Deposition and Microfabrication

Physical structures ranging in size from miniature objects (nanomaterials) to electrical devices (thin films) with planned properties can be made using the deposition and microfabrication capability. Materials with specific surface, bulk and interfacial properties for energy and environmental applications can be designed and made using these integrated capabilities.

Resources and Techniques

  • Functionalized surfaces – Design and manufacture surfaces optimized for specific functions related to catalysis and other areas.
  • Model systems for geochemistry/biogeochemistry – Grow model oxide and mineral films with varying structure and complexity.
  • Materials with designed properties – Film growth and ion implantation for materials with specific properties.
  • Chemical and biological sensing – Film and surface layer deposition and modification, micro and nano-lithography, and solution synthesis capabilities.
  • Microfabrication – Engineering, software development and fabrication are used to design and fabricate next-generation components.

Capability Details
• Unique oxygen-plasma-assisted molecular beam epitaxy system for designing and constructing high-quality oxide thin films
• Spin coating and wet chemical synthesis to prepare thin films and nanostructures
• Focused ion beam for nanolithography and deposition and manipulation of structures at the nano scale
• Microfabrication suite for designing and etching complex patterns into varied substrates
• Hybrid physical vapor deposition system for depositing thin films of metals, oxides, nitrides and alloys with high purity and thickness control
• Pulsed laser deposition for growing complex oxides films
• Low-energy ion deposition for preparing ultra-pure films of complex molecules, including biomolecules, through a mass-selected soft-landing process
• Diverse and unrivaled expertise in advanced signal acquisition and processing instrumentation, signal analysis algorithms, laboratory automation systems and scientific data management solutions

This instrument is newly available to EMSL users. For more information about this instrument and the science it will help enable, see the ...
Custodian(s): Ryan Kelly, Hardeep S Mehta
The FEI Helios Nanolab dual-beam focused ion beam/scanning electron microscopy (FIB/SEM) microscope combines two important high-resolution...
Custodian(s): Bruce Arey
Only available at EMSL, the Discovery Deposition System has been customized to be a fully automated multi-functional "hybrid" instrument with...
This instrument is newly available to EMSL users. For more information about this instrument and the science it will help enable, see the ...
Custodian(s): Ryan Kelly, Hardeep S Mehta
The mass-selected ion deposition system is a new instrument constructed at EMSL. The apparatus, shown in Figure 1, includes a high-transmission...
Custodian(s): Julia Laskin
Charge injection and transport in bottom-contact regioregular-poly(3-hexylthiophene) (rr-P3HT) based field-effect transistors (FETs), wherein the Au...
Extracellular polymeric substances (EPS) secreted by suspended cultures of microorganisms from an activated sludge plant in the presence of glucose...
With many technologies and applications downscaling to nanometer dimensions, the influence of single point defects on electronic structure has shown...
Lithium (Li) dendrite formation is one of the critical challenges for rechargeable Li metal batteries. The traditional method to suppress Li...
The absolute coverages of water and small aliphatic alcohols (C1-C4) were determined on TiO2(110) using a combination of temperature programmed...
Posted: August 22, 2014
Scientists at EMSL and Pacific Northwest National Laboratory have generated a material that allows oxygen to efficiently move through it at...
Posted: August 07, 2013
Predictive models of biogeochemical interactions in soils are more accurate and scalable if they consider the reaction chemistry that occurs in...
Posted: July 29, 2013
Scientists have gained the first quantitative insights into electron transfer from minerals to microbes by studying that transfer in a nature-...
Posted: May 20, 2013
Pacific Northwest National Laboratory scientists working at EMSL wrote a review of how microfluidic devices are being used in scientific instruments...
Posted: March 19, 2013
One of the most noteworthy concerns for the U.S. Department of Energy is controlling atmospheric carbon dioxide to mitigate its effects on global...

Physical structures ranging in size from miniature objects (nanomaterials) to electrical devices (thin films) with planned properties can be made using the deposition and microfabrication capability. Materials with specific surface, bulk and interfacial properties for energy and environmental applications can be designed and made using these integrated capabilities.

Resources and Techniques

  • Functionalized surfaces – Design and manufacture surfaces optimized for specific functions related to catalysis and other areas.
  • Model systems for geochemistry/biogeochemistry – Grow model oxide and mineral films with varying structure and complexity.
  • Materials with designed properties – Film growth and ion implantation for materials with specific properties.
  • Chemical and biological sensing – Film and surface layer deposition and modification, micro and nano-lithography, and solution synthesis capabilities.
  • Microfabrication – Engineering, software development and fabrication are used to design and fabricate next-generation components.

