Contents

  		PREFACE	

	1.	DESIGN OF PROTEIN BASED NANOMACHINES	

		Introduction

		Renowned Nanomachines of the Biological Cell Confirm Engineering Principles and Inspire Nanomachine Design

		De Novo Design of Diverse Elastic-Contractile Protein Machines

		Hydrophobic and Elastic Consilient Mechanisms: Definitions

		Hydrophobic Consilient Mechanism and the Inverse Temperature Transition

		The Elastic Consilient Mechanism and the Nature of Near Ideal Elasticity

		Coupled Hydrophobic and Elastic Consilient Mechanisms

		Principal Thermodynamic Quantities Controlling Diverse Energy Conversions in Model Proteins

		The Change in Gibbs Free Energy for Solubility, G(solubility) = H-TS

		The Change in Gibbs Free Energy for a Phase Transition

		The Change in Gibbs Free Energy for an Inverse Temperature Transition

		Apolar-Polar Repulsive Gibbs Free Energy of Hydration, Gap

		Calculations of the Entropic Elastic Force and Energy

		Biology’s Protein-based Nanomachines Confirm the Hydrophobic and Elastic Consilient Mechanisms

		The Three Classes of Energy Conversion Within the Cell

		Complex III of the Electron Transport Chain Within the Inner Mitochondrial Membrane

		ATP Synthase of the Inner Mitochondrial Membrane

		The Myosin II Motor of Muscle Contraction

		Confirmation of the Hydrophobic and Elastic Consilient Mechanisms

		Designing Protein-based Nanomachines Using the Hydrophobic and Elastic Consilient Mechanisms

		Design of an AFM-Based Stress-Strain Nanomachine for the Detection of a Single Molecular Event

		Use of the 3 kHz Mechanical Resonances in the Design of an AFM-Based Nanomachine for Detection of Interactions at Fixed Length

		An Additional Opportunity in the Deciphering of Engineering Principles for the Design of Protein-Based Nanomachines

	2.	METASTABILITIES IN NANOCRYSTALLINE 	

SILICON

		Experimental Procedure

		Results

		Discussion

		Conclusion	

	3.	INTERACTION OF SULPHURIC ACID WITH 		

GRAPHENE

		Sulphuric Acid in Gas and Solid Phases

		Sulphuric Acid on Graphene

		Conclusions	

	4.	NANOSCALE CHARACTERIZATION OF 	

NANOWIRES

		Experimental Methods

		Nanowire Morphology, Periodicity and Diameter

		Chemical Analysis of the CoPt/Pt Nanowires

		Structural Analysis of the CoPt/Pt Nanowires

		Discussion

		Conclusions	

	5.	THERMOPOWER MEASUREMENTS ON NICKEL	

NANOWIRES

		Experimental Details

		Results and Discussion

		Structural Characterization of the NWs

		Initial Characterization of the Measurement Device

	6.	MULTI-WALLED CARBON NANOTUBE EMITTERS	

		EXPERIMENT

		Fabrication of CNT Cathode

		Experimental Structures

		Current-Voltage Characteristics

		Simulations

		Simulated Structures

		Predicted I—V Characteristics

		Cathode Support Structure Geometry

		Conclusion

	7.	VIBRATION OF A CARBON NANOTUBE	

		The Model for a CNT filled with a C-chain

		Vibration of a CNT filled with a C-chain

		Axisymmetric Radial Breathing Vibration (n = 0)

		Coupled Vibration with n = 1

		Vibration of Higher-order Modes (n > 2)

