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MSE 598/494 Bio-inspired Materials and Biomaterials MSE 598/494 Bio-inspired Materials and Biomaterials
Instructor: Ximin He
TA: Xiying Chen Email: xchen128@asu.edu
2014-04-10
Lecture 15-16
Mimicking Biological Phenomena & Concepts
What you will learn in the next 75 minutes
I. Artificial Photosynthesis
Photosynthesis
Artificial Photosynthesis
Artificial Sunflower for Light Harvesting
(Option for Lit Rev Presentation and Original Research)
II. Neural Networks & Bioinspired Computers
Neural Network
Neural Computation
III. Biological Geological Technology
(Guest Lecture by Nasser Hamdan)
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4/10/2014
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MSE 598/494 Bio-inspired Materials and Biomaterials MSE 598/494 Bio-inspired Materials and Biomaterials
Instructor: Ximin He
TA: Xiying Chen Email: xchen128@asu.edu
2014-04-08
Lecture 15. Artificial Photosynthesis
Energy, Energy
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Earriving/hr = Ehuman usage/yr
Solar panel
Solar cell < 0.1% Electricity
The ultimate source of energy for life on earth is
the sun!
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3 billion-year strategy of nature - Photosynthesis
6 CO
2
+ 6 H
2
0 -----------> C
6
H
12
O
6
+ 6 O
2
sunlight
Light
energy
Chemical
energy
Photosynthesis Artificial Photosynthesis
Classic synthetic chemistry and
bioorganic chemistry
Biomimetic systems which aim to
imitate photosynthesis as a generic
process
Use non-biological building blocks
The process that plants undergo in order to
transform solar energy into chemical energy
stored in the bonds of sugar molecules.
What organism?
In plants, algae, and certain bacteria
Where it happens?
In chloroplasts, where pigments (i.e.
chlorophyll) embedded in specialized
protein matrixes called photosystems absorbs
light (usually in the blue region of the
visible spectrum)
How?
Via a cascade of chemical reactions,
structural transformations, and electron
transfer processes occurring chloroplasts
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Photosynthesis
Why leaves are green?
Chlorophyll (a/b) use blue & red
Photosynthesis
Anatomy of Leaf
small pores
- regulate the entrance and exit
of carbon dioxide, oxygen and
water
Where CO
2
and H
2
0 form
new bonds, generating
glucose, releasing oxygen
during the process
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Photosynthesis
Energy Conversions
Two parts of photosynthesis
1. Light-dependent reactions:
Production of the well-known energy-
storage molecules
1) adenosine triphosphate (ATP)
2) nicotinamide adenine dinucleotide
phosphate (NADPH).
2. Light-independent reaction:
Reduction of carbon dioxide into
carbohydrates a process generally
referred to as carbon fixation,
produces sugar.
Photosynthesis
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Biomimetic photosynthesis
solar fuel cell for carbon fixation
Components & Process:
a molecule responsible for light absorption and generating electrons (a metal-containing
macrocyclic molecule);
a chemical species - donates electrons (for regeneration of the dye molecule);
titanium oxide nanoparticles (NPs) acting both as transporters/storage of the donated
electrons, as well as scaffolds for enzyme molecules (carbon oxide dehydrogenase);
the enzymes catalyze the reduction of carbon dioxide to carbon monoxide (CO).
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F. A. Armstrong and colleagues at Oxford University
Synthetic Chlorophyll for photo harvesting & e transfer
Porphyrins, macrocyclic compounds encapsulating metal ions: considerable
light absorption properties core components of artificial pigments
1. Multi-porphyrin, a model light-harvesting antenna:
Covalently-bonded zinc-containing porphyrins (shown in the periphery) and
free-base porphyrin (center) enable efficient light-induced energy transfer
and electron transport.
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Holten D. et al., Nano Lett. 2002 35, 5769.