Changes in Translational Efficiency is a Dominant Regulatory Mechanism in the Environmental Response of Bacteria.

Abstract: 

To understand how cell physiological state affects mRNA translation, we used Shewanella oneidensis MR-1 grown under steady state conditions at either aerobic or suboxic conditions. Using a combination of quantitative proteomics and RNA-Seq, we generated high-confidence data on >1000 mRNA and protein pairs. By using a steady state model, we found that differences in protein-mRNA ratios were primarily caused by differences in the translational efficiency of specific genes. When oxygen levels were lowered, 28% of the proteins showed at least a 2-fold change in expression. Altered transcription levels appeared responsible for 26% of the protein changes, altered translational efficiency appeared responsible for 46% and a combination of both were responsible for the remaining 28%. Changes in translational efficiency were significantly correlated with the codon usage pattern of the genes and measurable tRNA pools changed in response to altered O2 levels. Our results suggest that changes in the translational efficiency of proteins, in part caused by altered tRNA pools, is a major determinant of regulated protein expression in bacteria.

Citation: 
Taylor RC, BJM Webb-Robertson, LM Markillie, MH Serres, BE Linggi, JT Aldrich, EA Hill, MF Romine, MS Lipton, and HS Wiley.2013."Changes in Translational Efficiency is a Dominant Regulatory Mechanism in the Environmental Response of Bacteria."Integrative Biology 5(11):1393-1406. doi:10.1039/C3IB40120K
Authors: 
RC Taylor
BJM Webb-Robertson
LM Markillie
MH Serres
BE Linggi
JT Aldrich
EA Hill
MF Romine
MS Lipton
HS Wiley
Facility: 
Volume: 
5
Issue: 
11
Pages: 
1393-1406
Publication year: 
2013

Amino acid treatment enhances protein recovery from sediment and soils for metaproteomic studies .

Abstract: 

Characterization of geomicrobial protein expression provides information necessary to better understand the unique biological pathways that occur within soil microbial communities and the role they play in regulating atmospheric CO2 levels and the Earth’s climate. A significant challenge in studying soil microbial proteins is their initial dissociation from the complex mixture of particles found in natural soil. Due to bias of the most robust cells, the removal of intact bacterial cells limits the characterization of the complete representation of a microbial community. However, in-situ lysis of bacterial cells leads to the expulsion of proteins to the soil surface, which can lead to potentially high levels of adsorption due to the physicochemical properties of both the protein and the soil. We investigated various compounds for their ability to block protein adsorption soil sites prior to in-situ lysis of bacterial cells, as well as their compatibility with both tryptic digestion and mass spectrometric analysis. The treatments were tested by adding lysed Escherichia coli proteins to representative treated and untreated soil samples. The results show that it is possible to significantly increase protein identifications through blockage of binding sites on a variety of soil textures; use of an optimized desorption buffer further increases the number of identifications.

Citation: 
Nicora CD, BJ Anderson, SJ Callister, AD Norbeck, SO Purvine, JK Jansson, OU Mason, M David, DD Jurelevicius, RD Smith, and MS Lipton.2013."Amino acid treatment enhances protein recovery from sediment and soils for metaproteomic studies ."Proteomics 13(18-19):2776-2785. doi:10.1002/pmic.201300003
Authors: 
CD Nicora
BJ Anderson
SJ Callister
AD Norbeck
SO Purvine
JK Jansson
OU Mason
M David
DD Jurelevicius
RD Smith
MS Lipton
Facility: 
Instruments: 
Volume: 
13
Pages: 
2776-2785
Publication year: 
2013

Proteome Analyses of Strains ATCC 51142 and PCC 7822 of the Diazotrophic Cyanobacterium Cyanothece sp under Culture Conditions

Abstract: 

