International Institute for Complex Adaptive Matter (I2CAM)

1. International Institute for Complex Adaptive Matter (I2CAM) Daniel Cox, University of California-Davis, DMR 0645461 Sequence Dependent Conductivity in Wet DNA: Molecular Dynamics and Ab-initio Studies--``Bandgap engineering of molecules’’(S.S. Mallajosyula et al., submitted to NanoLett 2007)Support from I2CAM Exchange Award, for S.S. Mallajosyula from Jawal Nehru Center for Advanced Scientific Research, Bangalore [group of S.K. Pati to D.L. Cox/R.R.P. Singh, UC Davis • From work of Xu et al (NanoLett 4, 1105 [2004]) - measurements of conductance of short DNA in water between gold electrodes • At right - (a) expontential decrease of electrical conductance with number of AT bases - like quantum mechanical tunneling! • (b) at right: linear increase of electrical conductance with more GC bases only - like an ordinary electrical resistor that is metallic. • Optics: DNA is an insulator which absorbs energy only in the ultraviolet (hence SUNSCREEN!!!)

2. International Institute for Complex Adaptive Matter (I2CAM) Daniel Cox, University of California-Davis, DMR 0645461 Many experiments suggest DNA is an insulator - how can we make DNA a metal? Theory answer: after water makes it easier to take electrons from the DNA, that is what the gold does! Below: Occupied orbital extends throughout DNA for GCGC.., blocked by ATAT… • Combine molecular dynamics (thousands of atoms) to generate possible configurations from among many fluctuating ones -- this approximates system as classical and solvable by Newton’s laws • Solve for quantum mechanical states for average configuration with approximate ``density functional theory approach’’ on about 1000 atoms • Water screens the DNA bases making them more ``oxidizable’’ • The position of the highest occupied electron state of the Gold overlaps with DNA base G of GC but not with A of AT. Hence, inserting A makes a ``tunneling’’ barrier and gives the observed exponential dependence. • For GCGC…. The overlap of the gold fermi energy with the occupied G states allows for electron transfer out of G and effectively renders the DNA metallic as observed. • Theoretical conductance is higher for GCGCGC than GCATGC by about 30x, but GGATGG is higher than either (a novel prediction to be tested), higher than GCGCGC by ~ 10. • Upshot: It is possible to ``bandgap engineer’’ DNA in contact with electrodes to tune the conductance properties. This may be of use in nanotechnology. Left: Schematic of energy levels as a function of position for gold-DNA-gold The overlap of GCGC.. with the gold fermi energy allows for electron depletion, but insertion of ATAT… adds a ``tunneling barrier’’