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light-harvesting antenna
2. Dendrimer prophrin: another light-harvesting antenna
a large number of identical chemical units on their surface
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Multitude of chromophores (pigments) is displayed upon the surface of the
dendrimer absorbing light in a broad spectral range (blue arrows);
the absorbed energy is transferred from the chromophores at the dendrimer
periphery through the branches, and to its core (green arrows);
subsequent enhanced emission is produced from the core (red arrow)
Energy and Substance Metabolism
Self-Oscillating Gels
R. Yoshida et al., JACS (1996); Adv. Mater.
(2010).
By immobilizing the chemical oscillation
catalyst into the polymer network, the gel
converts chemical substrates into mechanical
energy, swelling/deswelling oscillation.
Catabolism
(cellular respiration, etc.)
Anabolism
(photosynthesis, etc.)
Generation of
high-energy substance
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Photoblast-mimicking Photonic Crystals as Artificial Leaves
Bioinspiration: Anabolism (photosynthesis, etc.)
Innovation: using soft responsive materials, hybrid with inorganic materials
Impact: enhance H
2
generation efficiency, as soft electrode, for energy storage, fuel cells
H
2
has the largest energy-to-mass ratio of any fuel, storage is difficult)
solar
Yoshida, et al ChemComm. 20101, 2009, Adv. Funct. Mater. 2010
H
2
Periodically-structured
poly(NIPAAm-co-Ru(bpy)
3
) gel
film
Concept: H
2
-generating nano-gel; Assembly into photonic crystals
H
2
-generating nanogels - formed by using
poly(NIPAAm-co-Ru(bpy)
3
) gel containing Pt nanoparticles
Different catalysts and
photosensitizers
Fluorescence (excitation@~600nm):
- Nanogel v.s. solution
- Fluorescence as function of
[Ru(bpy)
3
2+
]
H
2
generation:
-Gas (mol) as function of [Ru(bpy)
3
2+
]
- Quantum efficiency
Integration into artificial plants
Negatively-charged positively-charged
Hypothesis:
Spatial control of the Ru(bpy)
3
2+
molecules, in a condensed, but
dispersed state, enhance the
photoenergy conversion to operate
the electronic transmission circuit for
H
2
generation.
High transparency
Tunability
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Light Harvesting
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Phototropism
Asymmetric growth
Sunflower
Artificial Sunflower
Light harvesting
Adaptive stem
Reading Resources
Prof. Daniel Nocera: Artificial Leaf Inventor and Patterson
Rockwood Professor of Energy, Harvard
ASU Center for Bioenergy & Photosynthesis
Phototropism: light-oriented adaptive material systems
(optional topic for original research)
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MSE 598/494 Bio-inspired Materials and Biomaterials MSE 598/494 Bio-inspired Materials and Biomaterials
Instructor: Ximin He
TA: Xiying Chen Email: xchen128@asu.edu
2014-04-08
Lecture 16.
Neural networks and bioinspired computers
Human Brains V.S. Conventional Computers
Human brain: a sophisticated
decision-making machine
Learning in neuronal networks
consists of chemical modulation of
the synaptic connections between
the neurons
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algorithms i.e. following a set of
specific instructions in order to
solve a problem.
The instructions, e.g. stages in the
problem-solving process, need to
be fed to the computer in
advance (via the software codes)
This fundamental precondition
restricts the problem-solving
capabilities - defining the
concrete steps required from the
computer to produce output
from the specific inputs.
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Computing based on Artificial Neural Networks (ANNs)
To mimic neural-based decision-making and computing
Core difference between neural network and conventional computers:
their intrinsic approach to information processing and analysis
A neural network:
composed of a large number of interconnected processing elements (neurons)
working in parallel.
cannot be programmed to perform a specific task
How does NN solve problems?
Through a learning process based upon cumulative modulation of the signals
transmitted between the processing elements, neurons.
What idea to borrow?
The combined action of many interconnected neurons, the neural network undergoes
chemical changes which underlie the learning process which subsequently bestows
the neural network with computing or decision-making capabilities.
