This work was supported by a Contract from DARPA (N66001-08-C-2040) and by a grant from the Emerging Technology Fund of the State of Texas. The authors would like to acknowledge Jiyoung Kim, Greg Mordi, Angela Azcatl, and Tom Scharf for their contributions related to selective atomic layer deposition, as well as Wallace Martin and Gordon Pollock for ex-situ sample processing.

1. Ex-Situ Sample Preparation
<ol>
	<li>Prepare chips
	<ol>
		<li>Design appropriate etch mask to put identifying markers in the Si(100) wafer. Using standard optical lithography and RIE, etch a grid of lines as fiducial marks into the wafer from which STM samples will be taken. The lines should be 10 &#956;m wide, 1 &#956;m deep, and at pitch of 500 &#956;m. After etching, strip remaining photoresist from sample. 
		Note: The fiducial marks must be identifiable in-situ for tip location on the sample as well as in AFM and SEM during metrology.</li>
		<li>Protect wafer surface by applying standard tack blue dicing tape, tacky side down.</li>
		<li>Dice wafers into chips using a diamond tipped ceramic dicing saw into sizes appropriate for the specific UHV-STM tool being used to perform HDL. Here, the samples were 8.1 mm x 8.1 mm squares.</li>
	</ol>
	</li>
	<li>After dicing, prepare chip for insertion into UHV-STM patterning tool by gently peeling back the dicing tape, taking care not to touch chip with any nickel-containing tools which will induce an unfavorable surface reconstruction after UHV prep in section 2 below.
	<ol>
		<li>Clean chip by rinsing the front face for 10 sec each with streams of acetone, isopropyl alcohol, methanol, and deionized water, respectively, while gripping the sides of the sample with polytetrafluoroethylene (PTFE) tweezers. Finally, dry with ultrapure N2 or Ar, still gripping with Teflon tweezers.</li>
		<li>Mount sample chip in STM sample holder using methods appropriate for the specific UHV-STM tool to be used for HDL.
		<ol>
			<li>If mounting in a nickel-containing sample holder, cut tantalum foil barrier strips (appx. 4 mm by sample height) using titanium scissors. Sonicate foil strips for 5 min each in ultrapure acetone, isopropyl alcohol, methanol, and DI water, respectively. Dry with ultrapure N2 gas by partially covering a beaker with aluminum foil and injecting an N2 nozzle into the opening. Flow gas until all liquid has evaporated. Using nickel free tweezers, form foil around ends of sample then clamp in sample holder to isolate front and back sides of sample from sample holder.</li>
		</ol>
		</li>
		<li>After mounting, plasma clean sample and sample holder in oxygen plasma to remove carbon contamination.28</li>
	</ol>
	</li>
</ol>
2. UHV Sample Preparation
<ol>
	<li>Introduce sample into UHV system via load-lock or another preferred UHV-safe method so that the UHV processing and HDL can typically remain below 1.3 x 10-9 mbar (except for step 2.5.1.1 below).</li>
	<li>Degas O/N at 650 &#176;C, monitoring the temperature with a pyrometer. Ensure that the chamber pressure is within 25% of background. In the case described here, typical background pressures are approximately 4.5 x 10-10 mbar.</li>
	<li>Degas tungsten hydrogen cracking filament at 1,500 &#176;C for 5 min. Activate titanium sublimation pumps if possible.</li>
	<li>Perform sample &#8220;Flash&#8221; cycle.
	<ol>
		<li>Flash sample by heating to 1,250 &#176;C for 20 sec, monitoring T with pyrometer and using a 10 &#176;C/sec heating gradient. Do not exceed a maximum pressure of 7 x 10-9 mbar. Cool by removing heating current in less than 5 sec.</li>
		<li>Rest sample at 350 &#176;C for 5 min. to allow pressure to recover to baseline. Repeat 3x.</li>
	</ol>
	</li>
	<li>Perform sample passivation.
	<ol>
		<li>Set sample temperature to 350 &#176;C using a pyrometer to monitor the temperature. Introduce 1.3 x 10-6 mbar ultra-pure H2 into prep chamber using leak valve.
		<ol>
			<li>Put a cold trap on the H2 line very near a leak valve in the system in order to further purify H2.</li>
			<li>If possible, pump system with high-velocity turbo pump instead of an ion pump. This is so the ion pump does not contaminate the sample from being exposed to the high pressured and ejecting contaminants. The pumps are put back in the normal state after most the hydrogen has been removed and the sample is still warm (350 &#176;C).</li>
		</ol>
		</li>
		<li>Turn on tungsten hydrogen cracking filament to a temperature of 1,400 &#176;C for 12 min, then turn off filament and H2 gas flow. Cool sample to RT.</li>
	</ol>
	</li>
</ol>
3. Scanning Tunneling Microscopy and Lithography
<ol>
	<li>Transfer sample to STM, and bring sample and STM tip into tunneling range. Using a camera with resolving power of better than a 20 &#956;m spot size, take high-resolution optical image of tip-sample junction. Deskew and resize the optical image so that it represents an undistorted reproduction of the fiducial marks.</li>
	<li>Remove any illumination to reduce system thermal instabilities. Determine surface quality.
	<ol>
		<li>Using conventional STM techniques with sample bias of -2.25 V and 200 pA, identify the number of defects on the surface.</li>
		<li>If surface defects are below acceptable levels, move to the next step. Maximum acceptable defect levels are as followed: Dangling bonds of 1%; Si vacancies of 3%; contaminants of 1%.</li>
	</ol>
	</li>
	<li>Design HDL patterns to be produced, including both experimental patterns and large (1 &#956;m x 1 &#956;m) serp identification patterns. The serp patterns should be drawn with a long vector axis perpendicular to expected AFM fast scan axis, using a pitch of 15-20 nm. Fracture overall pattern into fundamental shapes to define the path followed by the tip when applying HDL conditions.24</li>
	<li>Using vector outputs from the previous step, perform HDL using FE mode lithography for large areas with sample bias of 7-9 V, current of 1 nA, and 0.2 mC/cm and AP mode lithography for small areas or those areas requiring atomic precision edges.24
	<ol>
		<li>Determine optimal AP mode lithography conditions by performing HDL with an variety of conditions with sample bias ranging from 3.5 to 4.5 V, current ranging from 2 to 4 nA, and line dosages ranging from 2 to 4 mC/cm. Choose conditions that produce the narrowest completely depassivated line.</li>
	</ol>
	</li>
	<li>Perform STM metrology on desired HDL patterned areas by imaging at -2.25 V sample bias and 0.2 nA tunneling current.
