Supramolecular assembly of multifunctional maspin-mimetic nanostructures as a potent peptide-based angiogenesis inhibitor

DOE PAGES

Zha, R. Helen; Sur, Shantanu; Boekhoven, Job; ...

2014-11-08

Aberrant angiogenesis plays a large role in pathologies ranging from tumor growth to macular degeneration. Anti-angiogenic proteins have thus come under scrutiny as versatile, potent therapeutics but face problems with purification and tissue retention. We report here on the synthesis of supramolecular nanostructures that mimic the anti-angiogenic activity of maspin, a class II tumor suppressor protein. These maspin-mimetic nanostructures are formed via self-assembly of small peptide amphiphiles containing the g-helix motif of maspin. Using tubulogenesis assays with human umbilical vein endothelial cells, we demonstrate that maspin-mimetic nanostructures show anti-angiogenic activity at concentrations that are significantly lower than those necessary formore » the g-helix peptide. Furthermore, in vivo assays in the chick chorioallantoic membrane show maspin-mimetic nanostructures to be effective over controls at inhibiting angiogenesis. Thus, in conclusion, the nanostructures investigated here offer an attractive alternative to the use of anti-angiogenic recombinant proteins in the treatment of cancer or other diseases involving abnormal blood vessel formation.« less

Optimized Assembly of a Multifunctional RNA-Protein Nanostructure in a Cell-Free Gene Expression System.

PubMed

Schwarz-Schilling, Matthaeus; Dupin, Aurore; Chizzolini, Fabio; Krishnan, Swati; Mansy, Sheref S; Simmel, Friedrich C

2018-04-11

Molecular complexes composed of RNA molecules and proteins are promising multifunctional nanostructures for a wide variety of applications in biological cells or in artificial cellular systems. In this study, we systematically address some of the challenges associated with the expression and assembly of such hybrid structures using cell-free gene expression systems. As a model structure, we investigated a pRNA-derived RNA scaffold functionalized with four distinct aptamers, three of which bind to proteins, streptavidin and two fluorescent proteins, while one binds the small molecule dye malachite green (MG). Using MG fluorescence and Förster resonance energy transfer (FRET) between the RNA-scaffolded proteins, we assess critical assembly parameters such as chemical stability, binding efficiency, and also resource sharing effects within the reaction compartment. We then optimize simultaneous expression and coassembly of the RNA-protein nanostructure within a single-compartment cell-free gene expression system. We demonstrate expression and assembly of the multicomponent nanostructures inside of emulsion droplets and their aptamer-mediated localization onto streptavidin-coated substrates, plus the successful assembly of the hybrid structures inside of bacterial cells.

Plasmonic nanostructures for bioanalytical applications of SERS

NASA Astrophysics Data System (ADS)

Kahraman, Mehmet; Wachsmann-Hogiu, Sebastian

2016-03-01

Surface-enhanced Raman scattering (SERS) is a potential analytical technique for the detection and identification of chemicals and biological molecules and structures in the close vicinity of metallic nanostructures. We present a novel method to fabricate tunable plasmonic nanostructures and perform a comprehensive structural and optical characterization of the structures. Spherical latex particles are uniformly deposited on glass slides and used as templates to obtain nanovoid structures on polydimethylsiloxane surfaces. The diameter and depth of the nanovoids are controlled by the size of the latex particles. The nanovoids are coated with a thin Ag layer for fabrication of uniform plasmonic nanostructures. Structural characterization of the surfaces is performed by scanning electron microscopy (SEM) and atomic force microscopy (AFM). Optical properties of these plasmonic nanostructures are evaluated via UV/Vis spectroscopy, and SERS. The sample preparation step is the key point to obtain strong and reproducible SERS spectra from the biological structures. When the colloidal suspension is used as a SERS substrate for the protein detection, the electrostatic interaction of the proteins with the nanoparticles is described by the nature of their charge status, which influences the aggregation properties such as the size and shape of the aggregates, which is critical for the SERS experiment. However, when the solid SERS substrates are fabricated, SERS signal of the proteins that are background free and independent of the protein charge. Pros and cons of using plasmonic nano colloids and nanostructures as SERS substrate will be discussed for label-free detection of proteins using SERS.

Boundary Condition for Modeling Semiconductor Nanostructures

NASA Technical Reports Server (NTRS)

Lee, Seungwon; Oyafuso, Fabiano; von Allmen, Paul; Klimeck, Gerhard

2006-01-01

A recently proposed boundary condition for atomistic computational modeling of semiconductor nanostructures (particularly, quantum dots) is an improved alternative to two prior such boundary conditions. As explained, this boundary condition helps to reduce the amount of computation while maintaining accuracy.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zha, R. Helen; Sur, Shantanu; Boekhoven, Job

Aberrant angiogenesis plays a large role in pathologies ranging from tumor growth to macular degeneration. Anti-angiogenic proteins have thus come under scrutiny as versatile, potent therapeutics but face problems with purification and tissue retention. We report here on the synthesis of supramolecular nanostructures that mimic the anti-angiogenic activity of maspin, a class II tumor suppressor protein. These maspin-mimetic nanostructures are formed via self-assembly of small peptide amphiphiles containing the g-helix motif of maspin. Using tubulogenesis assays with human umbilical vein endothelial cells, we demonstrate that maspin-mimetic nanostructures show anti-angiogenic activity at concentrations that are significantly lower than those necessary formore » the g-helix peptide. Furthermore, in vivo assays in the chick chorioallantoic membrane show maspin-mimetic nanostructures to be effective over controls at inhibiting angiogenesis. Thus, in conclusion, the nanostructures investigated here offer an attractive alternative to the use of anti-angiogenic recombinant proteins in the treatment of cancer or other diseases involving abnormal blood vessel formation.« less

In vivo production of RNA nanostructures via programmed folding of single-stranded RNAs.

PubMed

Li, Mo; Zheng, Mengxi; Wu, Siyu; Tian, Cheng; Liu, Di; Weizmann, Yossi; Jiang, Wen; Wang, Guansong; Mao, Chengde

2018-06-06

Programmed self-assembly of nucleic acids is a powerful approach for nano-constructions. The assembled nanostructures have been explored for various applications. However, nucleic acid assembly often requires chemical or in vitro enzymatical synthesis of DNA or RNA, which is not a cost-effective production method on a large scale. In addition, the difficulty of cellular delivery limits the in vivo applications. Herein we report a strategy that mimics protein production. Gene-encoded DNA duplexes are transcribed into single-stranded RNAs, which self-fold into well-defined RNA nanostructures in the same way as polypeptide chains fold into proteins. The resulting nanostructure contains only one component RNA molecule. This approach allows both in vitro and in vivo production of RNA nanostructures. In vivo synthesized RNA strands can fold into designed nanostructures inside cells. This work not only suggests a way to synthesize RNA nanostructures on a large scale and at a low cost but also facilitates the in vivo applications.

Shape-specific nanostructured protein mimics from de novo designed chimeric peptides.

PubMed

Jiang, Linhai; Yang, Su; Lund, Reidar; Dong, He

2018-01-30

Natural proteins self-assemble into highly-ordered nanoscaled architectures to perform specific functions. The intricate functions of proteins have provided great impetus for researchers to develop strategies for designing and engineering synthetic nanostructures as protein mimics. Compared to the success in engineering fibrous protein mimetics, the design of discrete globular protein-like nanostructures has been challenging mainly due to the lack of precise control over geometric packing and intermolecular interactions among synthetic building blocks. In this contribution, we report an effective strategy to construct shape-specific nanostructures based on the self-assembly of chimeric peptides consisting of a coiled coil dimer and a collagen triple helix folding motif. Under salt-free conditions, we showed spontaneous self-assembly of the chimeric peptides into monodisperse, trigonal bipyramidal-like nanoparticles with precise control over the stoichiometry of two folding motifs and the geometrical arrangements relative to one another. Three coiled coil dimers are interdigitated on the equatorial plane while the two collagen triple helices are located in the axial position, perpendicular to the coiled coil plane. A detailed molecular model was proposed and further validated by small angle X-ray scattering experiments and molecular dynamics (MD) simulation. The results from this study indicated that the molecular folding of each motif within the chimeric peptides and their geometric packing played important roles in the formation of discrete protein-like nanoparticles. The peptide design and self-assembly mechanism may open up new routes for the construction of highly organized, discrete self-assembling protein-like nanostructures with greater levels of control over assembly accuracy.

T7 RNA polymerase non-specifically transcribes and induces disassembly of DNA nanostructures

PubMed Central

Schaffter, Samuel W; Green, Leopold N; Schneider, Joanna; Subramanian, Hari K K; Schulman, Rebecca

2018-01-01

Abstract The use of proteins that bind and catalyze reactions with DNA alongside DNA nanostructures has broadened the functionality of DNA devices. DNA binding proteins have been used to specifically pattern and tune structural properties of DNA nanostructures and polymerases have been employed to directly and indirectly drive structural changes in DNA structures and devices. Despite these advances, undesired and poorly understood interactions between DNA nanostructures and proteins that bind DNA continue to negatively affect the performance and stability of DNA devices used in conjunction with enzymes. A better understanding of these undesired interactions will enable the construction of robust DNA nanostructure-enzyme hybrid systems. Here, we investigate the undesired disassembly of DNA nanotubes in the presence of viral RNA polymerases (RNAPs) under conditions used for in vitro transcription. We show that nanotubes and individual nanotube monomers (tiles) are non-specifically transcribed by T7 RNAP, and that RNA transcripts produced during non-specific transcription disassemble the nanotubes. Disassembly requires a single-stranded overhang on the nanotube tiles where transcripts can bind and initiate disassembly through strand displacement, suggesting that single-stranded domains on other DNA nanostructures could cause unexpected interactions in the presence of viral RNA polymerases. PMID:29718412

T7 RNA polymerase non-specifically transcribes and induces disassembly of DNA nanostructures.

PubMed

Schaffter, Samuel W; Green, Leopold N; Schneider, Joanna; Subramanian, Hari K K; Schulman, Rebecca; Franco, Elisa

2018-06-01

The use of proteins that bind and catalyze reactions with DNA alongside DNA nanostructures has broadened the functionality of DNA devices. DNA binding proteins have been used to specifically pattern and tune structural properties of DNA nanostructures and polymerases have been employed to directly and indirectly drive structural changes in DNA structures and devices. Despite these advances, undesired and poorly understood interactions between DNA nanostructures and proteins that bind DNA continue to negatively affect the performance and stability of DNA devices used in conjunction with enzymes. A better understanding of these undesired interactions will enable the construction of robust DNA nanostructure-enzyme hybrid systems. Here, we investigate the undesired disassembly of DNA nanotubes in the presence of viral RNA polymerases (RNAPs) under conditions used for in vitro transcription. We show that nanotubes and individual nanotube monomers (tiles) are non-specifically transcribed by T7 RNAP, and that RNA transcripts produced during non-specific transcription disassemble the nanotubes. Disassembly requires a single-stranded overhang on the nanotube tiles where transcripts can bind and initiate disassembly through strand displacement, suggesting that single-stranded domains on other DNA nanostructures could cause unexpected interactions in the presence of viral RNA polymerases.

Cross-Discipline Bio-Nanostructured Enhanced Photonic Multimode-Sensor Science

DTIC Science & Technology

2017-05-23

experimental study aimed to combine soft material science with nanotechnology and multi-physics modeling to produce adaptable bio-nanostructure based on...degradation through optical analysis and tracking programs Protein and DNA engineering . - The properties of proteins to be used in sensors were studies

Synthesis and functionalization of gold nanorods for probing plasmonic enhancement mechanisms in organic photovoltaic active layers

NASA Astrophysics Data System (ADS)

Wadams, Robert Christopher

DNA nanotechnology is one of the most flourishing interdisciplinary research fields. Through the features of programmability and predictability, DNA nanostructures can be designed to self-assemble into a variety of periodic or aperiodic patterns of different shapes and length scales, and more importantly, they can be used as scaffolds for organizing other nanoparticles, proteins and chemical groups. By leveraging these molecules, DNA nanostructures can be used to direct the organization of complex bio-inspired materials that may serve as smart drug delivery systems and in vitro or in vivo bio-molecular computing and diagnostic devices. In this dissertation I describe a systematic study of the thermodynamic properties of complex DNA nanostructures, including 2D and 3D DNA origami, in order to understand their assembly, stability and functionality and inform future design endeavors. It is conceivable that a more thorough understanding of DNA self-assembly can be used to guide the structural design process and optimize the conditions for assembly, manipulation, and functionalization, thus benefiting both upstream design and downstream applications. As a biocompatible nanoscale motif, the successful integration, stabilization and separation of DNA nanostructures from cells/cell lysate suggests its potential to serve as a diagnostic platform at the cellular level. Here, DNA origami was used to capture and identify multiple T cell receptor mRNA species from single cells within a mixed cell population. This demonstrates the potential of DNA nanostructure as an ideal nano scale tool for biological applications.

Protocol for sortase-mediated construction of DNA-protein hybrids and functional nanostructures.

PubMed

Koussa, Mounir A; Sotomayor, Marcos; Wong, Wesley P

2014-05-15

Recent methods in DNA nanotechnology are enabling the creation of intricate nanostructures through the use of programmable, bottom-up self-assembly. However, structures consisting only of DNA are limited in their ability to act on other biomolecules. Proteins, on the other hand, perform a variety of functions on biological materials, but directed control of the self-assembly process remains a challenge. While DNA-protein hybrids have the potential to provide the best-of-both-worlds, they can be difficult to create as many of the conventional techniques for linking proteins to DNA render proteins dysfunctional. We present here a sortase-based protocol for covalently coupling proteins to DNA with minimal disturbance to protein function. To accomplish this we have developed a two-step process. First, a small synthetic peptide is bioorthogonally and covalently coupled to a DNA oligo using click chemistry. Next, the DNA-peptide chimera is covalently linked to a protein of interest under protein-compatible conditions using the enzyme sortase. Our protocol allows for the simple coupling and purification of a functional DNA-protein hybrid. We use this technique to form oligos bearing cadherin-23 and protocadherin-15 protein fragments. Upon incorporation into a linear M13 scaffold, these protein-DNA hybrids serve as the gate to a binary nanoswitch. The outlined protocol is reliable and modular, facilitating the construction of libraries of oligos and proteins that can be combined to form functional DNA-protein nanostructures. These structures will enable a new class of functional nanostructures, which could be used for therapeutic and industrial processes. Copyright © 2014. Published by Elsevier Inc.

Protocol for sortase-mediated construction of DNA-protein hybrids and functional nanostructures

PubMed Central

Koussa, Mounir A.; Sotomayor, Marcos; Wong, Wesley P.

2014-01-01

Recent methods in DNA nanotechnology are enabling the creation of intricate nanostructures through the use of programmable, bottom-up self-assembly. However, structures consisting only of DNA are limited in their ability to act on other biomolecules. Proteins, on the other hand, perform a variety of functions on biological materials, but directed control of the self-assembly process remains a challenge. While DNA-protein hybrids have the potential to provide the best-of-both-worlds, they can be difficult to create as many of the conventional techniques for linking proteins to DNA render proteins dysfunctional. We present here a sortase-based protocol for covalently coupling proteins to DNA with minimal disturbance to protein function. To accomplish this we have developed a two-step process. First, a small synthetic peptide is bioorthogonally and covalently coupled to a DNA oligo using click chemistry. Next, the DNA-peptide chimera is covalently linked to a protein of interest under protein-compatible conditions using the enzyme sortase. Our protocol allows for the simple coupling and purification of a functional DNA-protein hybrid. We use this technique to form oligos bearing cadherin-23 and protocadherin-15 protein fragments. Upon incorporation into a linear M13 scaffold, these protein-DNA hybrids serve as the gate to a binary nanoswitch. The outlined protocol is reliable and modular, facilitating the construction of libraries of oligos and proteins that can be combined to form functional DNA-protein nanostructures. These structures will enable a new class of functional nanostructures, which could be used for therapeutic and industrial processes. PMID:24568941

Protein Corona Influences Cell-Biomaterial Interactions in Nanostructured Tissue Engineering Scaffolds.

PubMed

Serpooshan, Vahid; Mahmoudi, Morteza; Zhao, Mingming; Wei, Ke; Sivanesan, Senthilkumar; Motamedchaboki, Khatereh; Malkovskiy, Andrey V; Gladstone, Andrew B; Cohen, Jeffrey E; Yang, Phillip C; Rajadas, Jayakumar; Bernstein, Daniel; Woo, Y Joseph; Ruiz-Lozano, Pilar

2015-07-22

Biomaterials are extensively used to restore damaged tissues, in the forms of implants (e.g. tissue engineered scaffolds) or biomedical devices (e.g. pacemakers). Once in contact with the physiological environment, nanostructured biomaterials undergo modifications as a result of endogenous proteins binding to their surface. The formation of this macromolecular coating complex, known as 'protein corona', onto the surface of nanoparticles and its effect on cell-particle interactions are currently under intense investigation. In striking contrast, protein corona constructs within nanostructured porous tissue engineering scaffolds remain poorly characterized. As organismal systems are highly dynamic, it is conceivable that the formation of distinct protein corona on implanted scaffolds might itself modulate cell-extracellular matrix interactions. Here, we report that corona complexes formed onto the fibrils of engineered collagen scaffolds display specific, distinct, and reproducible compositions that are a signature of the tissue microenvironment as well as being indicative of the subject's health condition. Protein corona formed on collagen matrices modulated cellular secretome in a context-specific manner ex-vivo , demonstrating their role in regulating scaffold-cellular interactions. Together, these findings underscore the importance of custom-designing personalized nanostructured biomaterials, according to the biological milieu and disease state. We propose the use of protein corona as in situ biosensor of temporal and local biomarkers.

Bio-mimetic Nanostructure Self-assembled from Au@Ag Heterogeneous Nanorods and Phage Fusion Proteins for Targeted Tumor Optical Detection and Photothermal Therapy

NASA Astrophysics Data System (ADS)

Wang, Fei; Liu, Pei; Sun, Lin; Li, Cuncheng; Petrenko, Valery A.; Liu, Aihua

2014-10-01

Nanomaterials with near-infrared (NIR) absorption have been widely studied in cancer detection and photothermal therapy (PTT), while it remains a great challenge in targeting tumor efficiently with minimal side effects. Herein we report a novel multifunctional phage-mimetic nanostructure, which was prepared by layer-by-layer self-assembly of Au@Ag heterogenous nanorods (NRs) with rhodamine 6G, and specific pVIII fusion proteins. Au@Ag NRs, first being applied for PTT, exhibited excellent stability, cost-effectivity, biocompatibility and tunable NIR absorption. The fusion proteins were isolated from phage DDAGNRQP specifically selected from f8/8 landscape phage library against colorectal cancer cells in a high-throughput way. Considering the definite charge distribution and low molecular weight, phage fusion proteins were assembled on the negatively charged NR core by electrostatic interactions, exposing the N-terminus fused with DDAGNRQP peptide on the surface. The fluorescent images showed that assembled phage fusion proteins can direct the nanostructure into cancer cells. The nanostructure was more efficient than gold nanorods and silver nanotriangle-based photothermal agents and was capable of specifically ablating SW620 cells after 10 min illumination with an 808 nm laser in the light intensity of 4 W/cm2. The prepared nanostructure would become an ideal reagent for simutaneously targeted optical imaging and PTT of tumor.

Computational Nanotechnology Program

NASA Technical Reports Server (NTRS)

Scuseria, Gustavo E.

1997-01-01

The objectives are: (1) development of methodological and computational tool for the quantum chemistry study of carbon nanostructures and (2) development of the fundamental understanding of the bonding, reactivity, and electronic structure of carbon nanostructures. Our calculations have continued to play a central role in understanding the outcome of the carbon nanotube macroscopic production experiment. The calculations on buckyonions offer the resolution of a long controversy between experiment and theory. Our new tight binding method offers increased speed for realistic simulations of large carbon nanostructures.

Multifunctional ferritin cage nanostructures for fluorescence and MR imaging of tumor cells

NASA Astrophysics Data System (ADS)

Li, Ke; Zhang, Zhi-Ping; Luo, Ming; Yu, Xiang; Han, Yu; Wei, Hong-Ping; Cui, Zong-Qiang; Zhang, Xian-En

2011-12-01

Bionanoparticles and nanostructures have attracted increasing interest as versatile and promising tools in many applications including biosensing and bioimaging. In this study, to image and detect tumor cells, ferritin cage-based multifunctional hybrid nanostructures were constructed that: (i) displayed both the green fluorescent protein and an Arg-Gly-Asp peptide on the exterior surface of the ferritin cages; and (ii) incorporated ferrimagnetic iron oxide nanoparticles into the ferritin interior cavity. The overall architecture of ferritin cages did not change after being integrated with fusion proteins and ferrimagnetic iron oxide nanoparticles. These multifunctional nanostructures were successfully used as a fluorescent imaging probe and an MRI contrast agent for specifically probing and imaging αvβ3 integrin upregulated tumor cells. The work provides a promising strategy for tumor cell detection by simultaneous fluorescence and MR imaging.Bionanoparticles and nanostructures have attracted increasing interest as versatile and promising tools in many applications including biosensing and bioimaging. In this study, to image and detect tumor cells, ferritin cage-based multifunctional hybrid nanostructures were constructed that: (i) displayed both the green fluorescent protein and an Arg-Gly-Asp peptide on the exterior surface of the ferritin cages; and (ii) incorporated ferrimagnetic iron oxide nanoparticles into the ferritin interior cavity. The overall architecture of ferritin cages did not change after being integrated with fusion proteins and ferrimagnetic iron oxide nanoparticles. These multifunctional nanostructures were successfully used as a fluorescent imaging probe and an MRI contrast agent for specifically probing and imaging αvβ3 integrin upregulated tumor cells. The work provides a promising strategy for tumor cell detection by simultaneous fluorescence and MR imaging. Electronic supplementary information (ESI) available. See DOI: 10.1039/c1nr11132a

Protein Biosensors Based on Polymer Nanowires, Carbon Nanotubes and Zinc Oxide Nanorods

PubMed Central

M., Anish Kumar; Jung, Soyoun; Ji, Taeksoo

2011-01-01

The development of biosensors using electrochemical methods is a promising application in the field of biotechnology. High sensitivity sensors for the bio-detection of proteins have been developed using several kinds of nanomaterials. The performance of the sensors depends on the type of nanostructures with which the biomaterials interact. One dimensional (1-D) structures such as nanowires, nanotubes and nanorods are proven to have high potential for bio-applications. In this paper we review these three different kinds of nanostructures that have attracted much attention at recent times with their great performance as biosensors. Materials such as polymers, carbon and zinc oxide have been widely used for the fabrication of nanostructures because of their enhanced performance in terms of sensitivity, biocompatibility, and ease of preparation. Thus we consider polymer nanowires, carbon nanotubes and zinc oxide nanorods for discussion in this paper. We consider three stages in the development of biosensors: (a) fabrication of biomaterials into nanostructures, (b) alignment of the nanostructures and (c) immobilization of proteins. Two different methods by which the biosensors can be developed at each stage for all the three nanostructures are examined. Finally, we conclude by mentioning some of the major challenges faced by many researchers who seek to fabricate biosensors for real time applications. PMID:22163892

Incorporation of native antibodies and Fc-fusion proteins on DNA nanostructures via a modular conjugation strategy† †Electronic supplementary information (ESI) available: Experimental methods, DNA origami design, DNA sequences, and additional experimental data. See DOI: 10.1039/c7cc04178k

PubMed Central

Rosier, Bas J. H. M.; Cremers, Glenn A. O.; Engelen, Wouter; Merkx, Maarten; Brunsveld, Luc

2017-01-01

A photocrosslinkable protein G variant was used as an adapter protein to covalently and site-specifically conjugate an antibody and an Fc-fusion protein to an oligonucleotide. This modular approach enables straightforward decoration of DNA nanostructures with complex native proteins while retaining their innate binding affinity, allowing precise control over the nanoscale spatial organization of such proteins for in vitro and in vivo biomedical applications. PMID:28617516

Packaging DNA Origami into Viral Protein Cages.