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from Neuronal Cells to Artificial Neurons
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Building blocks: neurons unique cells that can transmit electrical pulses.
Neurons comprise
several input-receiving protrusions called dendrites,
a single output-producing unit the axon
At the end of the axon are regions denoted synapses - connect the axon to dendrites
of other neurons; where communication is established between neighboring
neurons through chemical and electrical stimulation.
When a neuron receives an input signal through one of the dendrites and this input
is deemed sufficiently large (i.e. surpasses a certain signal threshold), the neuron
sends an electrical pulse down its axon which could then excite other neurons.
Synapses: chemical modification
Learning: quently affect the extent to which information (e.g.
electrical stimuli) is transmittedbetween neurons.
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Artificial neuron and its Truth Tables
The neuron has three inputs
(delivering 0 or 1 signals), and
one output.
The output signal produced by the
neuron is determined by the firing
rules:
1,1,1 or 0,1,0 give out 1 output,
0,0,0 or 0,0,1 trigger 0 output.
If the input signals are different to
the four combinations, the output
signal is determined by the overall
similarity between the input signal
and the four combinations (four right
columns)
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Neural network for pattern recognition
A 9-element matrix providing inputs for three neurons
neural outputs of the letters T and H and the
corresponding truth tables for the three neurons
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Reading Resources
More details in Neural Computing
Researchers:
UC Berkeley
MIT
Stergiou and Siganos, Imperial College, London
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MSE 598/494 Bio-inspired Materials and Biomaterials MSE 598/494 Bio-inspired Materials and Biomaterials
Guest Lecturer: Ximin He
TA: Xiying Chen Email: xchen128@asu.edu
2014-04-08
Lecture 17.
Bio-geotechnical Engineering:
Bio-mediated & Bio-inspired Geotechnics
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Bio-geotechnical Engineering:
Bio-mediated & Bio-inspired Geotechnics
Nasser Hamdan
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Stromatolites
Stromatolites
Stromatolites
Stromatolites
Stromatolites
Stromatolites
Stromatolites
Stromatolites
Stromatolites
What is geotechnical engineering?
Investigate behavior of earth materials such as soil and rock
Design & engineer ground systems to accommodate structures
What types of properties do soil and rock have?
Mechanical properties (bulk & micro-scale mechanics)
Physical (structure, porosity, swell/shrink, micro, nano-scale interaction)
Chemical/Biological properties (biochemical, geochemical, microbial)
Geotechnical Engineering
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What kinds of projects do they work on?
Earthquakes
Foundations
Slope stability
landslides
Mining
Tunneling/Excavations
Dams
Contaminant remediation
Landfills
Roadway construction
Geotechnical Engineering
Images (clockwise top left): en.wikipedia.com, cruxsub.com, www.reviewcivilpe.com, www.goic.org.qa, arizona-leasure.com, englishcqnews.net,
Bio-mediated & Bio-inspired Geotechnics
What is Bio-inspired?
Ideas rooted in the understanding of natural biological processes
Goal: try to understand natural biological processes to mimic them
What is Bio-mediated?
Using natural biological processes for engineering purposes
Goal: induce and/or accelerate these processes for a beneficial effect
Why do pursue bio-mediated & bio-inspired processes?
Sustainable engineering is critical
Nature seems to have perfected many things . . . lots of practice!
Bio-geotechnical Engineering
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Bio-inspiration
What do we see nature do?
An important area is Biomineralization/Biotransformation
Images (top-down): (left)NBCnews.com, en.wikipedia.org., cambridgecarbonates.com; (middle)www.artwet.fr, www.nhm.ac.uk;(right)www.madrimasd.org.dailycollegian.com
Biomineralization
Mineral precipitates are common in engineered systems & nature
Clog drainage systems, water treatment filters, etc.
