Physics-Based Simulation of Biological Structures

基于物理的生物结构模拟

基本信息

批准号：
8324542
负责人：
RUSS BIAGIO ALTMAN
金额：
$ 248.93万
依托单位：
STANFORD UNIVERSITY
依托单位国家：
美国
项目类别：
财政年份：
2004
资助国家：
美国
起止时间：
2004-09-15 至 2014-08-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/8324542
关键词：
Achievement Address Adverse drug effect Antibiotics Architecture Artificial Arm Automobile Driving Bacteria Biological Biology Biomechanics Biomedical Computing Blood flow Cardiovascular system Cell Shape Cells Code Collaborations Communities Complement Complex Computer software Data Development Devices Disease Drug Delivery Systems Drug Design Educational workshop Elements Engineering Ensure Environment Family Generations Grant Health Imagery Infection Internet Internships Journals Laboratories Language Lead Limb structure Liquid substance Mails Maintenance Measurement Mechanics Medical Device Medicine Minority-Serving Institution Modeling Molecular Molecular Models Motion Myosin ATPase Operative Surgical Procedures Organism Pharmaceutical Preparations Physics Postdoctoral Fellow Printing Process Prosthesis RNA Reporting Research Research Design Research Infrastructure Research Personnel Research Training Scientist Simulate Social Network Software Engineering Speed Structure Students System Technology Testing Therapeutic Tissues Training Underrepresented Minority Universities Virus Virus Diseases Vision Work base biomedical scientist design drug discovery experience graduate student improved macromolecular assembly macromolecule member mind control models and simulation molecular dynamics molecular modeling molecular scale motor control neural prosthesis neuromuscular next generation novel open source programs protein folding rapid growth simulation simulation software software development success trend virtual web site wiki

项目摘要

The Simbios National Center for Biomedical Computing is singularly focused on the application of physics-based simulation to problems in biology and medicine. Physics-based simulation provides a powerful framework for understanding biological form and function. Simulations are used by biologists to study macromolecular assemblies and by clinicians to analyze disease mechanisms and therapeutic options. Simulations help biomedical researchers understand the physical constraints on these systems as they engineer novel drugs, drug delivery mechanisms, synthetic tissues, medical devices, or surgical interventions. In the previous grant period, we have created a simulation toolkit (SimTK) that enables users to create and visualize accurate models and simulations of biological structures at all scales, from molecules to organisms. SimTK is an extensible, open source, freely available software package. Domain specific application software packages (built using SimTK) are distributed on our webportal, simtk.org, which has more than 8000 users and 300 software or data projects, and has enabled scientific impact in RNA biology, myosin biomechanics, protein folding, cardiovascular fluid dynamics, and neuromuscular biomechanics. SimTK applications have been developed and tested in close collaboration with biomedical scientists to ensure its utility and accuracy. In this proposal, we outline a plan to introduce three exciting new driving biological problems focusing on (1) the dynamics of neural prostheses, (2) the dynamics of cell shape, and (3) the dynamics of drug target macromolecules. We have identified the computational research challenges critical to these fields, and have assembled a strong team of researchers in modeling, simulation and visualization of biological structures that will address these challenges. The software engineering effort is lead by experienced professionals, who have previously developed and delivered complex software packages to thousands of users. Our dissemination plan includes workshops that will move online, a nationally recognized magazine, and technologies for community-based user support. Our initial efforts have established the vision, facilities, training environment, administrative organization, and collaborative relationships required for the success of Simbios. In the context of other centers focusing on complementary elements of biomedicine, our center is focused on the physical reality of biological structures. It thus provides a critical piece of a national biomedical computing infrastructure.

Simbios 国家生物医学计算中心专注于基于物理的模拟在生物学和医学问题中的应用。基于物理的模拟为理解生物形态和功能提供了强大的框架。生物学家利用模拟来研究大分子组装，临床医生利用模拟来分析疾病机制和治疗方案。模拟可以帮助生物医学研究人员了解这些系统在设计新药物、药物输送机制、合成组织、医疗设备或外科手术时的物理限制。在上一个资助期间，我们创建了一个模拟工具包（SimTK），使用户能够创建和可视化从分子到生物体的所有尺度的生物结构的精确模型和模拟。 SimTK 是一个可扩展、开源、免费的软件包。领域特定应用软件包（使用 SimTK 构建）分布在我们的门户网站 simtk.org 上，该门户拥有 8000 多名用户和 300 个软件或数据项目，并在 RNA 生物学、肌球蛋白生物力学、蛋白质折叠、心血管流体方面产生了科学影响动力学和神经肌肉生物力学。 SimTK 应用程序是与生物医学科学家密切合作开发和测试的，以确保其实用性和准确性。在本提案中，我们概述了一项计划，介绍三个令人兴奋的新驱动生物学问题，重点是（1）神经假体的动力学，（2）细胞形状的动力学，以及（3）药物靶标大分子的动力学。我们已经确定了对这些领域至关重要的计算研究挑战，并组建了一支强大的生物结构建模、模拟和可视化研究人员团队来应对这些挑战。软件工程工作由经验丰富的专业人员领导，他们之前开发过复杂的软件包并将其交付给数千名用户。我们的传播计划包括在线研讨会、全国认可的杂志以及基于社区的用户支持技术。我们最初的努力已经建立了 Simbios 成功所需的愿景、设施、培训环境、管理组织和协作关系。在其他中心专注于生物医学互补要素的背景下，我们的中心专注于生物结构的物理现实。因此，它提供了国家生物医学计算基础设施的关键部分。