PubMed

Linko, Veikko; Mikkilä, Joona; Kostiainen, Mauri A

2018-01-01

The DNA origami technique is a widely used method to create customized, complex, spatially well-defined two-dimensional (2D) and three-dimensional (3D) DNA nanostructures. These structures have huge potential to serve as smart drug-delivery vehicles and molecular devices in various nanomedical and biotechnological applications. However, so far only little is known about the behavior of these novel structures in living organisms or in cell culture/tissue models. Moreover, enhancing pharmacokinetic bioavailability and transfection properties of such structures still remains a challenge. One intriguing approach to overcome these issues is to coat DNA origami nanostructures with proteins or lipid membranes. Here, we show how cowpea chlorotic mottle virus (CCMV) capsid proteins (CPs) can be used for coating DNA origami nanostructures. We present a method for disassembling native CCMV particles and isolating the pure CP dimers, which can further bind and encapsulate a rectangular DNA origami shape. Owing to the highly programmable nature of DNA origami, packaging of DNA nanostructures into viral protein cages could find imminent uses in enhanced targeting and cellular delivery of various active nano-objects, such as enzymes and drug molecules.

A S-Layer Protein of Bacillus anthracis as a Building Block for Functional Protein Arrays by In Vitro Self-Assembly.

PubMed

Wang, Xu-Ying; Wang, Dian-Bing; Zhang, Zhi-Ping; Bi, Li-Jun; Zhang, Ji-Bin; Ding, Wei; Zhang, Xian-En

2015-11-18

S-layer proteins create a cell-surface layer architecture in both bacteria and archaea. Because S-layer proteins self-assemble into a native-like S-layer crystalline structure in vitro, they are attractive building blocks in nanotechnology. Here, the potential use of the S-layer protein EA1 from Bacillus anthracis in constructing a functional nanostructure is investigated, and apply this nanostructure in a proof-of-principle study for serological diagnosis of anthrax. EA1 is genetically fused with methyl parathion hydrolase (MPH), to degrade methyl parathion and provide a label for signal amplification. EA1 not only serves as a nanocarrier, but also as a specific antigen to capture anthrax-specific antibodies. As results, purified EA1-MPH forms a single layer of crystalline nanostructure through self-assembly. Our chimeric nanocatalyst greatly improves enzymatic stability of MPH. When applied to the detection of anthrax-specific antibodies in serum samples, the detection of our EA1-MPH nanostructure is nearly 300 times more sensitive than that of the unassembled complex. Together, it is shown that it is possible to build a functional and highly sensitive nanosensor based on S-layer protein. In conclusion, our present study should serve as a model for the development of other multifunctional nanomaterials using S-layer proteins. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Versatile multi-functionalization of protein nanofibrils for biosensor applications

NASA Astrophysics Data System (ADS)

Sasso, L.; Suei, S.; Domigan, L.; Healy, J.; Nock, V.; Williams, M. A. K.; Gerrard, J. A.

2014-01-01

Protein nanofibrils offer advantages over other nanostructures due to the ease in their self-assembly and the versatility of surface chemistry available. Yet, an efficient and general methodology for their post-assembly functionalization remains a significant challenge. We introduce a generic approach, based on biotinylation and thiolation, for the multi-functionalization of protein nanofibrils self-assembled from whey proteins. Biochemical characterization shows the effects of the functionalization onto the nanofibrils' surface, giving insights into the changes in surface chemistry of the nanostructures. We show how these methods can be used to decorate whey protein nanofibrils with several components such as fluorescent quantum dots, enzymes, and metal nanoparticles. A multi-functionalization approach is used, as a proof of principle, for the development of a glucose biosensor platform, where the protein nanofibrils act as nanoscaffolds for glucose oxidase. Biotinylation is used for enzyme attachment and thiolation for nanoscaffold anchoring onto a gold electrode surface. Characterization via cyclic voltammetry shows an increase in glucose-oxidase mediated current response due to thiol-metal interactions with the gold electrode. The presented approach for protein nanofibril multi-functionalization is novel and has the potential of being applied to other protein nanostructures with similar surface chemistry.Protein nanofibrils offer advantages over other nanostructures due to the ease in their self-assembly and the versatility of surface chemistry available. Yet, an efficient and general methodology for their post-assembly functionalization remains a significant challenge. We introduce a generic approach, based on biotinylation and thiolation, for the multi-functionalization of protein nanofibrils self-assembled from whey proteins. Biochemical characterization shows the effects of the functionalization onto the nanofibrils' surface, giving insights into the changes in surface chemistry of the nanostructures. We show how these methods can be used to decorate whey protein nanofibrils with several components such as fluorescent quantum dots, enzymes, and metal nanoparticles. A multi-functionalization approach is used, as a proof of principle, for the development of a glucose biosensor platform, where the protein nanofibrils act as nanoscaffolds for glucose oxidase. Biotinylation is used for enzyme attachment and thiolation for nanoscaffold anchoring onto a gold electrode surface. Characterization via cyclic voltammetry shows an increase in glucose-oxidase mediated current response due to thiol-metal interactions with the gold electrode. The presented approach for protein nanofibril multi-functionalization is novel and has the potential of being applied to other protein nanostructures with similar surface chemistry. Electronic supplementary information (ESI) available: Cyclic voltammetry characterization of biosensor platforms including bare Au electrodes (Fig. S1), biosensor response to various glucose concentrations (Fig. S2), and AFM roughness measurements due to WPNF modifications (Fig. S3). See DOI: 10.1039/c3nr05752f

Aptamer-based microspheres for highly sensitive protein detection using fluorescently-labeled DNA nanostructures.

PubMed

Han, Daehoon; Hong, Jinkee; Kim, Hyun Cheol; Sung, Jong Hwan; Lee, Jong Bum

2013-11-01

Many highly sensitive protein detection techniques have been developed and have played an important role in the analysis of proteins. Herein, we report a novel technique that can detect proteins sensitively and effectively using aptamer-based DNA nanostructures. Thrombin was used as a target protein and aptamer was used to capture fluorescent dye-labeled DNA nanobarcodes or thrombin on a microsphere. The captured DNA nanobarcodes were replaced by a thrombin and aptamer interaction. The detection ability of this approach was confirmed by flow cytometry with different concentrations of thrombin. Our detection method has great potential for rapid and simple protein detection with a variety of aptamers.

Microwave-Assisted Hydrothermal Rapid Synthesis of Calcium Phosphates: Structural Control and Application in Protein Adsorption

PubMed Central

Cai, Zhu-Yun; Peng, Fan; Zi, Yun-Peng; Chen, Feng; Qian, Qi-Rong

2015-01-01

Synthetic calcium phosphate (CaP)-based materials have attracted much attention in the biomedical field. In this study, we have investigated the effect of pH values on CaP nanostructures prepared using a microwave-assisted hydrothermal method. The hierarchical nanosheet-assembled hydroxyapatite (HAP) nanostructure was prepared under weak acidic conditions (pH 5), while the HAP nanorod was prepared under neutral (pH 7) and weak alkali (pH 9) condition. However, when the pH value increases to 11, a mixed product of HAP nanorod and tri-calcium phosphate nanoparticle was obtained. The results indicated that the pH value of the initial reaction solution played an important role in the phase and structure of the CaP. Furthermore, the protein adsorption and release performance of the as-prepared CaP nanostructures were investigated by using hemoglobin (Hb) as a model protein. The sample that was prepared at pH = 11 and consisted of mixed morphologies of nanorods and nanoprisms showed a higher Hb protein adsorption capacity than the sample prepared at pH 5, which could be explained by its smaller size and dispersed structure. The results revealed the relatively high protein adsorption capacity of the as-prepared CaP nanostructures, which show promise for applications in various biomedical fields such as drug delivery and protein adsorption. PMID:28347064

Microwave-Assisted Hydrothermal Rapid Synthesis of Calcium Phosphates: Structural Control and Application in Protein Adsorption.

PubMed

Cai, Zhu-Yun; Peng, Fan; Zi, Yun-Peng; Chen, Feng; Qian, Qi-Rong

2015-07-31

Synthetic calcium phosphate (CaP)-based materials have attracted much attention in the biomedical field. In this study, we have investigated the effect of pH values on CaP nanostructures prepared using a microwave-assisted hydrothermal method. The hierarchical nanosheet-assembled hydroxyapatite (HAP) nanostructure was prepared under weak acidic conditions (pH 5), while the HAP nanorod was prepared under neutral (pH 7) and weak alkali (pH 9) condition. However, when the pH value increases to 11, a mixed product of HAP nanorod and tri-calcium phosphate nanoparticle was obtained. The results indicated that the pH value of the initial reaction solution played an important role in the phase and structure of the CaP. Furthermore, the protein adsorption and release performance of the as-prepared CaP nanostructures were investigated by using hemoglobin (Hb) as a model protein. The sample that was prepared at pH = 11 and consisted of mixed morphologies of nanorods and nanoprisms showed a higher Hb protein adsorption capacity than the sample prepared at pH 5, which could be explained by its smaller size and dispersed structure. The results revealed the relatively high protein adsorption capacity of the as-prepared CaP nanostructures, which show promise for applications in various biomedical fields such as drug delivery and protein adsorption.

Functionalization of DNA Nanostructures for Cell Signaling Applications

NASA Astrophysics Data System (ADS)

Pedersen, Ronnie O.

Transforming growth factor beta (TGF-beta) is an important cytokine responsible for a wide range of different cellular functions including extracellular matrix formation, angiogenesis and epithelial-mesenchymal transition. We have sought to use self-assembling DNA nanostructures to influence TGF-beta signaling. The predictable Watson Crick base pairing allows for designing self-assembling nanoscale structures using oligonucleotides. We have used the method of DNA origami to assemble structures functionalized with multiple peptides that bind TGF-beta receptors outside the ligand binding domain. This allows the nanostructures to cluster TGF-beta receptors and lower the energy barrier of ligand binding thus sensitizing the cells to TGF-beta stimulation. To prove efficacy of our nanostructures we have utilized immunofluorescent staining of Smad2/4 in order to monitor TGF-beta mediated translocation of Smad2/4 to the cell nucleus. We have also utilized Smad2/4 responsive luminescence constructs that allows us to quantify TGF-beta stimulation with and without nanostructures. To functionalize our nanostructures we relied on biotin-streptavidin linkages. This introduces a multivalency that is not necessarily desirable in all designs. Therefore we have investigated alternative means of functionalization. The first approach is based on targeting DNA nanostructure by using zinc finger binding proteins. Efficacy of zinc finger binding proteins was assayed by the use of enzyme-linked immunosorbent (ELISA) assay and atomic force microscopy (AFM). While ELISA indicated a relative specificity of zinc finger proteins for target DNA sequences AFM showed a high degree of non-specific binding and insufficient affinity. The second approach is based on using peptide nucleic acid (PNA) incorporated in the nanostructure through base pairing. PNA is a synthetic DNA analog consisting of a backbone of repeating N-(2-aminoethyl)-glycine units to which purine and pyrimidine bases are linked by amide bonds. The solid phase synthesis of PNA allows for convenient extension of the backbone into a peptide segment enabling peptide functionalization of DNA nanostructures. We have investigated how the neutral character of PNA alters the incorporation in DNA based nanostructures compared to a DNA control using biotinylation and AFM. Results indicate that PNA can successfully be used as a way of functionalizing DNA nanostructures. Additionally we have shown that functionalized nanostructures are capable of sensitizing cells to TGF-beta stimulation.

Decoding the conformation-linked functional properties of nucleic acids by the use of computational tools.

PubMed

Iacovelli, Federico; Falconi, Mattia

2015-09-01

DNA and RNA are large and flexible polymers selected by nature to transmit information. The most common DNA three-dimensional structure is represented by the double helix, but this biopolymer is extremely flexible and polymorphic, and can easily change its conformation to adapt to different interactions and purposes. DNA can also adopt singular topologies, giving rise, for instance, to supercoils, formed because of the limited free rotation of the DNA domain flanking a replication or transcription complex. Our understanding of the importance of these unusual or transient structures is growing, as recent studies of DNA topology, supercoiling, knotting and linking have shown that the geometric changes can drive, or strongly influence, the interactions between protein and DNA, so altering its own metabolism. On the other hand, the unique self-recognition properties of DNA, determined by the strict Watson-Crick rules of base pairing, make this material ideal for the creation of self-assembling, predesigned nanostructures. The construction of such structures is one of the main focuses of the thriving area of DNA nanotechnology, where several assembly strategies have been employed to build increasingly complex DNA nanostructures. DNA nanodevices can have direct applications in biomedicine, but also in the materials science field, requiring the immersion of DNA in an environment far from the physiological one. Crucial help in the understanding and planning of natural and artificial nanostructures is given by modern computer simulation techniques, which are able to provide a reliable structural and dynamic description of nucleic acids. © 2015 FEBS.

Molecular Design of Performance Proteins With Repetitive Sequences

NASA Astrophysics Data System (ADS)

Vendrely, Charlotte; Ackerschott, Christian; Römer, Lin; Scheibel, Thomas

Most performance proteins responsible for the mechanical stability of cells and organisms reveal highly repetitive sequences. Mimicking such performance proteins is of high interest for the design of nanostructured biomaterials. In this article, flagelliform silk is exemplary introduced to describe a general principle for designing genes of repetitive performance proteins for recombinant expression in Escherichia coli . In the first step, repeating amino acid sequence motifs are reversely transcripted into DNA cassettes, which can in a second step be seamlessly ligated, yielding a designed gene. Recombinant expression thereof leads to proteins mimicking the natural ones. The recombinant proteins can be assembled into nanostructured materials in a controlled manner, allowing their use in several applications.

Multifunctional ferritin cage nanostructures for fluorescence and MR imaging of tumor cells.

PubMed

Li, Ke; Zhang, Zhi-Ping; Luo, Ming; Yu, Xiang; Han, Yu; Wei, Hong-Ping; Cui, Zong-Qiang; Zhang, Xian-En

2012-01-07

Bionanoparticles and nanostructures have attracted increasing interest as versatile and promising tools in many applications including biosensing and bioimaging. In this study, to image and detect tumor cells, ferritin cage-based multifunctional hybrid nanostructures were constructed that: (i) displayed both the green fluorescent protein and an Arg-Gly-Asp peptide on the exterior surface of the ferritin cages; and (ii) incorporated ferrimagnetic iron oxide nanoparticles into the ferritin interior cavity. The overall architecture of ferritin cages did not change after being integrated with fusion proteins and ferrimagnetic iron oxide nanoparticles. These multifunctional nanostructures were successfully used as a fluorescent imaging probe and an MRI contrast agent for specifically probing and imaging α(v)β(3) integrin upregulated tumor cells. The work provides a promising strategy for tumor cell detection by simultaneous fluorescence and MR imaging.

The Effect of Small Molecule Additives on the Self-Assembly and Functionality of Protein-Polymer Diblock Copolymers

NASA Astrophysics Data System (ADS)

Thomas, Carla; Xu, Liza; Olsen, Bradley

2013-03-01

Self-assembly of globular protein-polymer block copolymers into well-defined nanostructures provides a route towards the manufacture of protein-based materials which maintains protein fold and function. The model material mCherry-b-poly(N-isopropyl acrylamide) forms self-assembled nanostructures from aqueous solutions via solvent evaporation. To improve retention of protein functionality when dehydrated, small molecules such as trehalose and glycerol are added in solution prior to solvent removal. With as little as 10 wt% additive, improvements in retained functionality of 20-60% are observed in the solid-state as compared to samples in which no additive is present. Higher additive levels (up to 50%) continue to show improvement until approximately 100% of the protein function is retained. These large gains are hypothesized to originate from the ability of the additives to replace hydrogen bonds normally fulfilled by water. The addition of trehalose in the bulk material also improves the thermal stability of the protein by 15-20 °C, while glycerol decreases the thermal stability. Materials containing up to 50% additives remain microphase separated, and, upon incorporation of additives, nanostructure domain spacing tends to increase, accompanied by order-order transitions.

Growth of single-layer boron nitride dome-shaped nanostructures catalysed by iron clusters.

PubMed

Torre, A La; Åhlgren, E H; Fay, M W; Ben Romdhane, F; Skowron, S T; Parmenter, C; Davies, A J; Jouhannaud, J; Pourroy, G; Khlobystov, A N; Brown, P D; Besley, E; Banhart, F

2016-08-11

We report on the growth and formation of single-layer boron nitride dome-shaped nanostructures mediated by small iron clusters located on flakes of hexagonal boron nitride. The nanostructures were synthesized in situ at high temperature inside a transmission electron microscope while the e-beam was blanked. The formation process, typically originating at defective step-edges on the boron nitride support, was investigated using a combination of transmission electron microscopy, electron energy loss spectroscopy and computational modelling. Computational modelling showed that the domes exhibit a nanotube-like structure with flat circular caps and that their stability was comparable to that of a single boron nitride layer.

2-d and 1-d Nanomaterials Construction through Peptide Computational Design and Solution Assembly

NASA Astrophysics Data System (ADS)

Pochan, Darrin

Self-assembly of molecules is an attractive materials construction strategy due to its simplicity in application. By considering peptidic molecules in the bottom-up materials self-assembly design process, one can take advantage of inherently biomolecular attributes; intramolecular folding events, secondary structure, and electrostatic/H-bonding/hydrophobic interactions to define hierarchical material structure and consequent properties. Importantly, while biomimicry has been a successful strategy for the design of new peptide molecules for intermolecular assembly, computational tools have been developed to de novo design peptide molecules required for construction of pre-determined, desired nanostructures and materials. A new system comprised of coiled coil bundle motifs theoretically designed to assemble into designed, one and two-dimensional nanostructures will be introduced. The strategy provides the opportunity for arbitrary nanostructure formation, i.e. structures not observed in nature, with peptide molecules. Importantly, the desired nanostructure was chosen first while the peptides needed for coiled coil formation and subsequent nanomaterial formation were determined computationally. Different interbundle, two-dimensional nanostructures are stabilized by differences in amino acid composition exposed on the exterior of the coiled coil bundles. Computation was able to determine molecules required for different interbundle symmetries within two-dimensional sheets stabilized by subtle differences in amino acid composition of the inherent peptides. Finally, polymers were also created through covalent interactions between bundles that allowed formation of architectures spanning flexible network forming chains to ultra-stiff polymers, all with the same building block peptides. The success of the computational design strategy is manifested in the nanomaterial results as characterized by electron microscopy, scattering methods, and biophysical techniques. Support from NSF DMREF program under awards DMR-1234161 and DMR-1235084.

Sequence basis of Barnacle Cement Nanostructure is Defined by Proteins with Silk Homology

NASA Astrophysics Data System (ADS)

So, Christopher R.; Fears, Kenan P.; Leary, Dagmar H.; Scancella, Jenifer M.; Wang, Zheng; Liu, Jinny L.; Orihuela, Beatriz; Rittschof, Dan; Spillmann, Christopher M.; Wahl, Kathryn J.

2016-11-01

Barnacles adhere by producing a mixture of cement proteins (CPs) that organize into a permanently bonded layer displayed as nanoscale fibers. These cement proteins share no homology with any other marine adhesives, and a common sequence-basis that defines how nanostructures function as adhesives remains undiscovered. Here we demonstrate that a significant unidentified portion of acorn barnacle cement is comprised of low complexity proteins; they are organized into repetitive sequence blocks and found to maintain homology to silk motifs. Proteomic analysis of aggregate bands from PAGE gels reveal an abundance of Gly/Ala/Ser/Thr repeats exemplified by a prominent, previously unidentified, 43 kDa protein in the solubilized adhesive. Low complexity regions found throughout the cement proteome, as well as multiple lysyl oxidases and peroxidases, establish homology with silk-associated materials such as fibroin, silk gum sericin, and pyriform spidroins from spider silk. Distinct primary structures defined by homologous domains shed light on how barnacles use low complexity in nanofibers to enable adhesion, and serves as a starting point for unraveling the molecular architecture of a robust and unique class of adhesive nanostructures.

Protein Design for Nanostructural Engineering: General Aspects.

PubMed

Grove, Tijana Z; Cortajarena, Aitziber L

2016-01-01

This chapter aims to introduce the main challenges in the field of protein design for engineering of nanostructures and functional materials. First, we introduce proteins and illustrate the key characteristics that open many possibilities for the use of proteins in nanotechnology. Then, we describe the current state of the art of nanopatterning techniques and the actual needs of the emerging field of nanotechnology to develop new tools in order to achieve precise control and manipulation of elements at the nanoscale. In this sense, the increasing knowledge of protein science and advances in protein design allow to tackle current challenges such as the design of nanodevices, nanopatterned surfaces, and nanomachines. This book highlights the recent progresses of protein nanotechnology over the last decade and emphasizes the power of protein engineering through illustrative examples of protein based-assemblies and their potential applications.

Effect of egg albumen protein addition on physicochemical properties and nanostructure of gelatin from fish skin.

PubMed

Cai, Luyun; Feng, Jianhui; Peng, Xichun; Regenstein, Joe M; Li, Xiuxia; Li, Jianrong; Zhao, Wei

2016-12-01

The physicochemical properties and nanostructure of mixtures of egg albumen protein (EAP) and gelatin from under-utilised grass carp ( Ctenopharyngodon idella ) skins were studied. The gelatin with 1% EAP had an acceptable gel strength. The addition of 5% EAP significantly increased the melting and gelling temperatures of gelatin gels. Additionally, the colour turned white and the crystallinity was higher in gelatin gels with gradient concentrations of EAP (1, 3, and 5%). Gelatin with 5% EAP had the highest G' values while gelatin with 1% EAP had the lowest G' values. Atomic force microscopy showed the heterogeneous nanostructure of fish gelatin, and a simple coacervate with a homogeneous distribution was only observed with the addition of 1% EAP, indicating interaction between gelatin and EAP. These results showed that EAP effect fish gelatin's physicochemical and nanostructure properties and has potential applications in foods and pharmaceuticals.

