Physics-Based Simulation of Biological Structures

基于物理的生物结构模拟

• 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
• 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

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唯一地集中在将基于物理的模拟应用于生物学和医学问题上。基于物理的模拟为理解生物学形式和功能提供了有力的框架。生物学家使用模拟来研究大分子组件和临床医生，以分析疾病机制和治疗选择。模拟有助于生物医学研究人员了解这些系统的物理限制，因为他们正在设计新型药物，药物输送机制，合成组织，医疗设备或手术干预措施。 在上一个赠款期间，我们创建了一个仿真工具包（SIMTK），该工具包（SIMTK）使用户能够创建和可视化从分子到生物体的各个尺度的生物结构的准确模型和模拟。 Simtk是一个可扩展的开源，可自由使用的软件包。特定域特定的应用程序软件包（使用SIMTK构建）分布在我们的WebPortal，Simtk.org上，该软件simtk.org具有8000多个用户和300个软件或数据项目，并且对RNA生物学，肌球蛋白生物力学，蛋白质折叠，心血管液体动力学以及神经肌肉肌肉肌肉肌肉的生物力学产生了科学影响。 SIMTK应用程序已与生物医学科学家密切合作开发和测试，以确保其效用和准确性。在此提案中，我们概述了一个计划，旨在引入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，并组建了一组强大的研究人员在建模，模拟和可视化生物结构方面，这将解决这些挑战。软件工程工作是由经验丰富的专业人员领导的，他们以前曾向数千名用户开发并交付了复杂的软件包。我们的传播计划包括将在线移动的研讨会，一本全国认可的杂志以及基于社区用户支持的技术。 我们的最初努力确定了Simbios成功所需的愿景，设施，培训环境，行政组织和协作关系。在其他关注生物医学互补元素的中心的背景下，我们的中心专注于生物结构的物理现实。因此，它提供了重要的国家生物医学计算基础架构。