Computational Nanotechnology: Designing Molecular Machines

1. Computational Nanotechnology By: Dr. Ralph C.Merkle Presented by: Roshan P.Harjani

2. About the Author • B.A., Computer Science, U.C. Berkeley • M.S., Computer Science, U.C. Berkeley • Ph.D., Electrical Engineering, Stanford University • Scientist at Xerox PARC • Vice President, Technology Assessment, Foresight Institute • Current research interest, Molecular Nanotechnology Introduction to Nanotechnology

3. Agenda • Introduction to Molecular Nanotechnology • Design and modeling of molecular machines • Modeling Techniques • Sufficiency of Current Modeling Methods • Molecular Compilers • Conclusion Introduction to Nanotechnology

4. IntroductionHistory of computation • “Universal Computer” • Dates back to 19th century • “Universal Constructor” • More recent • Well understood by von Neumann in the 1940's • “Assembler” • Recognized by Drexler • Analogous to von Neumann's Universal Constructor Introduction to Nanotechnology

5. Basic Design of Drexler's Assembler • A molecular computer • One or more molecular positioning devices • Robotic arms • A well defined set of chemical reactions • Takes place at the tip of the arm Introduction to Nanotechnology

6. Claims of Computational Nanotechnology • Fabricate molecular machines with atomic precision • Fabricate a wide range of molecular structures • Reduce the time frame for developing • Fabricate devices with decreasing costs Introduction to Nanotechnology

7. High payoffs arise some Questions • What??? • What such systems will look like? • How??? • How will they work? • How??? • How will we be building them? • If??? • If its feasible or not? • Will??? • Will the current understanding of chemistry and physics be sufficient? Introduction to Nanotechnology

8. Computational Nanotechnology • Design and Modeling of molecular machines • Molecular machines specified in atomic detail • Modeled using the tools of computational chemistry • Two modeling techniques of particular utility • Molecular Mechanics • Ab Initio Methods Introduction to Nanotechnology

9. Molecular MechanicsIntroduction • Computational modeling of the positions of the nuclei of individual atoms • Current packages on • PC - can handle systems with thousands of atoms • Supercomputers - can handle systems with hundreds of thousands of atoms or more • Concept • The individual nuclei are usually treated as point masses • Potential Energy (E), as a function of the distance between the nuclei Introduction to Nanotechnology

10. Example: The H2 molecule • Involves 2 nuclei • E is a simple function of the inter-nuclear distance r • Function E(r) takes into account • Inter-nuclear repulsion • Interactions between the electrons and the nuclei • Two hydrogen nuclei will adopt a position that minimizes E(r) Introduction to Nanotechnology

11. The H2 molecule… • As, r  larger • Potential Energy of the system increases • Nuclei experience a restoring force that returns them to their original distance • As, r  smaller • Two nuclei are pushed closer together • Restoring force pushes them farther apart Introduction to Nanotechnology

12. Summary • If we know the positions r1, r2, .... rN of N nuclei • E(r1, r2, .... rN) gives the potential energy of the system • Knowing the potential energy as a function of the nuclear positions • Determine the forces acting on the individual nuclei • Compute the evolution of their position over time • Potential energy E is a Newtonian concept • Particular values of E at particular points are determined by Schrodinger's equation • Many atomically precise stable structures can be modeled with an accuracy adequate to determine the behavior of molecular machines Introduction to Nanotechnology

13. Example: A Molecular bearing • This style of design has been called "Molecular Bridge Building" • Ripping apart bonds • Considering the stability • Class of bearings • Members of this class perform the desired function • The Computational tools that are capable of creating and modeling most of the members of a broad class of devices Introduction to Nanotechnology

14. Ab Initio Methods • Problem with “Molecular Mechanics” • Do not provide sufficient accuracy to deal with chemical transitions • Impose severe constraints on the number of atoms that can be modeled • Provide an accuracy sufficient to analyze the chemical reactions • Analyze the addition or removal of atoms from a specific site on a work piece Introduction to Nanotechnology

15. Sufficiency of Current Modeling Methods • It is quite possible to adequately model the behavior of molecular machines that satisfy two constraints • They are built from parts that are sufficiently stable • The synthesis of the parts is done by using positionally controlled reactions Introduction to Nanotechnology

16. Can we model Drexler's Assembler? • Fundamental purpose of an assembler is to position atoms • Molecular mechanics • Second fundamental requirement is the ability to make and break bonds at specific sites • Higher order Ab Initio Methods Introduction to Nanotechnology

17. Drexler's Assembler… • The Molecular Computer • Possible to model electronic behavior with some degree of accuracy • Molecular mechanical computation is sufficient for the molecular computer • Molecular mechanical proposals are better understood than Electronic designs • Using our current approaches and methods • Drexler's assembler can be modeled Introduction to Nanotechnology

18. Molecular Compilers • Tools to specify such Molecular Machines • Input • High level description of an object • Output • Atomic coordinates, atom types and bonding structure of the object Introduction to Nanotechnology

19. A simple Molecular Compiler • Already been written at PARC • The Specifications set consists of • “scale 0.9” • shrink the size of the structure by 10% compared with the normal size • “tube…” • tells the program to produce a tubular structure • “grid…” • specifies that a grid is to be laid down on the surface • “delete…” • specifies that the point at coordinates “…” is to be deleted • “change O_3 to S_3…” • causes all oxygen atoms to be changed to sulfur Introduction to Nanotechnology

20. Conclusion • Derive detailed description of the behavior of proposed systems • Substantially reduce the development time for complex molecular machines • It is possible to debate how long it will be before we achieve a robust molecular manufacturing capability. • We'll get there sooner if we develop and make intelligent use of molecular design tools and computational models Introduction to Nanotechnology

21. Topics of Interest / References • A simple Molecular Compiler written at PARC The C source code is available at URL ftp://ftp.parc.xerox.com/pub/nano/tube.c • Links to internet Computational Chemistry resources http://www.zyvex.com/nanotech/compChemLinks.html • Potential Energy for modeling molecular machine http://www.zyvex.com/nanotech/nano4/brennerAbstract.html • Chemical Reactions Mechanisms http://www.zyvex.com/nanotech/CDAarticle.html#makingdiamond • Computational Nanotechnology http://www.zyvex.com/nanotech/compNano.html Introduction to Nanotechnology