Nanostructured aligned CNT platforms enhance the controlled release of a neurotrophic protein from polypyrrole

NASA Astrophysics Data System (ADS)

Thompson, Brianna C.; Chen, Jun; Moulton, Simon E.; Wallace, Gordon G.

2010-04-01

An aligned CNT array membrane electrode has been used as a nanostructured supporting platform for polypyrrole (PPy) films, exhibiting significant improvement in the controlled release of neurotrophin. In terms of linearity of release, stimulated to unstimulated control of NT-3 release and increased mass and % release of incorporated NT-3, the nanostructured material performed more favourably than the flat PPy film.

Regular Nanoscale Protein Patterns via Directed Adsorption through Self-Assembled DNA Origami Masks.

PubMed

Ramakrishnan, Saminathan; Subramaniam, Sivaraman; Stewart, A Francis; Grundmeier, Guido; Keller, Adrian

2016-11-16

DNA origami has become a widely used method for synthesizing well-defined nanostructures with promising applications in various areas of nanotechnology, biophysics, and medicine. Recently, the possibility to transfer the shape of single DNA origami nanostructures into different materials via molecular lithography approaches has received growing interest due to the great structural control provided by the DNA origami technique. Here, we use ordered monolayers of DNA origami nanostructures with internal cavities on mica surfaces as molecular lithography masks for the fabrication of regular protein patterns over large surface areas. Exposure of the masked sample surface to negatively charged proteins results in the directed adsorption of the proteins onto the exposed surface areas in the holes of the mask. By controlling the buffer and adsorption conditions, the protein coverage of the exposed areas can be varied from single proteins to densely packed monolayers. To demonstrate the versatility of this approach, regular nanopatterns of four different proteins are fabricated: the single-strand annealing proteins Redβ and Sak, the iron-storage protein ferritin, and the blood protein bovine serum albumin (BSA). We furthermore demonstrate the desorption of the DNA origami mask after directed protein adsorption, which may enable the fabrication of hierarchical patterns composed of different protein species. Because selectivity in adsorption is achieved by electrostatic interactions between the proteins and the exposed surface areas, this approach may enable also the large-scale patterning of other charged molecular species or even nanoparticles.

The Structure and Properties of Silica Glass Nanostructures using Novel Computational Systems

NASA Astrophysics Data System (ADS)

Doblack, Benjamin N.

The structure and properties of silica glass nanostructures are examined using computational methods in this work. Standard synthesis methods of silica and its associated material properties are first discussed in brief. A review of prior experiments on this amorphous material is also presented. Background and methodology for the simulation of mechanical tests on amorphous bulk silica and nanostructures are later presented. A new computational system for the accurate and fast simulation of silica glass is also presented, using an appropriate interatomic potential for this material within the open-source molecular dynamics computer program LAMMPS. This alternative computational method uses modern graphics processors, Nvidia CUDA technology and specialized scientific codes to overcome processing speed barriers common to traditional computing methods. In conjunction with a virtual reality system used to model select materials, this enhancement allows the addition of accelerated molecular dynamics simulation capability. The motivation is to provide a novel research environment which simultaneously allows visualization, simulation, modeling and analysis. The research goal of this project is to investigate the structure and size dependent mechanical properties of silica glass nanohelical structures under tensile MD conditions using the innovative computational system. Specifically, silica nanoribbons and nanosprings are evaluated which revealed unique size dependent elastic moduli when compared to the bulk material. For the nanoribbons, the tensile behavior differed widely between the models simulated, with distinct characteristic extended elastic regions. In the case of the nanosprings simulated, more clear trends are observed. In particular, larger nanospring wire cross-sectional radii (r) lead to larger Young's moduli, while larger helical diameters (2R) resulted in smaller Young's moduli. Structural transformations and theoretical models are also analyzed to identify possible factors which might affect the mechanical response of silica nanostructures under tension. The work presented outlines an innovative simulation methodology, and discusses how results can be validated against prior experimental and simulation findings. The ultimate goal is to develop new computational methods for the study of nanostructures which will make the field of materials science more accessible, cost effective and efficient.

Protein Bricks: 2D and 3D Bio-Nanostructures with Shape and Function on Demand.

PubMed

Jiang, Jianjuan; Zhang, Shaoqing; Qian, Zhigang; Qin, Nan; Song, Wenwen; Sun, Long; Zhou, Zhitao; Shi, Zhifeng; Chen, Liang; Li, Xinxin; Mao, Ying; Kaplan, David L; Gilbert Corder, Stephanie N; Chen, Xinzhong; Liu, Mengkun; Omenetto, Fiorenzo G; Xia, Xiaoxia; Tao, Tiger H

2018-05-01

Precise patterning of polymer-based biomaterials for functional bio-nanostructures has extensive applications including biosensing, tissue engineering, and regenerative medicine. Remarkable progress is made in both top-down (based on lithographic methods) and bottom-up (via self-assembly) approaches with natural and synthetic biopolymers. However, most methods only yield 2D and pseudo-3D structures with restricted geometries and functionalities. Here, it is reported that precise nanostructuring on genetically engineered spider silk by accurately directing ion and electron beam interactions with the protein's matrix at the nanoscale to create well-defined 2D bionanopatterns and further assemble 3D bionanoarchitectures with shape and function on demand, termed "Protein Bricks." The added control over protein sequence and molecular weight of recombinant spider silk via genetic engineering provides unprecedented lithographic resolution (approaching the molecular limit), sharpness, and biological functions compared to natural proteins. This approach provides a facile method for patterning and immobilizing functional molecules within nanoscopic, hierarchical protein structures, which sheds light on a wide range of biomedical applications such as structure-enhanced fluorescence and biomimetic microenvironments for controlling cell fate. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Amyloid-like self-assembly of peptide sequences from the adenovirus fiber shaft: insights from molecular dynamics simulations.

PubMed

Tamamis, Phanourios; Kasotakis, Emmanouil; Mitraki, Anna; Archontis, Georgios

2009-11-26

The self-assembly of peptides and proteins into nanostructures is related to the fundamental problems of protein folding and misfolding and has potential applications in medicine, materials science and nanotechnology. Natural peptides, corresponding to sequence repeats from self-assembling proteins, may constitute elementary building blocks of such nanostructures. In this work, we study by implicit-solvent replica-exchange simulations the self-assembly of two amyloidogenic sequences derived from the naturally occurring fiber shaft of the adenovirus, the octapeptide NSGAITIG (asparagine-serine-glycine-alanine-isoleucine-threonine-isoleucine-glycine) and its hexapeptide counterpart, GAITIG. In accordance with their amyloidogenic capacity, both peptides form readily intermolecular beta-sheets, stabilized by extensive main- and side-chain contacts involving the C-terminal moieties (segments 3-8 and 2-6, respectively). The structural and energetic properties of these sheets are analyzed extensively. The N-terminal residues Asn1 and Ser2 of the octapeptide remain disordered in the sheets, suggesting that these residues are exposed at the exterior of the fibrils and accessible. On the basis of insight provided by the simulations, cysteine residues were recently substituted at positions 1 and 2 of NSGAITIG; the newly designed peptides maintain their amyloidogenic properties and can bind to silver, gold and platinum nanoparticles [Kasotakis et al. Biopolymers 2009, 92, 164-172]. Computational investigation can identify suitable positions for rational modification of peptide building blocks, aiming at the fabrication of novel biomaterials.

Electron transport theory in magnetic nanostructures

NASA Astrophysics Data System (ADS)

Choy, Tat-Sang

Magnetic nanostructure has been a new trend because of its application in making magnetic sensors, magnetic memories, and magnetic reading heads in hard disks drives. Although a variety of nanostructures have been realized in experiments in recent years by innovative sample growth techniques, the theoretical study of these devices remain a challenge. On one hand, atomic scale modeling is often required for studying the magnetic nanostructures; on the other, these structures often have a dimension on the order of one micrometer, which makes the calculation numerically intensive. In this work, we have studied the electron transport theory in magnetic nanostructures, with special attention to the giant magnetoresistance (GMR) structure. We have developed a model that includes the details of the band structure and disorder, both of which are both important in obtaining the conductivity. We have also developed an efficient algorithm to compute the conductivity in magnetic nanostructures. The model and the algorithm are general and can be applied to complicated structures. We have applied the theory to current-perpendicular-to-plane GMR structures and the results agree with experiments. Finally, we have searched for the atomic configuration with the highest GMR using the simulated annealing algorithm. This method is computationally intensive because we have to compute the GMR for 103 to 104 configurations. However it is still very efficient because the number of steps it takes to find the maximum is much smaller than the number of all possible GMR structures. We found that ultra-thin NiCu superlattices have surprisingly large GMR even at the moderate disorder in experiments. This finding may be useful in improving the GMR technology.

DNA nanotechnology and its applications in biomedical research.

PubMed

Sun, Lifan; Yu, Lu; Shen, Wanqiu

2014-09-01

DNA nanotechnology, which uses DNA as a material to self-assemble designed nanostructures, including DNA 2D arrays, 3D nanostructures, DNA nanotubes and DNA nanomechanical devices, has showed great promise in biomedical applications. Various DNA nanostructures have been used for protein characterization, enzyme assembly, biosensing, drug delivery and biomimetic assemblies. In this review, we will present recent advances of DNA nanotechnology and its applications in biomedical research field.

Magneto-optical Phase Transition in a Nanostructured Co/Pd Thin Film

NASA Astrophysics Data System (ADS)

Nwokoye, Chidubem; Bennett, Lawrence; Della Torre, Edward; Siddique, Abid; Zhang, Ming; Wagner, Michael; Narducci, Frank

Interest in the study of magnetism in nanostructures at low temperatures is growing. We report work that extends the magnetics experiments in that studied Bose-Einstein Condensation (BEC) of magnons in confined nanostructures. We report experimental investigation of the magneto-optical properties, influenced by photon-magnon interactions, of a Co/Pd thin film below and above the magnon BEC temperature. Comparison of results from SQUID and MOKE experiments revealed a phase transition temperature in both magnetic and magneto-optical properties of the material that is attributed to the magnon BEC. Recent research in magnonics has provided a realization scheme for developing magnon BEC qubit gates for a quantum computing processor. Future research work will explore this technology and find ways to apply quantum computing to address some computational challenges in communication systems. We recognize financial support from the Naval Air Systems Command Section 219 grant.

Molecular separations using nanostructured porous thin films fabricated by glancing angle deposition

NASA Astrophysics Data System (ADS)

Bezuidenhout, Louis Wentzel

Biomolecular separation techniques are an enabling technology that indirectly in.uence many aspects of our lives. Advances have led to faster analyses, reduced costs, higher specificity, and new analytical techniques, impacting areas such as health care, environmental monitoring, polymer sciences, agriculture, and nutrition. Further development of separations technology is anticipated to follow the path of computing technology such that miniaturization through the development of microfluidics technology, lab-on-a-chip systems, and other integrative, multi-component systems will further extend our analysis capabilities. Creation of new and improvement of existing separation technologies is an integral part of the pathway to miniaturized systems. the work of this thesis investigates molecular separations using porous nanostructured films fabricated by the thin film process glancing angle deposition (GLAD). Structural architecture, pore size and shape, and film density can be finely controlled to produce high-surface area thin films with engineered morphology. The characteristic size scales and structural control of GLAD films are well-suited to biomolecules and separation techniques, motivating investigation into the utility and performance of GLAD films for biomolecular separations. This project consisted of three phases. First, chromatographic separation of dye molecules on silica GLAD films was demonstrated by thin layer chromatography Direct control of film nanostructure altered the separation characteristics; most strikingly, anisotropic structures provided two-dimensional analyte migration. Second, nanostructures made with GLAD were integrated in PDMS microfluidic channels using a sacrificial etching process; DNA molecules (10/48 kbp and 6/10/20 kbp mixtures) were electrophoretically separated on a microfluidic chip using a porous bed of SiO2 vertical posts. Third, mass spectrometry of proteins and drugs in the mass range of 100-1300 m/z was performed using laser desorption/ionization (LDI) on silicon GLAD films, and the influence of film thickness, porosity, structure, and substrate on performance was characterized. The application of GLAD nanostructured thin films to biomolecular separations is demonstrated and validated in this thesis. Chromatographic separation of dye molecules, electrophoretic separation of DNA molecules, and mass spectrometric isolation of small proteins and drug molecules by laser desorption ionization were demonstrated using GLAD films. All three methods yielded promising results and establish GLAD as a potential technology for biomolecular separations.

Engineering metallic nanostructures for plasmonics and nanophotonics

PubMed Central

Lindquist, Nathan C; Nagpal, Prashant; McPeak, Kevin M; Norris, David J; Oh, Sang-Hyun

2012-01-01

Metallic nanostructures now play an important role in many applications. In particular, for the emerging fields of plasmonics and nanophotonics, the ability to engineer metals on nanometric scales allows the development of new devices and the study of exciting physics. This review focuses on top-down nanofabrication techniques for engineering metallic nanostructures, along with computational and experimental characterization techniques. A variety of current and emerging applications are also covered. PMID:22790420

Engineering metallic nanostructures for plasmonics and nanophotonics

NASA Astrophysics Data System (ADS)

Lindquist, Nathan C.; Nagpal, Prashant; McPeak, Kevin M.; Norris, David J.; Oh, Sang-Hyun

2012-03-01

Metallic nanostructures now play an important role in many applications. In particular, for the emerging fields of plasmonics and nanophotonics, the ability to engineer metals on nanometric scales allows the development of new devices and the study of exciting physics. This review focuses on top-down nanofabrication techniques for engineering metallic nanostructures, along with computational and experimental characterization techniques. A variety of current and emerging applications are also covered.

Synthesis of nanostructured barium phosphate and its application in micro-computed tomography of mouse brain vessels in ex vivo

NASA Astrophysics Data System (ADS)

Zhu, Bangshang; Yuan, Falei; Yuan, Xiaoya; Bo, Yang; Wang, Yongting; Yang, Guo-Yuan; Drummen, Gregor P. C.; Zhu, Xinyuan

2014-02-01

Micro-computed tomography (micro-CT) is a powerful tool for visualizing the vascular systems of tissues, organs, or entire small animals. Vascular contrast agents play a vital role in micro-CT imaging in order to obtain clear and high-quality images. In this study, a new kind of nanostructured barium phosphate was fabricated and used as a contrast agent for ex vivo micro-CT imaging of blood vessels in the mouse brain. Nanostructured barium phosphate was synthesized through a simple wet precipitation method using Ba(NO3)2, and (NH4)2HPO4 as starting materials. The physiochemical properties of barium phosphate were characterized by scanning electron microscopy, transmission electron microscopy, X-ray diffraction, Fourier transform infrared spectroscopy, and thermal analysis. Furthermore, the impact of the produced nanostructures on cell viability was evaluated via the MTT assay, which generally showed low to moderate cytotoxicity. Finally, the animal test images demonstrated that the use of nanostructured barium phosphate as a contrast agent in Micro-CT imaging produced sharp images with excellent contrast. Both major vessels and the microvasculature were clearly observable in the imaged mouse brain. Overall, the results indicate that nanostructured barium phosphate is a potential and useful vascular contrast agent for micro-CT imaging.

Modeling of space environment impact on nanostructured materials. General principles

NASA Astrophysics Data System (ADS)

Voronina, Ekaterina; Novikov, Lev

2016-07-01

In accordance with the resolution of ISO TC20/SC14 WG4/WG6 joint meeting, Technical Specification (TS) 'Modeling of space environment impact on nanostructured materials. General principles' which describes computer simulation methods of space environment impact on nanostructured materials is being prepared. Nanomaterials surpass traditional materials for space applications in many aspects due to their unique properties associated with nanoscale size of their constituents. This superiority in mechanical, thermal, electrical and optical properties will evidently inspire a wide range of applications in the next generation spacecraft intended for the long-term (~15-20 years) operation in near-Earth orbits and the automatic and manned interplanetary missions. Currently, ISO activity on developing standards concerning different issues of nanomaterials manufacturing and applications is high enough. Most such standards are related to production and characterization of nanostructures, however there is no ISO documents concerning nanomaterials behavior in different environmental conditions, including the space environment. The given TS deals with the peculiarities of the space environment impact on nanostructured materials (i.e. materials with structured objects which size in at least one dimension lies within 1-100 nm). The basic purpose of the document is the general description of the methodology of applying computer simulation methods which relate to different space and time scale to modeling processes occurring in nanostructured materials under the space environment impact. This document will emphasize the necessity of applying multiscale simulation approach and present the recommendations for the choice of the most appropriate methods (or a group of methods) for computer modeling of various processes that can occur in nanostructured materials under the influence of different space environment components. In addition, TS includes the description of possible approximations and limitations of proposed simulation methods as well as of widely used software codes. This TS may be used as a base for developing a new standard devoted to nanomaterials applications for spacecraft.

Mechanical properties of nanostructure of biological materials

NASA Astrophysics Data System (ADS)

Ji, Baohua; Gao, Huajian

2004-09-01

Natural biological materials such as bone, teeth and nacre are nanocomposites of protein and mineral with superior strength. It is quite a marvel that nature produces hard and tough materials out of protein as soft as human skin and mineral as brittle as classroom chalk. What are the secrets of nature? Can we learn from this to produce bio-inspired materials in the laboratory? These questions have motivated us to investigate the mechanics of protein-mineral nanocomposite structure. Large aspect ratios and a staggered alignment of mineral platelets are found to be the key factors contributing to the large stiffness of biomaterials. A tension-shear chain (TSC) model of biological nanostructure reveals that the strength of biomaterials hinges upon optimizing the tensile strength of the mineral crystals. As the size of the mineral crystals is reduced to nanoscale, they become insensitive to flaws with strength approaching the theoretical strength of atomic bonds. The optimized tensile strength of mineral crystals thus allows a large amount of fracture energy to be dissipated in protein via shear deformation and consequently enhances the fracture toughness of biocomposites. We derive viscoelastic properties of the protein-mineral nanostructure and show that the toughness of biocomposite can be further enhanced by the viscoelastic properties of protein.

Effects of cholesterol depletion on membrane nanostructure in MCF-7 cells by atomic force microscopy

NASA Astrophysics Data System (ADS)

Wang, Yuhua; Jiang, Ningcheng; Shi, Aisi; Zheng, Liqin; Yang, Hongqin; Xie, Shusen

2017-02-01

The cell membrane is composed of phospholipids, glycolipids, cholesterol and proteins that are dynamic and heterogeneous distributed in the bilayer structure and many researches have showed that the plasma membrane in eukaryotic cells contains microdomains termed "lipid raft" in which cholesterol, sphingolipids and specific membrane proteins are enriched. Cholesterol extraction induced lipid raft disruption is one of the most widely used methods for lipid raft research and MβCD is a type of solvent to extract the cholesterol from cell membranes. In this study, the effect of MβCD treatment on the membrane nanostructure in MCF-7 living cells was investigated by atomic force microscopy. Different concentrations of MβCD were selected to deplete cholesterol for 30 min and the viability of cells was tested by MTT assay to obtain the optimal concentration. Then the nanostructure of the cell membrane was detected. The results show that an appropriate concentration of MβCD can induce the alteration of cell membranes nanostructure and the roughness of membrane surface decreases significantly. This may indicate that microdomains of the cell membrane disappear and the cell membrane appears more smoothly. Cholesterol can affect nanostructure and inhomogeneity of the plasma membrane in living cells.

Fabry-Perot magnonic ballistic coherent transport across ultrathin ferromagnetic lamellar bcc Ni nanostructures between Fe leads

NASA Astrophysics Data System (ADS)

Khater, A.; Saim, L.; Tigrine, R.; Ghader, D.

2018-06-01

We propose thermodynamically stable systems of ultrathin lamellar bcc Ni nanostructures between bcc Fe leads, sbnd Fe[Ni(n)]Fesbnd , based on the available literature for bcc Ni overlayers on Fe(001) surfaces, and establish the necessary criteria for their structural and ferromagnetic order, for thicknesses n ≤ 6 bcc Ni monatomic layers. The system is globally ferromagnetic. A theoretical model is presented to investigate and understand the ballistic coherent scattering of Fe spin-waves, incident from the leads, at the ferromagnetic bcc Ni nanostructure. The Nisbnd Ni and Nisbnd Fe exchange are computed using the Ising effective field theory (EFT), and the magnetic ground state of the system is constructed in the Heisenberg representation. We compute the spin-wave eigenmodes localized on the bcc Ni nanostructure, using the phase field matching theory (PFMT), illustrating the effects of symmetry breaking on the confinement of localized spin excitations. The reflection and transmission scattering properties of spin-waves incident from the Fe leads, across the embedded Ni nanostructures are investigated within the framework of the same PFMT methodology. A highly refined Fabry-Perot magnonic ballistic coherent transmission spectra is observed for these sbnd Fe[Ni(n)]Fesbnd systems.

Computational Materials: Modeling and Simulation of Nanostructured Materials and Systems

NASA Technical Reports Server (NTRS)

Gates, Thomas S.; Hinkley, Jeffrey A.

2003-01-01

The paper provides details on the structure and implementation of the Computational Materials program at the NASA Langley Research Center. Examples are given that illustrate the suggested approaches to predicting the behavior and influencing the design of nanostructured materials such as high-performance polymers, composites, and nanotube-reinforced polymers. Primary simulation and measurement methods applicable to multi-scale modeling are outlined. Key challenges including verification and validation of models are highlighted and discussed within the context of NASA's broad mission objectives.

In silico assembly and nanomechanical characterization of carbon nanotube buckypaper.

PubMed

Cranford, Steven W; Buehler, Markus J

2010-07-02

Carbon nanotube sheets or films, also known as 'buckypaper', have been proposed for use in actuating, structural and filtration systems, based in part on their unique and robust mechanical properties. Computational modeling of such a fibrous nanostructure is hindered by both the random arrangement of the constituent elements as well as the time- and length-scales accessible to atomistic level molecular dynamics modeling. Here we present a novel in silico assembly procedure based on a coarse-grain model of carbon nanotubes, used to attain a representative mesoscopic buckypaper model that circumvents the need for probabilistic approaches. By variation in assembly parameters, including the initial nanotube density and ratio of nanotube type (single- and double-walled), the porosity of the resulting buckypaper can be varied threefold, from approximately 0.3 to 0.9. Further, through simulation of nanoindentation, the Young's modulus is shown to be tunable through manipulation of nanotube type and density over a range of approximately 0.2-3.1 GPa, in good agreement with experimental findings of the modulus of assembled carbon nanotube films. In addition to carbon nanotubes, the coarse-grain model and assembly process can be adapted for other fibrous nanostructures such as electrospun polymeric composites, high performance nonwoven ballistic materials, or fibrous protein aggregates, facilitating the development and characterization of novel nanomaterials and composites as well as the analysis of biological materials such as protein fiber films and bulk structures.

In silico assembly and nanomechanical characterization of carbon nanotube buckypaper

NASA Astrophysics Data System (ADS)

Cranford, Steven W.; Buehler, Markus J.

