Numerical Loop-Tree Duality: contour deformation and subtraction

We introduce a novel construction of a contour deformation within the framework of Loop-Tree Duality for the numerical computation of loop integrals featuring threshold singularities in momentum space. The functional form of our contour deformation automatically satisfies all constraints without the need for fine-tuning. We demonstrate that our construction is systematic and efficient by applying it to more than 100 examples of finite scalar integrals featuring up to six loops. We also showcase a first step towards handling non-integrable singularities by applying our work to one-loop infrared divergent scalar integrals and to the one-loop amplitude for the ordered production of two and three photons. This requires the combination of our contour deformation with local counterterms that regulate soft, collinear and ultraviolet divergences. This work is an important step towards computing higher-order corrections to relevant scattering cross-sections in a fully numerical fashion.Comment: 87 page

Liver segmentation using automatically defined patient specific B-Spline surface models

This paper presents a novel liver segmentation algorithm. This is a model-driven approach; however, unlike previous techniques which use a statistical model obtained from a training set, we initialize patient-specific models directly from their own pre-segmentation. As a result, the non-trivial problems such as landmark correspondences, model registration etc. can be avoided. Moreover, by dividing the liver region into three sub-regions, we convert the problem of building one complex shape model into constructing three much simpler models, which can be fitted independently, greatly improving the computation efficiency. A robust graph-based narrow band optimal surface fitting scheme is also presented. The proposed approach is evaluated on 35 CT images. Compared to contemporary approaches, our approach has no training requirement and requires significantly less processing time, with an RMS error of 2.440.53mm against manual segmentation

Information Surfaces in Systems Biology and Applications to Engineering Sustainable Agriculture

Systems biology of plants offers myriad opportunities and many challenges in modeling. A number of technical challenges stem from paucity of computational methods for discovery of the most fundamental properties of complex dynamical systems. In systems engineering, eigen-mode analysis have proved to be a powerful approach. Following this philosophy, we introduce a new theory that has the benefits of eigen-mode analysis, while it allows investigation of complex dynamics prior to estimation of optimal scales and resolutions. Information Surfaces organizes the many intricate relationships among "eigen-modes" of gene networks at multiple scales and via an adaptable multi-resolution analytic approach that permits discovery of the appropriate scale and resolution for discovery of functions of genes in the model plant Arabidopsis. Applications are many, and some pertain developments of crops that sustainable agriculture requires.Comment: 24 Pages, DoCEIS 1

Beyond fuzzy spheres

We study polynomial deformations of the fuzzy sphere, specifically given by the cubic or the Higgs algebra. We derive the Higgs algebra by quantizing the Poisson structure on a surface in $\mathbb{R}^3$. We find that several surfaces, differing by constants, are described by the Higgs algebra at the fuzzy level. Some of these surfaces have a singularity and we overcome this by quantizing this manifold using coherent states for this nonlinear algebra. This is seen in the measure constructed from these coherent states. We also find the star product for this non-commutative algebra as a first step in constructing field theories on such fuzzy spaces.Comment: 9 pages, 3 Figures, Minor changes in the abstract have been made. The manuscript has been modified for better clarity. A reference has also been adde

Stochastic Dynamics of Bionanosystems: Multiscale Analysis and Specialized Ensembles

An approach for simulating bionanosystems, such as viruses and ribosomes, is presented. This calibration-free approach is based on an all-atom description for bionanosystems, a universal interatomic force field, and a multiscale perspective. The supramillion-atom nature of these bionanosystems prohibits the use of a direct molecular dynamics approach for phenomena like viral structural transitions or self-assembly that develop over milliseconds or longer. A key element of these multiscale systems is the cross-talk between, and consequent strong coupling of, processes over many scales in space and time. We elucidate the role of interscale cross-talk and overcome bionanosystem simulation difficulties with automated construction of order parameters (OPs) describing supra-nanometer scale structural features, construction of OP dependent ensembles describing the statistical properties of atomistic variables that ultimately contribute to the entropies driving the dynamics of the OPs, and the derivation of a rigorous equation for the stochastic dynamics of the OPs. Since the atomic scale features of the system are treated statistically, several ensembles are constructed that reflect various experimental conditions. The theory provides a basis for a practical, quantitative bionanosystem modeling approach that preserves the cross-talk between the atomic and nanoscale features. A method for integrating information from nanotechnical experimental data in the derivation of equations of stochastic OP dynamics is also introduced.Comment: 24 page