Quantitative photoacoustic imaging in radiative transport regime

The objective of quantitative photoacoustic tomography (QPAT) is to reconstruct optical and thermodynamic properties of heterogeneous media from data of absorbed energy distribution inside the media. There have been extensive theoretical and computational studies on the inverse problem in QPAT, however, mostly in the diffusive regime. We present in this work some numerical reconstruction algorithms for multi-source QPAT in the radiative transport regime with energy data collected at either single or multiple wavelengths. We show that when the medium to be probed is non-scattering, explicit reconstruction schemes can be derived to reconstruct the absorption and the Gruneisen coefficients. When data at multiple wavelengths are utilized, we can reconstruct simultaneously the absorption, scattering and Gruneisen coefficients. We show by numerical simulations that the reconstructions are stable.Comment: 40 pages, 13 figure

Study of noise effects in electrical impedance tomography with resistor networks

We present a study of the numerical solution of the two dimensional electrical impedance tomography problem, with noisy measurements of the Dirichlet to Neumann map. The inversion uses parametrizations of the conductivity on optimal grids. The grids are optimal in the sense that finite volume discretizations on them give spectrally accurate approximations of the Dirichlet to Neumann map. The approximations are Dirichlet to Neumann maps of special resistor networks, that are uniquely recoverable from the measurements. Inversion on optimal grids has been proposed and analyzed recently, but the study of noise effects on the inversion has not been carried out. In this paper we present a numerical study of both the linearized and the nonlinear inverse problem. We take three different parametrizations of the unknown conductivity, with the same number of degrees of freedom. We obtain that the parametrization induced by the inversion on optimal grids is the most efficient of the three, because it gives the smallest standard deviation of the maximum a posteriori estimates of the conductivity, uniformly in the domain. For the nonlinear problem we compute the mean and variance of the maximum a posteriori estimates of the conductivity, on optimal grids. For small noise, we obtain that the estimates are unbiased and their variance is very close to the optimal one, given by the Cramer-Rao bound. For larger noise we use regularization and quantify the trade-off between reducing the variance and introducing bias in the solution. Both the full and partial measurement setups are considered.Comment: submitted to Inverse Problems and Imagin

Efficient equilibrium sampling of all-atom peptides using library-based Monte Carlo

We applied our previously developed library-based Monte Carlo (LBMC) to equilibrium sampling of several implicitly solvated all-atom peptides. LBMC can perform equilibrium sampling of molecules using the pre-calculated statistical libraries of molecular-fragment configurations and energies. For this study, we employed residue-based fragments distributed according to the Boltzmann factor of the OPLS-AA forcefield describing the individual fragments. Two solvent models were employed: a simple uniform dielectric and the Generalized Born/Surface Area (GBSA) model. The efficiency of LBMC was compared to standard Langevin dynamics (LD) using three different statistical tools. The statistical analyses indicate that LBMC is more than 100 times faster than LD not only for the simple solvent model but also for GBSA.Comment: 5 figure