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ItemBrownian dynamics simulation of macromolecule diffusion in a protocell(Georgia Institute of Technology, 2011) Ando, Tadashi ; Skolnick, JeffreyThe interiors of all living cells are highly crowded with macro molecules, which differs considerably the thermodynamics and kinetics of biological reactions between in vivo and in vitro. For example, the diffusion of green fluorescent protein (GFP) in E. coli is ~10-fold slower than in dilute conditions. In this study, we performed Brownian dynamics (BD) simulations of rigid macromolecules in a crowded environment mimicking the cytosol of E. coli to study the motions of macromolecules. The simulation systems contained 35 70S ribosomes, 750 glycolytic enzymes, 75 GFPs, and 392 tRNAs in a 100 nm × 100 nm × 100 nm simulation box, where the macromolecules were represented by rigid-objects of one bead per amino acid or four beads per nucleotide models. Diffusion tensors of these molecules in dilute solutions were estimated by using a hydrodynamic theory to take into account the diffusion anisotropy of arbitrary shaped objects in the BD simulations. BD simulations of the system where each macromolecule is represented by its Stokes radius were also performed for comparison. Excluded volume effects greatly reduce the mobility of molecules in crowded environments for both molecular-shaped and equivalent sphere systems. Additionally, there were no significant differences in the reduction of diffusivity over the entire range of molecular size between two systems. However, the reduction in diffusion of GFP in these systems was still 4-5 times larger than for the in vivo experiment. We will discuss other plausible factors that might cause the large reduction in diffusion in vivo.
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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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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.