Organizational Unit:

College of Sciences

Permanent Link

https://hdl.handle.net/1853/70627

Includes Organization(s)

Organizational Unit

School of Biological Sciences

Organizational Unit

School of Chemistry and Biochemistry

Organizational Unit

School of Earth and Atmospheric Sciences

Organizational Unit

School of Mathematics

Organizational Unit

School of Physics

Show 1 more

ArchiveSpace Name Record

https://finding-aids.library.gatech.edu/agents/corporate_entities/1130

Full item page

Publication Search Results

Now showing 1 - 10 of 16

Brownian dynamics simulation of macromolecule diffusion in a protocell

(Georgia Institute of Technology, 2011) Ando, Tadashi ; Skolnick, Jeffrey

The 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.
Biophysically inspired development of a sand-swimming robot

(Georgia Institute of Technology, 2011) Maladen, Ryan D. ; Ding, Yang ; Umbanhowar, Paul B. ; Kamor, Adam ; Goldman, Daniel I.

Previous study of a sand-swimming lizard, the sandfish, Scincus scincus, revealed that the animal swims within granular media at speeds up to 0:4 body-lengths/cycle using body undulation (approximately a single period sinusoidal traveling wave) without limb use [1]. Inspired by this biological experiment and challenged by the absence of robotic devices with comparable subterranean locomotor abilities, we developed a numerical simulation of a robot swimming in a granular medium (modeled using a multi-particle discrete element method simulation) to guide the design of a physical sand-swimming device built with off-the-shelf servo motors. Both in simulation and experiment the robot swims limblessly subsurface and, like the animal, increases its speed by increasing its oscillation frequency. It was able to achieve speeds of up to 0:3 body-lengths/cycle. The performance of the robot measured in terms of its wave efficiency, the ratio of its forward speed to wave speed, was 0:34 0:02, within 8 % of the simulation prediction. Our work provides a validated simulation tool and a functional initial design for the development of robots that can move within yielding terrestrial substrates.
Comparative studies reveal principles of movement on and within granular media

(Georgia Institute of Technology, 2010-06) Ding, Yang ; Gravish, Nick ; Li, Chen ; Maladen, Ryan D. ; Mazouchova, Nicole ; Sharpe, Sarah S. ; Umbanhowar, Paul B. ; Goldman, Daniel I.

Terrestrial locomotion can take place on complex substrates such as leaf litter, debris, and soil that flow or solidify in response to stress. While principles of movement in air and water are revealed through study of the hydrodynamic equations of fluid motion, discovery of principles of movement in complex terrestrial environments is less advanced in part because describing the physics of limb and body interaction with such environments remains challenging. We report progress our group has made in discovering principles of movement of organisms and models of organisms (robots) on and within granular materials (GM) like sand. We review current understanding of localized intrusion in GM relevant to foot and body interactions. We discuss the limb-ground interactions of a desert lizard, a hatchling sea turtle, and various robots and reveal that control of granular solidification can generate effective movement. We describe the sensitivity of movement on GM to gait parameters and discuss how changes in material state can strongly affect locomotor performance. We examine subsurface movement, common in desert animals like the sandfish lizard. High speed x-ray imaging resolves subsurface kinematics, while electromyography (EMG) allows muscle activation patterns to be studied. Our resistive force theory, numerical, and robotic models of sand-swimming reveal that subsurface swimming occurs in a “frictional fluid” whose properties differ from Newtonian fluids.
Systematic study of the performance of small robots on controlled laboratory substrates

(Georgia Institute of Technology, 2010-04) Li, Chen ; Hoover, Aaron M. ; Birkmeyer, Paul ; Umbanhowar, Paul B. ; Fearing, Ronald S. ; Goldman, Daniel I.

The design of robots able to locomote effectively over a diversity of terrain requires detailed ground interaction models; unfortunately such models are lacking due to the complicated response of real world substrates which can yield and flow in response to loading. To advance our understanding of the relevant modeling and design issues, we conduct a comparative study of the performance of DASH and RoACH, two small, biologically inspired, six legged, lightweight (~ 10 cm, ~ 20 g) robots fabricated using the smart composite microstructure (SCM) process. We systematically examine performance of both robots on rigid and °owing substrates. Varying both ground properties and limb stride frequency, we investigate average speed, mean mechanical power and cost of transport, and stability. We find that robot performance and stability is sensitive to the physics of ground interaction: on hard ground kinetic energy must be managed to prevent yaw, pitch, and roll instability to maintain high performance, while on sand the fluidizing interaction leads to increased cost of transport and lower running speeds. We also observe that the characteristic limb morphology and kinematics of each robot result in distinct differences in their abilities to traverse different terrains. Our systematic studies are the first step toward developing models of interaction of limbs with complex terrain as well as developing improved limb morphologies and control strategies.
Integrating 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.
An 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 Dongmei

Experimental 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.
Learning 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.
Computational 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 Dongmei

Studies 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.
Toward 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.
The RiSE Climbing Robot: Body and Leg Design

(Georgia Institute of Technology, 2006) Saunders, Aaron ; Goldman, Daniel I. ; Full, Robert J. ; Buehler, Martin

The 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.