Results for “process simulation modeling” — Page 15

DOE OSTI2016

WE-DE-202-00: Connecting Radiation Physics with Computational Biology

Radiation therapy for the treatment of cancer has been established as a highly precise and effective way to eradicate a localized region of diseased tissue. To achieve further significant gains in the therapeutic ratio, we need to move towards biologically optimized treatment planning. To achieve this goal, we need to understand how the radiation-type dependent patterns of induced energy depositions within the cell (physics) connect via molecular, cellular and tissue reactions to treatment outcome such as tumor control and undesirable effects on normal tissue. Several computational biology approaches have been developed connecting physics to biology. Monte Carlo simulations are the most accurate method to calculate physical dose distributions at the nanometer scale, however simulations at the DNA scale are slow and repair processes are generally not simulated. Alternative models that rely on the random formation of individual DNA lesions within one or two turns of the DNA have been shown to reproduce the clusters of DNA lesions, including single strand breaks (SSBs), double strand breaks (DSBs) without the need for detailed track structure simulations. Efficient computational simulations of initial DNA damage induction facilitate computational modeling of DNA repair and other molecular and cellular processes. Mechanistic, multiscale models provide a useful conceptual framework to test biological hypotheses and help connect fundamental information about track structure and dosimetry at the sub-cellular level to dose-response effects on larger scales. In this symposium we will learn about the current state of the art of computational approaches estimating radiation damage at the cellular and sub-cellular scale. How can understanding the physics interactions at the DNA level be used to predict biological outcome? We will discuss if and how such calculations are relevant to advance our understanding of radiation damage and its repair, or, if the underlying biological processes are too complex for a mechanistic approach. Can computer simulations be used to guide future biological research? We will debate the feasibility of explaining biology from a physicists’ perspective. Learning Objectives: Understand the potential applications and limitations of computational methods for dose-response modeling at the molecular, cellular and tissue levels Learn about mechanism of action underlying the induction, repair and biological processing of damage to DNA and other constituents Understand how effects and processes at one biological scale impact on biological processes and outcomes on other scales J. Schuemann, NCI/NIH grantsS. McMahon, Funding: European Commission FP7 (grant EC FP7 MC-IOF-623630)

60 APPLIED LIFE SCIENCES↗

DOE OSTI2016

WE-DE-202-02: Are Track Structure Simulations Truly Needed for Radiobiology at the Cellular and Tissue Levels?

Radiation therapy for the treatment of cancer has been established as a highly precise and effective way to eradicate a localized region of diseased tissue. To achieve further significant gains in the therapeutic ratio, we need to move towards biologically optimized treatment planning. To achieve this goal, we need to understand how the radiation-type dependent patterns of induced energy depositions within the cell (physics) connect via molecular, cellular and tissue reactions to treatment outcome such as tumor control and undesirable effects on normal tissue. Several computational biology approaches have been developed connecting physics to biology. Monte Carlo simulations are the most accurate method to calculate physical dose distributions at the nanometer scale, however simulations at the DNA scale are slow and repair processes are generally not simulated. Alternative models that rely on the random formation of individual DNA lesions within one or two turns of the DNA have been shown to reproduce the clusters of DNA lesions, including single strand breaks (SSBs), double strand breaks (DSBs) without the need for detailed track structure simulations. Efficient computational simulations of initial DNA damage induction facilitate computational modeling of DNA repair and other molecular and cellular processes. Mechanistic, multiscale models provide a useful conceptual framework to test biological hypotheses and help connect fundamental information about track structure and dosimetry at the sub-cellular level to dose-response effects on larger scales. In this symposium we will learn about the current state of the art of computational approaches estimating radiation damage at the cellular and sub-cellular scale. How can understanding the physics interactions at the DNA level be used to predict biological outcome? We will discuss if and how such calculations are relevant to advance our understanding of radiation damage and its repair, or, if the underlying biological processes are too complex for a mechanistic approach. Can computer simulations be used to guide future biological research? We will debate the feasibility of explaining biology from a physicists’ perspective. Learning Objectives: Understand the potential applications and limitations of computational methods for dose-response modeling at the molecular, cellular and tissue levels Learn about mechanism of action underlying the induction, repair and biological processing of damage to DNA and other constituents Understand how effects and processes at one biological scale impact on biological processes and outcomes on other scales J. Schuemann, NCI/NIH grantsS. McMahon, Funding: European Commission FP7 (grant EC FP7 MC-IOF-623630)