Cultures of the cyanobacterial genus Cyanothece have been shown to produce high levels of biohydrogen. These strains are diazotrophic and undergo pronounced diurnal cycles when grown under N2-fixing conditions in light-dark cycles. We seek to better understand the way in which proteins respond to these diurnal changes and we performed quantitative proteome analysis of Cyanothece ATCC 51142 and PCC 7822 grown under 8 different nutritional conditions. Nitrogenase expression was limited to N2-fixing conditions, and in the absence of glycerol, nitrogenase gene expression was linked to the dark period. However, glycerol induced expression of nitrogenase during part of the light period, together with cytochrome c oxidase (Cox), glycogen phosphorylase (Glp), and glycolytic and pentose-phosphate pathway (PPP) enzymes. This indicated that nitrogenase expression in the light was facilitated via higher respiration and glycogen breakdown. Key enzymes of the Calvin cycle were inhibited in Cyanothece ATCC 51142 in the presence of glycerol under H2 producing conditions, suggesting a competition between these sources of carbon. However, in Cyanothece PCC 7822, the Calvin cycle still played a role in cofactor recycling during H2 production. Our data comprise the first comprehensive profiling of proteome changes in Cyanothece PCC 7822, and allows an in-depth comparative analysis of major physiological and biochemical processes that influence H2-production in both the strains. Our results revealed many previously uncharacterized proteins that may play a role in nitrogenase activity and in other metabolic pathways and may provide suitable targets for genetic manipulation that would lead to improvement of large scale H2 production.

Citation: 
Aryal UK, SJ Callister, S Mishra, X Zhang, JI Shutthanandan, TE Angel, AK Shukla, ME Monroe, RJ Moore, DW Koppenaal, RD Smith, and L Sherman.2013."Proteome Analyses of Strains ATCC 51142 and PCC 7822 of the Diazotrophic Cyanobacterium Cyanothece sp under Culture Conditions Resulting in Enhanced H-2 Production."Applied and Environmental Microbiology 79(4):1070-1077. doi:10.1128/AEM.02864-12
Authors: 
UK Aryal
SJ Callister
S Mishra
X Zhang
JI Shutthanan
TE Angel
AK Shukla
ME Monroe
RJ Moore
DW Koppenaal
RD Smith
L Sherman
Facility: 
Instruments: 
Volume: 
79
Issue: 
4
Pages: 
1070-1077
Publication year: 
2013

Aerosolized ZnO nanoparticles induce toxicity in alveolar type II epithelial cells at the air-liquid interface.

Abstract: 

The majority of in vitro studies characterizing the impact of engineered nanoparticles (NPs) on cells that line the respiratory tract were conducted in cells exposed to NPs in suspension. This approach introduces processes that are unlikely to occur during inhaled NP exposures in vivo, such as the shedding of toxic doses of dissolved ions. ZnO NPs are used extensively and pose significant sources for human exposure. Exposures to airborne ZnO NPs can induce adverse effects, but the relevance of the dissolved Zn2+ to the observed effects in vivo is still unclear. Our goal was to mimic in vivo exposures to airborne NPs and decipher the contribution of the intact NP from the contribution of the dissolved ions to airborne ZnO NP toxicity. We established the exposure of alveolar type II epithelial cells to aerosolized NPs at the air-liquid interface (ALI), and compared the impact of aerosolized ZnO NPs and NPs in suspension at the same cellular doses, measured as the number of particles per cell. By evaluating membrane integrity and cell viability 6 and 24 hours post exposure we found that aerosolized NPs induced toxicity at the ALI at doses that were in the same order of magnitude as doses required to induce toxicity in submersed cultures. In addition, distinct patterns of oxidative stress were observed in the two exposure systems. These observations unravel the ability of airborne ZnO NPs to induce toxicity without the contribution of dissolved Zn2+ and suggest distinct mechanisms at the ALI and in submersed cultures.

Citation: 
Xie Y, NG Williams, A Tolic, WB Chrisler, JG Teeguarden, BL Maddux, JG Pounds, A Laskin, and G Orr.2012."Aerosolized ZnO nanoparticles induce toxicity in alveolar type II epithelial cells at the air-liquid interface."Toxicological Sciences 125(2):450-461. doi:10.1093/toxsci/kfr251
Authors: 
Y Xie
NG Williams
A Tolic
WB Chrisler
JG Teeguarden
BL Maddux
JG Pounds
A Laskin
G Orr
Facility: 
Volume: 
125
Issue: 
2
Pages: 
450-461
Publication year: 
2012

Cellular Recognition and Trafficking of Amorphous Silica Nanoparticles by Macrophage Scavenger Receptor A.

