Bio Molecular Materials

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Cover Illustrations (from top):

Molecular graphics representation looking into the channel of the a hemolysin pore. Song et al.,1996 (Figure 24).

Complexation of F-actin and cationic lipids leads to the hierarchical self-assembly of a network oftubules; shown here in cross-section. Wong 2000 (Figure 9).

Depiction of an array of hybrid nanodevices powered by F1-ATPase. Soong et al., 2000 (Figure 1).

Electronmicrograph, after fixation, of neuron from the A cluster of the pedal ganglia in L. stagnalisimmobilized within a picket fence of polyimide after 3 days in culture on silicon chip. (Scale bar =20 mm.). Zeck and Fromherz 2001 (Figure 16).


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Biomolecular Materials

Report of the January 13-15, 2002 WorkshopSupported by the Basic Energy Sciences

Advisory Committee

U.S. Department of Energy

Co-Chairs:

Mark D. AlperMaterials Sciences Division

Lawrence Berkeley National Laboratoryand

Department of Molecular and Cell BiologyUniversity of California at BerkeleyBerkeley, CA 94720

Samuel I. StuppDepartment of Materials Science and Engineering

Department of ChemistryFeinberg School of Medicine

Northwestern UniversityEvanston, IL 60208

This work was supported by the Director, Office of Science, Office of Basic Energy Sciences, of the U.S.Department of Energy under contract DE-AC03-76SF00098


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Table of Contents

Executive Summary...........................................................................................................................................iForeword ............................................................................................................................................................v

1. Introduction...................................................................................................................................................12. What Does Biology Offer.............................................................................................................................42.1 Introduction....................................................................................................................................4

2.1.1 Adaptation to the Environment........................................................................................42.1.2 Amplification of Signals.....................................................................................................42.1.3 Atomic Level Control of Structure...................................................................................42.1.4 Benign Processing. ..............................................................................................................52.1.5 Color. ..................................................................................................................................... 52.1.6 Combinatorial Synthesis....................................................................................................52.1.7 Computation. .......................................................................................................................52.1.8 Conformational Change..................................................................................................... 62.1.9 Control of Interfaces. ..........................................................................................................62.1.10 Control of Polymer Properties........................................................................................6

2.1.11 Energy Conversion. ..........................................................................................................82.1.12 Enzymes..............................................................................................................................82.1.13 Evolution.............................................................................................................................82.1.14 Extreme Environments.....................................................................................................92.1.15 Hierarchical Construction................................................................................................92.1.16 Lightweight Materials. ..................................................................................................... 92.1.17 Lubricants. .......................................................................................................................... 92.1.18 Mass Production..............................................................................................................102.1.19 Materials Recycling.........................................................................................................102.1.20 Membranes.......................................................................................................................102.1.21 Model Materials for Studies of Basic Materials Physics...........................................102.1.22 Molecular Recognition. ..................................................................................................11

2.1.23 Motors, Rotors, Pumps, Transporters, Tractors, Springs, Switches, Ratchets. ....112.1.24 Multi-Functional Materials............................................................................................122.1.25 Organic Synthesis............................................................................................................132.1.26 Optical Systems. ..............................................................................................................132.1.27 Self-Assembly. .................................................................................................................132.1.28 Self Healing, Repair, Damage and Fault Resistance or Tolerance. ........................ 142.1.29 Signal Transduction........................................................................................................142.1.30 Smart Materials/Sensors. ..............................................................................................142.1.31 Structural Materials. .......................................................................................................152.1.32 Systems..............................................................................................................................162.1.33 Template Directed Synthesis.........................................................................................162.1.34 Transport Systems...........................................................................................................17

3. Self-Assembled, Templated and Hierarchical Structures....................................................................18

3.1 Introduction..................................................................................................................................183.2 Organic Materials........................................................................................................................19

3.2.1 DNA-Based Materials.......................................................................................................193.2.2 Polymer-Organic Hybrid Structures. ............................................................................213.2.3 Lipid-Protein-Nucleic Acid Hybrid Structures. ..........................................................223.2.4 Biomolecular Materials in Microchannels.................................................................... 23

3.3 Organic-Inorganic Hybrid Structures. ....................................................................................233.3.1 Natural Mineralized Tissues........................................................................................... 233.3.2 Polymer-Directed Mineralized Composites.................................................................243.3.3 DNA-Inorganic Hybrids..................................................................................................253.3.4 Protein-Inorganic Hybrids...............................................................................................27

3.4 Abiological Molecules Mimicking Biological Structures.....................................................27


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3.4.1 Colloidal Particles with a Valence..................................................................................273.4.2 Hydrophilic/Hydrophobic Coatings on Inorganic Materials...................................28

4. The Living Cell in Hybrid Materials Systems........................................................................................294.1 Introduction..................................................................................................................................294.2 Metabolic Engineering................................................................................................................304.3 Engineering the Cell/Materials Interface. ..............................................................................324.4 Artificial Cells...............................................................................................................................35

4.5 Model System Cell-Based Biosensors...................................................................................355. Biomolecular Functional Systems ............................................................................................................375.1 Introduction..................................................................................................................................375.2 Energy Transducing Membranes and Processes...................................................................385.3 Motors, Rotors, Ratchets, Switches. .........................................................................................395.4 Enzymes. .......................................................................................................................................425.5 Pores, Gates, Channels. ..............................................................................................................43

6. Promise and Challenges.............................................................................................................................45

References .........................................................................................................................................................47


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Executive Summary

The Office of Basic Energy Sciences in the

Department of Energy Office of Science, andthe Basic Energy Sciences AdvisoryCommittee convened a workshop in January,2002 to explore the potential impact of biologyon the physical sciences, in particular thematerials and chemical sciences.

Twenty-two scientists from around the nationand the world met to discuss the way that themolecules, structures, processes and conceptsof the biological world could be used or

mimicked in designing novel materials,processes or devices of potential practicalsignificance. The emphasis was on basicresearch, although the long-term goal is, inaddition to increased knowledge, thedevelopment of applications to further themission of the Department of Energy.

The charge to the workshop was to identifythe most important and potentially fruitful

areas of research in the field of Biomolecular

Materials and to identify challenges that mustbe overcome to achieve success. This reportsummarizes the response of the workshopparticipants to this charge, and provides, byway of example, a description of progress that

has been made in selected areas of the field.

The participants agreed on severalconclusions. First and foremost, they agreed

that:

The world of biology offers an

extraordinary source of molecules andinspiration for the development of newmaterials, devices and processes. Progressin research in a number of areas in this

field has been rapid and the panel foreseesa revolutionary impact of the linkage ofbiology and materials science on scienceand technology in general, and the missionof the Department of Energy in particular.

In particular the panelists agreed that:

The interest of the Department of Energy

in biomolecular materials and biologicalprocesses is very broad. There is a need forlighter and stronger materials to improve

fuel economy. There is a need forfunctional materials to control transportacross membranes, to make separationsand purification processes more efficient.There is a need to increase energyefficiency by using low temperature

processes to make materials. There is aneed for energy producing processes that

can convert light, carbon dioxide, andwater to high-density fuels and therebydecrease, at least to some extent, ourdependence on fossil fuels. Finally thehigh specificity of biological reactions,

producing little or no side products, andthe inherent biodegradability ofbiological systems strongly suggest thatthese systems need to be explored by DOE

for their potential beneficial effects on theenvironment.

Having agreed on these principles, theparticipants stepped back to explore potentialresearch directions in the field. The world of

biology is immense. As described in Section 2of this report, living organisms perform anextraordinary number of functions, virtuallyall of which can be seen to have relevance tomaterials, processes or devices. Some of theseimpacts have already been explored, at least tosome extent, most have not. At this stage anoutline of productive directions in the field

can be identified only through broad brushstrokes.

Specifically, the participants felt that a DOEprogram in this area should focus on thedevelopment of a greater understanding of theunderlying biology, and tools to manipulate

biological systems both in vitro and in vivorather than on the attempted identification ofnarrowly defined applications or devices. The


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field is too immature to be subject to arbitrarylimitations on research and the exclusion ofareas that could have great impact.

Future Directions.

These limitations aside, the group did respond

to the charge and develop a series ofrecommendations. Three major areas ofresearch were identified as central to theexploitation of biology for the physicalsciences. Sections 3, 4 and 5 in this report aredevoted to those areas.

Self Assembled, Templated and Hierarchical

Structures. Biology acts at the nanoscale,synthesizing and manipulating molecules withdimensions as small as tenths of nanometers.