		Conclusions

	8.	A NANOPOROUS TiO2 ELECTRODE

		Experimental Details

		Preparation of the ILSE Films

		Characterization of the ILSE Films

		Electrode and DSSC Fabrication Containing the ILSE

		Electrode Characterization

		Results and Discussion

		Conclusions

	9.	FREEZING BEHAVIOUR OF AN NANOMETER-	

SIZED Au DROPLET

		Numerical Simulations

		Results and Discussion

		Conclusions	

	10.	NANOSCALE IN INVESTIGATION OF ULTRATHIN	 

SILICONE OXIDE THERMAL DECOMPOSITION	

		Experimental Details

		Results and Discussion

		High Temperature STM in situ Observation of the Thermal Decomposition Process

		Individual Void Growth Kinetics at the Initial Decomposition Stage

		Decomposition Rate Variation and Rate Limiting Steps

		Morphology Effects on the Decomposition Process

		Conclusions

	11.	CARBON NANOTUBE FIELD-EFFECT	

TRANSISTOR	

		Methodology

		Results and Discussion

		Conclusions

	12.	CYLINDRICAL NANODOT ARRAYS	

		System and Units

		Theoretical Model

		Vortex-core Magnetization

		Total Energy Calculation

		Results and Discussion

		Conclusions

	13.	SUPERELASTICITY OF ENGINEERING	

CERAMICS BY NANOTUBES

		Experimental Details

		Results and Discussion

		Conclusion	

	14.	POROUS ANODIC ALUMINA	

		Experimental Details

		Results

		Initial Specimens and Anodizing 

		Film Morphology

		Film Composition

		Discussion

		Conclusions

	15.	METAL NANOCLUSTERS IN GLASS	

		Experimental Procedure 

		Results and Discussion

		Ion-Beam Mixed Ag in Silica

		Ion-Exchanged Ag in Soda Lime Glass 

		Conclusion

	16.	LIGHT EMISSION FROM NANOCOMPOSITES	

		Experiments

		Results and Discussion

		Conclusion

	17.	NANOCRYSTALLINE SILICON FILMS	

		Experimental Details

		Results

		Optical Absorption Study

		X-ray Diffraction Study

		Infrared Absorption Study

		Raman Study

		Electron Microscopy

		Discussion

		Conclusion

	18.	CARBON NANOTUBES IN CHEMICAL VAPOUR	

DEPOSITION	

	19.	NANOSCALE DEEP INDENTATION	

		Simulation Methodology

		Results and Discussion

		Conclusion

	20.	REDUCTION OF NANOWIRES	

		Experimental Details

		Results and Discussions

		Summary and Conclusion

	21.	DISPERSION OF CARBON NANOTUBES	

		Experimental Details

		Purification and Dispersion of MWCNTs

		Preparation of Nanocomposite Films

		Carbon Nanotube Dispersion Study in Solution and in Nanocomposite Films

		Electrical Conductivity Measurement

		Results and Discussion

		MWCNT Dispersion in Solution

		Nanocomposite Preparation and Carbon Nanotube Distribution in Composite Films

		Electrical Conductivity Study of Nanocomposite Films

		Conclusion

	22.	CREATION OF CARBON ONIONS AND COILS	

		Experimental Details

		Result and Discussion

		Conclusions

	23.	MAGNETIC PROPERTIES OF NANOSPHERES	

		Experimental Details

		Results and Discussion

		Conclusion

	24.	LUMINESCENCE OF CRYSTALS NANORODS	

		Experimental Section

		Results and Discussion

		Conclusions

	25.	NANONECKLACE MORPHOLOGY	

		Experimental Details

		Growth of Cu-Pt Nanoparticles

		Growth of Cu-Pt Nanonecklace Nanowires

		Conclusions

	26.	OPTICAL PROPERTIES OF NANODOT ARRAYS	

		Experimental Details

		Results and Discussion

		Conclusions

	27.	GENERATION SPECTROSCOPY OF NANOPARTICLE MONOLAYER	

		Experimental Section

		Materials

		Synthesis of AuNPs

		Synthesis of Dense AuNPs Monolayer

		Dodecanethiol SAM Formation

		Characterization

		SFG Set-up

		Results and Discussion

		Conclusions

	28.	CHEMICAL DOPING WITH CARBON NANOTUBES	

		Experimental Details

		Results and Discussion 

		Summary

	29.	DIRECT-WRITE PROGRAMMING OF 	

NANOSCALE DEMULTIPLEXER ARRAYS	

	30.	POLY(N-ISOPROPYLACRYLAMIDE)	

NANOPARTICLES	

		Introduction 

		Experimental Details

		PNIPAM-coated Fe3O4@SiO4@CdTe Nanoparticles and ZnPcS Loading

		Biological Systems 

		PL and Fluorescence Measurements