60 APPLIED LIFE SCIENCES↗

DOE OSTI2016

WE-DE-202-01: Connecting Nanoscale Physics to Initial DNA Damage Through Track Structure Simulations

Radiation therapy for the treatment of cancer has been established as a highly precise and effective way to eradicate a localized region of diseased tissue. To achieve further significant gains in the therapeutic ratio, we need to move towards biologically optimized treatment planning. To achieve this goal, we need to understand how the radiation-type dependent patterns of induced energy depositions within the cell (physics) connect via molecular, cellular and tissue reactions to treatment outcome such as tumor control and undesirable effects on normal tissue. Several computational biology approaches have been developed connecting physics to biology. Monte Carlo simulations are the most accurate method to calculate physical dose distributions at the nanometer scale, however simulations at the DNA scale are slow and repair processes are generally not simulated. Alternative models that rely on the random formation of individual DNA lesions within one or two turns of the DNA have been shown to reproduce the clusters of DNA lesions, including single strand breaks (SSBs), double strand breaks (DSBs) without the need for detailed track structure simulations. Efficient computational simulations of initial DNA damage induction facilitate computational modeling of DNA repair and other molecular and cellular processes. Mechanistic, multiscale models provide a useful conceptual framework to test biological hypotheses and help connect fundamental information about track structure and dosimetry at the sub-cellular level to dose-response effects on larger scales. In this symposium we will learn about the current state of the art of computational approaches estimating radiation damage at the cellular and sub-cellular scale. How can understanding the physics interactions at the DNA level be used to predict biological outcome? We will discuss if and how such calculations are relevant to advance our understanding of radiation damage and its repair, or, if the underlying biological processes are too complex for a mechanistic approach. Can computer simulations be used to guide future biological research? We will debate the feasibility of explaining biology from a physicists’ perspective. Learning Objectives: Understand the potential applications and limitations of computational methods for dose-response modeling at the molecular, cellular and tissue levels Learn about mechanism of action underlying the induction, repair and biological processing of damage to DNA and other constituents Understand how effects and processes at one biological scale impact on biological processes and outcomes on other scales J. Schuemann, NCI/NIH grantsS. McMahon, Funding: European Commission FP7 (grant EC FP7 MC-IOF-623630)

60 APPLIED LIFE SCIENCES↗

DOE OSTI2022

The Application of a Genetic Algorithm to the Optimization of a Mesoscale Model for Emergency Response

Besides solving the equations of momentum, heat, and moisture transport on the model grid, mesoscale weather models must account for subgrid-scale processes that affect the resolved model variables. These are simulated with model parameterizations, which often rely on values preset by the user. Such “free” model parameters, along with others set to initialize the model, are often poorly constrained, requiring that a user select each from a range of plausible values. Finding the values to optimize any forecasting tool can be accomplished with a search algorithm, and one such process—the genetic algorithm (GA)—has become especially popular. As applied to modeling, GAs represent a Darwinian process: an ensemble of simulations is run with a different set of parameter values for each member, and the members subsequently judged to be most accurate are selected as “parents” who pass their parameters onto a new generation. At the U.S. Department of Energy’s Savannah River Site in South Carolina, we are applying a GA to the Regional Atmospheric Modeling System (RAMS) mesoscale weather model, which supplies input to a model to simulate the dispersion of an airborne contaminant as part of the site’s emergency response preparations. An ensemble of forecasts is run each day, weather data are used to “score” the individual members of the ensemble, and the parameters from the best members are used for the next day’s forecasts. As meteorological conditions change, the parameters change as well, maintaining a model configuration that is best adapted to atmospheric conditions. Significance Statement We wanted to develop a forecasting system by which a weather model is run over the Savannah River Site each day and repeatedly adjusted according to how well it performed the previous day. To run the model, a series of values (parameters) must be set to control how the model will calculate winds, temperatures, and other desired variables. Each day the model was run several times using different combinations of these parameters and later compared with observed meteorological conditions. Parameters that produced the most accurate forecasts were preferentially reused to create the forecasts for the next day. The process was tested for the summer of 2020 and exhibited lower errors than forecasts produced by the model using default values of the parameters.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Adsorption Thermodynamics for Process Simulation

