for comparison. An impedance tube was developed specifically for exploring this regime. Using the instrument, unique phase speed and attenuation measurements were made for void fractions ranging from 6.2 × 10^−5 to 2.7 × 10^−3 and bubble sizes centered around 0.62 mm in radius. Improved measurement speed, accuracy and precision is possible with the new instrument, and both instantaneous and time-averaged measurements were obtained. Behavior at resonance was observed to be sensitive to the bubble population statistics and agreed with existing theory, within the uncertainty of the bubble population parameters. Scattering from acoustically compact bubble clouds can be predicted from classical scattering theory by using an effective medium description of the bubbly fluid interior. Experimental verification was previously obtained up to the lowest resonance frequency. A novel bubble production technique has been employed to obtain unique scattering measurements with a bubbly-liquid-filled latex tube in a large indoor tank. The effective scattering model described these measurements up to three times the lowest resonance frequency of the structure.

PROPAGATION OF SONIC BOOMS THROUGH A REAL, STRATIFIED ATMOSPHERE

Sonic boom propagation in a quiet) stratified) lossy atmosphere is the subject of this dissertation. Two questions are considered in detail: (1) Does waveform freezing occur? (2) Are sonic booms shocks in steady state? Both assumptions have been invoked in the past to predict sonic boom waveforms at the ground. A very general form of the Burgers equation is derived and used as the model for the problem. The derivation begins with the basic conservation equations. The effects of nonlinearity) attenuation and dispersion due to multiple relaxations) viscosity) and heat conduction) geometrical spreading) and stratification of the medium are included. When the absorption and dispersion terms are neglected) an analytical solution is available. The analytical solution is used to answer the first question. Geometrical spreading and stratification of the medium are found to slow down the nonlinear distortion of finite-amplitude waves. In certain cases the distortion reaches an absolute limit) a phenomenon called waveform freezing. Judging by the maturity of the distortion mechanism, sonic booms generated by aircraft at 18 km altitude are not frozen when they reach the ground. On the other hand, judging by the approach of the waveform to its asymptotic shape, N waves generated by aircraft at 18 km altitude are frozen when they reach the ground. To answer the second question we solve the full Burgers equation and for this purpose develop a new computer code, THOR. The code is based on an algorithm by Lee and Hamilton (J. Acoust. Soc. Am. 97, 906-917, 1995) and has the novel feature that all its calculations are done in the time domain, including absorption and dispersion. Results from the code compare very well with analytical solutions. In a NASA exercise to compare sonic boom computer programs, THOR gave results that agree well with those of other participants and ran faster. We show that sonic booms are not steady state waves because they travel through a varying medium, suffer spreading, and fail to approximate step shocks closely enough. Although developed to predict sonic boom propagation, THOR can solve other problems for which the extended Burgers equation is a good propagation model.

EVALUATION OF HARMONIC MOTION ELASTOGRAPHY AND ACOUSTO-­OPTIC IMAGING FOR MONITORING LESION FORMATION BY HIGH INTENSITY FOCUSED ULTRASOUND

Malignant or benign tumors may be ablated with high‐intensity focused ultrasound (HIFU). This technique, known as focused ultrasound surgery (FUS), has been actively investigated for decades, but slow to be implemented and difficult to control due to lack of real‐time feedback during ablation. Two methods of imaging and monitoring HIFU lesions during formation were implemented simultaneously, in order to investigate the efficacy of each and to increase confidence in the detection of the lesion. The first, Acousto‐Optic Imaging (AOI) detects the increasing optical absorption and scattering in the lesion. The intensity of a diffuse optical field in illuminated tissue is mapped at the spatial resolution of an ultrasound focal spot, using the acousto‐optic effect. The second, Harmonic Motion Imaging (HMI), detects the changing stiffness in the lesion. The HIFU beam is modulated to force oscillatory motion in the tissue, and the amplitude of this motion, measured by ultrasound pulse‐echo techniques, is influenced by the stiffness. Experiments were performed on store‐bought chicken breast and freshly slaughtered bovine liver. The AOI results correlated with the onset and relative size of forming lesions much better than prior knowledge of the HIFU power and duration. For HMI, a significant artifact was discovered due to acoustic nonlinearity. The artifact was mitigated by adjusting the phase of the HIFU and imaging pulses. A more detailed model of the HMI process than previously published was made using finite element analysis. The model showed that the amplitude of harmonic motion was primarily affected by increases in acoustic attenuation and stiffness as the lesion formed and the interaction of these effects was complex and often counteracted each other. Further biological variability in tissue properties meant that changes in motion were masked by sample‐to‐sample variation. The HMI experiments predicted lesion formation in only about a quarter of the lesions made. In simultaneous AOI/HMI experiments it appeared that AOI was a more robust method for lesion detection.

An Omniscient Scheduling Oracle for Systems with Harmonic Periods

Most real-time scheduling problems are known to be NP-complete. To enable accurate comparison between the schedules of heuristic algorithms and the optimal schedule, we introduce an omniscient oracle. This oracle provides schedules for periodic task sets with harmonic periods and variable resource requirements. Three different job value functions are described and implemented. Each corresponds to a different system goal. The oracle is used to examine the performance of different on-line schedulers under varying loads, including overload. We have compared the oracle against Rate Monotonic Scheduling, Statistical Rate Monotonic Scheduling, and Slack Stealing Job Admission Control Scheduling. Consistently, the oracle provides an upper bound on performance for the metric under consideration.

Orientational Harmonic Model for Illusory Boundary Formation in Biological Vision

An extension to the Boundary Contour System model is proposed to account for boundary completion through vertices with arbitrary numbers of orientations, in a manner consistent with psychophysical observartions, by way of harmonic resonance in a neural architecture.

Orientational Harmonic Model for Rotation, Translation, and Scale Invariant Pattern Representation in Biological Vision

An extension to the orientational harmonic model is presented as a rotation, translation, and scale invariant representation of geometrical form in biological vision.

Orientational Harmonic Model for Rotation, Translation, and Scale Invariant Pattern Representation in Biological Vision

The proposed model, called the combinatorial and competitive spatio-temporal memory or CCSTM, provides an elegant solution to the general problem of having to store and recall spatio-temporal patterns in which states or sequences of states can recur in various contexts. For example, fig. 1 shows two state sequences that have a common subsequence, C and D. The CCSTM assumes that any state has a distributed representation as a collection of features. Each feature has an associated competitive module (CM) containing K cells. On any given occurrence of a particular feature, A, exactly one of the cells in CMA will be chosen to represent it. It is the particular set of cells active on the previous time step that determines which cells are chosen to represent instances of their associated features on the current time step. If we assume that typically S features are active in any state then any state has K^S different neural representations. This huge space of possible neural representations of any state is what underlies the model's ability to store and recall numerous context-sensitive state sequences. The purpose of this paper is simply to describe this mechanism.

Comparative Performance Measures of Fuzzy ARTMAP, Learned Vector Quantization, and Back Propagation for Handwritten Character Recognition

This article compares the performance of Fuzzy ARTMAP with that of Learned Vector Quantization and Back Propagation on a handwritten character recognition task. Training with Fuzzy ARTMAP to a fixed criterion used many fewer epochs. Voting with Fuzzy ARTMAP yielded the highest recognition rates.