		ZnPcS Released from the Nanoparticles in PBS Solution 

		ZnPcS Released from the Nanoparticles in the CHO Cells 

		Results and Discussion

		ZnPcS Embedded in the PNIPAM of Nanoparticles 

		Release of ZnPcS from the ZnPcS–loaded Nanoparticles in PBS Solution

		Release of ZnPcS from the ZnPcS-loaded Nanoparticles in CHO Cells

		Release of ZnPcS from the ZnPcS-loaded Nanoparticles in Zebra Fish 

		Movement of the Nanoparticles in Zebra Fish by the Magnetic Field Gradient 

		Phthalocyanines and PDT

		Conclusion

	31.	COBALT FERRITE NANOPARTICLES	

		Experimental Details

		Sythesis

		Characterization Methods

		Results and Discussion

		Fundamental Characteristics, Crystallite size Versus Coercivity and Remanence

		Mossbauer Spectra and Distribution of Cations

		Heating Efficiency from Calorimetric Measurements and ac 	

Hysteresis Loops

		Conclusions

	32.	Au NANOPARTICLES ON LIGHT-EMITTING POLYMERS

		Experimental Section

		Measurements

		Device Fabrication and Characterization

		Materials

		Synthesis of PDOFT-bis-4-thiol

		End-capping at AuNP onto PDOFT-bis-4-thiol (PDOFT-Au 10, PDOFT-Au15, PDOFT-Au 20 and PDOFT-Au 30)

		Results and Discussion

		Synthesis and Characterization

		Photophysical Properties

		Electroluminescent Properties and Current Density-Voltage-Luminescence (J-V-L) Characteristics of the PLED Devices

		Conclusions

	33.	CARBON NANOSTRUCTURE BASED NANOCOMPOSITES

		Experimental Details

		Results and Discussion

		Conclusions

	34.	Au NANOPARTICLE CHAINS	

		Experimental Results and Discussion

		Sample Preparation and Measuring System

		General Considerations on Dielectrophoresis 

		Dielectrophoresis on Flat Substrates

		Dielectrophoresis on V-groove-etched Substrates

		Discussion of Results on Patterned Substrates, Electric Field Numerical Calculation

		CONCLUSION

	35.	GOLD-SILICA NANOCOMPOSITES	

	36.	NANOPINS BY CHEMICAL VAPOUR DEPOSITION	

		Experimental Section

		Preparation

		Characterization

		Results and Discussion

		Conclusions

	37.	OXIDATION RESISTANT METAL NANOPARTICLES	

		Experimental Details

		Thermo-Gravimetric Studies

		Particle Size Reduction

		Synthesis and Coating of Metal Nanoparticles

		Results and Discussion

		Thermo-Gravimetric Analysis

		Fluidized Bed Processing

		Particle Size Reduction

		Passivation of Metal Nanoparticles by in situ ALD

		Conclusions 

	38.	MOLECULAR CARBON-ONIONS	

		Experimental Details

		Discussion of Results

		Conclusion

	39.	ATOMIC SCALE MANIPULATION	

		Tip-Surface Interaction

		Experimental Response

		Discussion and Conclusion

	40.	SILICONE NANOWIRES	

		Experimental Session

		Results and Discussion

		Conclusion

	41.	CARBON NANOFIBERS	

		Experimental Details

		Results

		Discussion and Conclusion

	42.	SINGLE-CRYSTALLINE NANOWIRES	

		Experiments

		Results and Discussion

		Conclusion

	43.	SILICONE OXIDE NANOSTRUCTURES	

		Experimental Details

		Results and Discussion

		Conclusion

	44.	A SQUARE TITANIUM NANOMESH	

		Experimental Details 

		Results and Discussion

		Conclusions

	45.	NANO-POROUS ANODIC ALUMINIUM OXIDE MEMBRANES

		Experimental Details

		Results and Discussion

		Conclusions	

	46.	Co NANOPARTICLES	

		Experimental Section

		Materials

		Synthesis and Assembly of Cobalt Nanoparticles

		Characterization

		Results and Discussion

		Conclusions

	47.	ZERO-BIAS CONDUCTANCE OF GOLD MOLECULAR 

JUNCTION	

		Methodology

		Results and Discussion

		Conclusion

	48.	ALL-INKJET-PRINTED ELECTRONICS OF METAL NANOPARTICLES

		Fabrication and Experimental Details

		Nanoparticle Solution Preparation

		Semi-conducting Polymer Preparation

		Organic Field Effect Transistor Fabrication Process and Characterization (Inkjet Printing of Nanoparticle Solution, Polymer Dielectric Layer and Semi-conducting Polymer)