Through successive rounds of complexationand linkage of these molecules, it developsstructures on the meter length scale. All of thisis accomplished without conscious direction.Understanding and control of the processesinvolved in this self-fabrication are critical tothe successful exploitation of biology. This isdiscussed in Section 3.

The Living Cell in Hybrid Materials Systems.

Despite the extraordinary advances in the past

decade in our understanding of biologicalsystems, many remain far too complex for usto use, mimic or recreate. As a result, it must

be expected that for well into the future, manyof the cellular functions we wish to exploit willhave to be performed by intact, living cellsthemselves. Thus, methods to incorporateliving cells or tissues into non-living structuresand devices, and to have them communicatewith those structures and devices will berequired. This area is discussed in Section 4.

Biomolecular Functional Systems.Livingsystems perform a wide variety of functionsthat could be controlled and used in vitro.Critical to this goal is the thoroughunderstanding of the molecular components ofthese systems and how they interact, leadingto our ability to manipulate those componentsand interactions. In some cases, intact cells (asfound in nature or altered by design) will need

to be used (see Section 4). However, in othercases, this will involve removal of theparticular functional system from theorganism. In still other cases it will involve therecreation or mimicking of it outside theorganism. This area is discussed in Section 5.

Workshop participants also discussed thechallenges and impediments that stand in theway of our attaining the goal of fullyexploiting biology in the physical sciences.Some are cultural, others are scientific andtechnical.

Barriers.

Cultural Challenges. Those who know thebiology, the biologists, are, more often than

not, descriptive scientists, whose goal is toidentify the molecular components of

biological systems and understand how theywork together to produce the observedfunction. They are, in general, not focused onsynthesis or creation of these molecules orsystems, or mimics of them, nor are theyfocused on their adaptation to functionalsystems working outside the organism. Thisculture has changed somewhat in recent yearswith the focus on the molecular basis ofdisease and the identification of targets andthen lead compounds for pharmaceuticals.The number of biologists with an explicitinterest in the non-biomedical application oftheir systems however, remains small.

1. On the other hand, until recently,chemists, physicists and materialsscientists, who traditionally do have aninterest in creating materials, processesand devices, have had little formal

training in the biological sciences. A verysophisticated understanding of a field isrequired to exploit it, thus trulyinterdisciplinary training needs to besignificantly enhanced. We are alreadyseeing this, with the organization ofdepartments and groups in chemical

biology and the significant increase inthe enrollment of chemistry, physics andmaterials science students in biological


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science classes.

2. The application of biology to the physicalsciences is by definition amultidisciplinary activity requiringextensive collaboration. There have,

however, historically been fewcollaborations between biologists andmaterials scientists, although there have

been some with physicists and more withchemists.

Scientific and Technical Challenges.

1. Biological systems are not generallyrobust. They function best at roomtemperature, although some have beenfound in freezing or boiling

environments. They are subject todeterioration in non-sterile environments.They generally require an aqueous milieu.Thus issues of the adaptation of biologicalsystems to the harsher environments ofmaterials, processes and devices, andtheir strengthening for long-term viabilitymust be addressed.

2. We do not, even after the revolutionaryadvances of the past few decades,

understand biological systems wellenough to control and manipulate them.Basic research into the molecules,structures and processes is required

before adaptation and mimicry can be

achieved. Processes such as molecularrecognition, self-assembly, proteinfolding, energy transduction, nervoussystem function must be furtherelucidated.

3.

Biological systems are, at their highestlevel of function, exceptionally complex,with large numbers of componentsinteracting in very specific ways. Many

systems are multifunctional and highlyresponsive to their environment. Issues ofsimplification or of precise assembly ofmulticomponent complex objects withoutsacrificing their function need to beaddressed

4. Theory, simulation and modeling havenot been applied to biological systems tothe extent that they have become routinein the materials sciences, physics andchemistry. This field must be developed.

5. Characterization tools, especially at thesingle molecule level need to bedeveloped. This is a particularlychallenging issue because the NationalInstitutes of Health, the primary federalagency for support of biological and bio-medical research has, in the past, notemphasized instrument development tothe extent that the DOE programs have.

Recommendations.

Program Relevance.In view of what hasrecently developed into a generally recognizedopinion that biology offers a rich source ofstructures, functions and inspiration for thedevelopment of novel materials, processes anddevices support for this research should be acomponent of the broad Office of Basic EnergySciences Program.

Broad Support.The field is in its early stagesand is not as well defined as other areas. Thus,

although it is recommended that support befocused in the three areas identified in thisreport, it should be broadly applied. Goodideas in other areas proposed by investigatorswith good track records should be supportedas well. There should not be an emphasis onpicking winning applications because it issimply too difficult to reliably identify them atthis time.

Support of the Underlying Biology.Basic

research focused on understanding thebiological structures and processes in areasthat show potential for applicationssupporting the DOE mission should besupported.

Multidisplinary Teams.Research undertaken bymultidisciplinary teams across the spectrum of

materials science, physics, chemistry andbiology should be encouraged but not


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artificially arranged.

Training.Research that involves the training ofstudents and postdocs in multiple disciplines,preferably co-advised by two or more seniorinvestigators representing different relevant

disciplines, should be encouraged withoutsacrificing the students thorough studieswithin the individual disciplines.

Long-Term Investment.Returns, in terms of

functioning materials, processes or devicesshould not be expected in the very short term,

although it can reasonably be assumed thatapplications will, as they have already, ariseunexpectedly.

The workshop participants wish to thank andacknowledge Patricia Dehmer, Director of the

Office of Basic Energy Sciences; Iran Thomas,Director of the Division of Materials Sciences;and the Basic Energy Sciences AdvisoryCommittee for their vision in identifying

biomolecular materials as an important newfield and in sponsoring this workshop.


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Foreword

In 1999, the Basic Energy Sciences AdvisoryCommittee (BESAC) convened a workshop to

design a roadmap for research in complexsystems. The report of the workshop, ComplexSystems Science for the 21st Century, outlined anexciting science agenda that both integrated thedisciplines of physics, materials sciences,chemistry, biology, and high-performancecomputing, and also could be built on thefoundations that had been put in place a yearbefore by theNationalNanotechnolo

gy Initiative.In June 2001,Dr. JamesDecker, ActingDirector of theOffice ofScience, U.S.Department ofEnergy, askedBESAC to helprefine that

researchagenda. Inthe worldbeyond nano,Dr. Deckerwrote in hischarge letter tothe Chair ofBESAC, itwill benecessary to

use atoms,molecules, andnanoscalematerials as the building blocks for largersupramolecules and hierarchical assemblies. Aswas described in Complex Systems Science forthe 21st Century, the promise is nanometer-scale(and larger) chemical factories, molecularpumps, and sensors. This has the potential toprovide new routes to high-performance

materials such as adhesives and composites,highly specific membrane and filtration

systems, low-friction bearings, wear-resistantmaterials, high-strength lightweight materials,photosynthetic materials with built-in energystorage devices, and much more. Themagnitude of the challenge is perhaps moredaunting than any faced before by thesedisciplines. I would greatly appreciate BESACshelp in defining these challenges.

BESACconsidered a

number ofworkshoptopics thatweresuggested bythis charge.One involvedtheexploration ofbiomolecularmaterials,

materialsbased onbiologicalstructures andprinciples butwhose studyand useencompassesresearch at theinterfacesamong the

manydisciplinesenumerated in

Dr. Deckers charge. As a result of the rapidlyincreasing interest in research applying theprinciples and structures of biological systemsto the physical sciences, this BESAC workshopwas held in San Diego, California, January 13-15, 2002. Mark D. Alper of the LawrenceBerkeley National Laboratory and the

Table 1. Speakers

Mark AlperLawrence Berkeley National Laboratory/

University of California at BerkeleySamuel Stupp Northwestern University

Lia Addadi Weizmann Institute of Science

Paul AlivisatosUniversity of California at Berkeley/

Lawrence Berkeley National LaboratoryHagan Bayley Texas A&M University

Angela Belcher University of Texas at Austin

Carolyn BertozziUniversity of California at Berkeley/

Lawrence Berkeley National Laboratory

Jean FrchetUniversity of California at Berkeley/

Lawrence Berkeley National LaboratoryReza Ghadiri Scripps Research Institute

Wolfgang Knoll Max-Planck Institute for Polymer Research,MainzChad Mirkin Northwestern University

Carlo Montemagno University of California at Los Angeles

Thomas Moore Arizona State University

Daniel Morse University of California at Santa Barbara

David Nelson Harvard University

Cyrus Safinya University of California at Santa Barbara

Peter Schultz Scripps Research Institute

Nadrian Seeman New York University

Douglas Smith University of California at San Diego

Viola Vogel University of WashingtonUlrich Wiesner Cornell University

X. Sunney Xie Harvard University


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University of California at Berkeley and SamuelI. Stupp of Northwestern University were co-chairs. Twenty-two leaders (Table 1) in a widevariety of areas linking biology, physics,materials sciences, and chemistry were invitedto discuss progress in the field, define

promising future directions and identifybarriers to their pursuits. Thirty otherparticipants attended. The agenda for themeeting is shown in Table 2. This report of thepresentations and discussion at the workshop

begins with an introduction followed by a

discussion outlining the wide potential forresearch in the field, identifying molecules,structures and principles in biology that couldreasonably be applied to solving problemsimportant to the Department. This is followed

by three sections discussing areas in this broad

field the workshop attendees felt were ofparticular interest at this time, and alsoamenable for productive research, given ourpresent knowledge of the underlying biologyand the tools and techniques existing for theirmanipulation.

