One great challenge of genomic research is to efficiently and accurately identify complex gene regulatory networks. The development of high-throughput technologies provides numerous experimental data such as DNA sequences, protein sequence, and RNA expression profiles makes it possible to study interactions and regulations among genes or other substance in an organism. However, it is crucial to make inference of genetic regulatory networks from gene expression profiles and protein interaction data for systems biology. This study will develop a new approach to reconstruct time delay Boolean networks as a tool for exploring biological pathways. In the inference strategy, we will compare all pairs of input genes in those basic relationships by their corresponding -scores for every output gene. Then, we will combine those consistent relationships to reveal the most probable relationship and reconstruct the genetic network. Specifically, we will prove that state transition pairs are sufficient and necessary to reconstruct the time delay Boolean network of nodes with high accuracy if the number of input genes to each gene is bounded. We also have implemented this method on simulated and empirical yeast gene expression data sets. The test results show that this proposed method is extensible for realistic networks.

We propose a novel method to apply Teichmller space theory to study the signature of a family of nonintersecting closed 3D curves on a general genus zero closed surface. Our algorithm provides an efficient method to encode both global surface and local contour shape information. The signatureTeichmller shape descriptoris computed by surface Ricci flow method, which is equivalent to solving an elliptic partial differential equation on surfaces and is numerically stable. We propose to apply the new signature to analyze abnormalities in brain cortical morphometry. Experimental results with 3D MRI data from Alzheimers disease neuroimaging initiative (ADNI) dataset [152 healthy control subjects versus 169 Alzheimers disease (AD) patients] demonstrate the effectiveness of our method and illustrate its potential as a novel surface-based cortical morphometry measurement in AD research.

We study Hawking radiation from three-dimensional black holes. For this purpose the emission of charged scalar and charged fermionic particles is investigated from charged BTZ black holes, with and without rotation. We use the quantum tunneling approach incorporating WKB approximation and spacetime symmetries. Another class of black holes which is asymptotic to a Sol three-manifold has also been investigated. This procedure gives us the tunneling probability of outgoing particles, and we compute the temperature of the radiation for these black holes. We also consider the quantum tunneling of particles from black hole asymptotic to Sol geometry.

In this paper we introduce a path complex that can be regarded as a generalization of the notion of a simplicial complex. The main motivation for considering path complexes comes from directed graphs (digraphs). We obtain a new notion of the path homology and cohomology of a digraph.

Let <i>L</i> be a holomorphic line bundle over a compact Khler manifold <i>X</i>. Motivated by mirror symmetry, we study the deformed HermitianYangMills equation on <i>L</i>, which is the line bundle analogue of the special Lagrangian equation in the case that <i>X</i> is CalabiYau. We show that this equation is the Euler-Lagrange equation for a positive functional, and that solutions are unique global minimizers. We provide a necessary and sufficient criterion for existence in the case that <i>X</i> is a Khler surface. For the higher dimensional cases, we introduce a line bundle version of the Lagrangian mean curvature flow, and prove convergence when <i>L</i> is ample and <i>X</i> has non-negative orthogonal bisectional curvature.