		Results and Discussion

		Nanoparticle Sintering Characterization

		OFET Charactrization

		Summary

	49.	TRIODE TYPE CARBON NANOTUBE FIELD EMITTER

		Experimental Details

		Results and Discussion

		Conclusions	

	50.	PROTEIN AND POLYMER IMMOBILIZED NANOPARTICLES FOR BIOMEDICAL APPLICATIONS

		Methodology

		Chemicals and Materials

		Experimental Set-up

		Analyses

		Results and Discussion

		Protein Estimation

		Conjugation Studies

		Magnetic Studies

		Microscopy Studies

		Cytotoxicity Studies

		Leaching Studies

		Hyperthermia Studies

		Conclusion	

	51.	3D STRUCTURES OF NANOWIRES	

		Methods

		Nanowire Growth

		TEM Characterization

		Image Simulations

		Result

		Crystal Structure

		lmage Simulations

		Discussion

		Summary

	52.	SUPERIOR CONDUCTIVITY OF NANOPARTICLES	

		Experimental Details

		Synthesis of Nanocomposites

		Characterization

		Results and Discussion

		Conclusions

	53.	STRUCTURAL AND ELECTRONIC PROPERTIES OF ZnO 

NANOTUBES	

		Computational Method

		Results and Discussion

		Conclusions

	54.	SYNTHESIS OF NANOCRYSTALLINE CERAMIC POWDERS

		Experimental Procedure

		Results and Discussion 

		Nanocrystalline CeO2 Powders Through Glycine-Nitrate and Citrate-Nitrate Combustion

		Auto-Ignition Synthesis of Monophasic BaTi4O9 and Ba2Ti9O12 Powders

		Combustion Synthesis of TbO2, and MTbO3 (M = Ba and Sr)

		Conclusions	

	55.	NANOCLUSTERS ON POLYMER SURFACES	

		Organization of Nanoparticles on the Polymer Matrices: Why?

		Nanoclusters Organization on Polymers: How?

		Electrostatic Organization

		Covalent Organization

		Vander-Waals Organization

		Different Preparation Strategies

		Nanocomposites Versus Surface Functionalisation

		Selection of Polymers 

		Selection of Clusters 

		Metallic Nanoclusters

		Semi-conducting Nanoclusters

		Characterisation Techniques

		Selected Applications

		Catalytic Applications 

		Photovoltaic Applications 

		Biological Applications

		Limiations of Cluster Organization on Polymers

		Conclusion

Sample Chapters

Design of Protein Based Nanomachines

Introduction

Renowned Nanomachines of the Biological Cell Confirm Engineering Principles and Inspire Nanomachine Design

Definition of a Machine

 A combination of rigid or resistant bodies having definite motions and capable of performing useful work.

Proteins and protein based polymers constitute the resistant bodies of interest here. Proteins are polypeptides and protein based polymers are composed of repeating peptide sequences in which the repeating unit may be as small as a dipeptide or as large as hundreds of residues. The definite motions of protein arise from changing hydrophobic associations that result in deformations and relaxations of protein chain segments capable of performing mechanical work. The changing hydrophobic associations are also capable of performing a range of other forms of work most commonly chemical work.

A de novo design approach using elastic contractile model proteins gives rise to engineering principles

The approach to the elucidation of engineering principles required for the design of protein based nanomachines as reviewed in the following section began with a relatively simple repeating pentapeptide sequence from an extra cellular matrix protein. Then without recourse to an already known protein based machine de novo design involving stepwise introduction of compositional changes in elastic contractile model proteins resulted in the demonstration of diverse energy converting capacities. The approach of designing and characterizing elastic contractile model proteins allowed recognition of engineering principles that have now been used as demonstrated in the following section to describe the function of key intracellular protein machines. By this means engineering principles for design of protein based nanomachines have been developed and substantiated.