Sandstone, calcrete/caliche and other carbonates
Cementing agents include carbonates, silicates & metal oxides
Microbes can induce the formation of these precipitates
Carbonates are most interesting, partially due to their abundance
Carbonate precipitation is widely studied in biogeotechnical engineering
Engineering Challenge
Induce and/or accelerate mineral precipitation process for a beneficial
effect: Improve mechanical/chemical properties of soils
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Recall the Potential Pathways
CaCO
3
Precipitation Mechanism
o HCO
3
-
(aq)
+ OH
-
(aq)
H
2
O + CO
3
2-
(aq)
o Ca
2+
(aq)
+ CO
3
-
(aq)
CaCO
3
(s)
Microbial Denitrification: Dissimilatory reduction of nitrate
o NO
3
-
NO
2
-
NO N
2
O N
2
o NO
3
-
+ 1.25CH
2
O 0.5N
2
+ 1.25CO
2
+ 0.75H
2
O + OH
-
Ureolysis: Hydrolysis of urea via microbial OR free enzyme:
o CO(NH
2
)
2
+ 3H
2
O = CO
2
+ 2NH
4
+
+ 2OH
-
Algae & Cyanobacteria:
o Autotrophic organisms perform directed mineral precipitation
Biotransformation: Bio-mediated, direct redox rxns
o Results in a new substance or precipitation (TCEethene, Cr
6+
Cr
3+
)
Liquefaction mitigation is a potentially major application
Certain soils will liquefy (lose strength) under cyclic loading (earthquakes)
Carbonate Mineral Precipitation for Soil Improvement
Application to liquefaction
CourtesyofNationalGeophysicalDataCenter
CourtesyofNationalGeophysicalDataCenter
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Earthquake shaking causes soil structure to collapse
In saturated soil, pore pressure rises, strength decreases
Liquefaction is a major source of damage in earthquakes
Billions of dollars of property at risk
Earthquake-Induced Liquefaction of Cohesionless Soils
Photos (clockwise): Unknown, USGS, USGS.
Slopes fail, buildings settle, underground structures rise to surface
o Example: Christchurch, New Zealand (2011):
Magnitude 6.3 (same as 1932 Long Beach EQ)
Killed 185 people
7000 single family homes abandoned & razed
Approximately (US) $20 billion in total cost
Earthquake Induced Liquefaction
Photos (clockwise): PNSN, NZ Herald, PNSN.
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How can carbonate precipitation improve soil properties?
Mechanical & Physical Properties
Soil improvement through carbonate mineral precipitation(Calcite e.g.)
Calcite formed at inter-particle soil contacts cementation
Calcite can also fill voids increase density
Produce biogas desaturation
Cementation, density , desaturation improve mechanical properties
Increases strength & stiffness, and desaturates soil
If microbes are
involved
If microbes are
involved
Loose, cohesionless soil most susceptible to liquefaction
Saturation is also a necessary condition
Mitigate liquefaction potential by:
Cementing the soil
Increasing the soil density
Desaturating the soil
Bio-mediated Geotechnics
Note: Mitigation under existing structures particularly challenging
Mitigation of Liquefaction via Microbial Denitrification
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Biogrouted shallow footing
foundation, DeJong et al. (2010)
Cemented sand mass via Biogrout,
van Paassen et al. (2010)
Soil Cementation for Mass Stabilization
Columns produced strongly cemented bulbs of sand
Very little to ~ no hydraulic conductivity
Soil Cementation for Columnar Stabilization
Strengthover520kPa
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Large Columnar Stabilization
3 ft x 3 ft box filled with soil and treated
Several technical (delivery) problems during injection
Hydraulic fracturing, fluid leaked to surface & lost
Mass & columnar stabilization: Bio-inspired geotechnics
Soil block stood
vertically 2-ft high
on the other side.
Bottom of box
SEM images from Columnar Stabilization Experiments
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What is the Connection to Biomaterials?