	<ol>
		<li>[optional] Perform error correction. After STM metrology, compare depassivation pattern in the STM images with the desired pattern from step 3.5. If any areas show insufficient dangling bond formation, repeat the lithography cycle in those areas.</li>
	</ol>
	</li>
	<li>After completing STM HDL, disengage tip from sample, and move sample to load lock.</li>
	<li>Vent and remove sample. During vent with ultrapure N2, protect sample by contacting it with inert, flat substrate such as clean sapphire.29 After surface protection, close valves to any pumps then introduce vent gas as quickly as possible. Remove sample from system.</li>
</ol>
4. Sample Transport
<ol>
	<li>Remove sample from load lock. Release sample from sample holder, including removing the foil barrier pieces if possible. Using PTFE (or Ti) tweezers, move sample to transporter, keeping front side of sample protected, attempting to keep atmosphere exposure to less than 10 min.</li>
	<li>Install cover over sample and loosely assemble a pressurized sample transporter. Flush with ultrapure Ar for 1 min. Do not evacuate system at any point, or surface damage may occur.29 Finally, seal sample transporter with a small positive pressure (~50-100 mbar) of Ar so that the sample remains stable for up to a month.</li>
</ol>
5. Atomic Layer Deposition
<ol>
	<li>Ensure the ALD is at the proper deposition temperature (100 &#176;C). Slowly increase the argon pressure in the ALD chamber until atmospheric pressure has been achieved.</li>
	<li>Open ALD chamber.</li>
	<li>Open sample transporter and quickly transfer to ALD chamber using a pair of PTFE tweezers grasping the sample on edge, then close the ALD chamber and purge using a flow of argon at a pressure of &#60; 2 &#215; 10-1 mbar for 1 hr to degas the sample. Set a process to perform 80 repeated cycles of ALD to grow 2.8 nm of amorphous titania.
	<ol>
		<li>Using an unmodified commercial ALD system at a sample temperature of 100-150 &#176;C, with titanium tetrachloride (TiCl4) and water (H2O) as precursors perform deposition with reactants at pressures of 0.3 mbar and 0.8 mbar, with pulse times of 0.1 sec and 0.05 sec, respectively.27</li>
		<li>Following each gas pulse, purge the reactor with Ar for 60 sec at 0.2 mbar to ensure minimal background deposition due to physisorbed reactants. For the masks in this work, 80 ALD cycles are used to grow approximately 2.8 nm of amorphous titania at 100 &#176;C.</li>
	</ol>
	</li>
	<li>Slowly vent ALD chamber with Ar gas and open. Repeat steps 4.1 and 4.2 for sample transport.</li>
</ol>
6. Atomic Force Microscopy (AFM)
<ol>
	<li>Ensure proper calibration of the AFM according to manufacturer&#8217;s protocol. Open sample transporter and gently remove sample using tweezers.</li>
	<li>After removing from transporter, securely install the sample into the AFM using a mechanical mounting method such as a clamping system if possible. Focus the AFM camera onto the sample, and locate the fiducial markings on the sample surface to align the AFM tip to the pattern based on the optical metrology in step 3.2.</li>
	<li>Ensure that the AFM settings will show both the height and phase information and set the scan size to be between 20 and 40 &#956;m wide. Engage the AFM tip onto the sample.</li>
	<li>Using the height and phase information at highest resolution, scan until the locator patterns region are identified. Zoom into the patterned region and locate the region in which an image is desired.</li>
	<li>Take an image of the desired regions using the appropriate image quality and resolution (typically the highest possible). Once all desired regions have been scanned, disengage the tip from the sample. Unload the sample. Repeat steps 4.1 and 4.2 for sample transport.</li>
</ol>
7. Reactive Ion Etching
<ol>
	<li>Chill capacitively coupled RIE reactor to -110 &#176;C, then load the sample into its intro chamber and pump down to 7.5 x 10-6 mbar.
	<ol>
		<li>Stabilize the temperature for 3 min. Then turn the gas on with flow rates of O2 at 8 sccm (standard cubic centimeter per minute), Ar at 40 sccm, and SF6 at 20 sccm.</li>
		<li>Strike plasma using a 150 W RF discharge, then modify the gas flow to etch for 1 min using SF6 at 52 sccm and O2 at 8 sccm. Interaction of these gases with Si will etch at a rate of approximately 20 nm/min.30</li>
		<li>Pump vacuum to 7.5 x 10-6 mbar. Vent RIE system. Repeat steps 4.1 and 4.2 for sample transport.</li>
	</ol>
	</li>
</ol>
8. Scanning Electron Microscopy (SEM)
<ol>
	<li>SEM Sample Mounting and introduction of sample to system.
	<ol>
		<li>Place non-adhesive sample mount into a convenient location to facilitate sample mounting.</li>
		<li>Open sample transporter and gently remove sample using tweezers to grab the sample by the edges and securely install into SEM mount, then introduce sample assembly into SEM.</li>
		<li>Vent and open SEM chamber. Securely install sample assembly to the SEM sample stage. Pump down SEM chamber.</li>
	</ol>
	</li>
	<li>Locate the fiducials.
	<ol>
		<li>Bring the magnification to lowest possible value. Select the accelerating voltage and beam current settings that would give good resolution. Start with lowest acceptable settings. Go up as needed.</li>
		<li>Turn on the electron beam. Bring the general region of interest to recommended working distance and eucentric height.</li>
		<li>Locate and focus on fiducials described in section 1.1. Adjust working distance as necessary. Optimize the focus, brightness and contrast.</li>
	</ol>
	</li>
	<li>Locate and image the patterns.
	<ol>
		<li>Relative to the fiducials, locate the patterns based on the optical metrology of section 3.2 and AFM metrology of section 6. To minimize carbon deposition on patterns, optimize focus using nearby non-essential features. Once optimized, move to the patterns and acquire plan view images and measurements.</li>
		<li>If needed, tilt the sample for 3D images and pattern height measurements. For other patterns, repeat from 8.3 as needed.</li>
	</ol>
	</li>
	<li>Perform SEM system closing routine and dismount sample/s, as prescribed by the SEM manufacturer. Secure the sample back into the transporter.</li>
	<li>Repeat steps 4.3 and 4.4 for sample transport and storage. At this point, the samples are robust and can be stored for an indefinite period of time. Perform post-imaging analyses if necessary.</li>
</ol>