2010-07-01

Carbon nanotube sheets or films, also known as 'buckypaper', have been proposed for use in actuating, structural and filtration systems, based in part on their unique and robust mechanical properties. Computational modeling of such a fibrous nanostructure is hindered by both the random arrangement of the constituent elements as well as the time- and length-scales accessible to atomistic level molecular dynamics modeling. Here we present a novel in silico assembly procedure based on a coarse-grain model of carbon nanotubes, used to attain a representative mesoscopic buckypaper model that circumvents the need for probabilistic approaches. By variation in assembly parameters, including the initial nanotube density and ratio of nanotube type (single- and double-walled), the porosity of the resulting buckypaper can be varied threefold, from approximately 0.3 to 0.9. Further, through simulation of nanoindentation, the Young's modulus is shown to be tunable through manipulation of nanotube type and density over a range of approximately 0.2-3.1 GPa, in good agreement with experimental findings of the modulus of assembled carbon nanotube films. In addition to carbon nanotubes, the coarse-grain model and assembly process can be adapted for other fibrous nanostructures such as electrospun polymeric composites, high performance nonwoven ballistic materials, or fibrous protein aggregates, facilitating the development and characterization of novel nanomaterials and composites as well as the analysis of biological materials such as protein fiber films and bulk structures.

Comparative study of label-free electrochemical immunoassay on various gold nanostructures

NASA Astrophysics Data System (ADS)

Rafique, S.; Gao, C.; Li, C. M.; Bhatti, A. S.

2013-10-01

Electrochemical methods such as amperometry and impedance spectroscopy provide the feasibility of label-free immunoassay. However, the performance of electrochemical interfaces varies with the shape of gold nanostructures. In the present work three types of gold nanostructures including pyramid, spherical, and rod-like nanostructures were electrochemically synthesized on the gold electrode and were further transformed into immunosensor by covalent binding of antibodies. As a model protein, a cancer biomarker, Carcinoembryonic Antigen (CEA) was detected using amperometric and impedimetric techniques on three nanostructured electrodes, which enabled to evaluate and compare the immunoassay's performance. It was found that all three immunosensors showed improved linear electrochemical response to the concentration of CEA compared to bare Au electrode. Among all the spherical gold nanostructure based immunosensors displayed superior performance. Under optimal condition, the immunosensors exhibited a limit of detection of 4.1 pg ml-1 over a concentration range of five orders of magnitude. This paper emphasizes that fine control over the geometry of nanostructures is essentially important for high-performance electrochemical immunoassay.

Protocols for Molecular Dynamics Simulations of RNA Nanostructures.

PubMed

Kim, Taejin; Kasprzak, Wojciech K; Shapiro, Bruce A

2017-01-01

Molecular dynamics (MD) simulations have been used as one of the main research tools to study a wide range of biological systems and bridge the gap between X-ray crystallography or NMR structures and biological mechanism. In the field of RNA nanostructures, MD simulations have been used to fix steric clashes in computationally designed RNA nanostructures, characterize the dynamics, and investigate the interaction between RNA and other biomolecules such as delivery agents and membranes.In this chapter we present examples of computational protocols for molecular dynamics simulations in explicit and implicit solvent using the Amber Molecular Dynamics Package. We also show examples of post-simulation analysis steps and briefly mention selected tools beyond the Amber package. Limitations of the methods, tools, and protocols are also discussed. Most of the examples are illustrated for a small RNA duplex (helix), but the protocols are applicable to any nucleic acid structure, subject only to the computational speed and memory limitations of the hardware available to the user.

Crossing Over: Nanostructures that Move Electrons and Ions Across Cellular Membranes

DOE PAGES

Ajo-Franklin, C. M.; Noy, A.

2015-04-27

Critical biological processes such as energy generation and signal transduction are driven by the flow of electrons and ions across the membranes of living cells. As a result, there is substantial interest in creating nanostructured materials that control transport of these charged species across biomembranes. The recent advances in the synthesis of de novo and protein nanostructures for transmembrane ion and electron transport and the mechanistic understanding underlying this transport are described. Moreover, this body of work highlights the promise such nanostructures hold for directing transmembrane transport of charged species as well as challenges that must be overcome to realizemore » that potential.« less

Amphiphilic gold nanoparticles as modulators of lipid membrane fusion

NASA Astrophysics Data System (ADS)

Tahir, Mukarram; Alexander-Katz, Alfredo

The fusion of lipid membranes is central to biological functions like inter-cellular transport and signaling and is coordinated by proteins of the soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) superfamily. We utilize molecular dynamics simulations to demonstrate that gold nanoparticles functionalized with a mixed-monolayer of hydrophobic and hydrophilic alkanethiol ligands can act as synthetic analogues of these fusion proteins and mediate lipid membrane fusion by catalyzing the formation of a toroidal stalk between adjacent membranes and enabling the formation of a fusion pore upon influx of Ca2+ into the exterior solvent. The fusion pathway enabled by these synthetic nanostructures is analogous to the regulated fast fusion pathway observed during synaptic vesicle fusion; it therefore provides novel physical insights into this important biological process while also being relevant in a number of single-cell therapeutic applications. Computational resources from NSF XSEDE contract TG-DMR130042. Financial support from DOE CSGF fellowship DE-FG02-97ER25308.

Topographically Engineered Large Scale Nanostructures for Plasmonic Biosensing

NASA Astrophysics Data System (ADS)

Xiao, Bo; Pradhan, Sangram K.; Santiago, Kevin C.; Rutherford, Gugu N.; Pradhan, Aswini K.

2016-04-01

We demonstrate that a nanostructured metal thin film can achieve enhanced transmission efficiency and sharp resonances and use a large-scale and high-throughput nanofabrication technique for the plasmonic structures. The fabrication technique combines the features of nanoimprint and soft lithography to topographically construct metal thin films with nanoscale patterns. Metal nanogratings developed using this method show significantly enhanced optical transmission (up to a one-order-of-magnitude enhancement) and sharp resonances with full width at half maximum (FWHM) of ~15nm in the zero-order transmission using an incoherent white light source. These nanostructures are sensitive to the surrounding environment, and the resonance can shift as the refractive index changes. We derive an analytical method using a spatial Fourier transformation to understand the enhancement phenomenon and the sensing mechanism. The use of real-time monitoring of protein-protein interactions in microfluidic cells integrated with these nanostructures is demonstrated to be effective for biosensing. The perpendicular transmission configuration and large-scale structures provide a feasible platform without sophisticated optical instrumentation to realize label-free surface plasmon resonance (SPR) sensing.

Nanostructures for delivery of natural antimicrobials in food.

PubMed

Lopes, Nathalie Almeida; Brandelli, Adriano

2017-04-10

Natural antimicrobial compounds are a topic of utmost interest in food science due to the increased demand for safe and high-quality foods with minimal processing. The use of nanostructures is an interesting alternative to protect and delivery antimicrobials in food, also providing controlled release of natural compounds such as bacteriocins and antimicrobial proteins, and also for delivery of plant derived antimicrobials. A diversity of nanostructures are capable of trapping natural antimicrobials maintaining the stability of substances that are frequently sensitive to food processing and storage conditions. This article provides an overview on natural antimicrobials incorporated in nanostructures, showing an effective antimicrobial activity on a diversity of food spoilage and pathogenic microorganisms.

Crossing Over: Nanostructures that Move Electrons and Ions across Cellular Membranes.

PubMed

Ajo-Franklin, Caroline M; Noy, Aleksandr

2015-10-14

Critical biological processes such as energy generation and signal transduction are driven by the flow of electrons and ions across the membranes of living cells. As a result, there is substantial interest in creating nanostructured materials that control transport of these charged species across biomembranes. Recent advances in the synthesis of de novo and protein nanostructures for transmembrane ion and electron transport and the mechanistic understanding underlying this transport are described. This body of work highlights the promise such nanostructures hold for directing transmembrane transport of charged species as well as challenges that must be overcome to realize that potential. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Ion-Specific Control of the Self-Assembly Dynamics of a Nanostructured Protein Lattice

DOE PAGES

Rad, Behzad; Haxton, Thomas K.; Shon, Albert; ...

2014-12-10

Self-assembling proteins offer a potential means of creating nanostructures with complex structure and function. However, using self-assembly to create nanostructures with long-range order whose size is tunable is challenging, because the kinetics and thermodynamics of protein interactions depend sensitively on solution conditions. Here we systematically investigate the impact of varying solution conditions on the self-assembly of SbpA, a surface-layer protein from Lysinibacillus sphaericus that forms two-dimensional nanosheets. Using high-throughput light scattering measurements, we mapped out diagrams that reveal the relative yield of self-assembly of nanosheets over a wide range of concentrations of SbpA and Ca 2+. These diagrams revealed amore » localized region of optimum yield of nanosheets at intermediate Ca 2+ concentration. Replacement of Mg 2+ or Ba 2+ for Ca 2+ indicates that Ca 2+ acts both as a specific ion that is required to induce self-assembly and as a general divalent cation. In addition, we use competitive titration experiments to find that 5 Ca 2+ bind to SbpA with an affinity of 67.1 ± 0.3 μM. Finally, we show via modeling that nanosheet assembly occurs by growth from a negligibly small critical nucleus. We also chart the dynamics of nanosheet size over a variety of conditions. In conclusion, our results demonstrate control of the dynamics and size of the self-assembly of a nanostructured lattice, the constituents of which are one of a class of building blocks able to form novel hybrid nanomaterials.« less

Bottom-Up Synthesis and Sensor Applications of Biomimetic Nanostructures

PubMed Central

Wang, Li; Sun, Yujing; Li, Zhuang; Wu, Aiguo; Wei, Gang

2016-01-01

The combination of nanotechnology, biology, and bioengineering greatly improved the developments of nanomaterials with unique functions and properties. Biomolecules as the nanoscale building blocks play very important roles for the final formation of functional nanostructures. Many kinds of novel nanostructures have been created by using the bioinspired self-assembly and subsequent binding with various nanoparticles. In this review, we summarized the studies on the fabrications and sensor applications of biomimetic nanostructures. The strategies for creating different bottom-up nanostructures by using biomolecules like DNA, protein, peptide, and virus, as well as microorganisms like bacteria and plant leaf are introduced. In addition, the potential applications of the synthesized biomimetic nanostructures for colorimetry, fluorescence, surface plasmon resonance, surface-enhanced Raman scattering, electrical resistance, electrochemistry, and quartz crystal microbalance sensors are presented. This review will promote the understanding of relationships between biomolecules/microorganisms and functional nanomaterials in one way, and in another way it will guide the design and synthesis of biomimetic nanomaterials with unique properties in the future. PMID:28787853

Orientational imaging of a single plasmonic nanoparticle using dark-field hyperspectral imaging

NASA Astrophysics Data System (ADS)

Mehta, Nishir; Mahigir, Amirreza; Veronis, Georgios; Gartia, Manas Ranjan

2017-08-01

Orientation of plasmonic nanostructures is an important feature in many nanoscale applications such as catalyst, biosensors DNA interactions, protein detections, hotspot of surface enhanced Raman spectroscopy (SERS), and fluorescence resonant energy transfer (FRET) experiments. However, due to diffraction limit, it is challenging to obtain the exact orientation of the nanostructure using standard optical microscope. Hyperspectral Imaging Microscopy is a state-of-the-art visualization technology that combines modern optics with hyperspectral imaging and computer system to provide the identification and quantitative spectral analysis of nano- and microscale structures. In this work, initially we use transmitted dark field imaging technique to locate single nanoparticle on a glass substrate. Then we employ hyperspectral imaging technique at the same spot to investigate orientation of single nanoparticle. No special tagging or staining of nanoparticle has been done, as more likely required in traditional microscopy techniques. Different orientations have been identified by carefully understanding and calibrating shift in spectral response from each different orientations of similar sized nanoparticles. Wavelengths recorded are between 300 nm to 900 nm. The orientations measured by hyperspectral microscopy was validated using finite difference time domain (FDTD) electrodynamics calculations and scanning electron microscopy (SEM) analysis. The combination of high resolution nanometer-scale imaging techniques and the modern numerical modeling capacities thus enables a meaningful advance in our knowledge of manipulating and fabricating shaped nanostructures. This work will advance our understanding of the behavior of small nanoparticle clusters useful for sensing, nanomedicine, and surface sciences.

Acoustically modulated magnetic resonance imaging of gas-filled protein nanostructures

NASA Astrophysics Data System (ADS)

Lu, George J.; Farhadi, Arash; Szablowski, Jerzy O.; Lee-Gosselin, Audrey; Barnes, Samuel R.; Lakshmanan, Anupama; Bourdeau, Raymond W.; Shapiro, Mikhail G.

2018-05-01

Non-invasive biological imaging requires materials capable of interacting with deeply penetrant forms of energy such as magnetic fields and sound waves. Here, we show that gas vesicles (GVs), a unique class of gas-filled protein nanostructures with differential magnetic susceptibility relative to water, can produce robust contrast in magnetic resonance imaging (MRI) at sub-nanomolar concentrations, and that this contrast can be inactivated with ultrasound in situ to enable background-free imaging. We demonstrate this capability in vitro, in cells expressing these nanostructures as genetically encoded reporters, and in three model in vivo scenarios. Genetic variants of GVs, differing in their magnetic or mechanical phenotypes, allow multiplexed imaging using parametric MRI and differential acoustic sensitivity. Additionally, clustering-induced changes in MRI contrast enable the design of dynamic molecular sensors. By coupling the complementary physics of MRI and ultrasound, this nanomaterial gives rise to a distinct modality for molecular imaging with unique advantages and capabilities.

Computational Nanotechnology of Molecular Materials, Electronics and Machines

NASA Technical Reports Server (NTRS)

Srivastava, D.; Biegel, Bryan A. (Technical Monitor)

2002-01-01

This viewgraph presentation covers carbon nanotubes, their characteristics, and their potential future applications. The presentation include predictions on the development of nanostructures and their applications, the thermal characteristics of carbon nanotubes, mechano-chemical effects upon carbon nanotubes, molecular electronics, and models for possible future nanostructure devices. The presentation also proposes a neural model for signal processing.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lu, Dingjie; Xie, Yi Min; Huang, Xiaodong

Analytical studies on the size effects of a simply-shaped beam fixed at both ends have successfully explained the sudden changes of effective Young's modulus as its diameter decreases below 100 nm. Yet they are invalid for complex nanostructures ubiquitously existing in nature. In accordance with a generalized Young-Laplace equation, one of the representative size effects is transferred to non-uniformly distributed pressure against an external surface due to the imbalance of inward and outward loads. Because the magnitude of pressure depends on the principal curvatures, iterative steps have to be adopted to gradually stabilize the structure in finite element analysis. Computational resultsmore » are in good agreement with both experiment data and theoretical prediction. Furthermore, the investigation on strengthened and softened Young's modulus for two complex nanostructures demonstrates that the proposed computational method provides a general and effective approach to analyze the size effects for nanostructures in arbitrary shape.« less

Modulation of chondrocyte motility by tetrahedral DNA nanostructures.

PubMed

Shi, Sirong; Lin, Shiyu; Shao, Xiaoru; Li, Qianshun; Tao, Zhang; Lin, Yunfeng

2017-10-01

Contemporarily, a highly increasing attention was paid to nanoconstructs, particularly DNA nanostructures possessing precise organization, functional manipulation, biocompatibility and biodegradability. Amongst these DNA nanomaterials, tetrahedral DNA nanostructures (TDNs) are a significantly ideal bionanomaterials with focusing on the property that can be internalized into cytoplasm in the absence of transfection. Therefore, the focus of this study was on investigating the influence of TDNs on the chondrocytes locomotion. Tetrahedral DNA nanostructures was confirmed by 6% polyacrylamide gel electrophoresis (PAGE) and dynamic light scattering (DLS). Subsequently, the effect of TDNs on chondrocyte locomotion was investigated by real-time cell analysis (RTCA) and wound healing assay. The variation of relevant genes and proteins was detected by quantitative polymerase chain reaction (qPCR), western blotting and immunofluorescence respectively. We demonstrated that tetrahedral DNA nanostructures have positive influence on chondrocytes locomotion and promoted the expression of RhoA, ROCK2 and vinculin. Additionally, upon exposure to TDNs with the concentration of 250 nmol L -1 , the chondrocytes were showed the highest motility via both RTCA and wound healing assay. Meanwhile, the mRNA and protein expression of RhoA, ROCK2 and vinculin were also significantly enhanced with the same concentration. It can be concluded that the TDNs with the optimal concentration of 250 nmol L -1 could extremely promoted the chondrocytes locomotion through facilitating the expression of RhoA, ROCK2 and vinculin. These results seemed to reveal that this special three-dimensional DNA tetrahedral nanostructures may be applied to cartilage repair and treatment in the future. © 2017 John Wiley & Sons Ltd.

Silicon nanostructures for cancer diagnosis and therapy.

PubMed

Peng, Fei; Cao, Zhaohui; Ji, Xiaoyuan; Chu, Binbin; Su, Yuanyuan; He, Yao

2015-01-01

The emergence of nanotechnology suggests new and exciting opportunities for early diagnosis and therapy of cancer. During the recent years, silicon-based nanomaterials featuring unique properties have received great attention, showing high promise for myriad biological and biomedical applications. In this review, we will particularly summarize latest representative achievements on the development of silicon nanostructures as a powerful platform for cancer early diagnosis and therapy. First, we introduce the silicon nanomaterial-based biosensors for detecting cancer markers (e.g., proteins, tumor-suppressor genes and telomerase activity, among others) with high sensitivity and selectivity under molecular level. Then, we summarize in vitro and in vivo applications of silicon nanostructures as efficient nanoagents for cancer therapy. Finally, we discuss the future perspective of silicon nanostructures for cancer diagnosis and therapy.

Carbon nanostructure-based field-effect transistors for label-free chemical/biological sensors.

PubMed

Hu, PingAn; Zhang, Jia; Li, Le; Wang, Zhenlong; O'Neill, William; Estrela, Pedro

2010-01-01

Over the past decade, electrical detection of chemical and biological species using novel nanostructure-based devices has attracted significant attention for chemical, genomics, biomedical diagnostics, and drug discovery applications. The use of nanostructured devices in chemical/biological sensors in place of conventional sensing technologies has advantages of high sensitivity, low decreased energy consumption and potentially highly miniaturized integration. Owing to their particular structure, excellent electrical properties and high chemical stability, carbon nanotube and graphene based electrical devices have been widely developed for high performance label-free chemical/biological sensors. Here, we review the latest developments of carbon nanostructure-based transistor sensors in ultrasensitive detection of chemical/biological entities, such as poisonous gases, nucleic acids, proteins and cells.

Enhanced protein adsorption and patterning on nanostructured latex-coated paper.

PubMed

Juvonen, Helka; Määttänen, Anni; Ihalainen, Petri; Viitala, Tapani; Sarfraz, Jawad; Peltonen, Jouko

2014-06-01

Specific interactions of extracellular matrix proteins with cells and their adhesion to the substrate are important for cell growth. A nanopatterned latex-coated paper substrate previously shown to be an excellent substrate for cell adhesion and 2D growth was studied for directed immobilization of proteins. The nanostructured latex surface was formed by short-wavelength IR irradiation of a two-component latex coating consisting of a hydrophilic film-forming styrene butadiene acrylonitrile copolymer and hydrophobic polystyrene particles. The hydrophobic regions of the IR-treated latex coating showed strong adhesion of bovine serum albumin (cell repelling protein), fibronectin (cell adhesive protein) and streptavidin. Opposite to the IR-treated surface, fibronectin and streptavidin had a poor affinity toward the untreated pristine latex coating. Detailed characterization of the physicochemical surface properties of the latex-coated substrates revealed that the observed differences in protein affinity were mainly due to the presence or absence of the protein repelling polar and charged surface groups. The protein adsorption was assisted by hydrophobic (dehydration) interactions. Copyright © 2014 Elsevier B.V. All rights reserved.

Electron-transfer dynamics of photosynthetic reaction centers in thermoresponsive soft materials.

PubMed

Laible, Philip D; Kelley, Richard F; Wasielewski, Michael R; Firestone, Millicent A

2005-12-15

Poly(ethylene glycol)-grafted, lipid-based, thermoresponsive, soft nanostructures are shown to serve as scaffolding into which reconstituted integral membrane proteins, such as the bacterial photosynthetic reaction centers (RCs) can be stabilized, and their packing arrangement, and hence photophysical properties, can be controlled. The self-assembled nanostructures exist in two distinct states: a liquid-crystalline gel phase at temperatures above 21 degrees C and a non-birefringent, reduced viscosity state at lower temperatures. Characterization of the effect of protein introduction on the mesoscopic structure of the materials by 31P NMR and small-angle X-ray scattering shows that the expanded lamellar structure of the protein-free material is retained. At reduced temperatures, however, the aggregate structure is found to convert from a two-dimensional normal hexagonal structure to a three-dimensional cubic phase upon introduction of the RCs. Structural and functional characteristics of the RCs were determined by ground-state and femtosecond transient absorption spectroscopy. Time-resolved results indicate that the kinetics of primary electron transfer for the RCs in the low-viscosity cold phase of the self-assembled nanostructures are identical to those observed in a detergent-solubilized state in buffered aqueous solutions (approximately 4 ps) over a wide range of protein concentrations and experimental conditions. This is also true for RCs held within the lamellar gel phase at low protein concentrations and at short sample storage times. In contrast are kinetics from samples that are prepared with high RC concentrations and stored for several hours, which display additional kinetic components with extended electron-transfer times (approximately 10-12 ps). This observation is tentatively attributed to energy transfer between RCs that have laterally (in-plane) organized within the lipid bilayers of the lamellar gel phase prior to charge separation. These results not only demonstrate the use of soft nanostructures as a matrix in which to stabilize and organize membrane proteins but also suggest the possibility of using them to control the interactions between proteins and thus to tune their collective optical/electronic properties.

Synthesis of nanostructured materials in inverse miniemulsions and their applications.

PubMed

Cao, Zhihai; Ziener, Ulrich

2013-11-07

Polymeric nanogels, inorganic nanoparticles, and organic-inorganic hybrid nanoparticles can be prepared via the inverse miniemulsion technique. Hydrophilic functional cargos, such as proteins, DNA, and macromolecular fluoresceins, may be conveniently encapsulated in these nanostructured materials. In this review, the progress of inverse miniemulsions since 2000 is summarized on the basis of the types of reactions carried out in inverse miniemulsions, including conventional free radical polymerization, controlled/living radical polymerization, polycondensation, polyaddition, anionic polymerization, catalytic oxidation reaction, sol-gel process, and precipitation reaction of inorganic precursors. In addition, the applications of the nanostructured materials synthesized in inverse miniemulsions are also reviewed.

