A computational model for real-time calculation of electric field due to transcranial magnetic stimulation in clinics

The aim of this paper is to propose an approach for an accurate and fast (real-time) computation of the electric field induced inside the whole brain volume during a transcranial magnetic stimulation (TMS) procedure. The numerical solution implements the admittance method for a discretized realistic brain model derived from Magnetic Resonance Imaging (MRI). Results are in a good agreement with those obtained using commercial codes and require much less computational time. An integration of the developed codewith neuronavigation toolswill permit real-time evaluation of the stimulated brain regions during the TMSdelivery, thus improving the efficacy of clinical applications

CRANKITE: a fast polypeptide backbone conformation sampler

Background: CRANKITE is a suite of programs for simulating backbone conformations of polypeptides and proteins. The core of the suite is an efficient Metropolis Monte Carlo sampler of backbone conformations in continuous three-dimensional space in atomic details. Methods: In contrast to other programs relying on local Metropolis moves in the space of dihedral angles, our sampler utilizes local crankshaft rotations of rigid peptide bonds in Cartesian space. Results: The sampler allows fast simulation and analysis of secondary structure formation and conformational changes for proteins of average length

Beam Energy Considerations for Gold Nano-Particle Enhanced Radiation Treatment

Purpose: A novel approach using nano technology enhanced radiation modalities is investigated. The proposed methodology uses antibodies labeled with organically inert metals with a high atomic number. Irradiation using photons with energies in the kilo--electron volt (keV) range show an increase in dose due to a combination of an increase in photo-electric interactions and a pronounced generation of Auger and/or Coster-Kronig (A-CK) electrons. Methods: The dependency of the dose deposition on various factors is investigated using Monte Carlo simulation models. The factors investigated include: agent concentration, spectral dependency looking at mono--energetic sources as well as classical bremsstrahlung sources. The optimization of the energy spectrum is performed in terms of physical dose enhancement as well as the dose deposited by Auger and/or Coster-Kronig electrons and their biological effectiveness. Results: A quasi-linear dependency on concentration and an exponential decrease within the target medium is observed. The maximal dose enhancement is dependent on the position of the target in the beam. Apart from irradiation with low photon energies (10 - 20 keV) there is no added benefit from the increase in generation of Auger electrons. Interestingly, a regular 110kVp bremsstrahlung spectrum shows a comparable enhancement in comparison with the optimized mono--energetic sources. Conclusions: In conclusion we find that the use of nano-particle enhanced shows promise to be implemented quite easily in regular clinic on a physical level due to the advantageous properties in classical beams.Comment: Preprint submitted to Phys Med Bio

J-PET Framework: Software platform for PET tomography data reconstruction and analysis

J-PET Framework is an open-source software platform for data analysis, written in C++ and based on the ROOT package. It provides a common environment for implementation of reconstruction, calibration and filtering procedures, as well as for user-level analyses of Positron Emission Tomography data. The library contains a set of building blocks that can be combined by users with even little programming experience, into chains of processing tasks through a convenient, simple and well-documented API. The generic input-output interface allows processing the data from various sources: low-level data from the tomography acquisition system or from diagnostic setups such as digital oscilloscopes, as well as high-level tomography structures e.g. sinograms or a list of lines-of-response. Moreover, the environment can be interfaced with Monte Carlo simulation packages such as GEANT and GATE, which are commonly used in the medical scientific community.Comment: 14 pages, 5 figure

Fast Monte Carlo Simulation for Patient-specific CT/CBCT Imaging Dose Calculation

Recently, X-ray imaging dose from computed tomography (CT) or cone beam CT (CBCT) scans has become a serious concern. Patient-specific imaging dose calculation has been proposed for the purpose of dose management. While Monte Carlo (MC) dose calculation can be quite accurate for this purpose, it suffers from low computational efficiency. In response to this problem, we have successfully developed a MC dose calculation package, gCTD, on GPU architecture under the NVIDIA CUDA platform for fast and accurate estimation of the x-ray imaging dose received by a patient during a CT or CBCT scan. Techniques have been developed particularly for the GPU architecture to achieve high computational efficiency. Dose calculations using CBCT scanning geometry in a homogeneous water phantom and a heterogeneous Zubal head phantom have shown good agreement between gCTD and EGSnrc, indicating the accuracy of our code. In terms of improved efficiency, it is found that gCTD attains a speed-up of ~400 times in the homogeneous water phantom and ~76.6 times in the Zubal phantom compared to EGSnrc. As for absolute computation time, imaging dose calculation for the Zubal phantom can be accomplished in ~17 sec with the average relative standard deviation of 0.4%. Though our gCTD code has been developed and tested in the context of CBCT scans, with simple modification of geometry it can be used for assessing imaging dose in CT scans as well.Comment: 18 pages, 7 figures, and 1 tabl

Finding Cures for Tropical Diseases: Is Open Source an Answer?

We construct polar codes for binary relay channels with orthogonal receiver components. We show that polar codes achieve the cut-set bound when the channels are symmetric and the relay-destination link supports compress-and-forward relaying based on Slepian-Wolf coding. More generally, we show that a particular version of the compress-and-forward rate is achievable using polar codes for Wyner-Ziv coding. In both cases the block error probability can be bounded as O(2-Nβ) for 0 &lt; β &lt; 1/2 and sufficiently large block length N.Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works. QC 20111207</p