Table 2. Agenda.

Doubletree Golf Resort San Diego, 14455 Penasquitas Drive, San Diego, CA 92129

Sunday, January 13, 2002

7:30 pm Speakers DinnerMonday, January 14, 2002

8:00 am WelcomePat Dehmer, Iran ThomasDOE/BES

8:10 am Introduction Mark Alper

8:20 am Workshop Organization Samuel Stupp

Bio-Inorganic Systems Angela Belcher , Chair

8:30 am Opportunities at the Biology/Materials Interface Paul Alivisatos

8:50 amSilicon Biotechnology: Proteins, Genes andBiomolecular Mechanisms

Daniel Morse

9:10 amControl of Minerals by Organisms - Nanometers toMillimeters and More

Lia Addadi

9:50 am Protein Control of Inorganic Materials Angela Belcher

10:10 am Towards a Tetravalent Chemistry of Colloids David Nelson

10:30 am Discussion

Biomimetics and Biomolecular Self Assembly Sam Stupp, Chair

11:00 am Self-Assembly of Cell Cytoskeletal Proteins Samuel Stupp

11:20 amFunctional Materials Design, System Construction,and Computation. Adventures in Information Space &

Complexity

Reza Ghadiri

11:40 amSupramolecular Assembly of Cell CytoskeletalProteins

Cyrus Safinya

12:00 pm Working Lunch

1:00 pm DNA Nanotechnology Nadrian Seeman

1:20 pmFunctional 2-3 Dimensional Bio-inorganicNanostructures

Chad Mirkin

1:40 pm Discussion


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Biomolecular Functional Systems Mark Alper, Chair

2:20 pmSignal Transduction and Active Transport at theNanoscale

Viola Vogel

2:40 pmDendridic Macromolecules and Bioinspired Functional

Nanoscale Assemblies

Jean Frchet

3:00 pmEngineered Protein Pores with Applications inBiotechnology

Hagan Bayley

3:20 pmProviding Energy of Biomolecular Processes with anArtificial Photosynthetic Membrane

Thomas Moore

3:40 pm Using Biology to Make New Materials Peter Schultz

4:00 pm Discussion

6:30 pm Working Dinner

Tuesday, January 15, 2002

8:30 am Discussion

Cell Engineering and Cells in Artificial Environments C. Bertozzi, Chair

9:00 am NanoEngineering Biotextiles Carlo Montemagno

9:20 amProbing Biochemical Reactions: From Single Moleculesto Single Cells

Sunney Xie

9:40 amSupramolecular (Bio-) Functional InterfacialArchitectures

Wolfgang Knoll

10:00 am Artificial and Biological Machines Carolyn Bertozzi

10:20 am Structure and Shape Control in Hybrid Materials Ulrich Wiesner

10:30 amManipulation and Visualization of SingleBiomolecules: Applications in Materials Science and

Biophysics

Doug Smith

10:40 am Discussion

12:00 pm Working lunch

1:30 pm Individual Group Discussions

4:00 pm Group reports Chairs

6:00 pm Dinner


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1.Introduction

Mankind has made use of biological materialsfor millennia. Through most of this time, theywere used as nature made them. Homes were

built with wood, straw, leaves; ropes werefashioned from vines; tools were shaped from

bone, antler, horn; living yeast was used tocatalytically ferment alcohol or to leaven

bread. More recently, mankind sought toextend his exploitation of nature by mimickingher principles, building, for example, bird-likewings to free him from the ground, and

Velcro, reported to have been inspired by themechanism by which burred seed shells stickto a dogs coat (Ball 1999).

For most of recorded time, however, naturesliving systems were regarded as special. Itwas not until the 19th century that the principleof the vital force was finally set aside andthe concept of making biological moleculesand employing biological processes outsidethe living cell was demonstrated. The

extracellular synthesis of urea from cyanate byFriedrich Whler in 1828 demonstrated thatlife was not a requirement for the synthesisof molecules found naturally only in livingorganisms. [As Whler wrote to Berzelius, Imust tell you that I can make urea without theuse of kidneys, either man or dog.] Yearslater, in 1897, Buchner demonstrated that theentire 12 step/12 enzyme pathway convertingglucose to ethanol could proceed in extractsfrom yeast cells that had been killed and

completely disrupted through grinding withsand.

The impact of these discoveries on materialsscience was immense although not, to thisday, fully exploited. Nature, throughevolution the extraordinary linkage ofnatural variation and selection has, over

billions of years, learned to develop thousandsof extraordinarily sophisticated materials and

chemical processes that can serve us well inour search for the advanced materials requiredto meet our demand for improvements inproductivity, conservation, and safety. As inother fields, opportunities often lie untappeduntil the need and the tools to exploit themarise. In this area, biomedical applicationscame first driven by human healthconsiderations. But the time for applications tothe physical sciences is now here, and the pastfew years have seen a burgeoning of our

interest in pursuing this exciting field ofendeavor.

Despite the great interest over the past decade,successful and widespread use of biology inmaterials science remains a formidablechallenge. The application of biologicalmaterials or of materials that mimic biologicalsystems lags far behind our enthusiasm forthem. Our ability to control chemical reactionswith natures exquisite sensitivity, to make

polymers with precise molecular weight, or toassemble macromolecules into large-scalestructures is at a very primitive, descriptivestage. We are even further from anunderstanding, much less the ability toimitate, the metabolic, catalytic, andregulatory processes that harness energy forvital processes and synthesize all vitalsubstances.

There is however reason to be optimistic thatwe will, in the not too distant future, come tounderstand the very complex physics andchemistry of biological processes. A revolutionhas taken place in biology over the past fewdecades. We now have a vastly increasedknowledge and understanding of the

biochemistry and molecular biology ofbiological materials and how their uniqueproperties arise from their structure. We nowhave a vastly increased arsenal of tools to


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analyze, characterize and manipulate thesesystems and we now have theories and highlydeveloped simulations to guide and interpretexperiments. We are, as a result, developing avastly increased ability to modify biologicalmaterials and processes for our needs and to

synthesize, de novo, new materials that arebased on biological principles.

As Whler and Buchner demonstrated, thereare no mysterious vital forces governing the

behavior of biological systems. They are,instead, governed by the coulomb andchemical potentials that govern everything inthe universe. Quantum mechanics, Newtonslaws, and thermodynamics determine themotions of particles, mass transport, and

energy balance. Geometry influences howthings can be packed. The difficulty is that wedont yet understand how these relativelysimple forces can give rise to such complexphenomena. At the molecular level, we dontfully understand the relationships amongstructures, properties, and functions. We dontunderstand chemistry well enough to makethese complicated molecules easily. At thelevel of molecular assemblies and sub-cellularcomponents, we dont understand how they

are organized and how they functioncollectively. The cellular level, with all of itsinteracting components, mass and energyflows, is beyond our ability to even describecompletely.

Section 2 outlines the awe inspiring array ofmolecules, structures, and processesdeveloped by living organisms and availablefor our use or modification. It is an impressivelist, providing, in effect, an existence proof

of what can be done and challenging us toexploit it. It must be remembered, however,that even this impressive catalogue does notdescribe the upper limits. Despite their manyinteresting and useful properties, biologicalmaterials and processes evolved under severeconstraints that limited their development. Forone, nature does not optimize structures andprocesses evolution stops when it has madestructures and processes that are good

enough for their specific, or narrowly definedpurpose and successfully adapt their hostorganism to its environment. Further, eachstructure or process is limited by the fact thatit must co-exist and interact with the otherstructures and processes on that organism. On

a more fundamental level, only a smallnumber of the 92 naturally occurring elementshave been used, and only small ranges of pH,temperature, and pressure have beenexplored. Often, the constraints do not preventour use of these materials and processes.Clearly wood is a ubiquitous structuralmaterial, and fermentation is a well-developedindustrial process. However, these processesare limited in their properties and applicationsof biomolecular materials. Wood cannot

substitute for carbon fiber reinforcedcomposites in airplanes, and fermentation byitself will not produce absolute alcohol. Thereis a real possibility that, once we understandthe principles of natures construction, we will

be able to use these principles for our owndesign goals and improve on nature.

