Publications (11) View all
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Article: Minimal formulation of joint motion for biomechanisms.
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ABSTRACT: Biomechanical systems share many properties with mechanically engineered systems, and researchers have successfully employed mechanical engineering simulation software to investigate the mechanical behavior of diverse biological mechanisms, ranging from biomolecules to human joints. Unlike their man-made counterparts, however, biomechanisms rarely exhibit the simple, uncoupled, pure-axial motion that is engineered into mechanical joints such as sliders, pins, and ball-and-socket joints. Current mechanical modeling software based on internal-coordinate multibody dynamics can formulate engineered joints directly in minimal coordinates, but requires additional coordinates restricted by constraints to model more complex motions. This approach can be inefficient, inaccurate, and difficult for biomechanists to customize. Since complex motion is the rule rather than the exception in biomechanisms, the benefits of minimal coordinate modeling are not fully realized in biomedical research. Here we introduce a practical implementation for empirically-defined internal-coordinate joints, which we call "mobilizers." A mobilizer encapsulates the observations, measurement frame, and modeling requirements into a hinge specification of the permissible-motion manifold for a minimal set of internal coordinates. Mobilizers support nonlinear mappings that are mathematically equivalent to constraint manifolds but have the advantages of fewer coordinates, no constraints, and exact representation of the biomechanical motion-space-the benefits long enjoyed for internal-coordinate models of mechanical joints. Hinge matrices within the mobilizer are easily specified by user-supplied functions, and provide a direct means of mapping permissible motion derived from empirical data. We present computational results showing substantial performance and accuracy gains for mobilizers versus equivalent joints implemented with constraints. Examples of mobilizers for joints from human biomechanics and molecular dynamics are given. All methods and examples were implemented in Simbody™-an open source multibody-dynamics solver available at https://Simtk.org.Nonlinear Dynamics 10/2010; 62(1):291-303. · 1.25 Impact Factor -
Article: Simbios: an NIH national center for physics-based simulation of biological structures.
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ABSTRACT: Physics-based simulation provides a powerful framework for understanding biological form and function. Simulations can be used by biologists to study macromolecular assemblies and by clinicians to design treatments for diseases. Simulations help biomedical researchers understand the physical constraints on biological systems as they engineer novel drugs, synthetic tissues, medical devices, and surgical interventions. Although individual biomedical investigators make outstanding contributions to physics-based simulation, the field has been fragmented. Applications are typically limited to a single physical scale, and individual investigators usually must create their own software. These conditions created a major barrier to advancing simulation capabilities. In 2004, we established a National Center for Physics-Based Simulation of Biological Structures (Simbios) to help integrate the field and accelerate biomedical research. In 6 years, Simbios has become a vibrant national center, with collaborators in 16 states and eight countries. Simbios focuses on problems at both the molecular scale and the organismal level, with a long-term goal of uniting these in accurate multiscale simulations.Journal of the American Medical Informatics Association 11/2011; 19(2):186-9. · 3.61 Impact Factor -
Article: The Simbios National Center: Systems Biology in Motion.
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ABSTRACT: Physics-based simulation is needed to understand the function of biological structures and can be applied across a wide range of scales, from molecules to organisms. Simbios (the National Center for Physics-Based Simulation of Biological Structures, http://www.simbios.stanford.edu/) is one of seven NIH-supported National Centers for Biomedical Computation. This article provides an overview of the mission and achievements of Simbios, and describes its place within systems biology. Understanding the interactions between various parts of a biological system and integrating this information to understand how biological systems function is the goal of systems biology. Many important biological systems comprise complex structural systems whose components interact through the exchange of physical forces, and whose movement and function is dictated by those forces. In particular, systems that are made of multiple identifiable components that move relative to one another in a constrained manner are multibody systems. Simbios' focus is creating methods for their simulation. Simbios is also investigating the biomechanical forces that govern fluid flow through deformable vessels, a central problem in cardiovascular dynamics. In this application, the system is governed by the interplay of classical forces, but the motion is distributed smoothly through the materials and fluids, requiring the use of continuum methods. In addition to the research aims, Simbios is working to disseminate information, software and other resources relevant to biological systems in motion.Proceedings of the IEEE 08/2008; 96(8):1266. · 6.81 Impact Factor -
Article: iTools: a framework for classification, categorization and integration of computational biology resources.
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ABSTRACT: The advancement of the computational biology field hinges on progress in three fundamental directions--the development of new computational algorithms, the availability of informatics resource management infrastructures and the capability of tools to interoperate and synergize. There is an explosion in algorithms and tools for computational biology, which makes it difficult for biologists to find, compare and integrate such resources. We describe a new infrastructure, iTools, for managing the query, traversal and comparison of diverse computational biology resources. Specifically, iTools stores information about three types of resources--data, software tools and web-services. The iTools design, implementation and resource meta-data content reflect the broad research, computational, applied and scientific expertise available at the seven National Centers for Biomedical Computing. iTools provides a system for classification, categorization and integration of different computational biology resources across space-and-time scales, biomedical problems, computational infrastructures and mathematical foundations. A large number of resources are already iTools-accessible to the community and this infrastructure is rapidly growing. iTools includes human and machine interfaces to its resource meta-data repository. Investigators or computer programs may utilize these interfaces to search, compare, expand, revise and mine meta-data descriptions of existent computational biology resources. We propose two ways to browse and display the iTools dynamic collection of resources. The first one is based on an ontology of computational biology resources, and the second one is derived from hyperbolic projections of manifolds or complex structures onto planar discs. iTools is an open source project both in terms of the source code development as well as its meta-data content. iTools employs a decentralized, portable, scalable and lightweight framework for long-term resource management. We demonstrate several applications of iTools as a framework for integrated bioinformatics. iTools and the complete details about its specifications, usage and interfaces are available at the iTools web page http://iTools.ccb.ucla.edu.PLoS ONE 02/2008; 3(5):e2265. · 4.09 Impact Factor -
Article: Simbody: multibody dynamics for biomedical research
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ABSTRACT: Multibody software designed for mechanical engineering has been successfully employed in biomedical research for many years. For real time operation some biomedical researchers have also adapted game physics engines. However, these tools were built for other purposes and do not fully address the needs of biomedical researchers using them to analyze the dynamics of biological structures and make clinically meaningful recommendations. We are addressing this problem through the development of an open source, extensible, high performance toolkit including a multibody mechanics library aimed at the needs of biomedical researchers. The resulting code, Simbody, supports research in a variety of fields including neuromuscular, prosthetic, and biomolecular simulation, and related research such as biologically-inspired design and control of humanoid robots and avatars. Simbody is the dynamics engine behind OpenSim, a widely used biomechanics simulation application. This article reviews issues that arise uniquely in biomedical research, and reports on the architecture, theory, and computational methods Simbody uses to address them. By addressing these needs explicitly Simbody provides a better match to the needs of researchers than can be obtained by adaptation of mechanical engineering or gaming codes. Simbody is a community resource, free for any purpose. We encourage wide adoption and invite contributions to the code base at https://simtk.org/home/simbody.Procedia IUTAM. 01/2011; 2(2):241-261.