<ol>
	<li>Yoffe, A. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Low-dimensional+systems:+quantum+size+effects+and+electronic+properties+of+semiconductor+microcrystallites+(zero-dimensional+systems)+and+some+quasi-two-dimensional+systems.">Low-dimensional systems: quantum size effects and electronic properties of semiconductor microcrystallites (zero-dimensional systems) and some quasi-two-dimensional systems.</a> Adv. in Phy. 42 (2), 173-262 (1993).</li><li>Alivisatos, A. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Semiconductor+Clusters,+Nanocrystals,+and+Quantum+Dots.">Semiconductor Clusters, Nanocrystals, and Quantum Dots.</a> Science. 271 (5251), 933-937 (1996).</li><li>Craighead, H. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nanoelectromechanical+Systems.">Nanoelectromechanical Systems.</a> Science. 290 (5496), 1532-1535 (2000).</li><li>Dai, M. D., Kim, C. -. W., Eom, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Finite+size+effect+on+nanomechanical+mass+detection:+the+role+of+surface+elasticity.">Finite size effect on nanomechanical mass detection: the role of surface elasticity.</a> Nanotechnology. 22 (26), 265502 (2011).</li><li>Personick, M., Mirkin, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Making+sense+of+the+mayhem+behind+shape+control+in+the+synthesis+of+gold+nanoparticles.">Making sense of the mayhem behind shape control in the synthesis of gold nanoparticles.</a> J. Am. Chem. Soc. 135 (C), 18238-18247 (2013).</li><li>Rothemund, P. W. K., Ekani-Nkodo, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Design+and+Characterization+of+Programmable+DNA.">Design and Characterization of Programmable DNA.</a> Nanotubes. J. Am. Chem. Soc. 26, 16344-16353 (2004).</li><li>Hersam, M. C., Guisinger, N. P., Lyding, J. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Silicon-based+molecular+nanotechnology.">Silicon-based molecular nanotechnology.</a> Nanotechnology. 11 (2), 70-76 (2000).</li><li>Eigler, D. M., Schweizer, E. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Positioning+single+atoms+with+a+scanning+tunnelling+microscope.">Positioning single atoms with a scanning tunnelling microscope.</a> Nature. 344, 524-526 (1990).</li><li>Heinrich, A. J., Lutz, C. P., Gupta, J. A., Eigler, D. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Molecular+cascades.">Molecular cascades.</a> Science. 298, 1381-1387 (2002).</li><li>Crommie, M. F., Lutz, C. P., Eigler, D. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Confinement+of+Electrons+to+Quantum+Corrals+on+a+Metal+Surface.">Confinement of Electrons to Quantum Corrals on a Metal Surface.</a> Science. 262 (5131), 218-220 (1993).</li><li>Shen, T. -. C., Wang, C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Atomic-Scale+Desorption+Through+Electronic+and+Vibrational+Excitation+Mechanisms.">Atomic-Scale Desorption Through Electronic and Vibrational Excitation Mechanisms.</a> Science. 268, 1590-1592 (1995).</li><li>Randall, J. N., Lyding, J. W., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Atomic+precision+lithography+on+Si.">Atomic precision lithography on Si.</a> J. Vac. Sci. Tech. B. 27 (6), 2764-2768 (2009).</li><li>Tong, X., Wolkow, R. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Electron-induced+H+atom+desorption+patterns+created+with+a+scanning+tunneling+microscope:+Implications+for+controlled+atomic-scale+patterning+on+H-Si(100).">Electron-induced H atom desorption patterns created with a scanning tunneling microscope: Implications for controlled atomic-scale patterning on H-Si(100).</a> Surf. Sci. 600 (16), L199-L203 (2006).</li><li>Hitosugi, T., Hashizume, T., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Scanning+Tunneling+Spectroscopy+of+Dangling-Bond+Wires+Fabricated+on+the+Si(100)-2x1-H+Surface.">Scanning Tunneling Spectroscopy of Dangling-Bond Wires Fabricated on the Si(100)-2x1-H Surface.</a> Jap. J. App. Phys, Pt 2 2. 36 (3B), L361-L364 (1997).</li><li>Bird, C. F., Fisher, A. J., Bowler, D. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Soliton+effects+in+dangling-bond+wires+on+Si(001).">Soliton effects in dangling-bond wires on Si(001).</a> Phys. Rev B. 68, 115318 (2003).</li><li>Wolkow, R. A., Livadaru, L., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Beyond-CMOS Electronics. , 1-28 (2013).</li><li>Lyding, J. W., Shen, T. -. C., Hubacek, J. S., Tucker, J. R., Abeln, G. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nanoscale+patterning+and+oxidation+of+H-passivated+Si(100)-2&#215;1+surfaces+with+an+ultrahigh+vacuum+scanning+tunneling+microscope.">Nanoscale patterning and oxidation of H-passivated Si(100)-2&#215;1 surfaces with an ultrahigh vacuum scanning tunneling microscope.</a> App. Phys. Lett. 64 (15), 2010-2012 (1994).</li><li>Lyding, J. W., Shen, T. -. C., Abeln, G. C., Wang, C., Tucker, J. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nanoscale+patterning+and+selective+chemistry+of+silicon+surfaces+by+ultrahigh-vacuum+scanning+tunneling+microscopy.">Nanoscale patterning and selective chemistry of silicon surfaces by ultrahigh-vacuum scanning tunneling microscopy.</a> Nanotechnology. 7, 128-133 (1996).</li><li>Owen, J. H. G., Ballard, J., Randall, J. N., Alexander, J., Von Ehr, J. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Patterned+Atomic+Layer+Epitaxy+of+Si+/+Si(001):H.">Patterned Atomic Layer Epitaxy of Si / Si(001):H.</a> J. Vac. Sci. Tech. B. 29 (6), 06F201 (2011).