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Chemical Force Microscopy of Chemical and Biological Interactions

Description: Interactions between chemical functionalities define outcomes of the vast majority of important events in chemistry, biology and materials science. Chemical Force Microscopy (CFM)--a technique that uses direct chemical functionalization of AFM probes with specific functionalities--allows researchers to investigate these important interactions directly. We review the basic principles of CFM, some examples of its application, and theoretical models that provide the basis for understanding the experimental results. We also emphasize application of modern kinetic theory of non-covalent interactions strength to the analysis of CFM data.
Date: January 2, 2006
Creator: Noy, A
Partner: UNT Libraries Government Documents Department

Fabrication and Characterization of Suspended Carbon Nanotube Devices in Liquid

Description: Suspended carbon nanotube devices are a promising platform for future bio-electronic applications. Suspended carbon nanotube transistors have been previously fabricated in air; however all previous attempts to bring them into liquid failed. We analyze forces acting on the suspended nanotube devices during immersion into liquids and during device operation and show that surface tension forces acting on the suspended nanotubes during transfer into the liquid phase are responsible for the nanotube damage. We have developed a new strategy that circumvents these limitations by coating suspended nanotubes with a rigid inorganic shell in the gas phase. The coating reinforces the nanotubes and allows them to survive transfer through the interface. Subsequent removal of the coating in the solution phase restores pristine suspended nanotubes. We demonstrate that devices fabricated using this technique preserve their original electrical characteristics.
Date: October 30, 2006
Creator: Artyukhin, A; Stadermann, M; Stroeve, P; Bakajin, O & Noy, A
Partner: UNT Libraries Government Documents Department

Chemical Force Microscopy: Probing Chemical Origin of Interfacial Forces and Adhesion

Description: Experimental methods of measuring intermolecular interactions have had several recent developments which have improved our understanding of chemical forces. First, they allowed direct exploration of the role that different functionalities, solvents and environmental variables play in shaping the strength of intermolecular interactions. Chemical force microscopy approach, in particular, became an extremely effective tool for exploring the contributions of each of these factors. Second, CFM studies clearly debunked the naive notion that intermolecular interaction strength is determined only by the nature of the interacting groups. These studies showed that the interaction strength between two chemical species must always considered in context of the environment surrounding these species. Third, CFM studies highlighted the critical role solvent plays in shaping intermolecular interactions in condensed phases. Emerging kinetic view of the intermolecular interactions introduced a completely new paradigm for understanding these interactions. Kinetic modeling showed that the measured interactions strength depends not only on the energy landscape of the system, but also on the loading history prior to the bond break-up. This new paradigm refocused our attention to the energy landscape as a fundamental characteristic of the interaction. Moreover, dynamic force spectroscopy, derived from kinetic models, allowed direct characterization of the geometry of the potential energy barrier, while some other methods attempt to probe the equilibrium energy landscape directly. Further investigations of the interactions in different systems, especially interactions between biomolecules, will uncover many interesting characteristics of intermolecular potentials. These studies have the potential to reveal, for the first time, a true picture of the energy landscapes of adhesion processes in complex chemical and biological systems.
Date: March 21, 2005
Creator: Vezenov, D V; Noy, A & Ashby, P
Partner: UNT Libraries Government Documents Department

Single Molecule Studies of Chromatin

Description: In eukaryotic cells, DNA is packaged as chromatin, a highly ordered structure formed through the wrapping of the DNA around histone proteins, and further packed through interactions with a number of other proteins. In order for processes such as DNA replication, DNA repair, and transcription to occur, the structure of chromatin must be remodeled such that the necessary enzymes can access the DNA. A number of remodeling enzymes have been described, but our understanding of the remodeling process is hindered by a lack of knowledge of the fine structure of chromatin, and how this structure is modulated in the living cell. We have carried out single molecule experiments using atomic force microscopy (AFM) to study the packaging arrangements in chromatin from a variety of cell types. Comparison of the structures observed reveals differences which can be explained in terms of the cell type and its transcriptional activity. During the course of this project, sample preparation and AFM techniques were developed and optimized. Several opportunities for follow-up work are outlined which could provide further insight into the dynamic structural rearrangements of chromatin.
Date: February 6, 2006
Creator: Jeans, C; Thelen, M P & Noy, A
Partner: UNT Libraries Government Documents Department

