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

Indexing Methods for Efficient Multiclass Recognition

Many real world image analysis problems, such as face recognition and hand pose estimation, involve recognizing a large number of classes of objects or shapes. Large margin methods, such as AdaBoost and Support Vector Machines (SVMs), often provide competitive accuracy rates, but at the cost of evaluating a large number of binary classifiers, thus making it difficult to apply such methods when thousands or millions of classes need to be recognized. This thesis proposes a filter-and-refine framework, whereby, given a test pattern, a small number of candidate classes can be identified efficiently at the filter step, and computationally expensive large margin classifiers are used to evaluate these candidates at the refine step. Two different filtering methods are proposed, ClassMap and OVA-VS (One-vs.-All classification using Vector Search). ClassMap is an embedding-based method, works for both boosted classifiers and SVMs, and tends to map the patterns and their associated classes close to each other in a vector space. OVA-VS maps OVA classifiers and test patterns to vectors based on the weights and outputs of weak classifiers of the boosting scheme. At runtime, finding the strongest-responding OVA classifier becomes a classical vector search problem, where well-known methods can be used to gain efficiency. In our experiments, the proposed methods achieve significant speed-ups, in some cases up to two orders of magnitude, compared to exhaustive evaluation of all OVA classifiers. This was achieved in hand pose recognition and face recognition systems where the number of classes ranges from 535 to 48,600.

Neural Network and Bioinformatic Methods for Predicting HIV-1 Protease Inhibitor Resistance

This article presents a new method for predicting viral resistance to seven protease inhibitors from the HIV-1 genotype, and for identifying the positions in the protease gene at which the specific nature of the mutation affects resistance. The neural network Analog ARTMAP predicts protease inhibitor resistance from viral genotypes. A feature selection method detects genetic positions that contribute to resistance both alone and through interactions with other positions. This method has identified positions 35, 37, 62, and 77, where traditional feature selection methods have not detected a contribution to resistance. At several positions in the protease gene, mutations confer differing degress of resistance, depending on the specific amino acid to which the sequence has mutated. To find these positions, an Amino Acid Space is introduced to represent genes in a vector space that captures the functional similarity between amino acid pairs. Feature selection identifies several new positions, including 36, 37, and 43, with amino acid-specific contributions to resistance. Analog ARTMAP networks applied to inputs that represent specific amino acids at these positions perform better than networks that use only mutation locations.