</li><li>Goh, K. E. J., Chen, S., Xu, H., Ballard, J., Randall, J. N., Ehr, J. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Von+Using+patterned+H-resist+for+controlled+three-dimensional+growth+of+nanostructures.">Von Using patterned H-resist for controlled three-dimensional growth of nanostructures.</a> App. Phys. Lett. 98 (16), 163102 (2011).</li><li>Ye, W., Pe&#241;a Martin, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Direct+writing+of+sub-5+nm+hafnium+diboride+metallic+nanostructures.">Direct writing of sub-5 nm hafnium diboride metallic nanostructures.</a> ACS Nano. 4 (11), 6818-6824 (2010).</li><li>Brien, J. L., Schofield, S. R., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Scanning+tunnelling+microscope+fabrication+of+arrays+of+phosphorus+atom+qubits+for+a+silicon+quantum+computer.">Scanning tunnelling microscope fabrication of arrays of phosphorus atom qubits for a silicon quantum computer.</a> Smart. 11 (5), 741-748 (2002).</li><li>Van Oven, J. C., Berwald, F., Berggren, K. K., Kruit, P., Hagen, C. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Electron-beam-induced+deposition+of+3-nm-half-pitch+patterns+on+bulk+Si.">Electron-beam-induced deposition of 3-nm-half-pitch patterns on bulk Si.</a> J. Vac. Sci. Tech. B. 29 (6), 06F305 (2011).</li><li>Ballard, J. B., Sisson, T. W., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Multimode+hydrogen+depassivation+lithography:+A+method+for+optimizing+atomically+precise+write+times.">Multimode hydrogen depassivation lithography: A method for optimizing atomically precise write times.</a> J. Vac. Sci. Tech. B. 31 (6), 06FC01 (2013).</li><li>Randall, J. N., Ballard, J. B., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Atomic+precision+patterning+on+Si:+An+opportunity+for+a+digitized+process.">Atomic precision patterning on Si: An opportunity for a digitized process.</a> Microelec. Eng. 87 (5-8), 955-958 (2010).</li><li>Perrine, K. A., Teplyakov, A. V. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Reactivity+of+selectively+terminated+single+crystal+silicon+surfaces.">Reactivity of selectively terminated single crystal silicon surfaces.</a> Chem. Soc. Rev. 39 (8), 3256-3274 (2010).</li><li>McDonnell, S., Longo, R. C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Controlling+the+Atomic+Layer+Deposition+of+Titanium+Dioxide+on+Silicon:+Dependence+on+Surface+Termination.">Controlling the Atomic Layer Deposition of Titanium Dioxide on Silicon: Dependence on Surface Termination.</a> The J. Phys. Chem. C. 117 (39), 20250-20259 (2013).</li><li>Kane, D. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Plasma+cleaning+of+metal+surfaces.">Plasma cleaning of metal surfaces.</a> J. Vac. Sci. Tech. 11 (3), 567 (1974).</li><li>Hersam, M. C., Guisinger, N. P., Lyding, J. W., Thompson, D. S., Moore, J. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Atomic-level+study+of+the+robustness+of+the+Si(100)-2&#215;1:H+surface+following+exposure+to+ambient+conditions.">Atomic-level study of the robustness of the Si(100)-2&#215;1:H surface following exposure to ambient conditions.</a> App. Phys. Lett. 78 (7), 886-888 (2001).</li><li>Agostino, R., Flamm, D. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Plasma+etching+of+Si+and+SiO2+in+SF6&#8211;O2+mixtures.">Plasma etching of Si and SiO2 in SF6&#8211;O2 mixtures.</a> J. App. Phys. 52 (1), 162 (1981).</li><li>Longo, R. C., McDonnell, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Selectivity+of+metal+oxide+atomic+layer+deposition+on+hydrogen+terminated+and+oxidized+Si(001)-(2&#215;1)+surface.">Selectivity of metal oxide atomic layer deposition on hydrogen terminated and oxidized Si(001)-(2&#215;1) surface.</a> J. Vac. Sci Tech. B. 32 (3), 03D112 (2014).</li><li>Ruess, F. J., Oberbeck, L., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+use+of+etched+registration+markers+to+make+four-terminal+electrical+contacts+to+STM-patterned+nanostructures.">The use of etched registration markers to make four-terminal electrical contacts to STM-patterned nanostructures.</a> Nanotechnology. 16 (10), 2446-2449 (2005).</li><li>Ruess, F. J., Pok, W., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Realization+of+Atomically+Controlled+Dopant+Devices+in+Silicon.">Realization of Atomically Controlled Dopant Devices in Silicon.</a> Small. 3 (4), 563-567 (2007).</li><li>Li, K., Namboodiri, P., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Controlled+formation+of+atomic+step+morphology+on+micropatterned+Si+(100).">Controlled formation of atomic step morphology on micropatterned Si (100).</a> J. Vac. Sci. Tech. B. 29 (4), 041806 (2011).</li><li>Ballard, J. B., Owen, J. H. G., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Pattern+transfer+of+hydrogen+depassivation+lithography+patterns+into+silicon+with+atomically+traceable+placement+and+size+control.">Pattern transfer of hydrogen depassivation lithography patterns into silicon with atomically traceable placement and size control.</a> Journal of Vacuum Science and Technology B. 32 (4), 041804 (2014).</li><li>Gusev, E. P., Cabral, C., Copel, M., D&#8217;Emic, C., Gribelyuk, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=U+ltrathin+HfO+2+films+grown+on+silicon+by+atomic+layer+deposition+for+advanced+gate+dielectrics+applications.">U ltrathin HfO 2 films grown on silicon by atomic layer deposition for advanced gate dielectrics applications.</a> Microelectronic Engineering. 69, 145-151 (2003).</li></ol>