Strength of Multiple Parallel Biological Bonds

Description: Multivalent interactions play a critical role in a variety of biological processes on both molecular and cellular levels. We have used molecular force spectroscopy to investigate the strength of multiple parallel peptide-antibody bonds using a system that allowed us to determine the rupture forces and the number of ruptured bonds independently. In our experiments the interacting molecules were attached to the surfaces of the probe and sample of the atomic force microscope with flexible polymer tethers, and unique mechanical signature of the tethers determined the number of ruptured bonds. We show that the rupture forces increase with the number of interacting molecules and that the measured forces obey the predictions of a Markovian model for the strength of multiple parallel bonds. We also discuss the implications of our results to the interpretation of force spectroscopy measurements in multiple bond systems.
Date: December 7, 2005
Creator: Sulchek, T A; Friddle, R W & Noy, A
Partner: UNT Libraries Government Documents Department

Persistence Length Control of the Polyelectrolyte Layer-by-Layer Self-Assembly on Carbon Nanotubes

Description: One-dimensional inorganic materials such as carbon nanotubes1 and semiconductor nanowires have been central to important advances in materials science in the last decade. Unique mechanical and electronic properties of these molecular-scale wires enabled a variety of applications ranging from novel composite materials, to electronic circuits, to new sensors. Often, these applications require non-covalent modification of carbon nanotubes with organic compounds, DNA and biomolecules, and polymers to change nanotube properties or to add new functionality. We recently demonstrated a versatile and flexible strategy for non-covalent modification of carbon nanotubes using layer-by-layer self-assembly of polyelectrolytes. Researchers used this technique extensively for modification of flat surfaces, micro-, and nano-particles; however, little is known about the mechanism and the factors influencing layer-by-layer self-assembly in one-dimensional nanostructures. The exact conformation of polyelectrolyte chains deposited on single-walled carbon nanotubes (SWNT) is still unknown. There are two possible configurations: flexible polymers wrapping around the nanotube and stretched, rigid chains stacked parallel to the nanotube axis. Several factors, such as polymer rigidity, surface curvature, and strength of polymer-surface interactions, can determine the nature of assembly. Persistence length of the polymer chain should be one of the critical parameters, since it determines the chain's ability to wrap around the nanotube. Indeed, computer simulations for spherical substrates show that polymer rigidity and substrate surface curvature can influence the deposition process. Computational models also show that the persistence length of the polymer must fall below the threshold values determined by target surface curvature in order to initiate polyelectrolyte deposition process. Although these models described the effects of salt concentration and target surface curvature, they considered only nano-particles with radius 5 nanometer and larger. One-dimensional materials, such as carbon nanotubes, provide an even more interesting template for studying self-assembly mechanisms, since they give us access to even smaller surface curvatures down to ...
Date: April 30, 2005
Creator: Huang, S J; Artyukhin, A B; Wang, Y; Ju, J; Stroeve, P & Noy, A
Partner: UNT Libraries Government Documents Department

Dynamic force spectroscopy of parallel individual mucin1-antibody bonds

Description: We used atomic force microscopy (AFM) to measure the binding forces between Mucin1 (MUC1) peptide and a single chain antibody fragment (scFv) selected from a scFv library screened against MUC1. This binding interaction is central to the design of the molecules for targeted delivery of radioimmunotherapeutic agents for prostate and breast cancer treatment. Our experiments separated the specific binding interaction from non-specific interactions by tethering the antibody and MUC1 molecules to the AFM tip and sample surface with flexible polymer spacers. Rupture force magnitude and elastic characteristics of the spacers allowed identification of the bond rupture events corresponding to different number of interacting proteins. We used dynamic force spectroscopy to estimate the intermolecular potential widths and equivalent thermodynamic off rates for mono-, bi-, and tri-valent interactions. Measured interaction potential parameters agree with the results of molecular docking simulation. Our results demonstrate that an increase of the interaction valency leads to a precipitous decline in the dissociation rate. Binding forces measured for mono and multivalent interactions match the predictions of a Markovian model for the strength of multiple uncorrelated bonds in parallel configuration. Our approach is promising for comparison of the specific effects of molecular modifications as well as for determination of the best configuration of antibody-based multivalent targeting agents.
Date: May 2, 2005
Creator: Sulchek, T A; Friddle, R W; Langry, K; Lau, E; Albrecht, H; Ratto, T et al.
Partner: UNT Libraries Government Documents Department

