TOPAS - nBio, a Monte Carlo tool for radiation biology research

TOPAS - nBio，用于辐射生物学研究的蒙特卡罗工具

• 批准号: 10837209
• 负责人: Jan Patrick Oscar Schuemann
• 金额: $ 28.61万
• 依托单位: MASSACHUSETTS GENERAL HOSPITAL
• 依托单位国家: 美国
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-04-01 至 2024-01-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10837209
• 关键词: Administrative Supplement; Biological; Biology; Biophysics; Cells; Chemistry; Communication; Communities; Complex; Computer software; Deposition; Development; Diffusion; Discipline; Environment; Event; Face; Generations; Geometry; Hour; Individual; Institution; Modeling; Monitor; Monte Carlo Method; Names; Nature; Occupations; Organelles; Paper; Physics; Process; Radiobiology; Recording of previous events; Registries; Research; Research Personnel; Resources; Running; Source; Specific qualifier value; Structure; System; Text; Time; Work; base; chemical reaction; cloud based; cluster computing; computerized tools; computing resources; design; experience; experimental study; graphical user interface; improved; multidisciplinary; open data; open source; parent project; particle; prototype; repaired; response; simulation; simulation software; skills; statistics; success; tool

The parent project, TOPAS-nBio, focuses on developing a Monte Carlo simulation toolkit specifically designed to connect research disciplines. TOPAS-nBio simulates the initial energy deposition events (physics), then follows the diffusion and reaction of chemical species (chemistry) to infer biological ob- servables at the cell and organelle scale (biology). For the Administrative Supplement to TOPAS-nBio in response to NOT-OD-23-073, we propose to carry out three supplemental tasks which, acting together, enhance TOPAS-nBio for Open Science: 1. Develop an automated cloud-based system for users to build simulation executables from the TOPAS kernel plus any set of user-provided TOPAS extensions. The new system will generate executables suitable for standard desktop, cluster and cloud systems including containerized versions suitable for entry into tool registries. 2. Redesign TOPAS-nBio GitHub setup from current ad-hoc design to instead follow current best-prac- tices for open science. The improved design will make it possible for standard cloud tools to install TOPAS-nBio. 3. Provide tools to launch, monitor and collate results from TOPAS-nBio simulations on cluster and cloud systems. The new tools will be provided as new features within the existing TOPAS Graphical User Interface, removing the need for users to have scripting or other computing expertise to make use of cloud re- sources.

父项目 TOPAS-nBio 专注于专门开发蒙特卡罗模拟工具包 旨在连接研究学科。 TOPAS-nBio 模拟初始能量沉积事件 （物理学），然后根据化学物质（化学）的扩散和反应来推断生物现象 细胞和细胞器规模的服务（生物学）。 对于响应 NOT-OD-23-073 的 TOPAS-nBio 行政补充，我们建议 执行三项补充任务，共同行动，增强 TOPAS-nBio 的开放科学能力： 1. 开发一个基于云的自动化系统，供用户从 TOPAS 内核加上任何用户提供的 TOPAS 扩展集。 新系统将生成适用于标准桌面、集群和云系统的可执行文件 包括适合进入工具注册表的容器化版本。 2. 从当前的临时设计重新设计 TOPAS-nBio GitHub 设置，以遵循当前的最佳实践 开放科学的门票。 改进的设计将使标准云工具安装 TOPAS-nBio 成为可能。 3. 提供工具来启动、监控和整理集群和 TOPAS-nBio 模拟的结果 云系统。 新工具将作为现有 TOPAS 图形用户界面中的新功能提供， 用户无需具备脚本编写或其他计算专业知识即可利用云重新构建 来源。

项目成果

A parameter sensitivity study for simulating DNA damage after proton irradiation using TOPAS-nBio.

• DOI: 10.1088/1361-6560/ab7a6b
• 发表时间: 2020-04-23
• 期刊: Physics in medicine and biology
• 影响因子: 3.5
• 作者: Zhu H;McNamara AL;Ramos-Mendez J;McMahon SJ;Henthorn NT;Faddegon B;Held KD;Perl J;Li J;Paganetti H;Schuemann J
• 通讯作者: Schuemann J

Dose enhancement effects to the nucleus and mitochondria from gold nanoparticles in the cytosol.

• DOI: 10.1088/0031-9155/61/16/5993
• 发表时间: 2016-08-21
• 期刊: Physics in medicine and biology
• 影响因子: 3.5
• 作者: McNamara AL;Kam WW;Scales N;McMahon SJ;Bennett JW;Byrne HL;Schuemann J;Paganetti H;Banati R;Kuncic Z
• 通讯作者: Kuncic Z

Flagged uniform particle splitting for variance reduction in proton and carbon ion track-structure simulations.

标记的统一粒子拆分，以减少质子和碳离子轨道结构模拟的方差。

• DOI: 10.1088/1361-6560/aa7831
• 发表时间: 2017-07-06
• 期刊: Physics in medicine and biology
• 影响因子: 3.5
• 作者: Ramos-Méndez J;Schuemann J;Incerti S;Paganetti H;Schulte R;Faddegon B
• 通讯作者: Faddegon B

Application of High-Z Gold Nanoparticles in Targeted Cancer Radiotherapy-Pharmacokinetic Modeling, Monte Carlo Simulation and Radiobiological Effect Modeling.

• DOI: 10.3390/cancers13215370
• 发表时间: 2021-10-26
• 期刊: Cancers
• 影响因子: 5.2
• 作者: Li WB;Stangl S;Klapproth A;Shevtsov M;Hernandez A;Kimm MA;Schuemann J;Qiu R;Michalke B;Bernal MA;Li J;Hürkamp K;Zhang Y;Multhoff G
• 通讯作者: Multhoff G

An integrated Monte Carlo track-structure simulation framework for modeling inter and intra-track effects on homogenous chemistry.

集成的蒙特卡罗轨道结构模拟框架，用于模拟轨道间和轨道内对均质化学的影响。

• DOI: 10.1088/1361-6560/acd6d0
• 发表时间: 2023
• 期刊: Physics in medicine and biology
• 影响因子: 3.5
• 作者: D-Kondo,JNaoki;Garcia-Garcia,OmarR;LaVerne,JayA;Faddegon,Bruce;Schuemann,Jan;Shin,Wook-Geun;Ramos-Méndez,José
• 通讯作者: Ramos-Méndez,José