lect 15-16 photosynthesis neural computer biogeotech_print

8/11/2019 Lect 15-16 Photosynthesis Neural Computer Biogeotech_print

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MSE 598/494 Bio-inspired Materials and BiomaterialsMSE 598/494 Bio-inspired Materials and Biomaterials

Instructor: Ximin He

TA: Xiying Chen Email: [email protected]

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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2014-04-08

Lecture 15. Artificial Photosynthesis

Energy, Energy

4

E arriving/hr= E human usage/yr

Solar panel

Solar cell < 0.1% Electricity

The ultimate source of energy for life on earth isthe sun!


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3 billion-year strategy of nature - Photosynthesis

6 CO2 + 6 H

0 -----------> C6

H

O6

+ 6 O

sunlight

Lightenergy

Chemicalenergy

Photosynthesis Artificial Photosynthesis

Classic synthetic chemistry andbioorganic chemistry

Biomimetic systems which aim toimitate photosynthesis as a generic

process

Use non-biological building blocks

The process that plants undergo in order totransform 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 specializedprotein matrixes calledphotosystemsabsorbs

light (usually in the blue region of thevisible 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 andwater

Where CO2 and H20 form

new bonds, generating

glucose, releasing oxygenduring the process


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Photosynthesis

Energy ConversionsTwo parts of photosynthesis

1. Light-dependent reactions:

Production of the well-known energy-

storage molecules1) 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 andgenerating electrons (a metal-containingmacrocyclic 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).

11 F. A. Armstrong and colleagues at Oxford University

Synthetic Chlorophyll for photo harvesting & e transfer

Porphyrins, macrocyclic compounds encapsulating metal ions: considerablelight 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 transferand electron transport.

12Holten 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 thedendrimer absorbing light in a broad spectral range (blue arrows);

the absorbed energy is transferred from the chromophores at the dendrimerperiphery through the branches, and to its core (green arrows);

subsequent enhanced emission is produced from the core (red arrow)

Energy and Substance Metabol ism

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 o f

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 H2 generation efficiency, as soft electrode, for energy storage, fuel cells

H2 has the largest energy-to-mass ratio of any fuel, storage is difficult)

solar

Yoshida, et alChem Comm. 20101, 2009,Adv. Funct. Mater. 2010

H2

Periodically-structured

poly(NIPAAm-co-Ru(bpy)3) gel

film

Concept: H2 -generating nano-gel; Assembly into photonic crystals

H2-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)32+]

H2 generation:

-Gas (mol) as function of [Ru(bpy)32+]

- Quantum efficiency

Integration into artificial plants

Negatively-charged positively-charged

Hypothesis:

Spatial control of the Ru(bpy)32+

molecules, in a condensed, but

dispersed state, enhance the

photoenergy conversion to operate

the electronic transmission circuit for

H2 generation.

High transparency

Tunability


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Light Harvesting

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Phototropism

Asymmetric growth

Sunflower

Art if ic ial Sunflower

Light harvesting

Adaptive stem

Reading Resources

Prof. Daniel Nocera: Artificial Leaf Inventor and PattersonRockwood Professor of Energy, Harvard

ASU Center for Bioenergy & Photosynthesis

Phototropism: light-oriented adaptive material systems

(optional topic for original research)


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2014-04-08

Lecture 16.

Neural networks and bioinspired computers

Human Brains V.S. Conventional Computers

Human brain: a sophisticateddecision-making machine

Learning in neuronal networksconsists of chemical modulation ofthe synaptic connections between

the neurons

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algorithms i.e. following a set ofspecific instructions in order tosolve a problem.

The instructions, e.g. stages in theproblem-solving process, need to

be fed to the computer inadvance (via the software codes)

This fundamental preconditionrestricts the problem-solving

capabilities - defining theconcrete steps required from the

computer to produce outputfrom 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 signalstransmitted between the processing elements, neurons.

What idea to borrow?

The combined action of many interconnected neurons, the neural network undergoeschemical changes which underlie the learning process which subsequently bestowsthe 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 dendritesof 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 neuronsends 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), andone output.

The output signal produced by the

neuron is determined by the firingrules:

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 outputsignal is determined by the overallsimilarity between the input signal

and the four combinations (four rightcolumns)

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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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Guest Lecturer: Ximin He


2014-04-08

Lecture 17.

Bio-geotechnical Engineering:

Bio-mediated & Bio-inspired Geotechnics


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Bio-geotechnical Engineering:


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,


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

BiomineralizationMineral 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

CaCO3 Precipitation Mechanism

o HCO3-(aq) + OH

-(aq)H2O + CO3

2-(aq)

o Ca2+(aq) + CO3-(aq)CaCO3(s)

Microbial Denitrification: Dissimilatory reduction of nitrate

o NO3- NO2

- NO N2O N2

o NO3- + 1.25CH2O 0.5N2 + 1.25CO2 + 0.75H2O + OH

-

Ureolysis: Hydrolysis of urea via microbial OR free enzyme:

o CO(NH2)2+ 3H2O = CO2 + 2NH4++ 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, Cr6+Cr3+)

Liquefaction mitigation is a potentially major application

Certain soils will liquefy (lose strength) under cyclic loading (earthquakes)

Carbonate Mineral Precipitation for Soil ImprovementApplication to liquefaction

CourtesyofNationalGeophysical DataCenter

CourtesyofNationalGeophysical DataCenter


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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

Strength

over

520

kPa


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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

PM10 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 (CO32-) mineral

precipitation Calcite

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/CaCl2 only (red line)

Many other tests have been conducted


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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)

27

Homework of Lecture 13-14

1. Please talk about a current artificial photosynthesis technique inthe bio-inspiration perspective, in comparison to the naturalphotosynthesis process.

2. Please list several bio-inspired and/or bio-mediated topics ofresearch 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 [email protected] for questions.

lect 15-16 photosynthesis neural computer biogeotech_print

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