Ion Exclusion by Sub 2-nm Carbon Nanotube Pores

Description: Carbon nanotubes offer an outstanding platform for studying molecular transport at nanoscale, and have become promising materials for nanofluidics and membrane technology due to their unique combination of physical, chemical, mechanical, and electronic properties. In particular, both simulations and experiments have proved that fluid flow through carbon nanotubes of nanometer size diameter is exceptionally fast compared to what continuum hydrodynamic theories would predict when applied on this length scale, and also, compared to conventional membranes with pores of similar size, such as zeolites. For a variety of applications such as separation technology, molecular sensing, drug delivery, and biomimetics, selectivity is required together with fast flow. In particular, for water desalination, coupling the enhancement of the water flux with selective ion transport could drastically reduce the cost of brackish and seawater desalting. In this work, we study the ion selectivity of membranes made of aligned double-walled carbon nanotubes with sub-2 nm diameter. Negatively charged groups are introduced at the opening of the carbon nanotubes by oxygen plasma treatment. Reverse osmosis experiments coupled with capillary electrophoresis analysis of permeate and feed show significant anion and cation rejection. Ion exclusion declines by increasing ionic strength (concentration) of the feed and by lowering solution pH; also, the highest rejection is observed for the A{sub m}{sup Z{sub A}} C{sub n}{sup Z{sub C}} salts (A=anion, C=cation, z= valence) with the greatest Z{sub A}/Z{sub C} ratio. Our results strongly support a Donnan-type rejection mechanism, dominated by electrostatic interactions between fixed membrane charges and mobile ions, while steric and hydrodynamic effects appear to be less important. Comparison with commercial nanofiltration membranes for water softening reveals that our carbon nanotube membranes provides far superior water fluxes for similar ion rejection capabilities.
Date: April 9, 2008
Creator: Fornasiero, F; Park, H G; Holt, J K; Stadermann, M; Grigoropoulos, C P; Noy, A et al.
Partner: UNT Libraries Government Documents Department

A High-Flux, Flexible Membrane with Parylene-encapsulated Carbon Nanotubes

Description: We present fabrication and characterization of a membrane based on carbon nanotubes (CNTs) and parylene. Carbon nanotubes have shown orders of magnitude enhancement in gas and water permeability compared to estimates generated by conventional theories [1, 2]. Large area membranes that exhibit flux enhancement characteristics of carbon nanotubes may provide an economical solution to a variety of technologies including water desalination [3] and gas sequestration [4]. We report a novel method of making carbon nanotube-based, robust membranes with large areas. A vertically aligned dense carbon nanotube array is infiltrated with parylene. Parylene polymer creates a pinhole free transparent film by exhibiting high surface conformity and excellent crevice penetration. Using this moisture-, chemical- and solvent-resistant polymer creates carbon nanotube membranes that promise to exhibit high stability and biocompatibility. CNT membranes are formed by releasing a free-standing film that consists of parylene-infiltrated CNTs, followed by CNT uncapping on both sides of the composite material. Thus fabricated membranes show flexibility and ductility due to the parylene matrix material, as well as high permeability attributed to embedded carbon nanotubes. These membranes have a potential for applications that may require high flux, flexibility and durability.
Date: March 14, 2008
Creator: Park, H G; In, J; Kim, S; Fornasiero, F; Holt, J K; Grigoropoulos, C P et al.
Partner: UNT Libraries Government Documents Department

Nanofiltration of Electrolyte Solutions by Sub-2nm Carbon Nanotube Membranes

Description: Both MD simulations and experimental studies have shown that liquid and gas flow through carbon nanotubes with nanometer size diameter is exceptionally fast. For applications in separation technology, selectivity is required together with fast flow. In this work, we use pressure-driven filtration experiments to study ion exclusion in silicon nitride/sub-2-nm CNT composite membranes as a function of solution ionic strength, pH, and ion valence. We show that carbon nanotube membranes exhibit significant ion exclusion at low salt concentration. Our results support a rejection mechanism dominated by electrostatic interactions between fixed membrane charges and mobile ions, while steric and hydrodynamic effects appear to be less important. Comparison with commercial nanofiltration membranes for water softening reveals that our carbon nanotube membranes provides far superior water fluxes for similar ion rejection capabilities.
Date: March 13, 2008
Creator: Fornasiero, F; Park, H G; Holt, J K; Stadermann, M; Kim, S; In, J B et al.
Partner: UNT Libraries Government Documents Department

