CHESS DMR _01 p1 Carbon Nanotube Growth and Self-organization Joel D. Brock, Cornell University, DMR E.R. Meshot, E.A. Verploegen, M. Bedewy, S. Tawfick, A.R. Woll, K.S. Green, M. Hromalik, L.J. Koerner, H.T. Philipp, M.W. Tate, S.M. Gruner, and A.J. Hart; "High- speed in situ X-ray Scattering of Carbon Nanotube Film Nucleation and Self- organization", ACS Nano. 6: (2012) Intellectual Merit: Reporting in a recent issue of ACS Nano, the Hart group of the University of Michigan, in collaboration with researchers at Cornell University and the Cornell High Energy Synchrotron Source, describe the first high-speed, in situ grazing incident small angle scattering (GISAXS) x-ray studies of carbon nanotube (CNT) forest growth. Quantitative analysis of the results yielded insights into the coarsening of Fe catalyst particles prior to CNT nucleation and the size and ordering of CNTs once growth has begun. These insights allow optimization of the CNT- forest growth process. Experiments were conducted at the high-intensity wiggler-fed G1 hutch at CHESS, employing a custom glass-tube furnace (fabricated by Absolute Nano, Plymouth, MI) designed specifically for in situ x-ray studies. The experiments also utilized a novel, 2D x-ray detector fabricated by the Gruner group (Cornell), and originally designed as part of the principle 2D detector system for the Linac Coherent Light Source at SLAC, the world’s first hard x-ray free electron laser.

GISAXS images capture different stages of the CNT synthesis process: (left) before deposition, (right) during growth. Broader Impacts: Carbon nanotubes (CNTs), well known for their unique combination of mechanical, thermal, and electronic properties, are already commercially manufactured and used for many applications. Carbon nanotubes are most commonly grown as isolated tubes and fibers; however, many additional applications, such as for electro-optical devices, are enabled by densely packed, aligned bundles of CNTs known as CNT-forests. Although such forests are routinely produced, many mysteries surround the mechanisms by which they form and, critically, what factors control and limit their properties, including their maximum length. In situ measurements at CHESS revealed new insights into packed bundles of carbon nanotubes. Quantitative analysis of the results showed coarsening of Fe catalyst particles prior to CNT nucleation and the size and ordering of CNTs once growth has begun. These insights will allow optimization of the CNT-forest growth process and will benefit commercialization of CNT materials. E.R. Meshot, E.A. Verploegen, M. Bedewy, S. Tawfick, A.R. Woll, K.S. Green, M. Hromalik, L.J. Koerner, H.T. Philipp, M.W. Tate, S.M. Gruner, and A.J. Hart; "High-speed in situ X-ray Scattering of Carbon Nanotube Film Nucleation and Self-organization", ACS Nano. 6: (2012) CHESS DMR _01 p2 Carbon Nanotube Growth and Self-organization Joel D. Brock, Cornell University, DMR

Structural Basis of Transcription Initiation Joel D. Brock, Cornell University, DMR Yu Zhang, Yu Feng, Sujy Chatterjee, Steve Tuske, Mary X. Ho, Eddy Arnold, and Richard H. Ebright; "Structural Basis of Transcription Initiation", Science 338, 1076 (2012) DOI: /science Intellectual Merit: A group of Rutgers researchers has solved X-ray crystal structures of the RNA polymerase (RNAP)-promoter open complex, a key structure for understanding transcription initiation. Transcription is the copying of a gene to make a complementary RNA, which may then be translated by a ribosome to make a protein. In addition to the RNAP-promoter open complex, the researchers also solved a structure of the complex together with a ribodinucleotide primer, which reveals the interaction of the complex will have with the transcribed RNA once transcription begins. The structures divulge details about interaction of the polymerase with downstream sections of the DNA, and the conformation of the RNAP clamp within the complex. The group inserted bromine atom at particular locations to create an 'anomalous scattering' signal in the X- ray diffraction, making it possible to precisely locate that atom in crystallographic maps. X-ray diffraction data used to solve these structures were collected both at CHESS and at the National Synchrotron Light Source. Overall structure of Thermus thermophilus RNA polymerase. CHESS DMR _01 p3

Broader Impacts: Transcription and translation, along with DNA replication, are the three most fundamental molecular processes within cells. Understanding these processes is important for the rapid development of many pharmaceuticals, and, ultimately, human health. Before transcription the RNA polymerase, aided by initiation factors, must recognize the promoter, a special DNA sequence which marks the start of a gene. While various structures of the RNA polymerase have been solved, either alone or in complexes, these new structures are the first of a specific, promoter- dependent, initiation-factor-dependent transcription initiation complex. Although structural models of RNAP and the open promoter complex (RPo) have been generated based on data from electron microscopy, fluorescence-resonance-energy- transfer and protein-DNA crosslinking, this group reports the first high-resolution structural formation for a functional Rpo ever reported. Yu Zhang, Yu Feng, Sujy Chatterjee, Steve Tuske, Mary X. Ho, Eddy Arnold, and Richard H. Ebright; "Structural Basis of Transcription Initiation", Science 338, 1076 (2012) DOI: /science Structure of RPo-GpA, showing the transcription-bubble template strand ssDNA, downstream dsDNA, and ribodinucleotide primer GpA in structure of RPo-GpA CHESS DMR _01 p4 Structural Basis of Transcription Initiation Joel D Brock, Cornell University, DMR