The authors have nothing to disclose.

Performing metrology on the nanostructures described above requires the ability to bridge the tip positioning during HDL and pattern location using other tools such as AFM and SEM. In contrast to other well-developed patterning tools with high-resolution position encoding such as e-beam lithography, the HDL performed here was performed with an STM without well controlled coarse positioning, so extra position identification protocols were used, as shown in Figure 3. First, a long-focal-length microscope i...

As nanotechnology becomes more important in a wide variety of arenas, understanding the structures being formed gains importance, especially in fields of lithography and electronics. To emphasize the importance of metrology at the nanoscale, specifically at scales below 10 nm, it should be pointed out that a variation in feature size of only 1 nm indicates a fractional variation at least 10%. This variation can have significant implications for device performance and material character.1,2&#8211;4 Using synthetic methods, very precisely formed individual features such as quantum dots or other complex molecules can be fabricated,2,5,6 but generally lacking the same precision in feature placement and orientation, despite work toward improving size and placement control. This paper demonstrates an approach for fabricating nanostructures with near atomic size precision and atomic precision in feature placement, as well as with atomic metrology in feature placement. Using the atomic precision of Scanning Tunneling Microscope (STM) induced Hydrogen Depassivation Lithography (HDL), atomically precise patterns with chemically sensitive contrast are formed on a surface. Selective Atomic Layer Deposition (ALD) then applies a hard oxide material in the patterned areas, with Reactive Ion Etching (RIE) ultimately transferring the patterns into the bulk material, as shown schematically in Figure 1. Combining the highly precise HDL process with the standard ALD and RIE processes results in a flexible method to produce nanostructures on a surface with arbitrary shape and positioning.
<img alt="Figure 1" src="/files/ftp_upload/52900/52900fig1.jpg" /> 
Figure 1. Primary Nanofabrication Process Steps. As an example, a 200 nm x 200 nm square is shown. Each circled arrow indicates a step of atmospheric exposure and transport between sites. After UHV sample prep, the sample is patterned using UHV HDL followed by STM metrology (top left). ALD is then performed, followed by AFM metrology (right). RIE transfers the patterns into Si(100), followed by SEM metrology (bottom left). <a href="https://www.jove.com/files/ftp_upload/52900/52900fig1large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
The most precise lithography to date usually involves scanned probe techniques, specifically STM-based patterning where atomic resolution patterning and functionalization has been demonstrated for many applications.7 Previously, atom manipulation has produced nanostructures with ultimate precision by using individual atoms as building blocks,8,9,10 but the nanostructures required cryogenic conditions and thus lacked long-term robustness. RT atom manipulation by removal of hydrogen atoms from the surface has been shown, specifically HDL.11,12,13 HDL promises to enable new classes of electronic and other devices based on the spatial localization of surface contrast. Using HDL without further processing, various device architectures are possible including dangling bond wires or logic devices.14,15,16 In addition to providing electrical contrast, HDL can introduce chemical contrast on the surface where the passivating H layer has been removed, in effect creating a template for further chemical modification. This chemical modification has been demonstrated on silicon and other surfaces, showing selectivity for deposition of metals,17 insulators,18 and even semiconductors.16,19 Each of these examples produces two dimensional structures, so other processing steps must be used to produce true three dimensional structures with the atomically resolved control promised by HDL. Previously, this has required repeated patterning,19,20,21 annealing,22 or less well resolved processes such as tip-based e-beam induced deposition.23
Similar to e-beam lithography, HDL uses a localized flux of electrons to expose a resist. Several similarities exist such as the capacity to perform multi-mode lithography with variable spot size and patterning efficiency.24 However, the true power of HDL arises from how it differs from e-beam lithography. First, the resist in HDL is a monolayer of atomic hydrogen so that resist exposure becomes a digital process; the resist atom either is or is not present.25 Since the H atom placement corresponds to the underlying Si(100) lattice the HDL process can be an atomically precise process, although it should be noted that in this paper the HDL has nanometer precision as opposed to having atomic perfection and thus is not digital in this case. Since the electron source in HDL is local to the surface, the various modes of STM operation facilitate both throughput optimization as well as error checking. At tip-sample biases below ~4.5 V, lithography may be performed at the single atom level with atomic precision, known as Atomically Precise mode (AP mode). In contrast, at biases above ~7 V, electrons are emitted directly from the tip to the sample with wide linewidths and high depassivation efficiencies, known here as Field Emission mode (FE mode). HDL throughputs can then be optimized by careful combination of these two modes, although the overall throughputs remain small relative to e-beam lithography with patterning up to 1 &#956;m2/minute possible. When the bias is reversed so that the sample is held at ~-2.25 V, electrons tunnel from the sample to the tip with extremely low depassivation efficiency, thus permitting inspection of the atomic structure of the surface both for error correction and for atomic scale metrology.
This nanostructure fabrication process shown in Figure 1 starts with an UHV-HDL step, as described above. Following HDL, the sample is vented to atmosphere, at which time the patterned areas become saturated with water, forming a thin (i.e., ~1 monolayer) SiO2 layer.26 After transport, the sample is inserted into an ALD chamber for deposition of titania (TiO2), with thicknesses around 2-3 nm deposited here, as measured by AFM and XPS.27 Since the titania reaction depends upon a water saturation of the surface, this process is possible despite atmosphere exposure which saturates the surface with water. Next, to transfer the ALD mask pattern into the bulk the sample was etched using RIE so that 20 nm of Si is removed, with the etch depth determined by AFM and SEM. In order to facilitate metrology steps, an Si(100) wafer is patterned with a grid of lines which are designed to be visible after UHV preparation by a long working distance optical microscope, AFM plan-view optical imaging, and low-magnification plan-view SEM imaging. To help identify the nanoscale structures, 1 &#956;m2 serpentine patterns (serps) are patterned onto the samples with the most isolated nanopatterns located at fixed locations relative to the serps.
This combination of HDL, selective ALD, and RIE can be an important process for nanostructure fabrication, and it includes an atomic scale metrology as a natural byproduct of the process. Below, we include a detailed description of the steps involved to fabricate sub-10 nm nanostructures in Si(100) using HDL, selective ALD, and RIE. It is assumed that one is skilled in each of these processes, but information will be included related to how to integrate the various processes. Particular emphasis will be given to those unexpected difficulties experienced by the authors in order to prevent the same difficulties, especially related to transport and metrology.

<table><tbody><tr><td>Si Wafer</td><td>VA Semiconductor</td><td></td><td>P type (Boron) Si&amp;lt;100&gt; &amp;#177; 2 degrees, 280 mm &amp;#177; 25 mm thick, 0.01-0.02 ohm-cm</td></tr><tr><td>Ta foil</td><td>Alfa Aesar</td><td>335</td><td>0.025&amp;nbsp;mm (0.001&amp;nbsp;in) thick, 99.997% (metals basis)</td></tr><tr><td>Methanol</td><td>Alfa Aesar</td><td>19393</td><td>Semiconductor Grade, 99.9%</td></tr><tr><td>2-Propanol</td><td>Alfa Aesar</td><td>19397</td><td>Semiconductor Grade, 99.5%</td></tr><tr><td>Acetone</td><td>Alfa Aesar</td><td>19392</td><td>Semiconductor Grade, 99.5%</td></tr><tr><td>Argon</td><td>Praxair</td><td></td><td>Ultra high purity (grade 5.0)</td></tr><tr><td>Deionized water</td><td>Millipore</td><td>Milli-Q Water Purification System</td><td>&gt;18 MW resistance water produced on demand.</td></tr><tr><td>TiCl&lt;sub&gt;4&lt;/sub&gt;</td><td>Sigma Aldrigh</td><td>254312</td><td>&amp;ge;99.995% trace metals basis</td></tr><tr><td>O&lt;sub&gt;2&lt;/sub&gt;</td><td>Matheson</td><td>G2182101</td><td>Research Grade</td></tr><tr><td>SF&lt;sub&gt;6&lt;/sub&gt;</td><td>Matheson</td><td>G2658922</td><td>Ultra high purity (grade 4.7)</td></tr><tr><td>Blue Medium Tack Roll</td><td>Semiconductor Equipment Corporation</td><td>18074</td><td>Thickness 75 &amp;#956;m / 0.003&amp;rdquo;&amp;nbsp; Length 200 M / 660&amp;rsquo;&amp;nbsp;</td></tr></tbody></table>

atomically traceable nanostructure fabrication

Reducing the scale of etched nanostructures below the 10 nm range eventually will require an atomic scale understanding of the entire fabrication process being used in order to maintain exquisite control over both feature size and feature density. Here, we demonstrate a method for tracking atomically resolved and controlled structures from initial template definition through final nanostructure metrology, opening up a pathway for top-down atomic control over nanofabrication. Hydrogen depassivation lithography is the first step of the nanoscale fabrication process followed by selective atomic layer deposition of up to 2.8 nm of titania to make a nanoscale etch mask. Contrast with the background is shown, indicating different mechanisms for growth on the desired patterns and on the H passivated background. The patterns are then transferred into the bulk using reactive ion etching to form 20 nm tall nanostructures with linewidths down to ~6 nm. To illustrate the limitations of this process, arrays of holes and lines are fabricated. The various nanofabrication process steps are performed at disparate locations, so process integration is discussed. Related issues are discussed including using fiducial marks for finding nanostructures on a macroscopic sample and protecting the chemically reactive patterned Si(100)-H surface against degradation due to atmospheric exposure.