Formation, Stability, and Mobility of One-Dimensional Lipid Bilayer on High Curvature Substrates

Description: Curved lipid membranes are ubiquitous in living systems and play an important role in many biological processes. To understand how curvature and lipid composition affect membrane formation and fluidity we have assembled and studied mixed 1,2-Dioleoyl-sn-Glycero-3-Phosphocholine (DOPC) and 1,2-Dioleoyl-sn-Glycero-3-Phosphoethanolamine (DOPE) supported lipid bilayers on amorphous silicon nanowires with controlled diameters ranging from 20 nm to 200 nm. Addition of cone-shaped DOPE molecules to cylindrical DOPC molecules promotes vesicle fusion and bilayer formation on smaller diameter nanowires. Our experiments demonstrate that nanowire-supported bilayers are mobile, exhibit fast recovery after photobleaching, and have low concentration of defects. Lipid diffusion coefficients in these high-curvature tubular membranes are comparable to the values reported for flat supported bilayers and increase with decreasing nanowire diameter.
Date: March 23, 2007
Creator: Huang, J; Martinez, J; Artyukhin, A; Sirbuly, D; Wang, Y; Ju, J W et al.
Partner: UNT Libraries Government Documents Department

High-resolution ab initio Three-dimensional X-ray Diffraction Microscopy

Description: Coherent X-ray diffraction microscopy is a method of imaging non-periodic isolated objects at resolutions only limited, in principle, by the largest scattering angles recorded. We demonstrate X-ray diffraction imaging with high resolution in all three dimensions, as determined by a quantitative analysis of the reconstructed volume images. These images are retrieved from the 3D diffraction data using no a priori knowledge about the shape or composition of the object, which has never before been demonstrated on a non-periodic object. We also construct 2D images of thick objects with infinite depth of focus (without loss of transverse spatial resolution). These methods can be used to image biological and materials science samples at high resolution using X-ray undulator radiation, and establishes the techniques to be used in atomic-resolution ultrafast imaging at X-ray free-electron laser sources.
Date: August 19, 2005
Creator: Chapman, H N; Barty, A; Marchesini, S; Noy, A; Cui, C; Howells, M R et al.
Partner: UNT Libraries Government Documents Department

Progress in Three-Dimensional Coherent X-Ray Diffraction Imaging

Description: The Fourier inversion of phased coherent diffraction patterns offers images without the resolution and depth-of-focus limitations of lens-based tomographic systems. We report on our recent experimental images inverted using recent developments in phase retrieval algorithms, and summarize efforts that led to these accomplishments. These include ab-initio reconstruction of a two-dimensional test pattern, infinite depth of focus image of a thick object, and its high-resolution ({approx}10 nm resolution) three-dimensional image. Developments on the structural imaging of low density aerogel samples are discussed.
Date: September 30, 2005
Creator: Marchesini, S; Chapman, H N; Barty, A; Howells, M R; Cui, C; Spence, J H et al.
Partner: UNT Libraries Government Documents Department

FY05 LDRD Final Report, A Revolution in Biological Imaging

Description: X-ray free-electron lasers (XFELs) are currently under development and will provide a peak brightness more than 10 orders of magnitude higher than modern synchrotrons. The goal of this project was to perform the fundamental research to evaluate the possibility of harnessing these unique x-ray sources to image single biological particles and molecules at atomic resolution. Using a combination of computational modeling and experimental verification where possible, they showed that it should indeed be possible to record coherent scattering patterns from single molecules with pulses that are shorter than the timescales for the degradation of the structure due to the interaction with those pulses. They used these models to determine the effectiveness of strategies to allow imaging using longer XFEL pulses and to design validation experiments to be carried out at interim ultrafast sources. They also developed and demonstrated methods to recover three-dimensional (3D) images from coherent diffraction patterns, similar to those expected from XFELs. The images of micron-sized test objects are the highest-resolution 3D images of any noncrystalline material ever formed with x-rays. The project resulted in 14 publications in peer-reviewed journals and four records of invention.
Date: January 20, 2006
Creator: Chapman, H N; Bajt, S; Balhorn, R; Barty, A; Barsky, D; Bogan, M et al.
Partner: UNT Libraries Government Documents Department