Nanomachines of living cell confirm engineering principles

Driving forces for cellular machines differ from those of man made macroscopic machines. The protein machines within the cell are of nanometer dimensions and require an aqueous milieu in which to function. These protein nanomachines are remarkable structures capable of operating at high efficiencies. In some cases they bear astonishing structural analogy to machines of the macroscopic world even though composed of very different rigid or resistant materials that operate by means of very different forces. The forces that dominate in protein based machines are not so familiar to the mechanical engineer. The forces of hydrophobic association/dissociation and those concerned with the extent of irreversible deformation of single protein chain segments replace gravitation and surface frictional loss of the macroscopic world. The interior of the living cell therefore provides the ultimate site for confirming model protein derived engineering principles for the design of protein based nanomachines.

The difficulty of determining engineering principles from cellular protein machines. The compositional complexity of the evolutionarily optimized protein nanomachine of the cell makes difficult a direct attack on elucidating the engineering principles. Rather a de novo design approach in which the energies and forces can be dissected by careful control of composition and selection of experimental method provides the opportunity one variable at a time to characterize the energies and forces involved in function. Elastic contractile model proteins capable of a phase transition unique to aqueous systems exhibit the properties essential for revealing the sought after engineering principles.

Engineering principles from designed elastic contractile model proteins confirmed by crystal structure in two key functional states of three vital cellular protein machines. Once a set of engineering principles is derived using elastic contractile model proteins these principles can be tested by detailed consideration of cellular protein machines for which crystal structural detail is available in critical functional states. In the present case the principles are remarkably demonstrated in Complex III of the electron transport chain of mitochondria that produces the proton gradient in the adenosine triphosphate (ATP) synthase of the inner mitochondrial membrane that uses the proton concentration gradient to produce nearly 90% of the ATP for an organism and in the myosin II motor of muscle contraction that uses ATP to produce motion essential to function of the organism.

Nanomachine designs inspired by intracellular protein constructs and properties

An elastic extracellular protein provided the starting point that led to the design of energy converting elastic contractile model proteins. On the other hand the elastic intracellular protein titin composed of a linear array of repeating small globular units functions within the muscle cell as a series of shock absorbing elements that irreversibly absorb energy of deformation. When a single globular element is combined with subtending elastic contractile model protein the potential exists for the detection of single molecular events. As seen by single chain force extension studies using the atomic force micro scope (AFM) a single chain of titin globular elements gives a sawtooth profile. Each sawtooth represents a single unfolding globular protein element irreversibly absorbing a unique packet of deformation energy. On the other hand the elastic contractile model proteins give a simple monotonic curve in the AFM single chain force extension curve. By the design of a single globular sensing element subtended by elastic contractile sequences a single chain force extension curve is obtained with a single sawtooth. As a single interaction with the globular element can change the characteristic sawtooth for that globular element it becomes a sensing element for detection of that interaction.

De Novo Design of Diverse Elastic Contractile Protein Machines

The potential for more effective design of new protein based nanomachines arises from the previous de novo design of elastic contractile model proteins capable of performing the set of energy conversions familiar in living organisms. The set of energy conversions involves the intensive variables of mechanical force pressure chemical potential temperature electrochemical potential and electromagnetic radiation covering the frequency range from the ultraviolet to the acoustic. The interconversions of energy involving the 6 intensive variables result in 15 possible pair wise energy conversions. When chemo chemical transduction (the conversion of one chemical energy into another) electro electrical transduction (the use of the reduction of one redox group to change the reduction potential of another redox group) and energy conversions between different frequencies of the electromagnetic radiation spectra are included the number of 15 expands to 18 classes of pair wise energy conversions.

The initial elastic contractile model protein

The starting protein based polymer was found as a repeating pentapeptide sequence in the mammalian elastic protein elastin. The repeating pentapeptide sequence is glycine valine glycine valine proline or Gly Val Gly Val Pro or simply GVGVP which in bovine elastin is found to repeat as many as 11 times in a single unbroken sequence. High molecular weight protein based polymers of this repeating sequence (GVGVP)n were found to be soluble in water at temperatures below 25°C and phase separate on raising the temperature above 25°C to form a more ordered viscoelastic and filamentous state. When cross linked for example by  irradiation the resulting elastic sheets swell on lowering the temperature and contract on raising the temperature above 25ºC and do so when loaded with a weight. Thus the cross linked polymer is capable of thermo mechanical transduction.

