Physics-based Simulation of Biological Structures

基于物理的模拟为理解生物的形式和功能提供了一个强大的框架。模拟 生物学家可以使用它来研究大分子组装，临床医生也可以使用它来分析疾病机制。 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、医疗器械或外科手术。 我们建议建立国家生物结构模拟中心（SimBioS）。我们会发展， 传播和支持模拟工具包（SimTK），使用户能够创建和可视化准确的模型， 从原子到有机体的所有尺度的生物结构模拟。SimTK将是一个可扩展的，开源的， 免费提供的软件系统，将建立在项目参与者开发的组件软件系统之上 等人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。最初的驾驶生物问题将立即行使全方位的尺度： 模拟RNA折叠、分子机器、神经肌肉动力学和心血管力学。我们有 确定了必须解决的生物计算研究挑战，以超越目前的能力。 我们已经组建了一个研究团队，他们在建模、仿真和 [生物结构的可视化。软件工程工作将由经验丰富的专业人员领导， 我以前开发过复杂的软件包，并交付给成千上万的用户。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中心在线培训， iProfessional发展。 我们的规划工作已经建立了愿景，设施，培训环境，行政组织， 这是成功完成这一具有挑战性的项目所需的合作关系。在其他中心关注的背景下， 在生物医学的互补元素方面，我们的中心专注于生物结构的物理现实。它将 从而提供了国家生物医学计算基础设施的关键部分。

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 ihave 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 iProfessional 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.