Localized entrapment of green fluorescent protein within nanostructured polymer films

NASA Astrophysics Data System (ADS)

Ankner, John; Kozlovskaya, Veronika; O'Neill, Hugh; Zhang, Qiu; Kharlampieva, Eugenia

2012-02-01

Protein entrapment within ultrathin polymer films is of interest for applications in biosensing, drug delivery, and bioconversion, but controlling protein distribution within the films is difficult. We report on nanostructured protein/polyelectrolyte (PE) materials obtained through incorporation of green fluorescent protein (GFP) within poly(styrene sulfonate)/poly(allylamine hydrochloride) multilayer films assembled via the spin-assisted layer-by-layer method. By using deuterated GFP as a marker for neutron scattering contrast we have inferred the architecture of the films in both normal and lateral directions. We find that films assembled with a single GFP layer exhibit a strong localization of the GFP without intermixing into the PE matrix. The GFP volume fraction approaches the monolayer density of close-packed randomly oriented GFP molecules. However, intermixing of the GFP with the PE matrix occurs in multiple-GFP layer films. Our results yield new insight into the organization of immobilized proteins within polyelectrolyte matrices and open opportunities for fabrication of protein-containing films with well-organized structure and controllable function, a crucial requirement for advanced sensing applications.

Hydroxyapatite hierarchically nanostructured porous hollow microspheres: rapid, sustainable microwave-hydrothermal synthesis by using creatine phosphate as an organic phosphorus source and application in drug delivery and protein adsorption.

PubMed

Qi, Chao; Zhu, Ying-Jie; Lu, Bing-Qiang; Zhao, Xin-Yu; Zhao, Jing; Chen, Feng; Wu, Jin

2013-04-22

Hierarchically nanostructured porous hollow microspheres of hydroxyapatite (HAP) are a promising biomaterial, owing to their excellent biocompatibility and porous hollow structure. Traditionally, synthetic hydroxyapatite is prepared by using an inorganic phosphorus source. Herein, we report a new strategy for the rapid, sustainable synthesis of HAP hierarchically nanostructured porous hollow microspheres by using creatine phosphate disodium salt as an organic phosphorus source in aqueous solution through a microwave-assisted hydrothermal method. The as-obtained products are characterized by powder X-ray diffraction (XRD), Fourier-transform IR (FTIR) spectroscopy, SEM, TEM, Brunauer-Emmett-Teller (BET) nitrogen sorptometry, dynamic light scattering (DLS), and thermogravimetric analysis (TGA). SEM and TEM micrographs show that HAP hierarchically nanostructured porous hollow microspheres consist of HAP nanosheets or nanorods as the building blocks and DLS measurements show that the diameters of HAP hollow microspheres are within the range 0.8-1.5 μm. The specific surface area and average pore size of the HAP porous hollow microspheres are 87.3 m(2) g(-1) and 20.6 nm, respectively. The important role of creatine phosphate disodium salt and the influence of the experimental conditions on the products were systematically investigated. This method is facile, rapid, surfactant-free and environmentally friendly. The as-prepared HAP porous hollow microspheres show a relatively high drug-loading capacity and protein-adsorption ability, as well as sustained drug and protein release, by using ibuprofen as a model drug and hemoglobin (Hb) as a model protein, respectively. These experiments indicate that the as-prepared HAP porous hollow microspheres are promising for applications in biomedical fields, such as drug delivery and protein adsorption. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

First-principles study of the binding energy between nanostructures and its scaling with system size

NASA Astrophysics Data System (ADS)

Tao, Jianmin; Jiao, Yang; Mo, Yuxiang; Yang, Zeng-Hui; Zhu, Jian-Xin; Hyldgaard, Per; Perdew, John P.

2018-04-01

The equilibrium van der Waals binding energy is an important factor in the design of materials and devices. However, it presents great computational challenges for materials built up from nanostructures. Here we investigate the binding-energy scaling behavior from first-principles calculations. We show that the equilibrium binding energy per atom between identical nanostructures can scale up or down with nanostructure size, but can be parametrized for large N with an analytical formula (in meV/atom), Eb/N =a +b /N +c /N2+d /N3 , where N is the number of atoms in a nanostructure and a , b , c , and d are fitting parameters, depending on the properties of a nanostructure. The formula is consistent with a finite large-size limit of binding energy per atom. We find that there are two competing factors in the determination of the binding energy: Nonadditivities of van der Waals coefficients and center-to-center distance between nanostructures. To decode the detail, the nonadditivity of the static multipole polarizability is investigated from an accurate spherical-shell model. We find that the higher-order multipole polarizability displays ultrastrong intrinsic nonadditivity, no matter if the dipole polarizability is additive or not.

Kinetic Effects on Self-Assembly and Function of Protein-Polymer Bioconjugates in Thin Films Prepared by Flow Coating.

PubMed

Chang, Dongsook; Huang, Aaron; Olsen, Bradley D

2017-01-01

The self-assembly of nanostructured globular protein arrays in thin films is demonstrated using protein-polymer block copolymers based on a model protein mCherry and the polymer poly(oligoethylene glycol acrylate) (POEGA). Conjugates are flow coated into thin films on a poly(ethylene oxide) grafted Si surface, forming self-assembled cylindrical nanostructures with POEGA domains selectively segregating to the air-film interface. Long-range order and preferential arrangement of parallel cylinders templated by selective surfaces are demonstrated by controlling relative humidity. Long-range order increases with coating speed when the film thicknesses are kept constant, due to reduced nucleation per unit area of drying film. Fluorescence emission spectra of mCherry in films prepared at <25% relative humidity shows a small shift suggesting that proteins are more perturbed at low humidity than high humidity or the solution state. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Engineering DNA scaffolds for delivery of anticancer therapeutics.

PubMed

Sun, Wujin; Gu, Zhen

2015-07-01

Engineering DNA nanostructures with programmability in size, shape and surface chemistry holds tremendous promise in biomedical applications. As an emerging platform for drug delivery, DNA nanostructures have been extensively studied for delivering anticancer therapeutics, including small-molecule drug, nucleic acids and proteins. In this mini-review, current advances in utilizing DNA scaffolds as drug carriers for cancer treatment were summarized and future challenges were also discussed.

One-step fabrication of nanostructure-covered microstructures using selective aluminum anodization based on non-uniform electric field

NASA Astrophysics Data System (ADS)

Park, Yong Min; Kim, Byeong Hee; Seo, Young Ho

2016-06-01

This paper presents a selective aluminum anodization technique for the fabrication of microstructures covered by nanoscale dome structures. It is possible to fabricate bulging microstructures, utilizing the different growth rates of anodic aluminum oxide in non-uniform electric fields, because the growth rate of anodic aluminum oxide depends on the intensity of electric field, or current density. After anodizing under a non-uniform electric field, bulging microstructures covered by nanostructures were fabricated by removing the residual aluminum layer. The non-uniform electric field induced by insulative micropatterns was estimated by computational simulations and verified experimentally. Utilizing computational simulations, the intensity profile of the electric field was calculated according to the ratio of height and width of the insulative micropatterns. To compare computational simulation results and experimental results, insulative micropatterns were fabricated using SU-8 photoresist. The results verified that the shape of the bottom topology of anodic alumina was strongly dependent on the intensity profile of the applied electric field, or current density. The one-step fabrication of nanostructure-covered microstructures can be applied to various fields, such as nano-biochip and nano-optics, owing to its simplicity and cost effectiveness.

Molecular simulations of self-assembling bio-inspired supramolecular systems and their connection to experiments

PubMed Central

Patmanidis, Ilias

2018-01-01

In bionanotechnology, the field of creating functional materials consisting of bio-inspired molecules, the function and shape of a nanostructure only appear through the assembly of many small molecules together. The large number of building blocks required to define a nanostructure combined with the many degrees of freedom in packing small molecules has long precluded molecular simulations, but recent advances in computational hardware as well as software have made classical simulations available to this strongly expanding field. Here, we review the state of the art in simulations of self-assembling bio-inspired supramolecular systems. We will first discuss progress in force fields, simulation protocols and enhanced sampling techniques using recent examples. Secondly, we will focus on efforts to enable the comparison of experimentally accessible observables and computational results. Experimental quantities that can be measured by microscopy, spectroscopy and scattering can be linked to simulation output either directly or indirectly, via quantum mechanical or semi-empirical techniques. Overall, we aim to provide an overview of the various computational approaches to understand not only the molecular architecture of nanostructures, but also the mechanism of their formation. PMID:29688238

Use of a porous silicon-gold plasmonic nanostructure to enhance serum peptide signals in MALDI-TOF analysis.

PubMed

Li, Xiao; Tan, Jie; Yu, Jiekai; Feng, Jiandong; Pan, Aiwu; Zheng, Shu; Wu, Jianmin

2014-11-07

Small peptides in serum are potential biomarkers for the diagnosis of cancer and other diseases. The identification of peptide biomarkers in human plasma/serum has become an area of high interest in medical research. However, the direct analysis of peptides in serum samples using mass spectrometry is challenging due to the low concentration of peptides and the high abundance of high-molecular-weight proteins in serum, the latter of which causes severe signal suppression. Herein, we reported that porous semiconductor-noble metal hybrid nanostructures can both eliminate the interference from large proteins in serum samples and significantly enhance the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) yields of peptides captured on the nanostructure. Serum peptide fingerprints with high fidelity can be acquired rapidly, and successful discrimination of colorectal cancer patients based on peptide fingerprints is demonstrated. Copyright © 2014 Elsevier B.V. All rights reserved.

Biocompatibility of cluster-assembled nanostructured TiO2 with primary and cancer cells.

PubMed

Carbone, Roberta; Marangi, Ida; Zanardi, Andrea; Giorgetti, Luca; Chierici, Elisabetta; Berlanda, Giuseppe; Podestà, Alessandro; Fiorentini, Francesca; Bongiorno, Gero; Piseri, Paolo; Pelicci, Pier Giuseppe; Milani, Paolo

2006-06-01

We have characterized the biocompatibility of nanostructured TiO2 films produced by the deposition of a supersonic beam of TiOx clusters. Physical analysis shows that these films possess, at the nanoscale, a granularity and porosity mimicking those of typical extracellular matrix structures and adsorption properties that could allow surface functionalization with different macromolecules such as DNA, proteins, and peptides. To explore the biocompatibility of this novel nanostructured surface, different cancer and primary cells were analyzed in terms of morphological appearance (by bright field microscopy and immunofluorescence) and growth properties, with the aim to evaluate cluster-assembled TiO2 films as substrates for cell-based and tissue-based applications. Our results strongly suggest that this new biomaterial supports normal growth and adhesion of primary and cancer cells with no need for coating with ECM proteins; we thus propose this new material as an optimal substrate for different applications in cell-based assays, biosensors or microfabricated medical devices.

Rapid and label-free detection of protein a by aptamer-tethered porous silicon nanostructures.

PubMed

Urmann, Katharina; Reich, Peggy; Walter, Johanna-Gabriela; Beckmann, Dieter; Segal, Ester; Scheper, Thomas

2017-09-10

Protein A, which is secreted by and displayed on the cell membrane of Staphylococcus aureus is an important biomarker for S. aureus. Thus, its rapid and specific detection may facilitate the pathogen identification and initiation of proper treatment. Herein, we present a simple, label-free and rapid optical biosensor enabling specific detection of protein A. Protein A-binding aptamer serves as the capture probe and is immobilized onto a nanostructured porous silicon thin film, which serves as the optical transducer element. We demonstrate high sensitivity of the biosensor with a linear detection range between 8 and 23μM. The apparent dissociation constant was determined as 13.98μM and the LoD is 3.17μM. Harnessing the affinity between protein A and antibodies, a sandwich assay format was developed to amplify the optical signal associated with protein A capture by the aptamer. Using this approach, we increase the sensitivity of the biosensor, resulting in a three times lower LoD. Copyright © 2017 Elsevier B.V. All rights reserved.

(Poly)cation-induced protection of conventional and wireframe DNA origami nanostructures.

PubMed

Ahmadi, Yasaman; De Llano, Elisa; Barišić, Ivan

2018-04-26

DNA nanostructures hold immense potential to be used for biological and medical applications. However, they are extremely vulnerable towards salt depletion and nucleases, which are common under physiological conditions. In this contribution, we used chitosan and linear polyethyleneimine for coating and long-term stabilization of several three-dimensional DNA origami nanostructures. The impact of the degree of polymerization and the charge density of the polymer together with the N/P charge ratio (ratio of the amines in polycations to the phosphates in DNA) on the stability of encapsulated DNA origami nanostructures in the presence of nucleases and in low-salt media was examined. The polycation shells were compatible with enzyme- and aptamer-based functionalization of the DNA nanostructures. Additionally, we showed that despite being highly vulnerable to salt depletion and nucleolytic digestion, self-assembled DNA nanostructures are stable in cell culture media up to a week. This was contrary to unassembled DNA scaffolds that degraded in one hour, showing that placing DNA strands into a spatially designed configuration crucially affect the structural integrity. The stability of naked DNA nanostructures in cell culture was shown to be mediated by growth media. DNA origami nanostructures kept in growth media were significantly more resistant towards low-salt denaturation, DNase I and serum-mediated digestion than when in a conventional buffer. Moreover, we confirmed that DNA origami nanostructures remain not only structurally intact but also fully functional after exposure to cell media. Agarose gel electrophoresis and negative stain transmission electron microscopy analysis revealed the hybridization of DNA origami nanostructures to their targets in the presence of serum proteins and nucleases. The structural integrity and functionality of DNA nanostructures in physiological fluids validate their use particularly for short-time biological applications in which the shape and structural details of DNA nanodevices are functionally critical.

Synthesis of nanostructured porous silica coatings on titanium and their cell adhesive and osteogenic differentiation properties.

PubMed

Inzunza, Débora; Covarrubias, Cristian; Von Marttens, Alfredo; Leighton, Yerko; Carvajal, Juan Carlos; Valenzuela, Francisco; Díaz-Dosque, Mario; Méndez, Nicolás; Martínez, Constanza; Pino, Ana María; Rodríguez, Juan Pablo; Cáceres, Mónica; Smith, Patricio

2014-01-01

Nanostructured porous silica coatings were synthesized on titanium by the combined sol-gel and evaporation-induced self-assembly process. The silica-coating structures were characterized by X-ray diffraction, transmission electron microscopy, scanning electron microscopy, and nitrogen sorptometry. The effect of the nanoporous surface on apatite formation in simulated body fluid, protein adsorption, osteoblast cell adhesion behavior, and osteogenic differentiation of human bone marrow mesenchymal stem cells (hBMSCs) is reported. Silica coatings with highly ordered sub-10 nm porosity accelerate early osteoblast adhesive response, a favorable cell response that is attributed to an indirect effect due to the high protein adsorption observed on the large-specific surface area of the nanoporous coating but is also probably due to direct mechanical stimulus from the nanostructured topography. The nanoporous silica coatings, particularly those doped with calcium and phosphate, also promote the osteogenic differentiation of hBMSCs with spontaneous mineral nodule formation in basal conditions. The bioactive surface properties exhibited by the nanostructured porous silica coatings make these materials a promising alternative to improve the osseointegration properties of titanium dental implants and could have future impact on the nanoscale design of implant surfaces. Copyright © 2013 Wiley Periodicals, Inc., a Wiley Company.

Inorganic Nanomaterials as Carriers for Drug Delivery.

PubMed

Chen, Shizhu; Hao, Xiaohong; Liang, Xingjie; Zhang, Qun; Zhang, Cuimiao; Zhou, Guoqiang; Shen, Shigang; Jia, Guang; Zhang, Jinchao

2016-01-01

For safe and effective therapy, drugs must be delivered efficiently and with minimal systemic side effects. Nanostructured drug carriers enable the delivery of small-molecule drugs as well as nucleic acids and proteins. Inorganic nanomaterials are ideal for drug delivery platforms due to their unique physicochemical properties, such as facile preparation, good storage stability and biocompatibility. Many inorganic nanostructure-based drug delivery platforms have been prepared. Although there are still many obstacles to overcome, significant advances have been made in recent years. This review focuses on the status and development of inorganic nanostructures, including silica, quantum dots, gold, carbon-based and magnetic iron oxide-based nanostructures, as carriers for chemical and biological drugs. We specifically highlight the extensive use of these inorganic drug carriers for cancer therapy. Finally, we discuss the most important areas in the field that urgently require further study.

SAW based micro- and acousto-fluidics in biomedicine

NASA Astrophysics Data System (ADS)

Ramasamy, Mouli; Varadan, Vijay K.

2017-04-01

Protein association starts with random collisions of individual proteins. Multiple collisions and rotational diffusion brings the molecules to a state of orientation. Majority of the protein associations are influenced by electrostatic interactions. To introduce: electrostatic rate enhancement, Brownian dynamics and transient complex theory has been traditionally used. Due to the recent advances in interdisciplinary sciences, an array of molecular assembly methods is being studied. Protein nanostructural assembly and macromolecular crowding are derived from the subsets of biochemistry to study protein-protein interactions and protein self-assembly. This paper tries to investigate the issue of enhancing the protein self-association rate, and bridging the gap between the simulations and experimental results. The methods proposed here include: electrostatic rate enhancement, macromolecular crowing, nanostructural protein assembly, microfluidics based approaches and magnetic force based approaches. Despite the suggestions of several methods, microfluidic and magnetic force based approaches seem to serve the need of protein assembly in a wider scale. Congruence of these approaches may also yield better results. Even though, these methods prove to be conceptually strong, to prevent the disagreement of theory and practice, a wide range of experiments is required. This proposal intends to study theoretical and experimental methods to successfully implement the aforementioned assembly strategies, and conclude with an extensive analysis of experimental data to address practical feasibility.

Investigation of Transport Parameters of Graphene-Based Nanostructures

NASA Astrophysics Data System (ADS)

Sergeyev, D. M.; Shunkeyev, K. Sh.

2018-03-01

The paper presents results of computer simulation of the main transport parameters of nanostructures obtained through the row-by-row removal of carbon atoms from graphene ribbon. Research into the electrical parameters is carried out within the density functional theory using the non-equilibrium Green functions in the local-density approximation. Virtual NanoLab based on Atomistix ToolKit is used to construct structures and analyze simulation results. Current-voltage characteristics, differential conductivity and transmittance spectra of nanostructures are calculated at different values of bias voltage. It is found that there is a large region of negative differential resistance in current-voltage characteristics of nanostructures caused by resonant tunneling of quasi-particles. Differential (dI/dV) characteristic also has similar changes. The obtained results can be useful for building novel electronic devices in the field of nanoelectronics.

Atomistic Design and Simulations of Nanoscale Machines and Assembly

NASA Technical Reports Server (NTRS)

Goddard, William A., III; Cagin, Tahir; Walch, Stephen P.

2000-01-01

Over the three years of this project, we made significant progress on critical theoretical and computational issues in nanoscale science and technology, particularly in:(1) Fullerenes and nanotubes, (2) Characterization of surfaces of diamond and silicon for NEMS applications, (3) Nanoscale machine and assemblies, (4) Organic nanostructures and dendrimers, (5) Nanoscale confinement and nanotribology, (6) Dynamic response of nanoscale structures nanowires (metals, tubes, fullerenes), (7) Thermal transport in nanostructures.

Reflectance analysis of porosity gradient in nanostructured silicon layers

NASA Astrophysics Data System (ADS)

Jurečka, Stanislav; Imamura, Kentaro; Matsumoto, Taketoshi; Kobayashi, Hikaru

2017-12-01

In this work we study optical properties of nanostructured layers formed on silicon surface. Nanostructured layers on Si are formed in order to reach high suppression of the light reflectance. Low spectral reflectance is important for improvement of the conversion efficiency of solar cells and for other optoelectronic applications. Effective method of forming nanostructured layers with ultralow reflectance in a broad interval of wavelengths is in our approach based on metal assisted etching of Si. Si surface immersed in HF and H2O2 solution is etched in contact with the Pt mesh roller and the structure of the mesh is transferred on the etched surface. During this etching procedure the layer density evolves gradually and the spectral reflectance decreases exponentially with the depth in porous layer. We analyzed properties of the layer porosity by incorporating the porosity gradient into construction of the layer spectral reflectance theoretical model. Analyzed layer is splitted into 20 sublayers in our approach. Complex dielectric function in each sublayer is computed by using Bruggeman effective media theory and the theoretical spectral reflectance of modelled multilayer system is computed by using Abeles matrix formalism. Porosity gradient is extracted from the theoretical reflectance model optimized in comparison to the experimental values. Resulting values of the structure porosity development provide important information for optimization of the technological treatment operations.

New Computational Approach to Electron Transport in Irregular Graphene Nanostructures

NASA Astrophysics Data System (ADS)

Mason, Douglas; Heller, Eric; Prendergast, David; Neaton, Jeffrey

2009-03-01

For novel graphene devices of nanoscale-to-macroscopic scale, many aspects of their transport properties are not easily understood due to difficulties in fabricating devices with regular edges. Here we develop a framework to efficiently calculate and potentially screen electronic transport properties of arbitrary nanoscale graphene device structures. A generalization of the established recursive Green's function method is presented, providing access to arbitrary device and lead geometries with substantial computer-time savings. Using single-orbital nearest-neighbor tight-binding models and the Green's function-Landauer scattering formalism, we will explore the transmission function of irregular two-dimensional graphene-based nanostructures with arbitrary lead orientation. Prepared by LBNL under contract DE-AC02-05CH11231 and supported by the U.S. Dept. of Energy Computer Science Graduate Fellowship under grant DE-FG02-97ER25308.

Nanoscale manipulation of membrane curvature for probing endocytosis in live cells.

PubMed

Zhao, Wenting; Hanson, Lindsey; Lou, Hsin-Ya; Akamatsu, Matthew; Chowdary, Praveen D; Santoro, Francesca; Marks, Jessica R; Grassart, Alexandre; Drubin, David G; Cui, Yi; Cui, Bianxiao

2017-08-01

Clathrin-mediated endocytosis (CME) involves nanoscale bending and inward budding of the plasma membrane, by which cells regulate both the distribution of membrane proteins and the entry of extracellular species. Extensive studies have shown that CME proteins actively modulate the plasma membrane curvature. However, the reciprocal regulation of how the plasma membrane curvature affects the activities of endocytic proteins is much less explored, despite studies suggesting that membrane curvature itself can trigger biochemical reactions. This gap in our understanding is largely due to technical challenges in precisely controlling the membrane curvature in live cells. In this work, we use patterned nanostructures to generate well-defined membrane curvatures ranging from +50 nm to -500 nm radius of curvature. We find that the positively curved membranes are CME hotspots, and that key CME proteins, clathrin and dynamin, show a strong preference towards positive membrane curvatures with a radius <200 nm. Of ten CME-related proteins we examined, all show preferences for positively curved membrane. In contrast, other membrane-associated proteins and non-CME endocytic protein caveolin1 show no such curvature preference. Therefore, nanostructured substrates constitute a novel tool for investigating curvature-dependent processes in live cells.