Changing hydrophobicity to change temperature range for contraction

Changing the polymer composition by addition of a CH2 group per pentamer achieved by replacing a Val residue by an isoleucine (Ile I) residue makes the polymer more hydrophobic and the contraction begins at 10ºC. When deleting two CH2 groups by replacing a Val residue by an alanine (Ala A) residue the contraction begins on raising the temperature above 45°C. Accordingly the temperature at which contraction occurs becomes lower as a polymer becomes more hydrophobic and higher as a polymer becomes less hydrophobic.

Introduction of functional groups with different states of hydrophobicity

Now it becomes possible to change the temperature of the phase separation by substitution of an aliphatic amino acid residue by an amino acid residue with a functional side chain. For example the charged carboxylate of glutamic acid (Glu E) or of aspartic acid (Asp D) or the charged amino function of lysine (Lys K) are less hydrophobic and more polar than the uncharged (more hydrophobic) state of the side chain. Accordingly changing the pH to form the uncharged side chain lowers the temperature of the transition. When at an intermediate temperature therefore neutralizing the charged side chain lowers the temperature of the transition and drives contraction. Thus the suitably substituted cross linked polymer becomes capable of efficient chemo mechanical transduction. Similarly a redox function can be bound to the protein based polymer. Since the oxidized state can be more polar and the reduced state can be more hydrophobic designed polymers capable of electro mechanical transduction result.

Phenomenological control of diverse energy conversions

Thus de novo designs of diverse energy conversions utilizing elastic contractile model proteins are achieved pheno menologically by exercising design control of the temperature at which hydrophobic association occurs. These protein based motors were not simply derivative of then known biological machines. Subsequent extensive analysis of these phenomenological designs gave rise to new understandings of the factors that control hydrophobic association/dissociation and the nature of entropic elasticity. These new understandings referred to as the hydrophobic and elastic consilient mechanisms become the engineering principles for the design of diverse protein based nanomachines.

Relevance to biology s protein based machines

Coherence of phenomena between designed elastic contractile model protein machines and biology s protein machines. When considering coherence of phenomena between the behaviours of elastic contractile model proteins designed for energy conversion and the natural energy converting proteins of the cell the hydrophobically associated state is identified with the contracted (rigor) state of a muscle protein or the taut tense T state of a globular protein such as hemoglobin. Formation of this contracted or T state occurs with loss of hydration. As concerns muscle contraction clinically there are recognized acid rigor (association of protein caused by acids) calcium rigor (contraction caused by excess calcium ion) heat rigor (heating that drives hydrophobic association) and rigor mortis (contraction on loss of ATP e.g. dephosphorylation). These muscle phenomena have demonstrable correlation with the elastic contractile model proteins designed for energy conversion.

Another well characterized protein is hemoglobin with its T (taut) state and R (relaxed) state. Increased temperature favours the T state binding polar oxygen favours the R state that forms with the uptake of water and ionpairing decreases charge to favour the T state. Thus there exists a clear coherence of phenomena.

Remarkable positive cooperativity of designed elastic contractile model proteins when compared to biology s renowned protein machines. These elastic contractile model proteins of translational symmetry are designed as chemo mechanical transductional model proteins that exhibit positive cooperativities with Hill coefficients as large as 8. This is a greater positive cooperativity than seen by Monod and others when concerned with symmetries of associating globular proteins. This was not expected from the prevailing view of cooperativity. As stated by Monod  One may set aside the simple problem of fibrous proteins. Being used as scaffolding shrouds or halyards they fulfill these requirements by adopting relatively simple types of translational symmetries.

In the popular hemoglobin example the Hill coefficient found for the oxygen binding curve is 3.2 which indicates a degree of positive cooperativity much less than that obtained with the most efficient design of elastic contractile model proteins. Thus protein structure with translational symmetry is designed to exhibit positive cooperativity that is central to efficient function (e.g. energy conversion) of nanomachines and exceeds the positive cooperativity considered so remarkable in protein machines of biology.

