Bio-Nano-Machines for Space Applications - NASA's Institute for ...

Introduction and Objectives• Identify and study computationally andexperimentally protein and DNA configurationsthat can be used as bio-nano-machine components• Design two macro-scale devices with importantspace application that will be using bio-nanocomponentassemblies:– The Networked TerraXplorer (NTXp)– All Terrain Astronaut Bio-Nano Gears (ATB)

Space ApplicationsOur current research is focused on two main space based applications:• Networked TerraXplorers (NTXp)– Mapping and sensing of vast planetary terrains• All Terrain Astronaut Bionano Gears (ATB)– Space radiation detection & protection system

Space Conditions / Design Requirements

Space Atmospheric Environment• Targeting Martian environment• Atmosphere Carbon-di-oxide for energy production for bionano robots.Certain micro organisms – “Methanogens” (H + CO 2 )• Temperature -140 to 20 degree C (require thermal insulation andthermally stable bio-components)• Pressure 6.8 millibars as high as 9.0 millibars (1000 millibars on earth)– Materials of sustaining internal pressures– Bio-components which can sustain in lower pressures– Transport mechanism through skin layer (NTXp)

Space Conditions• Topography Scale of the bio nano machines (within meters or miles) andthe area of landing and deployment• Local dust storms The design for NTXp – capable of flowing through thelocal storms or resist it or both• Radiation UV radiations between the wavelengths of 190 and 300 nm.Strong oxidants on the upper surface of Mars (radiation resistant andoxidant resistant skins!)

Identification of Bionano Components• Focusing on components from micro-organisms• A positive correlation -The degree of stability of the organism The degree of stability of theirproteins• Studying enzymes (for their dynamics and model and ease of accessibility)- One key component is - RNA Polymerase- Found in many micro organisms - Thermoplasma acidophilum, Sulfolobusacidocaldarius, Thermoproteus tenax, Desulfurococcus mucosus

Extreme Micro - OrganismsD. radiodurans• Deinococcus radiodurans• Cold-acclimation protein – a protein fromPseudomonas• Some key attributes required for thebio nano machines and components:– Radiation resistant– Thermal resistance (high / low)– Acidic environment resistant– Dry condition resistantHalobacterium

Computational Framework

Characterization of Bionano Components• A control mechanism (chemical pathway) and its dependency on externalparameters (such as, pH, temperature, chemical signals, enzymes)• The change in the external environment triggers changes in the bionanocomponent:- conformation changes- variations in the pattern of their self-assembly• These changes (for instance) demonstrate motion and a desired trajectory• Reversibility• Synchronization of individual bio-components• Stochastic, less understood dynamics, complex chemical pathways

Computational Framework• Identification of the protein from the mentioned organisms characterization with respect to the following three main parameters:- high temperature variations- dry conditions- space radiations• Stability analysis Stability in various conditions is desired, such as, dryconditions, high temperature variations and radiations.S = f( x ; y ;....; t)a bdry 1 1S = g( x ; y ;....; t)j itemp 2 2S = h( x ; y ;....; t)v uradiations 3 3• The overall stability is a complex variable of all the individual stabilitiesβ ν λSnet ∝ F( Sdry; Stemp; Sradiations; t)

Framework for bio molecular dynamics

Space Radiations on Bionano System• Radiations can produce many effects– break bonds, change the structure, destroy the amino acid residues, form otherbonds• Coupling of radiation at atomic level– Hamiltonian for Radiation is coupled to the atomic systemH''H≡ H + H + HRADATOM– the term coupling the electrons of the atom with the radiation. Radiationscan produce many effects– break bonds, change the structure, destroy the amino acid residues, form otherbonds''• is the sum of A coupling terms H n =∑A''H H n

Space Applications – Networked TerraXplorers (NTXp)

Networked TerraXplorers (NTXp)Mapping of vast planetary terrainsA realistic scenario where the Networked TerraXplorers (NTXp) are employed.These meshes would be launched through the parachute and these would be spreadopen on the target surface. These NTXps could be launched in large quantities(hundreds) and hence the target terrain could be thoroughly mapped and sensed. Asingle NTXp could run into miles and when integrated with other NTXPs could covera vast terrain.