Adsorption has rapidly evolved in recent decades and is an established separation technology extensively practiced in gas separation industries and others. However, rigorous thermodynamic modeling of multicomponent adsorption equilibrium remains elusive, and industrial practitioners rely heavily on expensive and time-consuming trial-and-error pilot studies to develop adsorption units. Here, this article highlights the need for rigorous adsorption thermodynamic models and the limitations and deficiencies of existing models such as the extended Langmuir isotherm, dual-process Langmuir isotherm, and adsorbed solution theory. It further presents a series of recent advances in the generalization of the classical Langmuir isotherm of single-component adsorption by deriving an activity coefficient model to account for the adsorbed phase adsorbate–adsorbent interactions, substituting adsorbed phase adsorbate and vacant site concentrations with activities, and extending to multicomponent competitive adsorption equilibrium, both monolayer and multilayer. Requiring a minimum set of physically meaningful model parameters, the generalized Langmuir isotherm for monolayer adsorption and the generalized Brunauer–Emmett–Teller isotherm for multilayer adsorption address various thermodynamic modeling challenges including adsorbent surface heterogeneity, isosteric enthalpies of adsorption, BET surface areas, adsorbed phase nonideality, adsorption azeotrope formation, and multilayer adsorption. Also discussed is the importance of quality adsorption data that cover sufficient temperature, pressure, and composition ranges for reliable determination of the model parameters to support adsorption process simulation, design, and optimization.

09 BIOMASS FUELS↗

DOE OSTI2019

Detailed Modeling of Physical Processes in Electron Sources for Accelerator Applications

At present, electron sources are essential in a wide range of applications – from common technical use to exploring the nature of matter. Depending on the application requirements, different methods and materials are used to generate electrons. State of-the-art accelerator applications set a number of often-contradicting requirements for electron sources (e.g., high quantum efficiency vs. high spin-polarization, high current density vs. long lifetime, etc). Development of advanced electron sources includes modeling and design of cathodes, material growth, fabrication of cathodes, and cathode testing. The detailed simulation and modeling of physical processes are required in order to shed light on the exact mechanisms of electron emission and to develop new-generation electron sources with optimized efficiency. The purpose of the present work is to study physical processes in prominent electron sources and to develop scientific tools that could be used to predict electron emission from novel nano-structured materials. In particular, the Monte Carlo model has been implemented and used to study photoemission from Negative Electron Affinity (NEA) GaAs widely used to provide spin-polarized electron beams for many accelerator facilities, including Thomas Jefferson National Accelerator Facility. According to our best knowledge, this is the first to date scientific tool to simulate the complete from-excitation-to-emission-into-vacuum photoemission of spin-polarized electrons from NEA GaAs based on the details of material band structure. Moreover, an effective image-processing algorithm has been developed and used to study field emission properties of Nitrogen-incorporated UltraNanoCrystalline Diamond ((N)UNCD) films. The algorithm processes large sets of image micrographs representing field emission sites formed on the anode plate and therefore provides significant information about the field emission area and the current density. The field emission model from convenient semiconductors has been modified and used to study the influence of the space-charge region and the electric-field-dependent electron mobility on the field emission characteristics of (N)UNCD field emitters.

Chubenko, Oksana↗

DOE OSTI2021

Fission In R-Process Elements

The goal of the FIRE topical collaboration in nuclear theory is to determine the astrophysical conditions of the rapid neutron capture process (r-process), which is responsible for the formation of heavy elements. This will be achieved by including in r-process simulations the most advanced models of fission (spontaneous, neutron-induced, β-delayed) that have been developed at LLNL and LANL. The collaboration is composed of LLNL (lead) and LANL for fission work, BNL for nuclear data management, and the university of Notre Dame and North Carolina State University for r -process simulations. Under DOE/NNSA agreement, both universities receive funds from DOE Office of Science, while national laboratories receive funds directly from NA221.