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ItemIntegrating a Hierarchy of Simulation Tools for Legged Robot Locomotion(Georgia Institute of Technology, 2008-09) Slatton, Andrew ; Cohen, Daniel ; Ding, Yang ; Umbanhowar, Paul B. ; Goldman, Daniel I. ; Haynes, G. Clark ; Komsuoglu, Haldun ; Koditschek, Daniel E.We are interested in the development of a variety of legged robot platforms intended for operation in unstructured outdoor terrain. In such settings, the traditions of rational engineering design, driven by analytically informed and computationally assisted studies of robot-environment models, remain ineffective due to the complexity of both the robot designs and the terrain in which they must operate. Instead, empirical trial and error often drives the necessary incremental and iterative design process, hence the development of such robots remains expensive both in time and cost, and is often closely dependent upon the substrate properties of the locomotion terrain. This paper describes a series of concurrent but increasingly coordinated software development efforts that aim to diminish the gap between easily interfaced and physically sound computational models of a real robot’s operation in a complex natural environment. We describe a robot simulation environment in which simple robot modifications can be easily prototyped along and “played” into phenomenological models of contact mechanics. We particularly focus on the daunting but practically compelling example of robot feet interacting granular media, such as gravel or sand, offering a brief report of our progress in deriving and importing physically accurate but computationally tractable phenomenological substrate models into the robot execution simulation environment. With a goal of integration for future robot prototyping simulations, we review the prospects for diminishing the gap between the integrated computational models and the needs of physical platform development.
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ItemAn interactive visualization tool and data model for experimental design in systems biology(Georgia Institute of Technology, 2008-08) Kapoor, Shray ; Quo, Chang Feng ; Merrill, Alfred H. ; Wang, May DongmeiExperimental design is important, but is often under-supported, in systems biology research. To improve experimental design, we extend the visualization of complex sphingolipid pathways to study biosynthetic origin in SphinGOMAP. We use the ganglio-series sphingolipid dataset as a test bed and the Java Universal Network / Graph Framework (JUNG) visualization toolkit. The result is an interactive visualization tool and data model for experimental design in lipid systems biology research. We improve the current SphinGOMAP in terms of interactive visualization by allowing (i) choice of four different network layouts, (ii) dynamic addition / deletion of on-screen molecules and (iii) mouse-over to reveal detailed molecule data. Future work will focus on integrating various lipid-relevant data systematically i.e. SphinGOMAP biosynthetic data, Lipid Bank molecular data (Japan) and Lipid MAPS metabolic pathway data (USA). We aim to build a comprehensive and interactive communication platform to improve experimental design for scientists globally in high-throughput lipid systems biology research.
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ItemLearning About and Through Biologically Inspired Design(Georgia Institute of Technology, 2008-06-22) Vattam, Swaroop ; Helms, Michael E. ; Goel, Ashok K. ; Yen, Jeannette ; Weissburg, Marc J.Biologically inspired design (BID) uses biological systems as analogues to develop solutions for design problems. Although designers have been looking to nature for inspiration for eons, only recently is BID gaining in importance as a wide-spread movement in design for environmentally-conscious sustainable development (e.g., Benyus 1997). But it is the tendency of the “products” of BID to be radically innovative (Forbes 2005; French 1998; Vogel 2000) that makes BID an interesting case for research in design creativity.
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ItemComputational modeling of a metabolic pathway in ceramide de novo synthesis(Georgia Institute of Technology, 2007-08) Dhingra, Shobhika ; Freedenberg, Melissa ; Quo, Chang Feng ; Merrill, Alfred H. ; Wang, May DongmeiStudies have implicated ceramide as a key molecular agent in regulating programmed cell death, or apoptosis. Consequently, there is significant potential in targeting intracellular ceramide as a cancer therapeutic agent. The cell’s major ceramide source is the ceramide de novo synthesis pathway, which consists of a complex network of interdependent enzyme-catalyzed biochemical reactions. To understand how ceramide works, we have initiated the study of the ceramide de novo synthesis pathway using computational modeling based on fundamental principles of biochemical kinetics. Specifically, we designed and developed the model in MATLAB SIMULINK for the behavior of dihydroceramide desaturase. Dihydroceramide desaturase is one of three key enzymes in the ceramide de novo synthesis pathway, and it converts a relatively inert precursor molecule, dihydroceramide into biochemically reactive ceramide. A major issue in modeling is parameter estimation. We solved this problem by adopting a heuristic strategy based on a priori knowledge from literature and experimental data. We evaluated model accuracy by comparing the model prediction results with interpolated experimental data. Our future work includes more experimental validation of the model, dynamic rate constants assessment, and expansion of the model to include additional enzymes in the ceramide de novo synthesis pathway.
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ItemToward a dynamic climbing robot(Georgia Institute of Technology, 2006) Clark, Jonathan E. ; Goldman, Daniel I. ; Chen, Tao S. ; Full, Robert J. ; Koditschek, Daniel E.Simple mathematical models or ‘templates’ of locomotion have been effective tools in understanding how animals move and have inspired and guided the design of robots that emulate those behaviors. This paper describes a recently proposed biologically-based template for dynamic vertical climbing, and evaluates the feasibility of adapting it to build a vertical ‘running’ robot. We present the results a simulation study suggesting that appropriate mechanical and control alterations to the template result in fast stable climbing that preserves the characteristic body motions and foot forces found in the template model and in animals. These design changes should also allow the robot to operate with commercially available actuators and in the same power to weight range as other running and climbing robots.
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ItemThe RiSE Climbing Robot: Body and Leg Design(Georgia Institute of Technology, 2006) Saunders, Aaron ; Goldman, Daniel I. ; Full, Robert J. ; Buehler, MartinThe RiSE robot is a biologically inspired, six legged climbing robot, designed for general mobility in scansorial (vertical walls, horizontal ledges, ground level) environments. It exhibits ground reaction forces that are similar to animal climbers and does not rely on suction, magnets or other surface-dependent specializations to achieve adhesion and shear force. We describe RiSE’s body and leg design as well as its electromechanical, communications and computational infrastructure. We review design iterations that enable RiSE to climb 90o carpeted, cork covered and (a growing range of) stucco surfaces in the quasi-static regime.
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ItemRobotics in Scansorial Environments(Georgia Institute of Technology, 2005) Autumn, Kellar ; Buehler, Martin ; Cutkosky, Mark ; Fearing, Ronald S. ; Full, Robert J. ; Goldman, Daniel I. ; Groff, Richard ; Provancher, William ; Rizzi, Alfred E. ; Saranli, Uluc ; Saunders, Aaron ; Koditschek, Daniel E.
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ItemDynamic pathway modeling of sphingolipid metabolism(Georgia Institute of Technology, 2004-09) Henning, Peter A. ; Merrill, Alfred H. ; Wang, May DongmeiWe report our research results on computational metabolome study. The goal of this research is to extend the integrated experimental modeling methodologies in sphingolipid metabolism study to other complex biological process studies such as signal transduction or gene regulation. Another feature of this work is that the 3-D information representation enables the user orchestrate the simulated pathways in real time.