In the cases described here, HDL is performed using multi-mode lithography.24 In FE mode, performed with 8 V sample bias, 1 nA, and 0.2 mC/cm (equivalent to 50 nm/sec tip speed), the tip moves over the surface either parallel or perpendicular to the Si lattice, producing lines of depassivation. While this lineshape is very tip dependent, in the case here, the completely depassivated portion of the lines was approximately 6 nm wide, with tails of partial depassivation extending another 2 nm on either side of th...

Watch this Scientific Journal Video about Atomically Traceable Nanostructure Fabrication at JoVE.com

Atomically Traceable Nanostructure Fabrication

We report a protocol for combining the atomic metrology of the Scanning Tunneling Microscope for surface patterning with selective Atomic Layer Deposition and Reactive Ion Etching. Using a robust process involving numerous atmospheric exposures and transport, 3D nanostructures with atomic metrology are fabricated.

Reducing the scale of etched nanostructures below the 10 nm range eventually will require an atomic scale understanding of the entire fabrication process ...

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8.7K Views.  Zyvex Labs. We report a protocol for combining the atomic metrology of the Scanning Tunneling Microscope for surface patterning with selective Atomic Layer Deposition and Reactive Ion Etching. Using a robust process involving numerous atmospheric exposures and transport, 3D nanostructures with atomic metrology are fabricated. 

Video: Atomically Traceable Nanostructure Fabrication

Fabrication, Densification, and Replica Molding of 3D Carbon Nanotube Microstructures

The introduction of new materials and processes to microfabrication has, in large part, enabled many important advances in microsystems, lab-on-a-chip devices, and their applications. In particular, capabilities for cost-effective fabrication of polymer microstructures were transformed by the advent of soft lithography and other micromolding techniques 1, 2, and this led a revolution in applications of microfabrication to biomedical engineering and biology. Nevertheless, it remains challenging to fabricate microstructures with well-defined nanoscale surface textures, and to fabricate arbitrary 3D shapes at the micro-scale. Robustness of master molds and maintenance of shape integrity is especially important to achieve high fidelity replication of complex structures and preserving their nanoscale surface texture. The combination of hierarchical textures, and heterogeneous shapes, is a profound challenge to existing microfabrication methods that largely rely upon top-down etching using fixed mask templates. On the other hand, the bottom-up synthesis of nanostructures such as nanotubes and nanowires can offer new capabilities to microfabrication, in particular by taking advantage of the collective self-organization of nanostructures, and local control of their growth behavior with respect to microfabricated patterns. 
Our goal is to introduce vertically aligned carbon nanotubes (CNTs), which we refer to as CNT "forests", as a new microfabrication material. We present details of a suite of related methods recently developed by our group: fabrication of CNT forest microstructures by thermal CVD from lithographically patterned catalyst thin films; self-directed elastocapillary densification of CNT microstructures; and replica molding of polymer microstructures using CNT composite master molds. In particular, our work shows that self-directed capillary densification ("capillary forming"), which is performed by condensation of a solvent onto the substrate with CNT microstructures, significantly increases the packing density of CNTs. This process enables directed transformation of vertical CNT microstructures into straight, inclined, and twisted shapes, which have robust mechanical properties exceeding those of typical microfabrication polymers. This in turn enables formation of nanocomposite CNT master molds by capillary-driven infiltration of polymers. The replica structures exhibit the anisotropic nanoscale texture of the aligned CNTs, and can have walls with sub-micron thickness and aspect ratios exceeding 50:1. Integration of CNT microstructures in fabrication offers further opportunity to exploit the electrical and thermal properties of CNTs, and diverse capabilities for chemical and biochemical functionalization 3.

We present methods for fabrication of patterned microstructures of vertically aligned carbon nanotubes (CNTs), and their use as master molds for production of polymer microstructures with organized nanoscale surface texture. The CNT forests are densified by condensation of solvent onto the substrate, which significantly increases their packing density and enables self-directed formation of 3D shapes.

The introduction of new materials and processes to microfabrication has, in large part, enabled many important advances in microsystems, lab-on-a-chip ...

Fabricating Nanogaps by Nanoskiving

There are several methods of fabricating nanogaps with controlled spacings, but the precise control over the sub-nanometer spacing between two electrodes-and generating them in practical quantities-is still challenging. The preparation of nanogap electrodes using nanoskiving, which is a form of edge lithography, is a fast, simple and powerful technique. This method is an entirely mechanical process which does not include any photo- or electron-beam lithographic steps and does not require any special equipment or infrastructure such as clean rooms. Nanoskiving is used to fabricate electrically addressable nanogaps with control over all three dimensions; the smallest dimension of these structures is defined by the thickness of the sacrificial layer (Al or Ag) or self-assembled monolayers. These wires can be manually positioned by transporting them on drops of water and are directly electrically-addressable; no further lithography is required to connect them to an electrometer.

The fabrication of electrically addressable, high-aspect-ratio (> 1000:1) metal nanowires separated by gaps of single nanometers using either sacrificial layers of aluminum and silver or self-assembled monolayers as templates is described. These nanogap structures are fabricated without a clean room or any photo- or electron-beam lithographic processes by a form of edge lithography known as nanoskiving.

There are several methods of fabricating nanogaps with controlled spacings, but the precise control over the sub-nanometer spacing between two ...

