Physics-based Simulation of Biological Structures(RMI)

描述（由申请人提供）：基于物理的模拟为理解生物形式和功能提供了强大的框架。生物学家可以使用模拟来研究大分子组装，临床医生也可以使用模拟来分析疾病机制。模拟帮助生物医学研究人员了解这些系统的物理约束，因为他们设计新的药物，药物输送机制，合成组织，医疗设备或手术干预。 我们建议建立国家生物结构模拟中心（SimBioS）。我们将开发，传播和支持一个模拟工具包（SimTK），使用户能够创建和可视化精确的模型和模拟生物结构在所有尺度上，从原子到有机体。SimTK将是一个可扩展的、开放源码的、免费提供的软件系统，它将建立在项目参与者和其他人开发的组件软件系统之上。该软件将与生物医学科学家密切合作开发和测试，以确保其实用性和准确性。最初的驱动生物学问题将立即运用全方位的尺度：模拟RNA折叠，分子机器，神经肌肉动力学和心血管力学。我们已经确定了生物计算研究的挑战，必须解决，以超越目前的能力。我们已经组建了一个研究团队，在生物结构的建模，模拟和可视化方面取得了成就。软件工程工作将由经验丰富的专业人员领导，他们以前曾为数千名用户开发和交付过复杂的软件包。我们积极的传播计划包括定期研讨会，全国通讯，并通过斯坦福大学的专业发展中心在线培训。 我们的规划工作已经建立了这个具有挑战性的项目成功所需的愿景，设施，培训环境，行政组织和合作关系。在其他中心专注于生物医学的互补元素的背景下，我们的中心专注于生物结构的物理现实。因此，它将成为国家生物医学计算基础设施的关键组成部分。

DESCRIPTION (provided by applicant): Physics-based simulation provides a powerful framework for understanding biological form and function. Simulations may be used by biologists to study macromolecular assemblies or by clinicians to analyze disease mechanisms. 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. We propose to establish the National Center for Simulation of Biological Structures (SimBioS). We will develop, disseminate, and support a simulation toolkit (SimTK) that enables users to create and visualize accurate models and simulations of biological structures at all scales-from atoms to organisms. SimTK will be an extensible, open source, freely available software system that will build on component software systems developed by the project participants and others. The software will be developed and tested in close collaboration with biomedical scientists to ensure its utility and accuracy. The initial driving biological problems will immediately exercise a full range of scales: simulating RNA folding, molecular machines, neuromuscular dynamics, and cardiovascular mechanics. We have identified the biocomputation research challenges that must be addressed in order to move beyond current capabilities. We have assembled a team of researchers with a track record of accomplishments in modeling, simulation and visualization of biological structures. The software engineering effort will be lead by experienced professionals, who have previously developed and delivered complex software packages to thousands of users. Our aggressive dissemination plan includes regular workshops, a national newsletter, and on-line training through Stanford's Center for Professional Development. Our planning effort has established the vision, facilities, training environment, administrative organization, and collaborative relationships required for the success of this challenging project. In the context of other centers focusing on complementary elements of biomedicine, our center is focused on the physical reality of biological structures. It will thus provide a critical piece of a national biomedical computing infrastructure.