21st International Conference on DNA Computing and Molecular Programming: 8.1 Biochemistry

DTIC Science & Technology

include information storage and biological applications of DNA systems, biomolecular chemical reaction networks, applications of self -assembled DNA...nanostructures, tile self -assembly and computation, principles and models of self -assembly, and strand displacement and biomolecular circuits. The fund

Protein Calligraphy: A New Concept Begins To Take Shape

DTIC Science & Technology

2016-06-30

of nearly any conceivable material .47 Judicious selection of binding peptides combined with an appropriate protein nanostructure enables the...controllable size and symmetry is a long sought after goal of nanotechnology and material engineering. Proteins are particularly attractive for...of structurally defined materials with nanometer dimensions. Researchers have spent consid- erable effort attempting to mimic nature to sculpt

Immobilization and direct electrochemistry of glucose oxidase on a tetragonal pyramid-shaped porous ZnO nanostructure for a glucose biosensor.

PubMed

Dai, Zhihui; Shao, Guojian; Hong, Jianmin; Bao, Jianchun; Shen, Jian

2009-01-01

A tetragonal pyramid-shaped porous ZnO (TPSP-ZnO) nanostructure is used for the immobilization, direct electrochemistry and biosensing of proteins. The prepared ZnO has a large surface area and good biocompatibility. Using glucose oxidase (GOD) as a model, this shaped ZnO is tested for immobilization of proteins and the construction of electrochemical biosensors with good electrochemical performances. The interaction between GOD and TPSP-ZnO is examined by using AFM, N(2) adsorption isotherms and electrochemical methods. The immobilized GOD at a TPSP-ZnO-modified glassy carbon electrode shows a good direct electrochemical behavior, which depends on the properties of the TPSP-ZnO. Based on a decrease of the electrocatalytic response of the reduced form of GOD to dissolved oxygen, the proposed biosensor exhibits a linear response to glucose concentrations ranging from 0.05 to 8.2mM with a detection limit of 0.01mM at an applied potential of -0.50V which has better biosensing properties than those from other morphological ZnO nanoparticles. The biosensor shows good stability, reproducibility, low interferences and can diagnose diabetes very fast and sensitively. Such the TPSP-ZnO nanostructure provides a good matrix for protein immobilization and biosensor preparation.

Modeling of the interaction between osteoblasts and biocompatible substrates as a function of adhesion strength.

PubMed

Portan, D V; Deligianni, D D; Deligianni, K; Kroustalli, A A; Tyllianakis, M; Papanicolaou, G C

2018-03-01

A goal of current implantology research is to design devices that induce controlled, guided, and rapid healing. Nanoscale structured substrates [e.g., titania nanotubes (TNTs) or carbon nanotubes (CNTs)] dramatically improve the functions of conventional biomaterials. The present investigation evaluated the behavior of osteoblasts cells cultured on smooth and nanostructured substrates, by measuring osteoblasts specific biomarkers [alkaline phosphatase (AP) and total protein] and cells adhesion strength to substrates, followed by semi-empirical modeling to predict the experimental results. Findings were in total agreement with the current state of the art. The proliferation, as well as the AP and total protein levels were higher on the nanostructure phases (TNTs, CNTs) comparing to the smooth ones (plastic and pure titanium). Cells adhesion strength measured was found higher on the nanostructured materials. This coincided with a higher value of proteins which are directly implicated in the process of adherence. Results were accurately predicted through the Viscoelastic Hybrid Interphase Model. A gradual adherence of bone cells to implants using multilayered biomaterials that involve biodegradable polymeric films and a nanoscale modification of titanium surface is suggested to improve performance through an interphase-mediated osteointegration of orthopedic implants. © 2017 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 106A: 621-628, 2018. © 2017 Wiley Periodicals, Inc.

Selective CXCR4+ Cancer Cell Targeting and Potent Antineoplastic Effect by a Nanostructured Version of Recombinant Ricin.

PubMed

Díaz, Raquel; Pallarès, Victor; Cano-Garrido, Olivia; Serna, Naroa; Sánchez-García, Laura; Falgàs, Aïda; Pesarrodona, Mireia; Unzueta, Ugutz; Sánchez-Chardi, Alejandro; Sánchez, Julieta M; Casanova, Isolda; Vázquez, Esther; Mangues, Ramón; Villaverde, Antonio

2018-05-29

Under the unmet need of efficient tumor-targeting drugs for oncology, a recombinant version of the plant toxin ricin (the modular protein T22-mRTA-H6) is engineered to self-assemble as protein-only, CXCR4-targeted nanoparticles. The soluble version of the construct self-organizes as regular 11 nm planar entities that are highly cytotoxic in cultured CXCR4 + cancer cells upon short time exposure, with a determined IC50 in the nanomolar order of magnitude. The chemical inhibition of CXCR4 binding sites in exposed cells results in a dramatic reduction of the cytotoxic potency, proving the receptor-dependent mechanism of cytotoxicity. The insoluble version of T22-mRTA-H6 is, contrarily, moderately active, indicating that free, nanostructured protein is the optimal drug form. In animal models of acute myeloid leukemia, T22-mRTA-H6 nanoparticles show an impressive and highly selective therapeutic effect, dramatically reducing the leukemia cells affectation of clinically relevant organs. Functionalized T22-mRTA-H6 nanoparticles are then promising prototypes of chemically homogeneous, highly potent antitumor nanostructured toxins for precise oncotherapies based on self-mediated intracellular drug delivery. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Icosahedral plant viral nanoparticles - bioinspired synthesis of nanomaterials/nanostructures.

PubMed

Narayanan, Kannan Badri; Han, Sung Soo

2017-10-01

Viral nanotechnology utilizes virus nanoparticles (VNPs) and virus-like nanoparticles (VLPs) of plant viruses as highly versatile platforms for materials synthesis and molecular entrapment that can be used in the nanotechnological fields, such as in next-generation nanoelectronics, nanocatalysis, biosensing and optics, and biomedical applications, such as for targeting, therapeutic delivery, and non-invasive in vivo imaging with high specificity and selectivity. In particular, plant virus capsids provide biotemplates for the production of novel nanostructured materials with organic/inorganic moieties incorporated in a very precise and controlled manner. Interestingly, capsid proteins of spherical plant viruses can self-assemble into well-organized icosahedral three-dimensional (3D) nanoscale multivalent architectures with high monodispersity and structural symmetry. Using viral genetic and protein engineering of icosahedral viruses with a variety of sizes, the interior, exterior and the interfaces between coat protein (CP) subunits can be manipulated to fabricate materials with a wide range of desirable properties allowing for biomineralization, encapsulation, infusion, controlled self-assembly, and multivalent ligand display of nanoparticles or molecules for varied applications. In this review, we discuss the various functional nanomaterials/nanostructures developed using the VNPs and VLPs of different icosahedral plant viruses and their nano(bio)technological and nanomedical applications. Copyright © 2017 Elsevier B.V. All rights reserved.

Atomistic model of the spider silk nanostructure

NASA Astrophysics Data System (ADS)

Keten, Sinan; Buehler, Markus J.

2010-04-01

Spider silk is an ultrastrong and extensible self-assembling biopolymer that outperforms the mechanical characteristics of many synthetic materials including steel. Here we report atomic-level structures that represent aggregates of MaSp1 proteins from the N. Clavipes silk sequence based on a bottom-up computational approach using replica exchange molecular dynamics. We discover that poly-alanine regions predominantly form distinct and orderly beta-sheet crystal domains while disorderly structures are formed by poly-glycine repeats, resembling 31-helices. These could be the molecular source of the large semicrystalline fraction observed in silks, and also form the basis of the so-called "prestretched" molecular configuration. Our structures are validated against experimental data based on dihedral angle pair calculations presented in Ramachandran plots, alpha-carbon atomic distances, as well as secondary structure content.

Virus-Based Nanoparticles of Simian Virus 40 in the Field of Nanobiotechnology.

PubMed

Zhang, Wenjing; Zhang, Xian-En; Li, Feng

2017-12-26

Biomolecular nanostructures derived from living organisms, such as protein cages, fibers, and layers are drawing increasing interests as natural biomaterials. The virus-based nanoparticles (VNPs) of simian virus 40 (SV40), with a cage-like structure assembled from the major capsid protein of SV40, have been developed as a platform for nanobiotechnology in the recent decade. Foreign nanomaterials (e.g., quantum dots (QDs) and gold nanoparticles (AuNPs)) can be positioned in the inner cavity or on the outer surface of SV40 VNPs, through self-assembly by engineering the nanoparticle (NP)-protein interfacial interactions. Construction of these hybrid nanostructures has enabled integration of different functionalities. This review briefly summarizes the applications of SV40 VNPs in this multidisciplinary field, including NP encapsulation, templated assembly of nanoarchitectures, nanophotonics, and fluorescence imaging. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Powering the programmed nanostructure and function of gold nanoparticles with catenated DNA machines

NASA Astrophysics Data System (ADS)

Elbaz, Johann; Cecconello, Alessandro; Fan, Zhiyuan; Govorov, Alexander O.; Willner, Itamar

2013-06-01

DNA nanotechnology is a rapidly developing research area in nanoscience. It includes the development of DNA machines, tailoring of DNA nanostructures, application of DNA nanostructures for computing, and more. Different DNA machines were reported in the past and DNA-guided assembly of nanoparticles represents an active research effort in DNA nanotechnology. Several DNA-dictated nanoparticle structures were reported, including a tetrahedron, a triangle or linear nanoengineered nanoparticle structures; however, the programmed, dynamic reversible switching of nanoparticle structures and, particularly, the dictated switchable functions emerging from the nanostructures, are missing elements in DNA nanotechnology. Here we introduce DNA catenane systems (interlocked DNA rings) as molecular DNA machines for the programmed, reversible and switchable arrangement of different-sized gold nanoparticles. We further demonstrate that the machine-powered gold nanoparticle structures reveal unique emerging switchable spectroscopic features, such as plasmonic coupling or surface-enhanced fluorescence.

The role of chemistry and pH of solid surfaces for specific adsorption of biomolecules in solution--accurate computational models and experiment.

PubMed

Heinz, Hendrik

2014-06-18

Adsorption of biomolecules and polymers to inorganic nanostructures plays a major role in the design of novel materials and therapeutics. The behavior of flexible molecules on solid surfaces at a scale of 1-1000 nm remains difficult and expensive to monitor using current laboratory techniques, while playing a critical role in energy conversion and composite materials as well as in understanding the origin of diseases. Approaches to implement key surface features and pH in molecular models of solids are explained, and distinct mechanisms of peptide recognition on metal nanostructures, silica and apatite surfaces in solution are described as illustrative examples. The influence of surface energies, specific surface features and protonation states on the structure of aqueous interfaces and selective biomolecular adsorption is found to be critical, comparable to the well-known influence of the charge state and pH of proteins and surfactants on their conformations and assembly. The representation of such details in molecular models according to experimental data and available chemical knowledge enables accurate simulations of unknown complex interfaces in atomic resolution in quantitative agreement with independent experimental measurements. In this context, the benefits of a uniform force field for all material classes and of a mineral surface structure database are discussed.

Determining suitable lego-structures to estimate stability of larger peptide nanostructures using computational methods.

PubMed

Beke, Tamás; Czajlik, András; Csizmadia, Imre G; Perczel, András

2006-02-02

Nanofibers, nanofilms and nanotubes constructed of one to four strands of oligo-alpha- and oligo-beta-peptides were obtained by using carefully selected building units. Lego-type approaches based on thermoneutral isodesmic reactions can be used to reconstruct the total energies of both linear and tubular periodic nanostructures with acceptable accuracy. Total energies of several different nanostructures were accurately determined with errors typically falling in the subchemical range. Thus, attention will be focused on the description of suitable isodesmic reactions that have enabled the determination of the total energy of polypeptides and therefore offer a very fast, efficient and accurate method to obtain energetic information on large and even very large nanosystems.

The Role of Membrane Curvature in Nanoscale Topography-Induced Intracellular Signaling.

PubMed

Lou, Hsin-Ya; Zhao, Wenting; Zeng, Yongpeng; Cui, Bianxiao

2018-05-15

Over the past decade, there has been growing interest in developing biosensors and devices with nanoscale and vertical topography. Vertical nanostructures induce spontaneous cell engulfment, which enhances the cell-probe coupling efficiency and the sensitivity of biosensors. Although local membranes in contact with the nanostructures are found to be fully fluidic for lipid and membrane protein diffusions, cells appear to actively sense and respond to the surface topography presented by vertical nanostructures. For future development of biodevices, it is important to understand how cells interact with these nanostructures and how their presence modulates cellular function and activities. How cells recognize nanoscale surface topography has been an area of active research for two decades before the recent biosensor works. Extensive studies show that surface topographies in the range of tens to hundreds of nanometers can significantly affect cell functions, behaviors, and ultimately the cell fate. For example, titanium implants having rough surfaces are better for osteoblast attachment and host-implant integration than those with smooth surfaces. At the cellular level, nanoscale surface topography has been shown by a large number of studies to modulate cell attachment, activity, and differentiation. However, a mechanistic understanding of how cells interact and respond to nanoscale topographic features is still lacking. In this Account, we focus on some recent studies that support a new mechanism that local membrane curvature induced by nanoscale topography directly acts as a biochemical signal to induce intracellular signaling, which we refer to as the curvature hypothesis. The curvature hypothesis proposes that some intracellular proteins can recognize membrane curvatures of a certain range at the cell-to-material interface. These proteins then recruit and activate downstream components to modulate cell signaling and behavior. We discuss current technologies allowing the visualization of membrane deformation at the cell membrane-to-substrate interface with nanometer precision and demonstrate that vertical nanostructures induce local curvatures on the plasma membrane. These local curvatures enhance the process of clathrin-mediated endocytosis and affect actin dynamics. We also present evidence that vertical nanostructures can induce significant deformation of the nuclear membrane, which can affect chromatin distribution and gene expression. Finally, we provide a brief perspective on the curvature hypothesis and the challenges and opportunities for the design of nanotopography for manipulating cell behavior.

Theoretical Investigations of Well-Defined Graphene Nanostructures: Catalysis, Spectroscopy, and Development of Novel Fragment-Based Models

NASA Astrophysics Data System (ADS)

Noffke, Benjamin W.

Carbon materials have the potential to replace some precious metals in renewable energy applications. These materials are particularly attractive because of the elemental abundance and relatively low nuclear mass of carbon, implying economically feasible and lightweight materials. Targeted design of carbon materials is hindered by the lack of fundamental understanding that is required to tailor their properties for the desired application. However, most available synthetic methods to create carbon materials involve harsh conditions that limit the control of the resulting structure. Without a well-defined structure, the system is too complex and fundamental studies cannot be definitive. This work seeks to gain fundamental understanding through the development and application of efficient computational models for these systems, in conjunction with experiments performed on soluble, well-defined graphene nanostructures prepared by our group using a bottom-up synthetic approach. Theory is used to determine mechanistic details for well-defined carbon systems in applications of catalysis and electrochemical transformations. The resulting computational models do well to explain previous observations of carbon materials and provide suggestions for future directions. However, as the system size of the nanostructures gets larger, the computational cost can become prohibitive. To reduce the computational scaling of quantum chemical calculations, a new fragmentation scheme has been developed that addresses the challenges of fragmenting conjugated molecules. By selecting fragments that retain important structural characteristics in graphene, a more efficient method is achieved. The new method paves the way for an automated, systematic fragmentation scheme of graphene molecules.

3D electron tomography of pretreated biomass informs atomic modeling of cellulose microfibrils.

PubMed

Ciesielski, Peter N; Matthews, James F; Tucker, Melvin P; Beckham, Gregg T; Crowley, Michael F; Himmel, Michael E; Donohoe, Bryon S

2013-09-24

Fundamental insights into the macromolecular architecture of plant cell walls will elucidate new structure-property relationships and facilitate optimization of catalytic processes that produce fuels and chemicals from biomass. Here we introduce computational methodology to extract nanoscale geometry of cellulose microfibrils within thermochemically treated biomass directly from electron tomographic data sets. We quantitatively compare the cell wall nanostructure in corn stover following two leading pretreatment strategies: dilute acid with iron sulfate co-catalyst and ammonia fiber expansion (AFEX). Computational analysis of the tomographic data is used to extract mathematical descriptions for longitudinal axes of cellulose microfibrils from which we calculate their nanoscale curvature. These nanostructural measurements are used to inform the construction of atomistic models that exhibit features of cellulose within real, process-relevant biomass. By computational evaluation of these atomic models, we propose relationships between the crystal structure of cellulose Iβ and the nanoscale geometry of cellulose microfibrils.

Computational Investigation of Graphene-Carbon Nanotube-Polymer Composite

NASA Astrophysics Data System (ADS)

Jha, Sanjiv; Roth, Michael; Todde, Guido; Subramanian, Gopinath; Shukla, Manoj; Univ of Southern Mississippi Collaboration; US Army Engineer Research; Development Center 3909 Halls Ferry Road Vicksburg, MS 39180, USA Collaboration

Graphene is a single atom thick two dimensional carbon sheet where sp2 -hybridized carbon atoms are arranged in a honeycomb structure. The functionalization of graphene and carbon nanotubes (CNTs) with polymer is a route for developing high performance nanocomposite materials. We study the interfacial interactions among graphene, CNT, and Nylon 6 polymer using computational methods based on density functional theory (DFT) and empirical force-field. Our DFT calculations are carried out using Quantum-ESPRESSO electronic structure code with van der Waals functional (vdW-DF2), whereas the empirical calculations are performed using LAMMPS with the COMPASS force-field. Our results demonstrated that the interactions between (8,8) CNT and graphene, and between CNT/graphene and Nylon 6 consist mostly of van der Waals type. The computed Young's moduli indicated that the mechanical properties of carbon nanostructures are enhanced by their interactions with polymer. The presence of Stone-Wales (SW) defects lowered the Young's moduli of carbon nanostructures.

Analysis of periodically patterned metallic nanostructures for infrared absorber

NASA Astrophysics Data System (ADS)

Peng, Sha; Yuan, Ying; Long, Huabao; Liu, Runhan; Wei, Dong; Zhang, Xinyu; Wang, Haiwei; Xie, Changsheng

2018-02-01

With rapid advancement of infrared detecting technology in both military and civil domains, the photo-electronic performances of near-infrared detectors have been widely concerned. Currently, near-infrared detectors demonstrate some problems such as low sensitivity, low detectivity, and relatively small array scale. The current studies show that surface plasmons (SPs) stimulated over the surface of metallic nanostructures by incident light can be used to break the diffraction limit and thus concentrate light into sub-wavelength scale, so as to indicate a method to develop a new type of infrared absorber or detector with very large array. In this paper, we present the design and characterization of periodically patterned metallic nanostructures that combine nanometer thickness aluminum film with silicon wafer. Numerical computations show that there are some valleys caused by surface plasmons in the reflection spectrum in the infrared region, and both red shift and blue shift of the reflection spectrum were observed through changing the nanostructural parameters such as angle α and diameters D. Moreover, the strong E-field intensity is located at the sharp corner of the nano-structures.

High-performance noncontact thermal diode via asymmetric nanostructures

NASA Astrophysics Data System (ADS)

Shen, Jiadong; Liu, Xianglei; He, Huan; Wu, Weitao; Liu, Baoan

2018-05-01

Electric diodes, though laying the foundation of modern electronics and information processing industries, suffer from ineffectiveness and even failure at high temperatures. Thermal diodes are promising alternatives to relieve above limitations, but usually possess low rectification ratios, and how to obtain a high-performance thermal rectification effect is still an open question. This paper proposes an efficient contactless thermal diode based on the near-field thermal radiation of asymmetric doped silicon nanostructures. The rectification ratio computed via exact scattering theories is demonstrated to be as high as 10 at a nanoscale gap distance and period, outperforming the counterpart flat-plate diode by more than one order of magnitude. This extraordinary performance mainly lies in the higher forward and lower reverse radiative heat flux within the low frequency band compared with the counterpart flat-plate diode, which is caused by a lower loss and smaller cut-off wavevector of nanostructures for the forward and reversed scheme, respectively. This work opens new routes to realize high performance thermal diodes, and may have wide applications in efficient thermal computing, thermal information processing, and thermal management.

How To Identify Plasmons from the Optical Response of Nanostructures

PubMed Central

2017-01-01

A promising trend in plasmonics involves shrinking the size of plasmon-supporting structures down to a few nanometers, thus enabling control over light–matter interaction at extreme-subwavelength scales. In this limit, quantum mechanical effects, such as nonlocal screening and size quantization, strongly affect the plasmonic response, rendering it substantially different from classical predictions. For very small clusters and molecules, collective plasmonic modes are hard to distinguish from other excitations such as single-electron transitions. Using rigorous quantum mechanical computational techniques for a wide variety of physical systems, we describe how an optical resonance of a nanostructure can be classified as either plasmonic or nonplasmonic. More precisely, we define a universal metric for such classification, the generalized plasmonicity index (GPI), which can be straightforwardly implemented in any computational electronic-structure method or classical electromagnetic approach to discriminate plasmons from single-particle excitations and photonic modes. Using the GPI, we investigate the plasmonicity of optical resonances in a wide range of systems including: the emergence of plasmonic behavior in small jellium spheres as the size and the number of electrons increase; atomic-scale metallic clusters as a function of the number of atoms; and nanostructured graphene as a function of size and doping down to the molecular plasmons in polycyclic aromatic hydrocarbons. Our study provides a rigorous foundation for the further development of ultrasmall nanostructures based on molecular plasmonics. PMID:28651057

Uncovering the self-assembly of DNA nanostructures by thermodynamics and kinetics.

PubMed

Wei, Xixi; Nangreave, Jeanette; Liu, Yan

2014-06-17

CONSPECTUS: DNA nanotechnology is one of the most flourishing interdisciplinary research fields. DNA nanostructures can be designed to self-assemble into a variety of periodic or aperiodic patterns of different shapes and length scales. They can be used as scaffolds for organizing other nanoparticles, proteins, and chemical groups, leveraging their functions for creating complex bioinspired materials that may serve as smart drug delivery systems, in vitro or in vivo biomolecular computing platforms, and diagnostic devices. Achieving optimal structural features, efficient assembly protocols, and precise functional group positioning and modification requires a thorough understanding of the thermodynamics and kinetics of the DNA nanostructure self-assembly process. The most common real-time measurement strategies include monitoring changes in UV absorbance based on the hyperchromic effect of DNA, and the emission signal changes of DNA intercalating dyes or covalently conjugated fluorescent dyes/pairs that accompany temperature dependent structural changes. Thermodynamic studies of a variety of DNA nanostructures have been performed, from simple double stranded DNA formation to more complex origami assembly. The key parameters that have been evaluated in terms of stability and cooperativity include the overall dimensions, the folding path of the scaffold, crossover and nick point arrangement, length and sequence of single strands, and salt and ion concentrations. DNA tile-tile interactions through sticky end hybridization have also been analyzed, and the steric inhibition and rigidity of tiles turn out to be important factors. Many kinetic studies have also been reported, and most are based on double stranded DNA formation. A two-state assumption and the hypothesis of several intermediate states have been applied to determine the rate constant and activation energy of the DNA hybridization process. A few simulated models were proposed to represent the structural, mechanical, and kinetic properties of DNA hybridization. The kinetics of strand displacement reactions has also been studied as a special case of DNA hybridization. The thermodynamic and kinetic characteristics of DNA nanostructures have been exploited to develop rapid and isothermal annealing protocols. It is conceivable that a more thorough understanding of the DNA assembly process could be used to guide the structural design process and optimize the conditions for assembly, manipulation, and functionalization, thus benefiting both upstream design and downstream applications.