Chemistry

A Method to Fabricate Disconnected Silver Nanostructures in 3D

The standard nanofabrication toolkit includes techniques primarily aimed at creating 2D patterns in dielectric media. Creating metal patterns on a submicron scale requires a combination of nanofabrication tools and several material processing steps. For example, steps to create planar metal structures using ultraviolet photolithography and electron-beam lithography can include sample exposure, sample development, metal deposition, and metal liftoff. To create 3D metal structures, the sequence is repeated multiple times. The complexity and difficulty of stacking and aligning multiple layers limits practical implementations of 3D metal structuring using standard nanofabrication tools. Femtosecond-laser direct-writing has emerged as a pre-eminent technique for 3D nanofabrication.1,2 Femtosecond lasers are frequently used to create 3D patterns in polymers and glasses.3-7 However, 3D metal direct-writing remains a challenge. Here, we describe a method to fabricate silver nanostructures embedded inside a polymer matrix using a femtosecond laser centered at 800 nm. The method enables the fabrication of patterns not feasible using other techniques, such as 3D arrays of disconnected silver voxels.8 Disconnected 3D metal patterns are useful for metamaterials where unit cells are not in contact with each other,9 such as coupled metal dot10,11or coupled metal rod12,13 resonators. Potential applications include negative index metamaterials, invisibility cloaks, and perfect lenses.
In femtosecond-laser direct-writing, the laser wavelength is chosen such that photons are not linearly absorbed in the target medium. When the laser pulse duration is compressed to the femtosecond time scale and the radiation is tightly focused inside the target, the extremely high intensity induces nonlinear absorption. Multiple photons are absorbed simultaneously to cause electronic transitions that lead to material modification within the focused region. Using this approach, one can form structures in the bulk of a material rather than on its surface.
Most work on 3D direct metal writing has focused on creating self-supported metal structures.14-16 The method described here yields sub-micrometer silver structures that do not need to be self-supported because they are embedded inside a matrix. A doped polymer matrix is prepared using a mixture of silver nitrate (AgNO3), polyvinylpyrrolidone (PVP) and water (H2O). Samples are then patterned by irradiation with an 11-MHz femtosecond laser producing 50-fs pulses. During irradiation, photoreduction of silver ions is induced through nonlinear absorption, creating an aggregate of silver nanoparticles in the focal region. Using this approach we create silver patterns embedded in a doped PVP matrix. Adding 3D translation of the sample extends the patterning to three dimensions.

Femtosecond-laser direct-writing is frequently used to create three-dimensional (3D) patterns in polymers and glasses. However, patterning metals in 3D remains a challenge. We describe a method for fabricating silver nanostructures embedded inside a polymer matrix using a femtosecond laser centered at 800 nm.

The standard nanofabrication toolkit includes  techniques primarily aimed at creating 2D patterns in dielectric media. Creating  metal patterns on a ...

Ultrahigh Density Array of Vertically Aligned Small-molecular Organic Nanowires on Arbitrary Substrates

In recent years &pi;-conjugated organic semiconductors have emerged as the active material in a number of diverse applications including large-area, low-cost displays, photovoltaics, printable and flexible electronics and organic spin valves. Organics allow (a) low-cost, low-temperature processing and (b) molecular-level design of electronic, optical and spin transport characteristics. Such features are not readily available for mainstream inorganic semiconductors, which have enabled organics to carve a niche in the silicon-dominated electronics market. The first generation of organic-based devices has focused on thin film geometries, grown by physical vapor deposition or solution processing. However, it has been realized that organic nanostructures can be used to enhance performance of above-mentioned applications and significant effort has been invested in exploring methods for organic nanostructure fabrication.	
A particularly interesting class of organic nanostructures is the one in which vertically oriented organic nanowires, nanorods or nanotubes are organized in a well-regimented, high-density array. Such structures are highly versatile and are ideal morphological architectures for various applications such as chemical sensors, split-dipole nanoantennas, photovoltaic devices with radially heterostructured "core-shell" nanowires, and memory devices with a cross-point geometry. Such architecture is generally realized by a template-directed approach. In the past this method has been used to grow metal and inorganic semiconductor nanowire arrays. More recently &pi;-conjugated polymer nanowires have been grown within nanoporous templates. However, these approaches have had limited success in growing nanowires of technologically important &pi;-conjugated small molecular weight organics, such as tris-8-hydroxyquinoline aluminum (Alq3), rubrene and methanofullerenes, which are commonly used in diverse areas including organic displays, photovoltaics, thin film transistors and spintronics.	
Recently we have been able to address the above-mentioned issue by employing a novel "centrifugation-assisted" approach. This method therefore broadens the spectrum of organic materials that can be patterned in a vertically ordered nanowire array. Due to the technological importance of Alq3, rubrene and methanofullerenes, our method can be used to explore how the nanostructuring of these materials affects the performance of aforementioned organic devices. The purpose of this article is to describe the technical details of the above-mentioned protocol, demonstrate how this process can be extended to grow small-molecular organic nanowires on arbitrary substrates and finally, to discuss the critical steps, limitations, possible modifications, trouble-shooting and future applications.

We report a simple method for fabricating an ultrahigh density array of vertically ordered small-molecular organic nanowires. This method allows for synthesis of complex heterostructured hybrid nanowire geometries, which can be inexpensively grown on arbitrary substrates. These structures have potential applications in organic electronics, optoelectronics, chemical sensing, photovoltaics and spintronics.

In  recent years &pi;-conjugated  organic semiconductors have emerged as the active material in a number of  diverse applications including large-area, ...

Writing and Low-Temperature Characterization of Oxide Nanostructures

Oxide nanoelectronics is a rapidly growing field which seeks to develop novel materials with multifunctional behavior at nanoscale dimensions. Oxide interfaces exhibit a wide range of properties that can be controlled include conduction, piezoelectric behavior, ferromagnetism, superconductivity and nonlinear optical properties. Recently, methods for controlling these properties at extreme nanoscale dimensions have been discovered and developed. Here are described explicit step-by-step procedures for creating LaAlO3/SrTiO3 nanostructures using a reversible conductive atomic force microscopy technique. The processing steps for creating electrical contacts to the LaAlO3/SrTiO3 interface are first described. Conductive nanostructures are created by applying voltages to a conductive atomic force microscope tip and locally switching the LaAlO3/SrTiO3 interface to a conductive state. A versatile nanolithography toolkit has been developed expressly for the purpose of controlling the atomic force microscope (AFM) tip path and voltage. Then, these nanostructures are placed in a cryostat and transport measurements are performed. The procedures described here should be useful to others wishing to conduct research in oxide nanoelectronics.

Oxide nanostructures provide new opportunities for science and technology. The interfacial conductivity between LaAlO3 and SrTiO3 can be controlled with near-atomic precision using a conductive atomic force microscopy technique. The protocol for creating and measuring conductive nanostructures at LaAlO3/SrTiO3 interfaces is demonstrated.

Oxide nanoelectronics is a rapidly growing field which seeks to develop novel materials with multifunctional behavior at nanoscale dimensions.  Oxide ...