The interest of the Department of Energy inbiomolecular materials and biologicalprocesses is very broad. There is a need for

lighter and stronger materials to improve fueleconomy. There is a need for functionalmaterials to control transport acrossmembranes, to make separations andpurification processes more efficient. There isa need to increase energy efficiency by usinglow temperature processes to make materials.There is a need for energy producingprocesses that can convert light, carbondioxide, and water to high-density fuels andthereby decrease, at least to some extent, our

dependence on fossil fuels. Finally the highspecificity of biological reactions, producinglittle or no side products, and the inherent

biodegradability of biological systems stronglysuggest that these systems need to be explored

by DOE for their potential beneficial effects onthe environment.

Following the cataloging of some of naturesstructures and processes in Section 2, we


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discuss, in Sections 3, 4, and 5, three broadareas of research that emerged at theworkshop as having significant discoverypotential because of the breadth of knowledgethat already exists in the underlying biology,

because of the applicability of this knowledge

to materials research in the physical sciences,and because of the promise seen in thepreliminary research already begun. Thesethree areas are:

self-assembled, templated, andhierarchical structures, both bio-inorganicand bio-organic,

the living cell in hybrid materials systems, biomolecular functional systems.Finally, it should be noted that this reportreflects the focus of the workshop on a

discussion of materials and processesdesigned for nonmedical applications,consistent with the mission of the EnergyDepartment as distinguished, for example,from the mission of National Institutes ofHealth (NIH).


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manufacturing, in which the product isproduced in the shape required; thus, noexpensive and wasteful machining isnecessary.

2.1.4 Benign Processing. Biological

processes are generally less hazardous andinvolve fewer toxic materials than theirsynthetic counterparts. For example, syntheticnanocrystals, which are of such great interestnow, are often synthesized at very hightemperatures with hazardous precursors.Organisms, on the other hand producemagnetic and semiconductor nanoparticles,often with great homogeneity, at roomtemperature and pressure. Teeth, shell andother ceramics are produced biologically

under far more benign conditions than aresynthetic ceramics.

2.1.5 Color. Certain birds (for example,peacocks) fish, snakes and butterflies appearcolorful, but without synthesizing thetraditional light absorbing pigments.Instead, they produce overlapping scalesmade of carbohydrate that impart iridescence

by creating interference patterns. These givethe appearance of different colors depending

on the nanometer scale spacing, the thicknessof the layers, the angle of viewing, thewavelength of the light illuminating them, therefractive index of the liquid between thelayers. At near grazing angles, for example,only ultraviolet light is reflected, making thematerial virtually invisible. It should bepossible to develop materials using similarproperties that change their response to lightin the presence of applied electrical ormagnetic fields. Such materials could be used,

for example, in smart windows that wouldreversibly reflect or transmit light, therebycontrolling the heat load in buildings.

2.1.6 Combinatorial Synthesis. Vertebratesproduce upwards of one hundred milliondifferent antibody molecules, each with aslightly different binding site. As a result, invirtually all cases, there are a few selectantibodies with a shape that allows them to

first bind to invading viruses or bacteria, andthen, after a few days time, to arrange for thesynthesis of many more copies of themselvesto overwhelm the invader and ward offdisease. In many cases, the current state oftheory and modeling is too primitive to allow

the prediction of the structure of a materialfrom the desired mix of properties. The ability,through combinatorial synthesis to developmillions of extremely similar, but criticallydifferent structures, and the ability to rapidlyscan them all for the desired properties, as isdone in the immune system, can potentiallysave enormous amounts of time and expensein the development of materials. A variety oftechniques can be employed. In phage display,variants of a given protein are presented on

the outer surface of bacterial viruses. Ininorganic combi-chem, ink jet printersdeposit nanoliter amounts of a variety ofcompounds in small wells that can beprocessed and analyzed in parallel. Batterymanufacturers have recently announced thattheir next generation cells will containmaterials discovered through combinatorialmethods. Combinatorial synthesis has becomea major focus in the search for better andcheaper catalysts for organic reactions.

2.1.7 Computation. The holy grail ofcomputer designers remains the developmentof a device that mimics the human brain.Nothing comes close to its ability to store andretrieve information, often from apparentlyunrelated data entry events. Its ability tofocus on a subset of the huge number ofsimultaneous stimuli and inputs it receives isalso unmatched, as is its ability to reason bycombining bits of information and weighting

them appropriately as it sums their input intothe solution of a problem. No device competesin use of spoken language. It is true thatsilicon computers are orders of magnitudefaster than the millisecond biological processesof the brain but none match the brain's abilityto process in parallel. It is interesting to notehowever, that the unit of biologicalinformation, the DNA or RNA nucleotide,occupies a volume of about one cubic


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nanometer, and can be accessed for readout with exceptional specificity.

A number of biological materials are beingstudied for their ability to compute,although clearly, nothing approaching a

biological computer has been developed.The protein bacteriorhodopsin has beenshown to have the capability for holographicdata storage. Adlemans report in Science(Adleman 1994) sparked a great deal ofinterest for his use of DNA to solve complexmathematical problems. Shapiro and hiscolleagues at the Weizmann Institute have alsoreported in Nature (Benenson et al., 2001) onthe use of DNA and its restriction and ligationenzymes in a system that can do computation.

Clearly an understanding of the method ofparallel processing and the mechanism of theself-assembly of the billions of neurons into afunctioning brain will be of great benefit, withmany, as yet undefinable, applications.

2.1.8 Conformational Change. Many cellularresponses to external stimuli are based on thefact that proteins can alter their structure, andtherefore their properties, in response tochanges in their environment. This response is

mediated through the binding of one or moremolecules from that environment at a specificsite on the protein. This binding event cancause one part of a ~10nm protein to movemore than 1nm relative to another. Enzymeactivity is regulated in this fashion, with theprotein shifting from an active conformationto one that is less effective either in bindingthe substrate, performing the chemistry of thereaction, or both. The oxygen binding proteinhemoglobin also exhibits conformational

changes. On a shorter time scale than that forthe increase in the concentration of 2,3 bis-phosphoglycerate (see Section 2.1.1),hemoglobin responds to a change in protonconcentration. In low proton environments, asin the lungs, it assumes a conformation thatenhances its ability to bind oxygen. In highproton environments, as in the muscles,however, these ions bind to hemoglobin andcause it to change shape, releasing oxygen for

its use in the metabolic processes that createenergy required for biosynthesis, musclecontraction and other functions.

2.1.9 Control of Interfaces. Organisms havelearned to control and exploit a wide variety

of interfaces with disparate materials. Inbiomineralized tissues such as bone, teeth,shell, inorganic materials of a variety ofcompositions are in direct contact with variousorganic materials. Proteins often direct thesynthesis of the inorganic phases. Theseprocesses serve as models that could, forexample, be applied to the controlled growthof mineralized phases for functional thin filmsor particulate applications (Klaus et al., 1999).Phage display and other such techniques have

been used to identify proteins that bindspecifically to semiconductor and othernanocrystals (Whaley et al., 2000; Whaley andBelcher 2000; Lee et al., 2002; Seeman andBelcher 2002). The crystalline ordering of viralparticles could be used to direct the orderingof nanocrystals in arrays that might promotecollective behavior. Biocompatibility, aninherent interfacial property of biomolecularmaterials is also becoming increasinglyimportant, as we design hybrid devices that

exploit the many cellular functions we cannotyet reproduce in the absence of the living cell(Section 4). Whole cells have been attached tosurfaces in bioreactors for fermentations.Hybrid circuits with both semiconductor chipsand synaptically connected neurons have beenexplored. Nerve cells from the snail Lymnaeastagnalis have been immobilized, through non-specific linkages, on silicon chips usingpolyimides such that a voltage pulse on thechip could excite the neuron (Zeck and

Fromherz 2001). Metabolic engineering hasbeen employed to alter the surfaces of cells toimprove their binding to specific sites on non-living surfaces including metals, polymers, orceramics, while the cells maintain their naturalfunctions (Section 4.3).

