Open-source Simulation Software Research Articles

THE GEANT4-DNA PROJECT

The Geant4-DNA project proposes to develop an open-source simulation software based and fully included in the general-purpose Geant4 Monte-Carlo simulation toolkit. The main objective of this software is to simulate biological damages induced by ionizing radiations at the cellular and sub-cellular scale. This project was originally initiated by the European Space Agency for the prediction of the deleterious effects of radiations that may affect astronauts during future long duration space exploration missions. In this paper, the Geant4-DNA collaboration presents an overview of the whole on-going project, including its most recent developments that are available in the Geant4 toolkit since December 2009 (release 9.3), as well as an illustration example simulating the direct irradiation of a biological chromatin fiber. Expected extensions involving several research domains, such as particle physics, chemistry and cellular and molecular biology, within a fully interdisciplinary activity of the Geant4 collaboration are also discussed.

The Improvement of Generalized Particle Method for Nano-Materials Molecular Dynamics Simulation

A generalized particle molecular dynamics simulation (GP) method has been proposed by J. Fan to solve the multi-scale problems in nano-materials. Although the method has attractive features, its acceleration equivalency hypothesis doesn’t meet the actual situation. In this paper an improved GP method is proposed. It assumes that the potential energy of generalized particles is equal to the potential energy of corresponding atomic groups in nano-materials. The parameters of improved GP method rest with the atomic structural details and corresponding atomic potential energy function. And by using open-source molecular simulation software DL-POLY, an example to compare the MD and the improved GP methods has been proposed, in which the Improved GP method presents sufficient accuracy

English

Subcooled flow boiling in vertical channels have many industrial applications, including heat removal from core of nuclears. In the present work, subcooled flow boiling is simulated using open source simulation software OpenFOAM. A new solver is developed based on the OpenFOAM framework to predict subcooled flow boiling by incorporating various flow boiling models. Vapor generation in the heated wall is modeled with a wall heat flux partitioning model. Additional source terms are added to the governing equations to account for the phase change process. Energy equation is implemented for the liquid phase. The solver is validated against benchmark calculation of the DEBORA subcooled boiling data.

Muscle Contributions to Propulsion and Support During Running

Understanding how muscles propel our body forward and support our body weight during running is challenging because important variables, such as muscle forces, are generally not measurable. Muscle-driven simulations of walking have been analyzed to gain insight into muscle actions; however, simulating running presents new challenges due to high accelerations and forces. PURPOSE: To create a 3-D, muscle-driven simulation of running and quantify how muscles contribute to propulsion and support (i.e., the forward and upward accelerations of the body mass center). METHODS: Motion and ground reaction force data were measured on an adult male subject running at 3.9 m/s on a treadmill. OpenSim, open-source dynamic simulation software, was used to determine the muscle activations and forces needed to drive a 31 degree-of-freedom musculoskeletal model to track the experimentally measured motion. Contributions of individual muscles to propulsion and support were examined by independently perturbing each muscle's force during the simulated movement to calculate its contribution to the acceleration of the subject's mass center. This analysis focused on the propulsive phase of stance, the time period when a foot is on the ground and the body mass center is accelerating forward. RESULTS: Gastrocnemius, soleus, and hamstrings contributed most to propulsion, while the quadriceps resisted forward propulsion. Soleus, gastrocnemius, and quadriceps contributed the most to vertical support, while hamstrings acted to pull the body mass center downward. CONCLUSIONS: The ankle plantarflexors are a key muscle group for both propulsion and support of the body mass center during the propulsive phase of running. Gastrocnemius contributes more to propulsion and soleus more to support, which is consistent with their actions during walking. We have used the first 3-D, muscle-driven simulation of a running gait cycle to answer the fundamental question of which muscles propel the body forward and support body weight during running. Supported by NSF and Stanford Fellowships, and NIH Grant GM63495.

Optimal control in NMR spectroscopy: Numerical implementation in SIMPSON

We present the implementation of optimal control into the open source simulation package SIMPSON for development and optimization of nuclear magnetic resonance experiments for a wide range of applications, including liquid- and solid-state NMR, magnetic resonance imaging, quantum computation, and combinations between NMR and other spectroscopies. Optimal control enables efficient optimization of NMR experiments in terms of amplitudes, phases, offsets etc. for hundreds-to-thousands of pulses to fully exploit the experimentally available high degree of freedom in pulse sequences to combat variations/limitations in experimental or spin system parameters or design experiments with specific properties typically not covered as easily by standard design procedures. This facilitates straightforward optimization of experiments under consideration of rf and static field inhomogeneities, limitations in available or desired rf field strengths (e.g., for reduction of sample heating), spread in resonance offsets or coupling parameters, variations in spin systems etc. to meet the actual experimental conditions as close as possible. The paper provides a brief account on the relevant theory and in particular the computational interface relevant for optimization of state-to-state transfer (on the density operator level) and the effective Hamiltonian on the level of propagators along with several representative examples within liquid- and solid-state NMR spectroscopy.

Modeling and Technical Feasibility Analysis of a Low-Emission Residential Energy System

An energy-efficient, renewable energy-based heating, ventilating, air-conditioning and domestic hot water heating system for houses is proposed and modeled to assess its end-use energy savings potential. The system that consists of a ground heat exchanger, ground source heat pump, in-floor radiant heating, heat recovery ventilation system, photovoltaic generation and net-metered grid storage, is modeled using the open-source building simulation software ESP-r. Potential end-use energy savings of more than 50 percent are found to be attainable when the proposed heating, ventilating and air-conditioning system is compared with a conventional system to heat common energy-efficient homes in four major climatic zones of Canada. The corresponding reduction in greenhouse gas emissions (carbon dioxide equivalent) ranges from 19 percent to close to 90 percent, depending on the types of fuels replaced.

Stanford University Medical Media and Information Technologies Hosts Open Source Surgical Simulation Workshop

Stanford University Medical Media and Information Technologies's technical workshop "Prototyping of Surgical Simulators using Open Source Simulation Software" was held in August 2006 at Stanford University. The objectives, program, and topics covered are presented in this short report.