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

Contour Generator Points for Threshold Selection and a Novel Photo-Consistency Measure for Space Carving

Space carving has emerged as a powerful method for multiview scene reconstruction. Although a wide variety of methods have been proposed, the quality of the reconstruction remains highly-dependent on the photometric consistency measure, and the threshold used to carve away voxels. In this paper, we present a novel photo-consistency measure that is motivated by a multiset variant of the chamfer distance. The new measure is robust to high amounts of within-view color variance and also takes into account the projection angles of back-projected pixels. Another critical issue in space carving is the selection of the photo-consistency threshold used to determine what surface voxels are kept or carved away. In this paper, a reliable threshold selection technique is proposed that examines the photo-consistency values at contour generator points. Contour generators are points that lie on both the surface of the object and the visual hull. To determine the threshold, a percentile ranking of the photo-consistency values of these generator points is used. This improved technique is applicable to a wide variety of photo-consistency measures, including the new measure presented in this paper. Also presented in this paper is a method to choose between photo-consistency measures, and voxel array resolutions prior to carving using receiver operating characteristic (ROC) curves.

Gismo: A Generator of Internet Streaming Media Objects and Workloads

This paper presents a tool called Gismo (Generator of Internet Streaming Media Objects and workloads). Gismo enables the specification of a number of streaming media access characteristics, including object popularity, temporal correlation of request, seasonal access patterns, user session durations, user interactivity times, and variable bit-rate (VBR) self-similarity and marginal distributions. The embodiment of these characteristics in Gismo enables the generation of realistic and scalable request streams for use in the benchmarking and comparative evaluation of Internet streaming media delivery techniques. To demonstrate the usefulness of Gismo, we present a case study that shows the importance of various workload characteristics in determining the effectiveness of proxy caching and server patching techniques in reducing bandwidth requirements.

On the Origin of Power Laws in Internet Topologies

Recent empirical studies have shown that Internet topologies exhibit power laws of the form for the following relationships: (P1) outdegree of node (domain or router) versus rank; (P2) number of nodes versus outdegree; (P3) number of node pairs y = x^α within a neighborhood versus neighborhood size (in hops); and (P4) eigenvalues of the adjacency matrix versus rank. However, causes for the appearance of such power laws have not been convincingly given. In this paper, we examine four factors in the formation of Internet topologies. These factors are (F1) preferential connectivity of a new node to existing nodes; (F2) incremental growth of the network; (F3) distribution of nodes in space; and (F4) locality of edge connections. In synthetically generated network topologies, we study the relevance of each factor in causing the aforementioned power laws as well as other properties, namely diameter, average path length and clustering coefficient. Different kinds of network topologies are generated: (T1) topologies generated using our parametrized generator, we call BRITE; (T2) random topologies generated using the well-known Waxman model; (T3) Transit-Stub topologies generated using GT-ITM tool; and (T4) regular grid topologies. We observe that some generated topologies may not obey power laws P1 and P2. Thus, the existence of these power laws can be used to validate the accuracy of a given tool in generating representative Internet topologies. Power laws P3 and P4 were observed in nearly all considered topologies, but different topologies showed different values of the power exponent α. Thus, while the presence of power laws P3 and P4 do not give strong evidence for the representativeness of a generated topology, the value of α in P3 and P4 can be used as a litmus test for the representativeness of a generated topology. We also find that factors F1 and F2 are the key contributors in our study which provide the resemblance of our generated topologies to that of the Internet.

A Neural Pattern Generator that Exhibits Arousal-Dependant Human Gait Transitions

A neural pattern generator based upon a non-linear cooperative-competitive feedback neural network is presented. It can generate the two standard human gaits: the walk and the run. A scalar arousal or GO signal causes a bifurcation from one gait to the next. Although these two gaits are qualitatively different, they both have the same limb order and may exhibit oscillation frequencies that overlap. The model simulates the walk and the run via qualitatively different waveform shapes. The fraction of cycle that activity is above threshold distinguishes the two gaits, much as the duty cycles of the feet are longer in the walk than in the run.

Quadruped Gait Transitions from a Neural Pattern Generator with Arousal Modulated Interactions

A four-channel neural pattern generator is described in which both the frequency and the relative phase of oscillations are controlled by a scalar arousal or GO signal. The generator is used to simulate quadruped gaits; in particular, rapid transitions are simulated in the order - walk, trot, pace, and gallop - that occurs in the cat. Precise switching control is achieved by using an arousal dependent modulation of the model's inhibitory interactions. This modulation generates a different functional connectivity in a single network at different arousal levels.

A Neural Pattern Generator that Exhibits Frequency-Dependent In-Phase and Anti-Phase Oscillations

This article describes a. neural pattern generator based on a cooperative-competitive feedback neural network. The two-channel version of the generator supports both in-phase and anti-phase oscillations. A scalar arousal level controls both the oscillation phase and frequency. As arousal increases, oscillation frequency increases and bifurcations from in-phase to anti-phase, or anti-phase to in-phase oscillations can occur. Coupled versions of the model exhibit oscillatory patterns which correspond to the gaits used in locomotion and other oscillatory movements by various animals.