2.1.10 Control of Polymer Properties. Theproperties of polymers depend on the typeand sequence of their constituent monomers.


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Increased numbers of types of monomersallow an increased variety of structures,properties and functions. Most syntheticpolymers are made from a single type ofmonomeric unit for example, styrene inpolystyrene, ethylene in polyethylene. To

achieve different properties, two or even threetypes of monomers can be incorporated into asingle polymer. Alternatively, a number ofdifferent polymers can be blended. Even thesesystems are at best rudimentary analogues ofnatural polymers. Biologically producednucleic acids, on the other hand, use fourprimary monomers (ATGC in DNA, AUGC inRNA), and a few others, in smaller amounts,that are methylated or acetylated. Proteinsgenerally use 20 primary amino acids as

monomers, some of which are modified afterinitial synthesis, for example to hydroxy-proline or gamma-carboxy-glutamate, to, ineffect, create a far larger library.Polysaccharides are even more complex.Although some are made of a single monomer,others draw from many, varying in size,stereochemistry, charge, and attachedfunctional groups, each affecting theproperties of the polymer in a different way.Cyclic polysaccharides have been used for

example to insulate photoluminescentpolymer chains (Cacialli et al 2002). Recentresearch has expanded the number ofmonomers beyond those nature uses in bothproteins and nucleic acids, allowing theincorporation of amino acids or nucleotideswith an almost unlimited variety of sizes orwith specific redox, optical, electrical,magnetic, and chemical properties. Equallyimportant to the materials properties ofpolymers of biological origin is the fact that

nucleic acids, proteins or many carbohydrates,are made to a precise, uniform length, givinggreater control of properties alignment andcrystallization. Naturally occurring

biopolymers do have a limited number ofdifferent backbone structures, but research hasprogressed in broadening this range, furtherincreasing the breadth of properties that canhe achieved. Techniques are being developedto use these materials in very imaginative

ways, for example, in a technology to writethin lines of proteins or nucleic acids on avariety of inorganic surfaces using the tip ofan atomic force microscope as a quill, and asolution of the polymer as the ink (Demers etal., 2002).

2.1.10.1 Nucleic Acids. DNA and RNA are ofcourse involved in the storage and use ofcellular information, and, in the case of RNA,in catalysis and as scaffolding insupramolecular structures. These materials arefound base-paired in double strands in thewell-known double helix form of DNA or insingle strands, which often, through the samemechanism, fold back on themselves and base-pair into precisely defined 3-dimensional

structures. Their role in information storageand retrieval is an impressive one, with, asmentioned above, one bit of informationoccupying only one cubic nanometer, yet stillallowing rigorous specific addressability(regulation of specific gene expression) andaccuracy in reading. The DNA double helixcan in fact serve not only as an informationcarrier but also as a structural material(Section 3.2.1), exhibiting the properties of along, relatively rigid rod with a persistence

length of approximately 50nm. Capitalizing onthis, nanocrystals and complex organic groupswith electronic or optical properties have beenlinked to individual single strands of DNA ofdefined sequence. These single strands thenare base paired with other defined sequenceoligonucleotides to align those functionalgroups in precise positions in space. Some ofthese structures have demonstrated energytransfer from donor to acceptor groups,presenting intriguing possibilities for

electronic materials. DNA molecules withcomplex topologies have been formed intospecific objects, nanomechanical devices andperiodic arrays, with potential ultimateapplications in nanoelectronics andnanorobotics. For example, DNA base pairinghas been exploited in the fabrication ofrudimentary structures, demonstrating and,nand, or and nor gates. Other devices,involving DNA single strands that compete


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with each other for binding complementarystrands demonstrate informationmanipulation (Seeman, 1999). DNA moleculeswith complex topologies have been formedinto specific objects, nanomechanical devicesand periodic arrays, with ultimate applications

for nanoelectronics and nanorobotics. Theprecise structures of folded single strands ofRNA, for example in transfer RNA, are criticalto the role of these molecules in geneticinformation storage and transfer, but couldalso be exploited in using them in materialsapplications. Opportunities for the use of thesematerials abound, especially when thedifficulties in producing large amounts ofnucleic acids are overcome.

2.1.10.2 Proteins. Proteins fold into precisethree-dimensional shapes, driven by theiramino acid sequence. The range of propertiesthat these polymers exhibit, or contribute to isenormous, including lubricity, adhesion,viscosity, stiffness, toughness, flexibility,optical clarity, and, in the case of, for example,aspartame, taste. A very large number ofproteins and their functions remainundiscovered or uncharacterized. Theemerging field of proteomics will, no doubt,

result in the discovery and understanding ofmany of these, some performing novel, usefulfunctions and others helping us understandhow the structure of proteins determines theirfunction.

2.1.11 Energy Conversion. Chemical energypowers organisms without the use offlammable fuels or high temperatures.Biological molecular motors involve the directconversion of chemical energy into mechanical

energy without the inefficient production ofheat seen in conventional motors and engines.Much of this process, and also the use ofenergy for biosynthesis of cellular materials,involves the recycling of energy carryingmolecules between their [incorrectly] so-calledhigh energy and low energy states. Inparticular, the molecule adenosinediphosphate can be activated in thepresence of metabolic energy through its

binding a third phosphate group to makeadenosine triphosphate (ATP). Removal ofthat group involves a significant negative freeenergy that can drive energy requiringprocesses. The photosynthetic sequence oflight energy capture, production of high

energy molecules, and the use of thosemolecules to produce metabolic andmechanical energy is one that, if duplicated,would revolutionize energy conversion.Chemical energy can also be stored as amolecular or ionic gradient across amembrane.

2.1.12 Enzymes. Enzymes accelerate reactionsby up to 13 orders of magnitude at roomtemperature and atmospheric pressure. Most

important is their exquisite specificity for bothstarting materials and products, and thus theirsynthesis of the desired molecules whileproducing no byproducts. The activity ofenzymes can be controlled over several ordersof magnitude through the binding of specificeffector molecules. Selective activation ofenzymes could allow control of complex,multi-component, specific chemicalconversions such as the synthesis of fuels fromcarbon dioxide and water using sunlight or

other energy sources.

2.1.13 Evolution. Materials ideally suited toperform in the environments for which theywere originally designed are often poorlysuited to new environments that have arisensince their design. Living organisms evolveconstantly to allow them to survive and in factthrive in new environments. One of the mostfrequently quoted (although recentlychallenged) cases involves the change in color

of moths in England from white to blackduring the industrial revolution and back towhite again after institution of pollutioncontrols. The principle lies in what might becalled error prone manufacture. Each unit(organism) manufactured (born) has anaturally occurring slight variation (mutation)from the norm in one or more of its thousandsof characteristics. In some cases, this alterationleads to death or decreased fertility. In most


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cases, these alterations are unnoticed innormal use (life), but when conditions change,those individuals with the particular mutationthat improves their survival, and hencefertility in that new environment take over thepopulation. In many cases, this process occurs

over several generations, each one slightlydifferent from its parents. Evolution has also

been employed in the laboratory in thematuration and optimization of antibodiesand other proteins where the continualproduction of variants and the selection of thebetter variants, has led to better functioningproducts (Yin 2001). Development of materialsthat themselves evolve is a very long termgoal, perhaps beyond our grasp. However, theuse of the principles of evolution to optimize

materials, as in the antibody work, is anexcellent example of biologically inspiredmaterials science.

2.1.14 Extreme Environments. In general,biological systems are regarded as impracticalfor many applications because of theirsensitivity to extremes of environment.Organisms have, however, adapted to live inthe below freezing waters of Antarctica or theocean depths, and in the near boiling

conditions of hot springs or deep oceanthermal vents. Those living at the oceandepths are protected against exceptionallyhigh pressures, those living in salt flats areprotected from high osmotic pressure, cellsthat line the stomach are adapted to extremeacidity (pH 1) and others have been shown to

be exceptionally resistant to ionizing radiation.In each case, specific protective mechanismshave evolved. Transferring these capabilitiesto organisms or systems that are employed for

specific functions could protect them fromthese biologically extreme environments,although it must be kept in mind that what isregarded as extreme biologically is not at allextreme in conventional materials synthesis.