Abstract: 

The internalization of engineered nanoparticles (ENPs) into cells is known to involve active transport mechanisms, yet the precise biological molecules involved are poorly understood. We demonstrate that the uptake of amorphous silica ENPs (92 nm) by macrophage cells is strongly inhibited by silencing expression of scavenger receptor A (SR-A). In addition, ENP uptake is augmented by introducing SR-A expression into human cells that are normally non-phagocytic. Confocal fluorescent microscopy analyses show that the majority of single or small clusters of silica ENPs co-localize intracellularly with SR-A and are internalized through a pathway characteristic of clathrin-dependent endocytosis. In contrast, larger silica NP agglomerates (>500 nm) are poorly co-localized with the receptor, suggesting independent trafficking or internalization pathways are involved. SR-A silencing also caused decreased cellular secretion of pro-inflammatory cytokines in response to silica ENPs. As SR-A is expressed in macrophages throughout the reticulo-endothelial system, this pathway is likely an important determinant of the biodistribution of, and cellular response to ENPs.

Citation: 
Orr G, WB Chrisler, KJ Cassens, R Tan, BJ Tarasevich, LM Markillie, RC Zangar, and BD Thrall.2011."Cellular Recognition and Trafficking of Amorphous Silica Nanoparticles by Macrophage Scavenger Receptor A."Nanotoxicology 5(3):296-311. doi:10.3109/17435390.2010.513836
Authors: 
G Orr
WB Chrisler
KJ Cassens
R Tan
BJ Tarasevich
LM Markillie
RC Zangar
BD Thrall
Facility: 
Volume: 
5
Issue: 
3
Pages: 
296-311
Publication year: 
2011

7 Å Resolution in Protein 2-Dimentional-Crystal X-Ray Diffraction at Linac Coherent Light Source.

Abstract: 

Membrane proteins arranged as two-dimensional (2D) crystals in the lipid en- vironment provide close-to-physiological structural information, which is essential for understanding the molecular mechanisms of protein function. X-ray diffraction from individual 2D crystals did not represent a suitable investigation tool because of radiation damage. The recent availability of ultrashort pulses from X-ray Free Electron Lasers (X-FELs) has now provided a mean to outrun the damage. Here we report on measurements performed at the LCLS X-FEL on bacteriorhodopsin 2D crystals mounted on a solid support and kept at room temperature. By merg- ing data from about a dozen of single crystal diffraction images, we unambiguously identified the diffraction peaks to a resolution of 7 °A, thus improving the observable resolution with respect to that achievable from a single pattern alone. This indicates that a larger dataset will allow for reliable quantification of peak intensities, and in turn a corresponding increase of resolution. The presented results pave the way to further X-FEL studies on 2D crystals, which may include pump-probe experiments at subpicosecond time resolution.

Citation: 
Pedrini B, CJ Tsai, G Capitani, C Padeste, M Hunter, NA Zatsepin, A Barty, H Benner, S Boutet, GK Feld, S Hau-Riege, R Kirian, C Kupitz, M Messerschmidt, JI Ogren, T Pardini, B Segelke, GJ Williams, JC Spence , R Abela, MA Coleman, JE Evans, G Schertler, M Frank, and XD Li.2014."7 Å Resolution in Protein 2-Dimentional-Crystal X-Ray Diffraction at Linac Coherent Light Source."Philosophical Transactions of the Royal Society of London Series B, Biological Sciences 369(1647):Article No. 20130500. doi:10.1098/rstb.2013.0500
Authors: 
B Pedrini
CJ Tsai
G Capitani
C Padeste
M Hunter
NA Zatsepin
A Barty
H Benner
S Boutet
GK Feld
S Hau-Riege
R Kirian
C Kupitz
M Messerschmidt
JI Ogren
T Pardini
B Segelke
GJ Williams
JC Spence
R Abela
MA Coleman
JE Evans
G Schertler
M Frank
XD Li
Instruments: 
Publication year: 
2014

In situ molecular imaging of hydrated biofilm in a microfluidic reactor by ToF-SIMS.

Abstract: 

The first results of using a novel single channel microfluidic reactor to enable Shewanella biofilm growth and in situ characterization using time-of-flight secondary ion mass spectrometry (ToF-SIMS) in the hydrated environment are presented. The new microfluidic interface allows direct probing of the liquid surface using ToF-SIMS, a vacuum surface technique. The detection window is an aperture of 2 m in diameter on a thin silicon nitride (SiN) membrane and it allows direct detection of the liquid surface. Surface tension of the liquid flowing inside the microchannel holds the liquid within the aperture. ToF-SIMS depth profiling was used to drill through the SiN membrane and the biofilm grown on the substrate. In situ 2D imaging of the biofilm in hydrated state was acquired, providing spatial distribution of the chemical compounds in the biofilm system. This data was compared with a medium filled microfluidic reactor devoid of biofilm and dried biofilm samples deposited on clean silicon wafers. Principle Component Analysis (PCA) was used to investigate these observations. Our results show that imaging biofilms in the hydrated environment using ToF-SIMS is possible using the unique microfluidic reactor. Moreover, characteristic biofilm fatty acids fragments were observed in the hydrated biofilm grown in the microfluidic channel, illustrating the advantage of imaging biofilm in its native environment.