Clogging is a significant problem
Pore spaces fill as calcite precipitates and/or microbes grow
Poor nutrient delivery
Lack of spatial and temporal control over the process
Limited applications due to clogging
Biomaterials may encapsulate reagents to delay reaction
Spatial & temporal control for inside-out reaction process
Better nutrient delivery
Soil erosion is a major sustainability issue
Air and water pollution
Soil loss
Soil erosion is driven by wind and surface water
Common sources include mining & construction sites
Bio-Inspired Soil Improvement for Erosion Control
Images (left-right clockwise): en.wikipedia.org., en.wikipedia.org, unknown, azomining.com
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The Soil Erosion Problem
Fugitive dust is a particular problem in Maricopa County
EPA air quality non-attainment zone
PM
10
is the primary problem
Significant health risk to local residents
Penalties for non-compliance with air quality standards
Fines & loss of federal transportation money
Image: en.wikipedia.org.
Bio-inspired Soil Erosion Control
Enzyme-induced carbonate precipitation, a bio-inspired process,
can stabilize surface soil against erosion
Ureolytic hydrolysis using plant-derived urease enzyme
Jack bean (C. ensiformis), a common drought-resistant legume contains
urease (best known & studied); also common in beans, melons, squash, etc.
Urease enzyme induces ureolytic carbonate (CO
3
2-
) mineral
precipitationCalcite
Precipitated calcite forms a crust, providing cementation at inter-
particle contacts
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Soil Erosion Control Experiment
Wind tunnel testing using NASA wind tunnel at ASU
Soil Erosion Control Experiment Results
Native Arizona silty sand used and treatment concentrations varied
Results compared with:
(a) Bare soil
(b) Wetting (current practice)
(c) 1.0 M Urea/CaCl
2
only (red line)
Many other tests have been conducted
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What is the Connection to Biomaterials?
Loss of cementation solution into deeper soil is a major problem
Dry soil quickly draws fluid into deeper layers
Reaction process is lost due to desiccation & dilution
Biomaterials may be able to help retain fluid on soil surface
Very hydrophilic fluid may slow water loss
A plugging biomaterial may help localize reaction to surface
Biomaterial may provide a more stable reaction matrix
Calcite precipitation can immobilize toxic metals
Sequestration of radionuclides & metal contaminants via co-precipitation
Carbonate minerals can widely vary MgCO
3
, (Ni, Mg, Fe)CO
3
(see below)
Example: Treatment at DOE sites via ureolysis
Radionuclide & metal contaminants
90
Sr
2+
,
60
Co
2+
, Cd
2+
Contaminants co-precipitated w/ calcite & Locked into stable form
Allows for decay of radionuclides and immobilization of other metals
Bioremediation: Chemical & Biological Properties of Soil
Calcite (CaCO
3
), Rhodochrosite (MnCO
3
) Smithsonite (ZnCO
3
) Gaspeite ((Ni, Mg, Fe
2+
)CO
3
)
Images: en.wikipedia.org
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Bioremediation: Bio-mediated & Bio-inspired
Biomineralization-
Geochemistry of carbonate precipitation not unique to any specific
microorganism.
Microbially induced carbonate precipitation is a consequence of an
organisms metabolism.
Biotransformation-
Geochemistry is unique to specific microorganisms
But, it is still a consequence of an organisms metabolism.
Thank you
Any Questions?
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Summary of Lecture 15-16
I. Artificial Photosynthesis
Photosynthesis
Artificial Photosynthesis
Advances in Dyes, Catalysts, etc
Artificial Sunflower for Light Harvesting
(Option for Lit Rev Presentation and Original Research)
II. Neural Networks & Bioinspired Computers
Neural Network
Neural Computation
III. Biological Geological Technology
(Guest Lecture by Nasser Hamdan)
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Homework of Lecture 13-14
1. Please talk about a current artificial photosynthesis technique in
the bio-inspiration perspective, in comparison to the natural
photosynthesis process.
2. Please list several bio-inspired and/or bio-mediated topics of
research in Biogeotech and pick one to explain the bio-
mediated/inspired process
Due by 04/17/2014
Hand in hard copy of homework at the TA, Xiying Chen, at the
beginning of the 04/17 class
Please contact xchen128@asu.edu for questions.