Direct demonstrations of relevance of the hydrophobic and elastic consilient mechanisms to biology s protein machines. Even though these demonstrations of energy conversion by de novo designed elastic contractile model proteins proceeded visually and convincingly with the above noted coherence of phenomena suggestions that biology s protein based machines functioned similarly were not well received by specialists in their particular protein machine. These new understandings nonetheless have now been demonstrated to be significant in three key classes of biological energy conversion the formation of the proton gradient in the mitochondrion the use of the proton gradient to produce ATP by ATP synthase and the use of ATP to produce motion essential to life. Thus the important new engineering principles did not arise from examination of the more complex site localized and evolutionarily optimized energy converting machines of biology. Instead the new engineering principles arose from the design preparation characterization and data analysis of relatively simple model proteins. In doing so the model proteins could be designed to perform the energy conversions of biology by simple changes made in an elastic repeating sequence derived from the mammalian elastic fiber a fiber not recognized as an energy converting machine of biology.

Hydrophobic and Elastic Consilient Mechanisms Definitions

Definition of consilience. Consilience reflects the presence of a pervasive basic law of nature that underlies otherwise seemingly disparate phenomena. In this case the phenomena involve a diverse set of energy conversions with an underlying common mechanism a common groundwork of explanation in the words of E.O. Wilson. Accordingly the common groundwork of explanation for diverse energy conversions as discovered using designed elastic contractile model proteins is called a consilient mechanism.

The hydrophobic and elastic consilient mechanisms. Two inter linked consilient mechanisms have been identified in studies on the de novo designed elastic contractile model protein machines and also observed in the energy conversion of biology s protein machines. These are the hydrophobic and elastic consilient mechanisms. They derive their consilience from a general applicability in the former case to all amphiphilic polymers in water and in the latter case to all polymers of whatever composition containing chain segments with a backbone mobility that can become damped on deformation whether by extension compression or repulsion.

Metastabilities in Nanocrystalline Silicon

Porous silicon (PS) is a form of nanocrystalline. Silicon and has attracted quite a lot of attention because of the possibility of it s wide range of applications in optoelectronic devices gas sensors vapour sensors and chemical sensors. PS consists of nanometer size crystallites of silicon and shows photoluminescence (PL) in the visible in room temperature. The as prepared PS surfaces are naturally terminated with a covalently bonded monolayer of hydrogen but this monolayer does not give protection against chemical absorption and exposure to light. Further it has been found that after short light exposures the dark current (DC) is higher than the annealed state dark current. This higher dark current called persistent photocurrent (PPC) persists for several hours even at room temperature. It has been reported that the LS decreases PL and increases electron spin resonance (ESR). Some of these changes are partly reversible with annealing. Some authors have found that PL does not change when the light soaking is done with the sample in vacuum or in nitrogen atmosphere. On the other hand Matsumoto have reported that for long exposures the dangling bond density (ESR) increases and PL decreases for their sample. Therefore there is a need to study these phenomena more closely.

In this paper it has been reported for the first time that the dangling bond density in the nanocrystalline silicon decreases after light exposures of short durations. This is accompanied by an increase in DC photocurrent (PC) and PL. Rapid cooling from high temperatures to room temperature also gives an increase in DC PC and PL and a decrease in ESR signal. Such an increase in DC after fast cooling has been observed by various authors in doped hydrogenated amorphous silicon (a Si H) also. However no decrease in ESR has been reported for a Si H. Further for long exposures the changes observed are in the opposite direction to the short exposures and are similar to the well known Staebler Wronski effect in a Si H. Authors suggest that the metastable changes caused by the thermal quenching and light exposures might be related to the structural changes in PS.

