Calculation of Relaxation Spectra from Stress Relaxation Measurements

Application of stress on materials increases the energy of the system. After removal of stress, macromolecules comprising the material shift towards equilibrium to minimize the total energy of the system. This process occurs through molecular rearrangements or “relaxation” during which macromolecules attain conformations of a lower energetic state. The time, however, that is required for these rearrangements can be short or long depending on the interactions between the macromolecular species that consist the material. When rearrangements occur faster than the time of observation (experimental timescale) then molecular motion is observed (flow) and the material is regarded as viscou

Direct and Inverse Computational Methods for Electromagnetic Scattering in Biological Diagnostics

Scattering theory has had a major roll in twentieth century mathematical physics. Mathematical modeling and algorithms of direct,- and inverse electromagnetic scattering formulation due to biological tissues are investigated. The algorithms are used for a model based illustration technique within the microwave range. A number of methods is given to solve the inverse electromagnetic scattering problem in which the nonlinear and ill-posed nature of the problem are acknowledged.Comment: 61 pages, 5 figure

Network estimation in State Space Model with L1-regularization constraint

Biological networks have arisen as an attractive paradigm of genomic science ever since the introduction of large scale genomic technologies which carried the promise of elucidating the relationship in functional genomics. Microarray technologies coupled with appropriate mathematical or statistical models have made it possible to identify dynamic regulatory networks or to measure time course of the expression level of many genes simultaneously. However one of the few limitations fall on the high-dimensional nature of such data coupled with the fact that these gene expression data are known to include some hidden process. In that regards, we are concerned with deriving a method for inferring a sparse dynamic network in a high dimensional data setting. We assume that the observations are noisy measurements of gene expression in the form of mRNAs, whose dynamics can be described by some unknown or hidden process. We build an input-dependent linear state space model from these hidden states and demonstrate how an incorporated $L_{1}$ regularization constraint in an Expectation-Maximization (EM) algorithm can be used to reverse engineer transcriptional networks from gene expression profiling data. This corresponds to estimating the model interaction parameters. The proposed method is illustrated on time-course microarray data obtained from a well established T-cell data. At the optimum tuning parameters we found genes TRAF5, JUND, CDK4, CASP4, CD69, and C3X1 to have higher number of inwards directed connections and FYB, CCNA2, AKT1 and CASP8 to be genes with higher number of outwards directed connections. We recommend these genes to be object for further investigation. Caspase 4 is also found to activate the expression of JunD which in turn represses the cell cycle regulator CDC2.Comment: arXiv admin note: substantial text overlap with arXiv:1308.359

Anomalies in Ward Identities for Three-Point Functions Revisited

A general calculational method is applied to investigate symmetry relations among divergent amplitudes in a free fermion model. A very traditional work on this subject is revisited. A systematic study of one, two and three point functions associated to scalar, pseudoscalar, vector and axial-vector densities is performed. The divergent content of the amplitudes are left in terms of five basic objects (external momentum independent). No specific assumptions about a regulator is adopted in the calculations. All ambiguities and symmetry violating terms are shown to be associated with only three combinations of the basic divergent objects. Our final results can be mapped in the corresponding Dimensional Regularization calculations (in cases where this technique could be applied) or in those of Gertsein and Jackiw which we will show in detail. The results emerging from our general approach allow us to extract, in a natural way, a set of reasonable conditions (e.g. crucial for QED consistency) that could lead us to obtain all Ward Identities satisfied. Consequently, we conclude that the traditional approach used to justify the famous triangular anomalies in perturbative calculations could be questionable. An alternative point of view, dismissed of ambiguities, which lead to a correct description of the associated phenomenology, is pointed out.Comment: 26 pages, Revtex, revised version, Refs. adde