2.1.15 Hierarchical Construction. Biologicalstructures are extraordinarily complex, farmore so than synthetic systems, and theirsophisticated properties reflect that

complexity. However, to a great degree, theirsynthesis is far less complex, relying onsequential hierarchical construction principles.For example, the synthesis of collagen fibers,whose thickness can be measured inmillimeters, can be described as a sequence of

relatively simple steps starting with theassociation of groups of atoms and gradually

building in complexity to generate advancedproperties. The groups of atoms in aminoacids are assembled in a linear polypeptidepolymer through the DNA-directed, proteinsynthesizing machinery. This single peptidechain then folds with two others of similarstructure into a triple helix collagen molecule.Collagen molecules than associate in aspontaneous but highly controlled process to

produce fibrils, which associate in a similarmanner to, eventually, produce the final,exceptionally strong collagen fibers. Each stepalong the path is programmed into thestructure of the material, allowing, throughkinetically and thermodynamically driven selfassembly, the development of great structuralcomplexity with minimal complexity ofdesign.

2.1.16 Lightweight Materials. Living systems

are inherently light-weight. They use, almostexclusively, carbon, hydrogen, nitrogen,oxygen, with lesser amounts of phosphorusand sulfur and very small amounts of others.They also produce low density hydrogels andrelated structures. Our ability to mimic livingsystems and develop lightweight structuraland functional materials would lead toenormous reductions in weight and fuel usein, for example, automobiles.

2.1.17 Lubricants. Enormous inefficiencies,loss of function and expense result frominadequate lubrication of the contact surfacesof moving parts. Living systems must solvethe same problems and have evolvedmolecules to lubricate joints, portions of theeye, and internal organ surfaces. These usuallyhighly charged molecules could serve as amodel for biomimetic lubrication.


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2.1.18 Mass Production. Large scaleproduction of materials can often beexpensive. Organisms can, and in fact already,serve as factories. Their regulatorymechanisms also allow for the control of thelevels of each molecule made. Certain proteins

can be present in as few as 10 copies per cell.Alternatively, activators and strongpromoters can lead to very high levels ofproduction of defined products, often atamounts approaching tens of percent of totalcell volume. Genes for the naturally occurringplastic polyhydroxybutyrate have beentransferred into plants. Acres of farmlanddevoted to these transgenic plants could beinexpensively harvested and the polymerextracted. Genes for proteins are now being

inserted into goats or cows in a manner thatleads to their secretion into the easily collectedmilk, which, of course, can be grown for thecost of animal feed.

2.1.19 Materials Recycling. Biosynthesis isaccomplished almost exclusively by enzymecatalysis of chemical reactions that make

bonds between small molecules to make largerones. These enzymes increase the rate ofreactions that would be otherwise far too slow

to support life. Other enzymes, produced by,for example, soil bacteria, and widely presentin the environment, break these bonds, bio-degrading the molecules, also at rates farexceeding those of the uncatalyzed reaction.Energy input is, of course, required in onedirection, usually the synthetic direction, since

bonds are being made and entropy is beingdecreased. As a result, the degradativereactions usually proceed exergonically, andwith relatively low activation energies. Easily

degraded structures are of increasingimportance. Industries are being required to

be responsible for the entire product cycle. Themanufacturing process will have to includerecycling: cradle-to-cradle (new product),rather than cradle-to-grave responsibility will

become the norm. The biological model couldserve well.

2.1.20 Membranes. Cellular membrane are

extraordinary multi-functional structures.They define the boundaries of cells and of sub-cellular organelles. Cell surface membraneshelp, through the use of embedded proteinsand carbohydrates, to identify the cell to theoutside world and receive signals from that

world. They house transport systems, motors,rotors, energy transduction devices andexquisitely sensitive and selective sensors.They create non-polar compartments in themidst of a fully aqueous environment. Theyare self-healing, self-assembling, can grow asthe cell it surrounds grows, and can split intotwo as the cell divides. Membranes are highlyflexible and can adapt their shape to a varietyof structures and also to perturbations in thosestructures as the cells progress through the

various stages of their lives or perform theirmyriad functions. They are also quite robust,despite the fact that the individual componentmolecules are not covalently linked to eachother. A great deal of effort has gone into themimicking of the cell membrane and muchsuccess has been achieved. Artificial, self-assembled monolayers serve in a wide varietyof efforts to study self-assembly or othermembrane associated properties. Membranemimics are made with artificial molecules,

mirroring the self-assembling amphiphilicproperties of membrane lipids, butincorporating greater rigidity through crosslinking, or functionality through lightabsorbing chromophores, inserted channels(Section 5.6)or molecular recognition groups.Use of other molecular components allows formultilayered membranes with their own setsof properties.

2.1.21 Model Materials for Studies of Basic

Materials Physics. Basic physical laws suchas those of Newtonian mechanics, statisticalmechanics and quantum mechanics provideour only rigorous foundation forunderstanding the properties of materials.However, factors such as complexity,nonlinearity, and many-body interactions tendto frustrate our ability to make connection

between the microscopic physical laws andmacroscopic materials properties.


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Fundamental experimental studies ofmaterials science must be aimed at elucidatingthe basic connections between physical lawsand materials properties; but, as a practicalmatter, an experimentalist has to pick exampleor model materials to study. Biological

materials can act as model materials thatrevolutionize such studies since they haveproperties that can currently be controlled to afar greater extent than synthetic materials. Anexample of this is in the field of polymermaterials and polymer rheology. Half acentury of theoretical and experimentalresearch had been dedicated to understandingthe connection between microscopic molecularand macroscopic materials properties ofpolymeric fluids without having the

experimental ability to directly control orvisualize the molecular dynamics. The fieldwas revolutionized in the early 1990s by theintroduction of techniques for directlyvisualizing and manipulating single DNAmolecules using optical tweezers andfluorescence microscopy (Perkins et al., 1994).Use of DNA allows the preparation of apolymer solution in which every polymer inthe solution has exactly the same length, andstructure. Optical tweezers allow individual

molecules to be mechanically manipulatedand the forces acting on the individualmolecules to be directly measured.Fluorescence microscopy allows the molecularconformation of individual polymers to bedirectly visualized. For the first time thisallowed rigorous testing and refinement ofmolecular theories by direct comparison withmolecular measurements (Smith et al., 1999;Babcock et al., 2000).

2.1.22 Molecular Recognition. Manybiological macromolecules have theextraordinary ability to recognize specificother molecules in an environment containinglarge numbers of very similar structures. Thisselectivity is the basis for the functioning ofthe cell membrane as a biosensor, the self-assembly of collagen and other structures, thestructure and replication of DNA as a geneticor structural material, the specificity of

enzymes for reactants and products. Themechanism of this recognition involves severalfactors. The first is a geometric fit similar tothat between two pieces of a jigsaw puzzle.Individual atoms in a molecule are in suchprecisely defined positions that each molecule

assumes a defined shape, which iscomplementary to the shape of the molecule towhich it will bind. In addition, groups ofopposite charge line the surfaces of two boundmolecules. Other binding forces including theso-called hydrophobic interactions and polarinteractions (hydrogen bonding, salt bridges)are also found along the interface. Complexityis added by the fact that proteins are not fixedin shape but rather are quite flexible, rapidlyand spontaneously shifting among a set of

possible conformations. Generally, only oneconformation of a given protein binds aparticular target molecule, and the binding ofthat molecule locks the protein into thatparticular configuration. This is a powerfultool in protein design and function but it doesadd complexity to the task of designingproteins for specific molecular recognitionfunctions.

2.1.23 Motors, Rotors, Pumps,

Transporters, Tractors, Springs, Switches,Ratchets. Cellular function depends to a greatextent on a variety of motors, rotors andrelated devices. These transport systems usechemical energy to move ions,macromolecules, organelles, chromosomes,and even whole cells. A newly characterizedmotor packs DNA into the heads of viruses asthey are produced in cells. Using a motorgenerating 60 piconewtons of force to counteran internal pressure 10 times that of a

champagne bottle (60 atm), the DNA ispackaged, perhaps to provide the spring torelease it into the next cell that is attacked(Smith 2001). The enzyme ATP synthase, andthe various components of the electrontransport chain, which are responsible for theproduction of most of the cellular ATP fromADP and phosphate, are themselves molecularpumps and motors. Energy released by theoxidation of nutrients is used by the electron


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transport chain to pump protons across themembrane. These protons flow backthrough the synthase, causing it to rotate anddrive the synthesis of ATP. Thermodynamicsrequires that this process can be run in reverse.Thus, the release of energy accompanying the

conversion of ATP to ADP and phosphatecauses the rotation of the protein and thepumping of protons out across the membrane.The synthase converts chemical to mechanicalenergy (or the reverse) with nearly 100%efficiency (Yasuda et al., 1998).