Atomistic Modeling of Nanostructures via the BFS Quantum Approximate Method

NASA Technical Reports Server (NTRS)

Bozzolo, Guillermo; Garces, Jorge E.; Noebe, Ronald D.; Farias, D.

2003-01-01

Ideally, computational modeling techniques for nanoscopic physics would be able to perform free of limitations on the type and number of elements, while providing comparable accuracy when dealing with bulk or surface problems. Computational efficiency is also desirable, if not mandatory, for properly dealing with the complexity of typical nano-strucured systems. A quantum approximate technique, the BFS method for alloys, which attempts to meet these demands, is introduced for the calculation of the energetics of nanostructures. The versatility of the technique is demonstrated through analysis of diverse systems, including multi-phase precipitation in a five element Ni-Al-Ti-Cr-Cu alloy and the formation of mixed composition Co-Cu islands on a metallic Cu(III) substrate.

Structure and optical function of amorphous photonic nanostructures from avian feather barbs: a comparative small angle X-ray scattering (SAXS) analysis of 230 bird species

PubMed Central

Saranathan, Vinodkumar; Forster, Jason D.; Noh, Heeso; Liew, Seng-Fatt; Mochrie, Simon G. J.; Cao, Hui; Dufresne, Eric R.; Prum, Richard O.

2012-01-01

Non-iridescent structural colours of feathers are a diverse and an important part of the phenotype of many birds. These colours are generally produced by three-dimensional, amorphous (or quasi-ordered) spongy β-keratin and air nanostructures found in the medullary cells of feather barbs. Two main classes of three-dimensional barb nanostructures are known, characterized by a tortuous network of air channels or a close packing of spheroidal air cavities. Using synchrotron small angle X-ray scattering (SAXS) and optical spectrophotometry, we characterized the nanostructure and optical function of 297 distinctly coloured feathers from 230 species belonging to 163 genera in 51 avian families. The SAXS data provided quantitative diagnoses of the channel- and sphere-type nanostructures, and confirmed the presence of a predominant, isotropic length scale of variation in refractive index that produces strong reinforcement of a narrow band of scattered wavelengths. The SAXS structural data identified a new class of rudimentary or weakly nanostructured feathers responsible for slate-grey, and blue-grey structural colours. SAXS structural data provided good predictions of the single-scattering peak of the optical reflectance of the feathers. The SAXS structural measurements of channel- and sphere-type nanostructures are also similar to experimental scattering data from synthetic soft matter systems that self-assemble by phase separation. These results further support the hypothesis that colour-producing protein and air nanostructures in feather barbs are probably self-assembled by arrested phase separation of polymerizing β-keratin from the cytoplasm of medullary cells. Such avian amorphous photonic nanostructures with isotropic optical properties may provide biomimetic inspiration for photonic technology. PMID:22572026

Assembly and microscopic characterization of DNA origami structures.

PubMed

Scheible, Max; Jungmann, Ralf; Simmel, Friedrich C

2012-01-01

DNA origami is a revolutionary method for the assembly of molecular nanostructures from DNA with precisely defined dimensions and with an unprecedented yield. This can be utilized to arrange nanoscale components such as proteins or nanoparticles into pre-defined patterns. For applications it will now be of interest to arrange such components into functional complexes and study their geometry-dependent interactions. While commonly DNA nanostructures are characterized by atomic force microscopy or electron microscopy, these techniques often lack the time-resolution to study dynamic processes. It is therefore of considerable interest to also apply fluorescence microscopic techniques to DNA nanostructures. Of particular importance here is the utilization of novel super-resolved microscopy methods that enable imaging beyond the classical diffraction limit.

Mesoscale Interfacial Dynamics in Magnetoelectric Nanocomposites

DOE Office of Scientific and Technical Information (OSTI.GOV)

Khachaturyan, Armen G.

Theory and modeling of chessboard-like self-assembling of vertically aligned columnar nanostructures in films has been developed. By means of modeling and three-dimensional computational simulations, we proposed a novel self-assembly process that can produce good chessboard nanostructure architectures through a pseudo-spinodal decomposition of an epitaxial film under optimal thermodynamic and crystallographic conditions (appropriate choice of the temperature, composition of the film, and crystal lattice parameters of the film and substrate). These conditions are formulated. The obtained results have been published on Nano Letters. Based on the principles of the formation of chessboard nanostructured films, we are currently trying to find goodmore » decomposing material systems that satisfy the optimal conditions to produce the chessboard nanostructure architecture. In addition we are under way doing 'computer experiments' to look for the appropriate materials with the chessboard columnar nanostructures, as a potential candidate for engineering of optical devices, high-efficiency multiferroics, and high-density magnetic perpendicular recording media. We are also currently to investigate the magnetoelectric response of multiferroic chessboard nanostructures under applied electric/magnetic fields. A unified 3-dimensional phase field theory of the strain-mediated magnetoelectric effect in magnetoelectric composites is developed. The theory is based on the established equivalency paradigm: we proved that by using a variational priciple the exact values of the electric, magnetic and strain fields in a magnetoelectric composite of arbitrary morphology and their coupled magneto-electric-mechanical response can be evaluated by considering an equivalent homogeneous system with the specially chosen effective eigenstrain, polarization and magnetization. These equivalency parameters are spatially inhomogeneous fields, which are obtained by solving the time-dependent Ginzburg-Landau equations. The paper summarizing these results is to be submitted to JAP. We are currently using the computational model based on the unified phase field theory to predict the local and overall response of the magnetoelectric composites with arbitrary configuration under applied fields, and to find the optimal composite microstructure that produces the strongest ME coupling. We have developed modeling and simulations to support Dr. S. Pryia efforts to produce the strongest ME coupling by searching the optimal configuration of applied electric/magnetic fields, and microstructure of polycrystalline multiferroics. An analytical model demonstrates that the optimization of a magnetoelectric (ME) coupling of a laminar magnetic/piezoelectric polycrystalline composite could be obtained by a proper choice of the magnetic and electric poling directions and the directions of the applied a.c. fields. The results have been published on JAP. Our next step is to determine the domain of optimal parameters and configurations by using our optimization theory and computational modeling.« less

Biomolecular Assembly of Gold Nanocrystals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Micheel, Christine Marya

2005-05-20

Over the past ten years, methods have been developed to construct discrete nanostructures using nanocrystals and biomolecules. While these frequently consist of gold nanocrystals and DNA, semiconductor nanocrystals as well as antibodies and enzymes have also been used. One example of discrete nanostructures is dimers of gold nanocrystals linked together with complementary DNA. This type of nanostructure is also known as a nanocrystal molecule. Discrete nanostructures of this kind have a number of potential applications, from highly parallel self-assembly of electronics components and rapid read-out of DNA computations to biological imaging and a variety of bioassays. My research focused inmore » three main areas. The first area, the refinement of electrophoresis as a purification and characterization method, included application of agarose gel electrophoresis to the purification of discrete gold nanocrystal/DNA conjugates and nanocrystal molecules, as well as development of a more detailed understanding of the hydrodynamic behavior of these materials in gels. The second area, the development of methods for quantitative analysis of transmission electron microscope data, used computer programs written to find pair correlations as well as higher order correlations. With these programs, it is possible to reliably locate and measure nanocrystal molecules in TEM images. The final area of research explored the use of DNA ligase in the formation of nanocrystal molecules. Synthesis of dimers of gold particles linked with a single strand of DNA possible through the use of DNA ligase opens the possibility for amplification of nanostructures in a manner similar to polymerase chain reaction. These three areas are discussed in the context of the work in the Alivisatos group, as well as the field as a whole.« less

Carbon nanotube-lipase hybrid nanoflowers with enhanced enzyme activity and enantioselectivity.

PubMed

Li, Kai; Wang, Jianhua; He, Yaojia; Abdulrazaq, Miaad Adnan; Yan, Yunjun

2018-06-19

Various nanoflowers are synthesized as supports for different methods of enzyme immobilization; however, the activities of these immobilized enzymes are limited because of their confinement in the nanoflowers. In order to increase the performance of nanoflowers, in this study, different protein-phosphate hybrid nanostructures were successfully synthesized and further enhanced by carbon nanotubes (CNTs) under the same conditions. Only Cu 3 (PO 4 ) 2 complex nanostructures exhibited flower-like structures and showed excellent results after enhancement with CNTs in this framework. An esterification reaction between lauric acid and 1-dodecanol was used to test enzyme activity during immobilization, revealing that the Cu 3 (PO 4 ) 2 /CNT/protein complex exhibited 68-fold higher activity relative to free lipase and 51-fold higher than that of Cu 3 (PO 4 ) 2 /Burkholderia cepacia lipase hybrid nanoflowers in the absence of CNTs. All three hybrid nanostructures showed good performance and exhibited excellent reusability in resolution reactions between 1-phenylethanol and vinyl acetate. Additionally, the substrate enantiomeric excess (ee s ) reached 98% in only 10 min, and the corresponding Cu 3 (PO 4 ) 2 /CNT/protein complex could be recycled eight times without obvious loss of activity. This approach involving nanoflowers enhanced with CNTs will be highly beneficial for decreasing mass-transfer resistance and providing enhanced enzyme loading along with promising potential for industrial application. Copyright © 2018 Elsevier B.V. All rights reserved.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Thomas, Carla S.; Xu, Liza; Olsen, Bradley D.

Blending the small molecule osmolytes glycerol and trehalose with the model globular protein–polymer block copolymer mCherry-b-poly(N-isopropyl acrylamide) (mCherry-b-PNIPAM) is demonstrated to improve protein functionality in self-assembled nanostructures. The incorporation of either additive into block copolymers results in functionality retention in the solid state of 80 and 100% for PNIPAM volume fractions of 40 and 55%, respectively. This represents a large improvement over the 50–60% functionality observed in the absence of any additive. Furthermore, glycerol decreases the thermal stability of block copolymer films by 15–20 °C, while trehalose results in an improvement in the thermal stability by 15–20 °C. These resultsmore » suggest that hydrogen bond replacement is responsible for the retention of protein function but suppression or enhancement of thermal motion based on the glass transition of the osmolyte primarily determines thermal stability. While both osmolytes are observed to have a disordering effect on the nanostructure morphology with increasing concentration, this effect is less pronounced in materials with a larger polymer volume fraction. Glycerol preferentially localizes in the protein domains and swells the nanostructures, inducing disordering or a change in morphology depending on the PNIPAM coil fraction. In contrast, trehalose is observed to macrophase separate from the block copolymer, which results in nanodomains becoming more disordered without changing significantly in size.« less

Two-qubit correlations via a periodic plasmonic nanostructure

NASA Astrophysics Data System (ADS)

Iliopoulos, Nikos; Terzis, Andreas F.; Yannopapas, Vassilios; Paspalakis, Emmanuel

2016-02-01

We theoretically investigate the generation of quantum correlations by using two distant qubits in free space or mediated by a plasmonic nanostructure. We report both entanglement of formation as well as quantum discord and classical correlations. We have found that for proper initial state of the two-qubit system and distance between the two qubits we can produce quantum correlations taking significant value for a relatively large time interval so that it can be useful in quantum information and computation processes.

Two-qubit correlations via a periodic plasmonic nanostructure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Iliopoulos, Nikos; Terzis, Andreas F.; Yannopapas, Vassilios

2016-02-15

We theoretically investigate the generation of quantum correlations by using two distant qubits in free space or mediated by a plasmonic nanostructure. We report both entanglement of formation as well as quantum discord and classical correlations. We have found that for proper initial state of the two-qubit system and distance between the two qubits we can produce quantum correlations taking significant value for a relatively large time interval so that it can be useful in quantum information and computation processes.

Nanostructured titanate with different metal ions on the surface of metallic titanium: a facile approach for regulation of rBMSCs fate on titanium implants.

PubMed

Ren, Na; Li, Jianhua; Qiu, Jichuan; Sang, Yuanhua; Jiang, Huaidong; Boughton, Robert I; Huang, Ling; Huang, Wei; Liu, Hong

2014-08-13

Titanium (Ti) is widely used for load-bearing bio-implants, however, it is bio-inert and exhibits poor osteo-inductive properties. Calcium and magnesium ions are considered to be involved in bone metabolism and play a physiological role in the angiogenesis, growth, and mineralization of bone tissue. In this study, a facile synthesis approach to the in situ construction of a nanostructure enriched with Ca(2+) and Mg(2+) on the surface of titanium foil is proposed by inserting Ca(2+) and Mg(2+) into the interlayers of sodium titanate nanostructures through an ion-substitution process. The characteriz 0.67, and 0.73 nm ation results validate that cations can be inserted into the interlayer regions of the layered nanostructure without any obvious change of morphology. The cation content is positively correlated to the concentration of the solutions employed. The biological assessments indicate that the type and the amount of cations in the titanate nanostructure can alter the bioactivity of titanium implants. Compared with a Na(+) filled titanate nanostructure, the incorporation of divalent ions (Mg(2+) , Ca(2+) ) can effectively enhance protein adsorption, and thus also enhance the adhesion and differentiation ability of rat bone-marrow stem cells (rBMSCs). The Mg(2+) /Ca(2+) -titanate nanostructure is a promising implantable material that will be widely applicable in artificial bones, joints, and dental implants. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Functional and in vitro gastric digestibility of the whey protein hydrogel loaded with nanostructured lipid carriers and gelled via citric acid-mediated crosslinking.

PubMed

Hashemi, Behnaz; Madadlou, Ashkan; Salami, Maryam

2017-12-15

Nanostructured lipid carriers (NLCs) with mean size of 347nm were fabricated and added into a heat-denatured whey protein solution. The subsequent crosslinking of proteins by citric acid or CaCl 2 resulted in the formation of cold-set hydrogels. Fourier transform infrared spectroscopy (FTIR) proposed formation of more hydrogen bonds in gel due to NLC loading or citric acid-mediated gelation. It was also found based on FITR spectroscopy that citric acid crosslinking disordered whey proteins. Scanning electron microscopy (SEM) imaging showed a non-porous and finely meshed microstructure for the crosslinked gels compared to non-crosslinked counterparts. Crosslinking also increased the firmness and water-holding capacity of gels. In pepsin-free fluid, a strong correlation existed between reduction in gel swellability and digestibility over periods up to 60min due to NLC loading and citric acid gelation. However, in peptic fluid, NLC loading and citric acid crosslinking brought about much higher decrease in digestibility than swellability. Copyright © 2017 Elsevier Ltd. All rights reserved.

Insight Center | Computational Science | NREL

Science.gov Websites

effectively convey information and illustrate research findings to stakeholders and visitors. The -turbine array simulations. Observational data span from the nanostructures of biomass pretreatments to the

The use of three-dimensional nanostructures to instruct cells to produce extracellular matrix for regenerative medicine strategies

PubMed Central

Schenke-Layland, Katja; Rofail, Fady; Heydarkhan, Sanaz; Gluck, Jessica M.; Ingle, Nilesh P.; Angelis, Ekaterini; Choi, Chang-Hwan; MacLellan, W Robb; Beygui, Ramin E; Shemin, Richard J; Heydarkhan-Hagvall, Sepideh

2009-01-01

Synthetic polymers or naturally-derived extracellular matrix (ECM) proteins have been used to create tissue engineering scaffolds; however, the need for surface modification in order to achieve polymer biocompatibility and the lack of biomechanical strength of constructs built using proteins alone remain major limitations. To overcome these obstacles, we developed novel hybrid constructs composed of both strong biosynthetic materials and natural human ECM proteins. Taking advantage of the ability of cells to produce their own ECM, human foreskin fibroblasts were grown on silicon-based nanostructures exhibiting various surface topographies that significantly enhanced ECM protein production. After 4 weeks, cell-derived sheets were harvested and histology, immunochemistry, biochemistry and multiphoton imaging revealed the presence of collagens, tropoelastin, fibronectin and glycosaminoglycans. Following decellularization, purified sheet-derived ECM proteins were mixed with poly(ε-caprolactone) to create fibrous scaffolds using electrospinning. These hybrid scaffolds exhibited excellent biomechanical properties with fiber and pore sizes that allowed attachment and migration of adipose tissue-derived stem cells. Our study represents an innovative approach to generate strong, non-cytotoxic scaffolds that could have broad applications in tissue regeneration strategies. PMID:19524289

A nanostructural basis for gloss of avian eggshells

PubMed Central

Igic, Branislav; Fecheyr-Lippens, Daphne; Xiao, Ming; Chan, Andrew; Hanley, Daniel; Brennan, Patricia R. L.; Grim, Tomas; Waterhouse, Geoffrey I. N.; Hauber, Mark E.; Shawkey, Matthew D.

2015-01-01

The role of pigments in generating the colour and maculation of birds' eggs is well characterized, whereas the effects of the eggshell's nanostructure on the visual appearance of eggs are little studied. Here, we examined the nanostructural basis of glossiness of tinamou eggs. Tinamou eggs are well known for their glossy appearance, but the underlying mechanism responsible for this optical effect is unclear. Using experimental manipulations in conjunction with angle-resolved spectrophotometry, scanning electron microscopy, atomic force microscopy and chemical analyses, we show that the glossy appearance of tinamou eggshells is produced by an extremely smooth cuticle, composed of calcium carbonate, calcium phosphate and, potentially, organic compounds such as proteins and pigments. Optical calculations corroborate surface smoothness as the main factor producing gloss. Furthermore, we reveal the presence of weak iridescence on eggs of the great tinamou (Tinamus major), an optical effect never previously documented for bird eggs. These data highlight the need for further exploration into the nanostructural mechanisms for the production of colour and other optical effects of avian eggshells. PMID:25505139

Multifunctional biophotonic nanostructures inspired by the longtail glasswing butterfly for medical devices

NASA Astrophysics Data System (ADS)

Narasimhan, Vinayak; Siddique, Radwanul Hasan; Lee, Jeong Oen; Kumar, Shailabh; Ndjamen, Blaise; Du, Juan; Hong, Natalie; Sretavan, David; Choo, Hyuck

2018-06-01

Numerous living organisms possess biophotonic nanostructures that provide colouration and other diverse functions for survival. While such structures have been actively studied and replicated in the laboratory, it remains unclear whether they can be used for biomedical applications. Here, we show a transparent photonic nanostructure inspired by the longtail glasswing butterfly (Chorinea faunus) and demonstrate its use in intraocular pressure (IOP) sensors in vivo. We exploit the phase separation between two immiscible polymers (poly(methyl methacrylate) and polystyrene) to form nanostructured features on top of a Si3N4 substrate. The membrane thus formed shows good angle-independent white-light transmission, strong hydrophilicity and anti-biofouling properties, which prevent adhesion of proteins, bacteria and eukaryotic cells. We then developed a microscale implantable IOP sensor using our photonic membrane as an optomechanical sensing element. Finally, we performed in vivo testing on New Zealand white rabbits, which showed that our device reduces the mean IOP measurement variation compared with conventional rebound tonometry without signs of inflammation.

Mutagenesis study to disrupt electrostatic interactions on the twofold symmetry interface of Escherichia coli bacterioferritin.

PubMed

Zhang, Yu; Wang, Lijun; Ardejani, Maziar S; Aris, Nur Fazlina; Li, Xun; Orner, Brendan P; Wang, Fei

2015-12-01

Ferritins and other cage proteins have been utilized as models to understand the fundamentals of protein folding and self-assembly. The bacterioferritin (BFR) from Escherichia coli, a maxi-ferritin made up of 24 subunits, was chosen as the basis for a mutagenesis study to investigate the role of electrostatic intermolecular interactions mediated through charged amino acids. Through structural and computational analyses, three charged amino acids R30, D56 and E60 which involved in an electrostatic interaction network were mutated to the opposite charge. Four mutants, R30D, D56R, E60H and D56R-E60H, were expressed, purified and characterized. All of the mutants fold into α-helical structures. Consistent with the computational prediction, they all show a lowered thermostability; double mutant D56R-E60H was found to be 16°C less stable than the wild type. Except for the mutant E60H, all the other mutations completely shut down the formation of protein cages to favour the dimer state in solution. The mutants, however, retain their ability to form cage-like nanostructures in the dried, surface immobilized conditions of transmission electron microscopy. Our findings confirm that even a single charge-inversion mutation at the 2-fold interface of BFR can affect the quaternary structure of its dimers and their ability to self-assemble into cage structures. © The Authors 2015. Published by Oxford University Press on behalf of the Japanese Biochemical Society. All rights reserved.

DNA-based construction at the nanoscale: emerging trends and applications

NASA Astrophysics Data System (ADS)

Lourdu Xavier, P.; Chandrasekaran, Arun Richard

2018-02-01

The field of structural DNA nanotechnology has evolved remarkably—from the creation of artificial immobile junctions to the recent DNA-protein hybrid nanoscale shapes—in a span of about 35 years. It is now possible to create complex DNA-based nanoscale shapes and large hierarchical assemblies with greater stability and predictability, thanks to the development of computational tools and advances in experimental techniques. Although it started with the original goal of DNA-assisted structure determination of difficult-to-crystallize molecules, DNA nanotechnology has found its applications in a myriad of fields. In this review, we cover some of the basic and emerging assembly principles: hybridization, base stacking/shape complementarity, and protein-mediated formation of nanoscale structures. We also review various applications of DNA nanostructures, with special emphasis on some of the biophysical applications that have been reported in recent years. In the outlook, we discuss further improvements in the assembly of such structures, and explore possible future applications involving super-resolved fluorescence, single-particle cryo-electron (cryo-EM) and x-ray free electron laser (XFEL) nanoscopic imaging techniques, and in creating new synergistic designer materials.

DNA-based construction at the nanoscale: emerging trends and applications.

PubMed

Xavier, P Lourdu; Chandrasekaran, Arun Richard

2018-02-09

The field of structural DNA nanotechnology has evolved remarkably-from the creation of artificial immobile junctions to the recent DNA-protein hybrid nanoscale shapes-in a span of about 35 years. It is now possible to create complex DNA-based nanoscale shapes and large hierarchical assemblies with greater stability and predictability, thanks to the development of computational tools and advances in experimental techniques. Although it started with the original goal of DNA-assisted structure determination of difficult-to-crystallize molecules, DNA nanotechnology has found its applications in a myriad of fields. In this review, we cover some of the basic and emerging assembly principles: hybridization, base stacking/shape complementarity, and protein-mediated formation of nanoscale structures. We also review various applications of DNA nanostructures, with special emphasis on some of the biophysical applications that have been reported in recent years. In the outlook, we discuss further improvements in the assembly of such structures, and explore possible future applications involving super-resolved fluorescence, single-particle cryo-electron (cryo-EM) and x-ray free electron laser (XFEL) nanoscopic imaging techniques, and in creating new synergistic designer materials.