Fabrication of Nanopillar-Based Split Ring Resonators for Displacement Current Mediated Resonances in Terahertz Metamaterials

Terahertz (THz) split ring resonator (SRR) metamaterials (MMs) has been studied for gas, chemical, and biomolecular sensing applications because the SRR is not affected by environmental characteristics such as the temperature and pressure surrounding the resonator. Electromagnetic radiation in THz frequencies is biocompatible, which is a critical condition especially for the application of the biomolecular sensing. However, the quality factor (Q-factor) and frequency responses of traditional thin-film based split ring resonator (SRR) MMs are very low, which limits their sensitivities and selectivity as sensors. In this work, novel nanopillar-based SRR MMs, utilizing displacement current, are designed to enhance the Q-factor up to 450, which is around 45 times higher than that of traditional thin-film-based MMs. In addition to the enhanced Q-factor, the nanopillar-based MMs induce a larger frequency shifts (17 times compared to the shift obtained by the traditional thin-film based MMs). Because of the significantly enhanced Q-factors and frequency shifts as well as the property of biocompatible radiation, the THz nanopillar-based SRR are ideal MMs for the development of biomolecular sensors with high sensitivity and selectivity without inducing damage or distortion to biomaterials. A novel fabrication process has been demonstrated to build the nanopillar-based SRRs for displacement current mediated THz MMs. A two-step gold (Au) electroplating process and an atomic layer deposition (ALD) process are used to create sub-10 nm scale gaps between Au nanopillars. Since the ALD process is a conformal coating process, a uniform aluminum oxide (Al2O3) layer with nanometer-scale thickness can be achieved. By sequentially electroplating another Au thin film to fill the spaces between Al2O3 and Au, a close-packed Au-Al2O3-Au structure with nano-scale Al2O3 gaps can be fabricated. The size of the nano-gaps can be well defined by precisely controlling the deposition cycles of the ALD process, which has an accuracy of 0.1 nm.

A protocol for the design and fabrication of a novel nanopillar-based split ring resonator (SRR) is presented.

Terahertz (THz) split ring resonator (SRR) metamaterials (MMs) has been studied for gas, chemical, and biomolecular sensing applications because the SRR ...

A Standard and Reliable Method to Fabricate Two-Dimensional Nanoelectronics

Two-dimensional (2D) materials have attracted huge attention due to their unique properties and potential applications. Since wafer scale synthesis of 2D materials is still in nascent stages, scientists cannot fully rely on traditional semiconductor techniques for related research. Delicate processes from locating the materials to electrode definition need to be well controlled. In this article, a universal fabrication protocol required in manufacturing nanoscale electronics, such as 2D quasi-heterojunction bipolar transistors (Q-HBT), and 2D back-gated transistors are demonstrated. This protocol includes the determination of material position, electron beam lithography (EBL), metal electrode definition, et al. A step by step narrative of the fabrication procedures for these devices are also presented. Furthermore, results show that each of the fabricated devices has achieved high performance with high repeatability. This work reveals a comprehensive description of process flow for preparing 2D nano-electronics, enables the research groups to access this information, and pave the way toward future electronics.

The article aims to introduce a standard and reliable fabrication procedure for the development of future low dimensional nanoelectronics.

Two-dimensional (2D) materials have attracted huge attention due to their unique properties and potential applications. Since wafer scale synthesis of 2D ...

Multiscale Structures Aggregated by Imprinted Nanofibers for Functional Surfaces

Multiscale surface structures have attracted increasing interest owing to several potential applications in surface devices. However, an existing challenge in the field is the fabrication of hybrid micro-nano structures using a facile, cost-effective, and high-throughput method. To overcome these challenges, this paper proposes a protocol to fabricate multiscale structures using only an imprint process with an anodic aluminum oxide (AAO) filter and an evaporative self-aggregation process of nanofibers. Unlike previous attempts that have aimed to straighten nanofibers, we demonstrate a unique fabrication method for multiscale aggregated nanofibers with high aspect ratios. Furthermore, the surface morphology and wettability of these structures on various liquids were investigated to facilitate their use in multifunctional surfaces.

Presented is an easy method to fabricate nano-micro multiscale structures, for functional surfaces, by aggregating nanofibers fabricated using an anodic aluminum oxide filter.

Multiscale surface structures have attracted increasing interest owing to several potential applications in surface devices. However, an existing ...

A Label-free Technique for the Spatio-temporal Imaging of Single Cell Secretions

Inter-cellular communication is an integral part of a complex system that helps in maintaining basic cellular activities. As a result, the malfunctioning of such signaling can lead to many disorders. To understand cell-to-cell signaling, it is essential to study the spatial and temporal nature of the secreted molecules from the cell without disturbing the local environment. Various assays have been developed to study protein secretion, however, these methods are typically based on fluorescent probes which disrupt the relevant signaling pathways. To overcome this limitation, a label-free technique is required.
In this paper, we describe the fabrication and application of a label-free localized surface plasmon resonance imaging (LSPRi) technology capable of detecting protein secretions from a single cell. The plasmonic nanostructures are lithographically patterned onto a standard glass coverslip and can be excited using visible light on commercially available light microscopes. Only a small fraction of the coverslip is covered by the nanostructures and hence this technique is well suited for combining common techniques such as fluorescence and bright-field imaging.
A multidisciplinary approach is used in this protocol which incorporates sensor nanofabrication and subsequent biofunctionalization, binding kinetics characterization of ligand and analyte, the integration of the chip and live cells, and the analysis of the measured signal. As a whole, this technology enables a general label-free approach towards mapping cellular secretions and correlating them with the responses of nearby cells.

Inter-cellular communication is critical for controlling various physiological activities within and outside the cell. This paper describes a protocol for measuring the spatio-temporal nature of single cell secretions. To achieve this, a multidisciplinary approach is used which integrates label-free nanoplasmonic sensing with live cell imaging.

Inter-cellular communication is an integral part of a complex system that helps in maintaining basic cellular activities. As a result, the malfunctioning ...

Bioengineering

DNA Origami-Mediated Substrate Nanopatterning of Inorganic Structures for Sensing Applications

Structural DNA nanotechnology provides a viable route for building from the bottom-up using DNA as construction material. The most common DNA nanofabrication technique is called DNA origami, and it allows high-throughput synthesis of accurate and highly versatile structures with nanometer-level precision. Here, it is shown how the spatial information of DNA origami can be transferred to metallic nanostructures by combining the bottom-up DNA origami with the conventionally used top-down lithography approaches. This allows fabrication of billions of tiny nanostructures in one step onto selected substrates. The method is demonstrated using bowtie DNA origami to create metallic bowtie-shaped antenna structures on silicon nitride or sapphire substrates. The method relies on the selective growth of a silicon oxide layer on top of the origami deposition substrate, thus resulting in a patterning mask for following lithographic steps. These nanostructure-equipped surfaces can be further used as molecular sensors (e.g., surface-enhanced Raman spectroscopy (SERS)) and in various other optical applications at the visible wavelength range owing to the small feature sizes (sub-10 nm). The technique can be extended to other materials through methodological modifications; therefore, the resulting optically active surfaces may find use in development of metamaterials and metasurfaces.

Here, we describe a protocol to create discrete and accurate inorganic nanostructures on substrates using DNA origami shapes as guiding templates. The method is demonstrated by creating plasmonic gold bowtie-shaped antennas on a transparent substrate (sapphire).