Another rotational motor imbedded in the cellmembrane drives the high-speed rotation offlagella, the tails of bacterial cells that enablethem to swim towards nutrients and away

from repellants. Linear motors such as myosin,kinesin, DNA polymerase also move withinthe cell using the direct conversion of chemicalenergy to mechanical energy. To a greatextent, the nature and structure of themolecules involved in these functions areknown. Some could replace micro-mechanicaldevices now made by lithographic techniques.For example, single steps in the motion of

these motors have been analyzed and resolvedto be on the order of 10 nanometers. Somemanipulation has also been achieved. Rigid

rods have been attached to the synthase andobserved in a microscope to rotate in a circle,driven by the rotation of the protein (Figure 1).Techniques, such as single moleculespectroscopy allow the study of individualmotors and rotors.

Biomolecular ratchets and springs store orrelease energy and rectify motion. The energyfor springs is provided by hydrolysis of anucleotide or binding of a ligand. Ratchets arepowered by Brownian motion in polymerizingfilaments. For example, the spasmoneme ofthe vorticellid contracts upon exposure tocalcium, by 40% of its length (2.3 mm) inmilliseconds, at a velocity approaching 8cm/sec. No energy source is required (Amos

1971, Moriyama et al., 1999, Mahadevan andMatsudaira 2000). Small changes in proteinsubunits, amplified by linear arrangements inthe filaments can lead to structures that storeenergy and then release it on demand, creatingmovement. Other structures act as molecularswitches or dimmers. For example, enzymeactivity can be controlled on a continuum fromfull activity to complete inactivity by a varietyof effectors (Zhou et al., 2001). Ion channelscan be controlled over the full spectrum of

activity by an equally diverse group of ionsand molecules. Some have speculated on theinterfacing of millions of these efficient

biological devices to produce macro levelsof power. Nature again shows the way,

bundling actin and myosin molecules to makemuscles. Jimnez and colleagues (Jimnez2000) have mimicked the system by designinga molecular assembly in which two syntheticfilaments mimicking actin and myosin slidealong each other to contract or stretch. Others

have done pioneering work to achieve self-assembly of these motor systems from theircomponents and, for example, to control themotion of kinesin using defined micro-butuletracks (Ndlec et al., 1997; Hiratsuka et al.,2001).

2.1.24 Multi-Functional Materials. Manybiological materials perform several functionssimultaneously. Skeletal plates of calcite

Figure 1. Depiction of an array of hybrid

nanodevices powered by F1-ATPase. Soong et al.,

2000.


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(calcium carbonate) on the arms of thebrittlestar Ophiocoma wendtii provide not

only structure and protection but also containthousands of lenses, which serve to focus lighton nerve receptors beneath, somewhat like acompound eye (Figure 2). The plates, whichare clear, birefringent single crystals of calcite,allow the organism to detect changes in lightintensity on its body surfaces and change colorfrom night to day (Aizenberg et al., 2001).Multifunctional scales coat the wings of

butterflies and simultaneously aid in theaerodynamics of the wing, assist in

temperature control, and provide colors andpatterns on the wing, serving as an avoidancedefense mechanism against predators.

2.1.25 Organic Synthesis. Living systems areperhaps the ultimate factories. Extraordinarilycomplex and large materials are synthesizedfrom an exceptionally small list of simpleprecursors. The key to this lies in the use of acomplex of interlinked metabolic pathways,charting a sequence of comparatively simple

organic chemical reactions that convert thestarting materials, through as many as 20reactions or more, to the product. Enzymaticcontrol of the reactions insures that no

byproducts are produced. A large number ofcommon intermediates insures that aminimum amount of duplication is involved.

2.1.26 Optical Systems. Organisms havedeveloped a variety of optical systems, not the

least of which is the eye of higher organisms.As described above (2.1.24) O. wendtiiproduce calcite micro lens arrays. This concepthas already been adapted for directionaldisplays and in micro-optics. Opals and

butterfly wings also manipulate light in a

manner that could serve as a model forphotonic systems (Sambles 2001).

2.1.27 Self-Assembly. Perhaps the mostpowerful of properties of biological systems istheir ability to assemble individual moleculesinto large, complex, functional structures. Theinformation for the assembly lies in themolecular structure of the components, theirgeometry and their precise alignment ofhydrogen-, ionic-, polar- and hydrophobic

bonding groups (Section 2.1.22). Membranes(Section 2.1.20) assemble themselves becausethe lowest energy state of their componentamphipathic molecules is the membrane lipid

bilayer. Proteins (Section 2.1.10.2), composedof multiple individual subunits, self-assemble,aligning the individual subunits precisely withrespect to one another to perform a function asdependent on the relationship of theindividual molecules as a watch is dependenton the meshing of its gears. The ribosome is

self-assembled from 80 proteins and 4 piecesof RNA. Hierarchical construction (Section2.1.15) is simply a process involvingsequential, increasingly complex, self-assembly steps.

Viral self-assembly is another remarkableexample. The bacteriophage phi29 has about20 genes coding for proteins out of which thevirus is constructed and a variety of otherproteins and RNA which transiently aid that

construction process. The phages capsid, orshell, self-assembles about a molecularscaffold which later disassembles itself. Theempty capsid is then filled with DNA by theaction of a transiently formed molecular motorpowered by ATP (Smith et al., 2001). Once theDNA is packaged, the motor falls apart. Whilethis assembly normally occurs inside the cell,molecular biologists have identified andcloned all of the genes of the proteins needed

Figure 2. Scanning electron micrograph of a dorsal armplate from a light-sensitive brittle star. The arm-plate,which is made up of single crystal calcite, is decorated

by myriads of microlenses that concentrate light on theunderlying nerve bundles. Courtesy of L. Addadi.


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to assemble the virus from purifiedcomponents in vitro (Guo et al., 1986). In a 20microliter test tube reaction each of 100 billionDNA molecules (end to end, 400 miles ofDNA) are packaged into 100 billion viralcapsids in approximately 5 minutes. These

viruses are all infectious and each one has thepotential to make an infinite number of copiesof itself by repeating the process. A variety ofsuccessful attempts at self-assembledstructures mimicking these sorts of biologicalsystems have been described (Ball 2001).

2.1.28 Self Healing, Repair, Damage and

Fault Resistance or Tolerance. Livingorganisms are, of course, capable, to varyingdegrees, of self-repair and healing. Simple

organisms, or very young organisms canreplace entire sections of their bodies. Morecomplex or older organisms are more limitedin this, although the human liver, for example,can regenerate itself even after much of it has

been removed. On a more molecular level,membranes have the capability to repair holes,and proteins can refold after being denatured.DNA polymerase, which copies DNA, reviewsits own work, and excises errors, replacingthem with the correct base. The application of

this principle to non-living materials anddevices is almost as difficult to imagine as it isto calculate the energy and cost savings thatwould result if it could be achieved.

2.1.29 Signal Transduction. Livingorganisms detect changes in their chemicaland physical environment and rapidlyrespond to them. The process involvesmolecular recognition and a resultingconformational change in receptor

molecules. This change in shape can lead toenhanced or reduced enzyme catalysis, ortransport of ions or molecules. Signalamplification (Section 2.1.2) is usually a criticalcomponent, as these systems often transduce achange in tens or hundreds of molecules into aphysiologically significant response. Manygroups have mimicked this stimulus-drivenconformational change (Krauss 2000).

2.1.30 Smart Materials/Sensors. Smartmaterials are those that alter their structureand properties in an almost immediateresponse to a change in their environment,thus, on a much shorter time scale thanadaptation and evolution. In many cases these

are reversible changes, and in some cases, theextent of the change is controlled to reflect thedegree of change in the environment. In somecases, individual molecules are smart(Section 2.1.8). In other cases a system ofmolecules responds. An individual moleculeof the enzyme glutamine synthetase, forexample, monitors the level of nineindependent factors in its environmentsimultaneously and adjusts its rate of catalysison the basis of a summation of these positive

and negative inputs. On a more complex level,entire metabolic pathways respond to singlemolecules, such as hormones, growth factorsor pathway products or other metabolicintermediates. In some cases the response tothe stimulus is a functional one. In other cases,it is simply a record of that stimulus. In cells,analytes are detected by surface mountedprotein and carbohydrate receptors whosestructure is defined at the level of each atomand the spatial relationship between those

atoms, allowing molecular recognition, withhigh affinity and specificity. In most cases,these responses are triggered by alterations inthe shape of the receptor resulting from the

binding of its target.