Citation: 
Hua X, XY Yu, Z Wang, L Yang, B Liu, Z Zhu, AE Tucker, WB Chrisler, EA Hill, S Thevuthasan, Y Lin, S Liu, and MJ Marshall.2014."In situ molecular imaging of hydrated biofilm in a microfluidic reactor by ToF-SIMS."Analyst 139:1609-1613. doi:10.1039/C3AN02262E
Authors: 
X Hua
XY Yu
Z Wang
L Yang
B Liu
Z Zhu
AE Tucker
WB Chrisler
EA Hill
S Thevuthasan
Y Lin
S Liu
MJ Marshall
Instruments: 
Publication year: 
2014

Absorption Mode FT-ICR Mass Spectrometry Imaging.

Abstract: 

Fourier transform ion cyclotron resonance mass spectrometry offers the highest mass resolving power for molecular imaging experiments. This high mass resolving power ensures that closely spaced peaks at the same nominal mass are resolved for proper image generation. Typically higher magnetic fields are used to increase mass resolving power. However, a gain in mass resolving power can also be realized by phase correction of the data for absorption mode display. In addition to mass resolving power, absorption mode offers higher mass accuracy and signal-to-noise ratio over the conventional magnitude mode. Here we present the first use of absorption mode for Fourier transform ion cyclotron resonance mass spectrometry imaging. The Autophaser algorithm is used to phase correct each spectrum (pixel) in the image and then these parameters are used by the Chameleon work-flow based data processing software to generate absorption mode ?Datacubes? for image and spectral viewing. Absorption mode reveals new mass and spatial features that are not resolved in magnitude mode and results in improved selected ion image contrast.

Citation: 
Smith DF, DP Kilgour, M Konijnenburg, PB O'Connor, and RM Heeren.2013."Absorption Mode FT-ICR Mass Spectrometry Imaging."Analytical Chemistry 85(23):11180-11184. doi:10.1021/ac403039t
Authors: 
DF Smith
DP Kilgour
M Konijnenburg
PB O'Connor
RM Heeren
Instruments: 
Volume: 
85
Issue: 
23
Pages: 
11180-11184
Publication year: 
2013

Current Understanding and Remaining Challenges in Modeling Long-Term Degradation of Borosilicate Nuclear Waste Glasses.

Abstract: 

Chemical durability is not a single material property that can be uniquely measured. Instead it is the response to a host of coupled material and environmental processes whose rates are estimated by a combination of theory, experiment, and modeling. High-level nuclear waste (HLW) glass is perhaps the most studied of any material yet there remain significant technical gaps regarding their chemical durability. The phenomena affecting the long-term performance of HLW glasses in their disposal environment include surface reactions, transport properties to and from the reacting glass surface, and ion exchange between the solid glass and the surrounding solution and alteration products. The rates of these processes are strongly influenced and are coupled through the solution chemistry, which is in turn influenced by the reacting glass and also by reaction with the near-field materials and precipitation of alteration products. Therefore, those processes must be understood sufficiently well to estimate or bound the performance of HLW glass in its disposal environment over geologic time-scales. This article summarizes the current state of understanding of surface reactions, transport properties, and ion exchange along with the near-field materials and alteration products influences on solution chemistry and glass reaction rates. Also summarized are the remaining technical gaps along with recommended approaches to fill those technical gaps.

Citation: 
Vienna JD, JV Ryan, S Gin, and Y Inagaki.2013."Current Understanding and Remaining Challenges in Modeling Long-Term Degradation of Borosilicate Nuclear Waste Glasses."International Journal of Applied Glass Science 4(4):283-294. doi:10.1111/ijag.12050
Authors: 
JD Vienna
JV Ryan
S Gin
Y Inagaki
Instruments: 
Volume: 
4
Issue: 
4
Pages: 
283-294
Publication year: 
2013

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