Space Applications – All Terrain Bionano (ATB)

Space Radiation – Molecular Damage• Space radiation – damage to DNA, breaking of bonds, mutations leading tocancerous conditions• Monitoring of the space radiations for the astronauts is the key requirements.Our existing design deals with radiation detection

Equivalence of Damage Effects• Health hazards from the space radiations - creating equivalence energetically

System Level Design of ATB

Overall Structure of Layer A on the ATB• Structure of the Layer A – vertical as well as horizontal directions• Non – continuum design (in patches)• Complimentary acceptor layer for electronic connections

Design of Layer - A• A surface view of theradiation detection layer –the probabilistic reactionlayer is represented byspheres.•The molecular components utilizedto make these reaction pathways• Survival of the molecularcomponent

The Number Game – Homological Settings• Represents maximum probability regime for the reaction.• Contains all the machinery (bionano robots) which will react with theradiation

Probabilistic Reaction Centers• Sphere modular design strategy• Probabilistic arrangement of radiation reactants and their signalingpathways• Electron / ionic transport reactionsFe+++ + e- « Fe++

Electron Transfer Reactions• Electron transfer reactions plays a key role in bioenergetics• Fermi’s Golden Rule describes the rates of the reactions• Light (radiation?) triggered electron transfer initiation takes placein the reaction centers of the Layer AStructure Of The Photosynthetic Reaction Centre FromRhodobacter Sphaeroides Carotenoidless Strain R-26.1

Radiation Resistant BacteriaThe many characteristics of D. radiodurans:• An extreme resistance to genotoxic chemicals• Resistance to oxidative damage• Resistance to high levels of ionizing and ultraviolet radiation• Resistance to dehydration• A cell wall forming three or more layersRepairs chromosome fragments, within 12-24 hoursUses a two-system processi. Single-strand annealing single strand re-connectionsii. Homologous recombination double-strand patch upDeinococcus radiodurans• RecA protein responsible for patch up and associated reactions for DNA repair• This bacterium might contain space resistant proteins and other mechanisms

Experimental Work• Peptide Selection – Loop 36 (chain of 36 amino acids)• Protein Expression• Protein Purification• Site-Directed Mutagenesis• Characterization of Protein Conformation as a Function of pH- Circular Dichroism Spectroscopy- Nuclear Magnetic Resonance (still to perform)

Future Activities• ATB gears for astronautsa) Design the reaction mechanism for radiation detection for ATBb) Design a detector layer complimentary to the Layer Ac) Integration with the electronic systems• NTXpa) Surface chemistry (water / mineral) detection networkb) Multi channel pumping / actuating mechanism for transportc) Space condition tolerant outer skin for NTXp

Future Activities• Computational frameworka) Integrate homology modeling of protein to expedite the design processb) Computationally analyze the effect of radiationc) Analyzing the radiation effects in ATB and how the ion / electrontransfer effects could be related to intensity of radiation damage.• Experimentala) Characterization of various bio-nano componentsb) Techniques from NMR would be used to exactly characterize thepeptide structure when it changes its conformationc) Explore the radiation resistant bacterium Deinococcus radiodurans forpossible radiation resistant bio-mechanisms and proteinsd) Experiments with carbon nano tube structures and bio-nano components

Publications / Presentations• Chapter in CRC Handbook on Biomimetics - Biologically InspiredTechnologies, Editor: Yoseph Bar-Cohen, JPL• Chapter in The Biomedical Engineering Handbook, 3rd Edition, Editor: M.L. Yarmush,• Paper Presented at the 7th NASA/DoD Conference on Evolvable Hardware(EH-2005), Washington DC, June 29 - July 1, 2005• Interview at The Scientist Volume 18 | Issue 18 | 26 | Sep. 27, 2004“Alternative Energy for Biomotors”• Interview at the http://science.nasa.gov/• Our research webpage: http://www.bionano.neu.edu

AcknowledgmentsNASA Institute of Advanced Concepts(NIAC) Phase II Grant, September 2004http://www.niac.usra.edu/

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