The ability to change chemical activity, color,electrical conduction, mechanical properties inresponse to a change in the environmentwould be quite valuable in a variety ofmaterials applications. Perhaps the most

advanced smart materials at this time aresensors, which translate their detection ofdefined targets into measurable optical,electrical or mechanical signals. Biologicalsystems provide a very high standard toattain, demonstrating discrimination,sensitivity and adaptability that can approachthe detection of single molecules or photons.Dogs can distinguish individual humans bysmell. Honeybees have been trained to detect


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explosives at levels as low as tens of parts pertrillion (Rodacy 2002). Other organisms haveexceptional senses of taste, touch, hearing,sight. The Melanophila beetle senses infraredemission of a forest fire at a distance of 50kilometers. A dish-like organ under its wings

contains structures that are tuned to absorbthe appropriate wavelengths and then increasetheir volume and apply pressure to structuresthat trigger nerve impulses. Vipers, pythonsand other snakes identify warm bloodedtargets objects by detecting the minutedifferences in radiated temperature, withexceptional discrimination levels. Asminiaturization progresses, and micro- andnano-scale devices are developed, sensors forextremely small forces will be required. Recent

work (Liphardt et al., 2001) has shown that theunfolding of single strands of RNA, whichinvolves only the breaking of hydrogen bonds,can be measured using optical tweezers,allowing speculation that these measurementtools could be adapted as (nano-) mechanicalsensors. Cantilevers have been shown to allowthe detection of the change in energy resultingfrom the binding of very small numbers ofmolecules, again allowing speculation aboutnew, ultrasensitive mechanical sensors.

Although investigators have had difficultyadapting these and other such systems toworking devices, it cannot be assumed thatthese problems will not be resolved.

2.1.31 Structural Materials. Naturesmaterials have exceptional strength andtoughness (Smith, B.L. et al., 1999; Hinman etal., 1993; Waite et al., 1998; Curry 1977;

Jackson1988). Spider dragline silk, synthesizedprimarily from carbon, hydrogen, oxygen and

nitrogen, has long been envied for its fractureenergy which is two orders of magnitudegreater than that of high tensile steel (Hinmanet al., 1993; Heslot 1998). Its use has beenhampered by the availability of the material,(which is more difficult to obtain than theweaker material from easily grown silkworms.) Recently, however, researchers have

been able to splice portions of the genes forspider silk into cells from a variety of other

organisms that can be grown in tissue culture(Lazaris et al., 2002). Systems also exist whichwould allow the transfer of the genes to goatsthat have been bred to produce the silk in theirmilk. The proteins produced are not yetidentical to natural silk; synthesis of only one

of the two proteins has been achieved, andeven that one is produced in a form that isshorter and weaker than the natural product.Unfortunately, we do not yet fully understandthe structure of the silk proteins, themechanism by which the spider processes theproteins into fibers, or the techniques requiredto manipulate the extremely long pieces ofDNA that code for the large silk proteins.

Other natural structural fibers such as collagen

and keratin, each with their own exceptionalproperties could find applications if theirsynthesis were possible. Research is alsoprogressing in the use of synthetic materials tomimic the biological models, for examplehydrogels that can reversibly bind water tomimic the ability of collagen to absorb shock.

Extensive work has been proceeding fordecades to improve our understanding andability to mimic the hard biological

structural materials such as bone, teeth, shell,which have exceptional combinations ofmechanical properties and light weight.Abalone shell, a composite of CaCO3 andorganic polymers is 3000 times more fractureresistant than a single crystal of CaCO3 (Curry1977; Jackson 1998) and artificial composites ofceramics and adhesives are also inferior to thenatural material (Smith B.L. et al., 1999;Almquist et al., 1999). Mineralizedcomponents are, as are the organic

components, usually made of a small group ofsimple compounds, in this case hydroxyapatite or calcium carbonate or phosphate.They do, however, form a wide variety ofstructures with these building blocks, thusachieving a wide variety of properties whichcan perform a wide variety of functions. Thisvariability in crystal structure arises becausethe organic protein phase controls the crystalstructure of the mineral and a variety of such


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structures are possible. The synthesis of thesilica needles in a marine sponge, for example,is achieved by the enzymatic condensation ofsilicon alkoxides. Enzyme molecules alignedin linear repeated assemblies in the form of arod, allow the deposition of the mineralized

spines of defined shape around them (Morse2001).

2.1.32 Systems. On a larger scale, theperformance of biological systems oftenexceeds that which is attainable with currenttechnology. Shark skin, for example, exhibits

better hydrodynamic behavior than polishedsurfaces, an effect attributed to theorganization and structure of the surface. Ithas served as a model for drag reducing

coatings (Bechert, D., in Ball 1999) (Figure 3).Lotus leaves are remarkable in their ability toreject dirt. Their fine surface roughnessprevents tight binding of dirt particles (andeven glues), which are then easily washedaway by water which is itself repelled by thewaxy coating. Structural surfaces on insectlegs allow for reversible adhesion to surfacesas do the microscopic setae on the feet ofgeckos, which can hang upside down and onvertical walls depending on van der Waals

bonds (Autumn et al. 2002). Valves in veinsare designed to allow blood flow in only onedirection; flow in the opposite direction forcesthe two flaps of the valve together, closing thechannel. Yu and coworkers (Yu 2001) designeda hydrogel valve that mimics these checkvalves and could find use as an actuatedcontrol in microfluidic systems.

2.1.33 Template Directed Synthesis. Muchof biological synthesis occurs through enzyme

catalyzed reactions, with the great specificityof these catalysts providing the high level ofefficiency and minimization of byproducts.Equally high fidelity is achieved throughtemplated synthesis, with the productproduced through its specific match to apreexisting model. DNA and RNA synthesisuses the sequences of bases on an existingsingle strand to determine the sequence of

bases to be organized in the daughter strand.

Deposition of mineral phases is directed by theshape of the underlying proteins. Thissynthetic strategy could be valuable in the

Figure 3. The riblets on shark skin (top) provided

the inspiration for modeling studies of the drag

reduction they confer, and eventually led to trials

on an aircraft coated with a plastic film with thissame microscopic texture (bottom), where an up

to 8% reduction in drag was observed. Ball 1999.

Figure 4. Model of a voltage-dependent K+

channel. Zhou et al., 2001.


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synthesis of many other types of materialsprovided that the design of the appropriatetemplate can be achieved.

2.1.34 Transport Systems. Living organismsmust transport a wide array of molecules and

structures both in and out of the organism orits constituent cells, or to various specificlocations within these organisms, cells ororganelles. Membranes are extraordinarilyselective in allowing materials to penetrate. Insome cases, even the hydrogen ion is

prevented from passing. On the other hand,membranes can develop systems tospecifically allow the passage of molecules ofchoice (Figure 4). In many cases thesechannels open or close in response to eithervoltage changes or the presence of other

molecules. In other cases, chemical or voltagegradients are used as energy sources to drivetransport against a concentration gradient(e.g., Gulbis et al., 2000). Separationstechnologies would benefit greatly from thesecapabilities.


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3. Self-Assembled, Templated and Hierarchical Structures2

3.1 Introduction. Nature, through the courseof evolution, has developed techniques toconstruct increasingly complex systems,reaching her most glorious achievement in theliving organism and, in particular, the human

brain. Perhaps as impressive as the productitself is the means employed to achieve it.Nature begins with a surprising small set of

building blocks, modifies some, producesvariants of others, and then organizes tens,hundreds, thousands or millions of them, in

most cases in precisely defined three-dimensional functional structures. Toaccomplish this, it uses the processes of self-,templated-, and hierarchical assembly,manufacturing techniques that are driven only

by the laws of kinetics and thermodynamicsacting on the structural and electronicproperties of the assembled building blocks. Itis as if all the parts of an automobile werethrown in a box and, within minutes, the fullyfunctioning car drove off on its own.

The long term goal of the study ofbiomolecular materials is the development ofsystems employing or based on biologicalprocesses that function independent of theliving organism. Construction is a criticalissue. At the nanoscale we cannot manipulate

building blocks one by one, placing each in itsrequired location relative to the others.(Techniques have been developed to usescanning probe microscopes to manipulate

and arrange individual atoms one-by-one (e.g.,Eigler and Schweizer 1990; Avouris et al.,1996)but these cannot, at least now, push moleculesor structures into place, or do more than one ata time. Thus, the concept of using naturesself-assembly principles outside the livingorganism to construct materials, structuresand devices in non-living systems hascaptivated imaginations for centuries. Now,however, with our newly achieved

understanding of these biological processes,and the structure/property/functionrelationships of the building blocks we wish touse, we can reasonably hope to achieve thisgoal.

The building blocks in this proc

Bio Molecular Materials

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