Experimental Procedure

PS layers were prepared by the standard method of electrochemical anodization of boron doped (100) crystalline silicon wafers having resistivity between 0.6 to 1.0   cm. The electrolyte was HF (49%) mixed with equal volume of ethanol. A current density  20 mA/cm2 was used and a two hours anodization yielded about 70 µm thick PS. Free standing PS were also made by passing 1A current for a few minutes after 2 h of anodization to lift off the PS from the silicon wafer. These gave flakes of size = 2 × 5 mm. After anodization PS was rinsed thoroughly in ethanol to remove HF and dried in air. Freestanding PS samples were mounted on Corning 7059 glass substrate by putting silver paint at the two ends of the sample which also served as electrodes for current measurements. Electrical measurements done on the free standing PS gave results similar to the PS samples attached to the silicon substrate. For the PL and ESR measurements PS removed from the Si wafer in the form of flakes was sealed in 10 1 torr helium atmosphere in a quartz tube. The samples were annealed at 150°C for 1 h in vacuum   10–6 torr for removing the effect of previous light exposures if any and slowly cooled (rate   0.5 K/min) to room temperature (state A). ESR was measured using a X band (Varian E 3) spectrometer at microwave power of 5 mW. For PL the sample was excited by a 15 mW He Ne laser (632 nm) and the emitted light was analyzed using a grating spectrometer and a CCD detector. A bias of 40 V was applied for the DC and PC measurements. The samples showed a symmetric sub ohmic I V behaviour upto this voltaged. For thermal quenching experiments the samples were heated in vacuum (10–6torr) at 150°C for one hour. Then the heater was switched off and chilled water was circulated without breaking the vacuum through the copper block upon which the sample had been mounted using silver paint. Using this set up we could obtain cooling rates upto 400 K/min.

Light soaking was done in vacuum using heat filtered white light from a 250W tungsten halogen lamp kept at a distance of about 15 Cm. X ray diffraction and atomic force microscopy (AFM) show that our PS consists of crystallites of sizes 2 5 nm and bigger. Our Raman measurements show the presence of a Si H (broad peak ~480cm 1) along with a nanocrystalline peak (~512 cm 1) whose position and width depend upon the size distribution of crystallites and the stress present in the porous silicon.

Results

Figure 1 shows the ESR signal of our PS in the annealed state (state A). This ESR signal is asymmetric and is similar to that reported by others. This can be fitted to three signals one isotropic signal with g 2.0055 ± 0.0006 (width ~ 6.4G ± 0.5G) corresponding to the dangling bonds in a Si and two anisotropic signals having g   2.0081 ± 0.0006 (width ~ 1.5G±0.5G) and g1 2.0028 ± 0.0006 (width ~ 1.8G±0.5G). The last two have been attributed to the dangling bonds in PS by some authors.

Fig. 2 shows the variation in current upon light exposures of durations varying between 30s and 4500s. After switching off the light the dark current reaches a value (B1 B8) which is higher than the annealed state (state A) dark current. For short exposures (upto 2700s) the excess DC increases with the duration of exposure (B1 B6 Fig. 2) but start decreasing for long exposures (> 3600 s B7 B8 Fig. 2). For very long exposures (> 6h not shown) the final state DC value is lower than the state A. This is similar to the Staebler Wronski effect in a Si H. The excess dark current persists for several hours even at room temperature.

Fig. 3 shows the effect of exposing the sample to infrared light ( 3600 s) exposures with a maximum at about 2700s exposure time. For the 900s exposure PL increases by about a factor of 2 and ESR decreases by   70% compared to the initial state A. Also it is seen that for very long exposures ESR increases with a decrease in DC PC and PL. Interestingly ESR shows a minimum at about the same exposure duration (2700s) at which DC PC and PL show a maximum.

Let us now look at the thermal quenching results. Fast cooling from I50ºC to room temperature (400 K/min) brings PS to another metastable state (C) which has higher DC PC and PL than the annealed state A. This is also accompanied by a decrease in the ESR signal. The state A can be recovered by annealing at 150°C (1h) and slow cooling but not by IR exposure. Table 1 shows the values of DC PC PL and ESR signal before (state A) and after rapid thermal quenching (state C).

It might be mentioned that the position and shape of the PL and ESR signals do not change significantly after various treatments. It is noted that the increase in DC PC and PL is always accompanied by a decrease in ESR and vice versa. Hence there is an anti correlation between DC PC PPC and PL on one hand and ESR on the other.

Discussion

The decrease in the ESR signal accompanies an increase in PC and PL for short exposures (