The application of the large particles method of numerical modeling of the process of carbonic nanostructures synthesis in plasma

NASA Astrophysics Data System (ADS)

Abramov, G. V.; Gavrilov, A. N.

2018-03-01

The article deals with the numerical solution of the mathematical model of the particles motion and interaction in multicomponent plasma by the example of electric arc synthesis of carbon nanostructures. The high order of the particles and the number of their interactions requires a significant input of machine resources and time for calculations. Application of the large particles method makes it possible to reduce the amount of computation and the requirements for hardware resources without affecting the accuracy of numerical calculations. The use of technology of GPGPU parallel computing using the Nvidia CUDA technology allows organizing all General purpose computation on the basis of the graphical processor graphics card. The comparative analysis of different approaches to parallelization of computations to speed up calculations with the choice of the algorithm in which to calculate the accuracy of the solution shared memory is used. Numerical study of the influence of particles density in the macro particle on the motion parameters and the total number of particle collisions in the plasma for different modes of synthesis has been carried out. The rational range of the coherence coefficient of particle in the macro particle is computed.

Hybrid lipid-based nanostructures

NASA Astrophysics Data System (ADS)

Dayani, Yasaman

Biological membranes serve several important roles, such as structural support of cells and organelles, regulation of ionic and molecular transport, barriers to non-mediated transport, contact between cells within tissues, and accommodation of membrane proteins. Membrane proteins and other vital biomolecules incorporated into the membrane need a lipid membrane to function. Due to importance of lipid bilayers and their vital function in governing many processes in the cell, the development of various models as artificial lipid membranes that can mimic cell membranes has become a subject of great interest. Using different models of artificial lipid membranes, such as liposomes, planar lipid bilayers and supported or tethered lipid bilayers, we are able to study many biophysical processes in biological membranes. The ability of different molecules to interact with and change the structure of lipid membranes can be also investigated in artificial lipid membranes. An important application of lipid bilayer-containing interfaces is characterization of novel membrane proteins for high throughput drug screening studies to investigate receptor-drug interactions and develop biosensor systems. Membrane proteins need a lipid bilayer environment to preserve their stability and functionality. Fabrication of materials that can interact with biomolecules like proteins necessitates the use of lipid bilayers as a mimic of cell membranes. The objective of this research is to develop novel hybrid lipid-based nanostructures mimicking biological membranes. Toward this aim, two hybrid biocompatible structures are introduced: lipid bilayer-coated multi-walled carbon nanotubes (MWCNTs) and hydrogel-anchored liposomes with double-stranded DNA anchors. These structures have potential applications in biosensing, drug targeting, drug delivery, and biophysical studies of cell membranes. In the first developed nanostructure, lipid molecules are covalently attached to the surfaces of MWCNTs, and then, using a sonication process, a uniform lipid bilayer that supports the incorporation of membrane proteins is formed. These bilayer-coated carbon nanotubes are highly dispersible and stable in aqueous solution, and they can be used in development of various biosensors and energy producing devices. In the other hybrid nanostructure, the lipid bilayer of a liposome is covalently anchored to a biocompatible poly(ethylene) glycol (PEG) hydrogel core using double-stranded DNA (dsDNA) linkers. Release studies shows that nano-size hydrogel-anchored liposomes are exceptionally stable, and they can be used as biomimetic model membranes that mimic the connectivity between the cytoskeleton and the plasma membrane. After lipid bilayer removal, dsDNA linkers can provide programmable nanogels decorated with oligonucleotides with potential sites for further molecular assembly. These stable nanostructures can be useful for oligonucleotide and drug delivery applications. The developed hydrogel-anchored liposomes are exploited for encapsulation and intracellular delivery of therapeutic peptide. Peptides with anti-cancer properties are successfully encapsulated in hydrogel core of pH-sensitive liposomes during rehydration process. Liposomes release their cargo at acidic pH. Confocal microscopy confirms the intracellular delivery of liposomes through an endocytotic pathway.

Photon-trapping micro/nanostructures for high linearity in ultra-fast photodiodes

NASA Astrophysics Data System (ADS)

Cansizoglu, Hilal; Gao, Yang; Perez, Cesar Bartolo; Ghandiparsi, Soroush; Ponizovskaya Devine, Ekaterina; Cansizoglu, Mehmet F.; Yamada, Toshishige; Elrefaie, Aly F.; Wang, Shih-Yuan; Islam, M. Saif

2017-08-01

Photodetectors (PDs) in datacom and computer networks where the link length is up to 300 m, need to handle higher than typical input power used in other communication links. Also, to reduce power consumption due to equalization at high speed (>25Gb/s), the datacom links will use PAM-4 signaling instead of NRZ with stringent receiver linearity requirements. Si PDs with photon-trapping micro/nanostructures are shown to have high linearity in output current verses input optical power. Though there is less silicon material due to the holes, the micro-/nanostructured holes collectively reradiate the light to an in-plane direction of the PD surface and can avoid current crowding in the PD. Consequently, the photocurrent per unit volume remains at a low level contributing to high linearity in the photocurrent. We present the effect of design and lattice patterns of micro/nanostructures on the linearity of ultra-fast silicon PDs designed for high speed multi gigabit data networks.

Silk fibroin nanostructured materials for biomedical applications

NASA Astrophysics Data System (ADS)

Mitropoulos, Alexander N.

Nanostructured biopolymers have proven to be promising to develop novel biomedical applications where forming structures at the nanoscale normally occurs by self-assembly. However, synthesizing these structures can also occur by inducing materials to transition into other forms by adding chemical cross-linkers, changing pH, or changing ionic composition. Understanding the generation of nanostructures in fluid environments, such as liquid organic solvents or supercritical fluids, has not been thoroughly examined, particularly those that are based on protein-based block-copolymers. Here, we examine the transformation of reconstituted silk fibroin, which has emerged as a promising biopolymer due to its biocompatibility, biodegradability, and ease of functionalization, into submicron spheres and gel networks which offer applications in tissue engineering and advanced sensors. Two types of gel networks, hydrogels and aerogels, have small pores and large surface areas that are defined by their structure. We design and analyze silk nanoparticle formation using a microfluidic device while offering an application for drug delivery. Additionally, we provide a model and characterize hydrogel formation from micelles to nanoparticles, while investigating cellular response to the hydrogel in an in vitro cell culture model. Lastly, we provide a second model of nanofiber formation during near-critical and supercritical drying and characterize the silk fibroin properties at different drying pressures which, when acting as a stabilizing matrix, shows to improve the activity of entrapped enzymes dried at different pressures. This work has created new nanostructured silk fibroin forms to benefit biomedical applications that could be applied to other fibrous proteins.

Rational Design of a Transferrin-Binding Peptide Sequence Tailored to Targeted Nanoparticle Internalization.

PubMed

Santi, Melissa; Maccari, Giuseppe; Mereghetti, Paolo; Voliani, Valerio; Rocchiccioli, Silvia; Ucciferri, Nadia; Luin, Stefano; Signore, Giovanni

2017-02-15

The transferrin receptor (TfR) is a promising target in cancer therapy owing to its overexpression in most solid tumors and on the blood-brain barrier. Nanostructures chemically derivatized with transferrin are employed in TfR targeting but often lose their functionality upon injection in the bloodstream. As an alternative strategy, we rationally designed a peptide coating able to bind transferrin on suitable pockets not involved in binding to TfR or iron by using an iterative multiscale-modeling approach coupled with quantitative structure-activity and relationship (QSAR) analysis and evolutionary algorithms. We tested that selected sequences have low aspecific protein adsorption and high binding energy toward transferrin, and one of them is efficiently internalized in cells with a transferrin-dependent pathway. Furthermore, it promotes transferrin-mediated endocytosis of gold nanoparticles by modifying their protein corona and promoting oriented adsorption of transferrin. This strategy leads to highly effective nanostructures, potentially useful in diagnostic and therapeutic applications, which exploit (and do not suffer) the protein solvation for achieving a better targeting.

Genetically engineered nanocarriers for drug delivery.

PubMed

Shi, Pu; Gustafson, Joshua A; MacKay, J Andrew

2014-01-01

Cytotoxicity, low water solubility, rapid clearance from circulation, and off-target side-effects are common drawbacks of conventional small-molecule drugs. To overcome these shortcomings, many multifunctional nanocarriers have been proposed to enhance drug delivery. In concept, multifunctional nanoparticles might carry multiple agents, control release rate, biodegrade, and utilize target-mediated drug delivery; however, the design of these particles presents many challenges at the stage of pharmaceutical development. An emerging solution to improve control over these particles is to turn to genetic engineering. Genetically engineered nanocarriers are precisely controlled in size and structure and can provide specific control over sites for chemical attachment of drugs. Genetically engineered drug carriers that assemble nanostructures including nanoparticles and nanofibers can be polymeric or non-polymeric. This review summarizes the recent development of applications in drug and gene delivery utilizing nanostructures of polymeric genetically engineered drug carriers such as elastin-like polypeptides, silk-like polypeptides, and silk-elastin-like protein polymers, and non-polymeric genetically engineered drug carriers such as vault proteins and viral proteins.

Genetically engineered nanocarriers for drug delivery

PubMed Central

Shi, Pu; Gustafson, Joshua A; MacKay, J Andrew

2014-01-01

Cytotoxicity, low water solubility, rapid clearance from circulation, and off-target side-effects are common drawbacks of conventional small-molecule drugs. To overcome these shortcomings, many multifunctional nanocarriers have been proposed to enhance drug delivery. In concept, multifunctional nanoparticles might carry multiple agents, control release rate, biodegrade, and utilize target-mediated drug delivery; however, the design of these particles presents many challenges at the stage of pharmaceutical development. An emerging solution to improve control over these particles is to turn to genetic engineering. Genetically engineered nanocarriers are precisely controlled in size and structure and can provide specific control over sites for chemical attachment of drugs. Genetically engineered drug carriers that assemble nanostructures including nanoparticles and nanofibers can be polymeric or non-polymeric. This review summarizes the recent development of applications in drug and gene delivery utilizing nanostructures of polymeric genetically engineered drug carriers such as elastin-like polypeptides, silk-like polypeptides, and silk-elastin-like protein polymers, and non-polymeric genetically engineered drug carriers such as vault proteins and viral proteins. PMID:24741309

Controlling Self-Assembly of Engineered Peptides on Graphite by Rational Mutation

PubMed Central

So, Christopher R.; Hayamizu, Yuhei; Yazici, Hilal; Gresswell, Carolyn; Khatayevich, Dmitriy; Tamerler, Candan; Sarikaya, Mehmet

2012-01-01

Self-assembly of proteins on surfaces is utilized in many fields to integrate intricate biological structures and diverse functions with engineered materials. Controlling proteins at bio-solid interfaces relies on establishing key correlations between their primary sequences and resulting spatial organizations on substrates. Protein self-assembly, however, remains an engineering challenge. As a novel approach, we demonstrate here that short dodecapeptides selected by phage display are capable of self-assembly on graphite and form long-range ordered biomolecular nanostructures. Using atomic force microscopy and contact angle studies, we identify three amino-acid domains along the primary sequence that steer peptide ordering and lead to nanostructures with uniformly displayed residues. The peptides are further engineered via simple mutations to control fundamental interfacial processes, including initial binding, surface aggregation and growth kinetics, and intermolecular interactions. Tailoring short peptides via their primary sequence offers versatile control over molecular self-assembly, resulting in well-defined surface properties essential in building engineered, chemically rich, bio-solid interfaces. PMID:22233341

Stability of biogenic metal(loid) nanomaterials related to the colloidal stabilization theory of chemical nanostructures.

PubMed

Piacenza, Elena; Presentato, Alessandro; Turner, Raymond J

2018-02-25

In the last 15 years, the exploitation of biological systems (i.e. plants, bacteria, mycelial fungi, yeasts, and algae) to produce metal(loid) (Me)-based nanomaterials has been evaluated as eco-friendly and a cost-effective alternative to the chemical synthesis processes. Although the biological mechanisms of biogenic Me-nanomaterial (Bio-Me-nanomaterials) production are not yet completely elucidated, a key advantage of such bio-nanostructures over those chemically synthesized is related to their natural thermodynamic stability, with several studies ascribed to the presence of an organic layer surrounding these Bio-Me-nanostructures. Different macromolecules (e.g. proteins, peptides, lipids, DNA, and polysaccharides) or secondary metabolites (e.g. flavonoids, terpenoids, glycosides, organic acids, and alkaloids) naturally produced by organisms have been indicated as main contributors to the stabilization of Bio-Me-nanostructures. Nevertheless, the chemical-physical mechanisms behind the ability of these molecules in providing stability to Bio-Me-nanomaterials are unknown. In this context, transposing the stabilization theory of chemically synthesized Me-nanomaterials (Ch-Me-nanomaterials) to biogenic materials can be used towards a better comprehension of macromolecules and secondary metabolites role as stabilizing agents of Bio-Me-nanomaterials. According to this theory, nanomaterials are generally featured by high thermodynamic instability in suspension, due to their high surface area and surface energy. This feature leads to the necessity to stabilize chemical nanostructures, even during or directly after their synthesis, through the development of (i) electrostatic, (ii) steric, or (iii) electrosteric interactions occurring between molecules and nanomaterials in suspension. Based on these three mechanisms, this review is focused on parallels between the stabilization of biogenic or chemical nanomaterials, suggesting which chemical-physical mechanisms may be involved in the natural stability of Bio-Me-nanomaterials. As a result, macromolecules such as DNA, polyphosphates and proteins may electrostatically interact with Bio-Me-nanomaterials in suspension through their charged moieties, showing the same properties of counterions in Ch-Me-nanostructure suspensions. Since several biomolecules (e.g. neutral lipids, nonionic biosurfactants, polysaccharides, and secondary metabolites) produced by metal(loid)-grown organisms can develop similar steric hindrance as compared to nonionic amphiphilic surfactants and block co-polymers generally used to sterically stabilize Ch-Me-nanomaterials. These biomolecules, most likely, are involved in the development of steric stabilization, because of their bulky structures. Finally, charged lipids and polysaccharides, ionic biosurfactants or proteins with amphiphilic properties can exert a dual effect (i.e. electrostatic and steric repulsion interactions) in the contest of Bio-Me-nanomaterials, leading to the high degree of stability observed.

Equivalent-Continuum Modeling of Nano-Structured Materials

NASA Technical Reports Server (NTRS)

Odegard, Gregory M.; Gates, Thomas S.; Nicholson, Lee M.; Wise, Kristopher E.

2001-01-01

A method has been developed for modeling structure-property relationships of nano-structured materials. This method serves as a link between computational chemistry and solid mechanics by substituting discrete molecular structures with an equivalent-continuum model. It has been shown that this substitution may be accomplished by equating the vibrational potential energy of a nano-structured material with the strain energy of representative truss and continuum models. As an important example with direct application to the development and characterization of single-walled carbon nanotubes, the model has been applied to determine the effective continuum geometry of a graphene sheet. A representative volume element of the equivalent-continuum model has been developed with an effective thickness. This effective thickness has been shown to be similar to, but slightly smaller than, the interatomic spacing of graphite.

DOE-EPSCoR Final Report Period: September 1, 2008- August 31, 2016

DOE Office of Scientific and Technical Information (OSTI.GOV)

Katiyar, Ram; Gomez, M.; Morell, G.

In this project, multifunctional nanostructured spintronic and magnetoelectric materials were investigated by experimental and computational efforts for applications in energy efficient electronic systems that integrate functionalities and thus have the potential to enable a new generation of faster responding devices and increased integration densities. The team systematically investigated transition metal (TM)-doped ZnO nanostructures, silicide nanorods, magnetoelectric oxides, and ferroelectric/ferromagnetic heterostructures. In what follows, we report the progress made by researchers during the above period in developing and understanding of 1) Spintronics nanostructures; 2) Resistive switching phenomenon in oxides for memory devices; 3) Magnetoelectric multiferroics; 4) Novel high-k gate oxides formore » logic devices; 5) Two dimensional (2D) materials; and 6) Theoretical studies in the above fields.« less

Picosecond ultrasonics study of the vibrational modes of a nanostructure

NASA Astrophysics Data System (ADS)

Antonelli, G. Andrew; Maris, Humphrey J.; Malhotra, Sandra G.; Harper, James M. E.

2002-03-01

We report experiments in which a subpicosecond pump light pulse is used to excite vibrations in a nanostructure consisting of a periodic array of copper wires embedded in a glass matrix on a silicon substrate. The motion of the wires after excitation is detected using a time-delayed probe light pulse. From the measured data, it is possible to determine the frequencies νn and damping rates Γn of a number of the normal modes of the structure. These modes have frequencies lying in the range 1-30 GHz. By comparison of the measured νn and Γn with the frequencies and damping rates calculated from a computer simulation of the vibrations of the nanostructure, we have been able to deduce the vibration patterns of six of the normal modes.

Effect of Lipid-Based Nanostructure on Protein Encapsulation within the Membrane Bilayer Mimetic Lipidic Cubic Phase Using Transmembrane and Lipo-proteins from the Beta-Barrel Assembly Machinery.

PubMed

van 't Hag, Leonie; Shen, Hsin-Hui; Lin, Tsung-Wu; Gras, Sally L; Drummond, Calum J; Conn, Charlotte E

2016-11-29

A fundamental understanding of the effect of amphiphilic protein encapsulation on the nanostructure of the bicontinuous cubic phase is crucial to progressing biomedical and biological applications of these hybrid protein-lipid materials, including as drug delivery vehicles, as biosensors, biofuel cells and for in meso crystallization. The relationship between the lipid nanomaterial and the encapsulated protein, however, remains poorly understood. In this study, we investigated the effect of incorporating the five transmembrane and lipo-proteins which make up the β-barrel assembly machinery from Gram-negative bacteria within a series of bicontinuous cubic phases. The transmembrane β-barrel BamA caused an increase in lattice parameter of the cubic phase upon encapsulation. By contrast, the mainly hydrophilic lipo-proteins BamB-E caused the cubic phase lattice parameters to decrease, despite their large size relative to the diameter of the cubic phase water channels. Analysis of the primary amino acid sequence was used to rationalize this effect, based on specific interactions between aromatic amino acids within the proteins and the polar-apolar interface. Other factors that were found to have an effect were lateral bilayer pressure and rigidity within the lipid bilayer, water channel diameter, and size and structure of the lipo-proteins. The data presented suggest that hydrophilic bioactive molecules can be selectively encapsulated within the cubic phase by using a lipid anchor or aromatic amino acids, for drug delivery or biosensing applications.

RNA Nanostructures – Methods and Protocols | Center for Cancer Research

Cancer.gov

RNA nanotechnology is a young field with many potential applications. The goal is to utilize designed RNA strands, such that the obtained constructs have specific properties in terms of shape and functionality. RNA has potential functionalities that are comparable to that of proteins, but possesses (compared to proteins) simpler design principles akin to DNA. The promise is

Self assembling proteins

DOEpatents

Yeates, Todd O.; Padilla, Jennifer; Colovos, Chris

2004-06-29

Novel fusion proteins capable of self-assembling into regular structures, as well as nucleic acids encoding the same, are provided. The subject fusion proteins comprise at least two oligomerization domains rigidly linked together, e.g. through an alpha helical linking group. Also provided are regular structures comprising a plurality of self-assembled fusion proteins of the subject invention, and methods for producing the same. The subject fusion proteins find use in the preparation of a variety of nanostructures, where such structures include: cages, shells, double-layer rings, two-dimensional layers, three-dimensional crystals, filaments, and tubes.

DNA nanotechnology and fluorescence applications.

PubMed

Schlichthaerle, Thomas; Strauss, Maximilian T; Schueder, Florian; Woehrstein, Johannes B; Jungmann, Ralf

2016-06-01

Structural DNA nanotechnology allow researchers to use the unique molecular recognition properties of DNA strands to construct nanoscale objects with almost arbitrary complexity in two and three dimensions. Abstracted as molecular breadboards, DNA nanostructures enable nanometer-precise placement of guest molecules such as proteins, fluorophores, or nanoparticles. These assemblies can be used to study biological phenomena with unprecedented control over number, spacing, and molecular identity. Here, we give a general introduction to structural DNA nanotechnology and more specifically discuss applications of DNA nanostructures in the field of fluorescence and plasmonics. Copyright © 2016 Elsevier Ltd. All rights reserved.

Nanomechanics—the whole is more than the sum of its parts

NASA Astrophysics Data System (ADS)

2016-09-01

Nanostructures, such as carbon nanotubes, are often added to polymers and composites to enhance their strength. The extreme mechanical properties of carbon nanotubes suggest an obvious rationale behind this approach. However as Markus Buehler and Isabelle Su at Massachusetts Institute of Technology in the US highlight in their recent topical review [1] the behaviour that renders nanomaterials soft or strong can be far from trivial, often involving interactions on a range of scales from macrostructures to nanostructures and—in the case of biostructures—the amino acids and proteins they are built from.

A New Computational Tool for Understanding Light-Matter Interactions

DTIC Science & Technology

2016-02-11

SECURITY CLASSIFICATION OF: Plasmonic resonance of a metallic nanostructure results from coherent motion of its conduction electrons driven by...Box 12211 Research Triangle Park, NC 27709-2211 Plasmonics , light-matter interaction, time-dependent density functional theory, modeling and...reviewed journals: Final Report: A New Computational Tool For Understanding Light-Matter Interactions Report Title Plasmonic resonance of a metallic

Novel 3D/VR interactive environment for MD simulations, visualization and analysis.

PubMed

Doblack, Benjamin N; Allis, Tim; Dávila, Lilian P

2014-12-18

The increasing development of computing (hardware and software) in the last decades has impacted scientific research in many fields including materials science, biology, chemistry and physics among many others. A new computational system for the accurate and fast simulation and 3D/VR visualization of nanostructures is presented here, using the open-source molecular dynamics (MD) computer program LAMMPS. This alternative computational method uses modern graphics processors, NVIDIA CUDA technology and specialized scientific codes to overcome processing speed barriers common to traditional computing methods. In conjunction with a virtual reality system used to model materials, this enhancement allows the addition of accelerated MD simulation capability. The motivation is to provide a novel research environment which simultaneously allows visualization, simulation, modeling and analysis. The research goal is to investigate the structure and properties of inorganic nanostructures (e.g., silica glass nanosprings) under different conditions using this innovative computational system. The work presented outlines a description of the 3D/VR Visualization System and basic components, an overview of important considerations such as the physical environment, details on the setup and use of the novel system, a general procedure for the accelerated MD enhancement, technical information, and relevant remarks. The impact of this work is the creation of a unique computational system combining nanoscale materials simulation, visualization and interactivity in a virtual environment, which is both a research and teaching instrument at UC Merced.

Novel 3D/VR Interactive Environment for MD Simulations, Visualization and Analysis

PubMed Central

Doblack, Benjamin N.; Allis, Tim; Dávila, Lilian P.

2014-01-01

The increasing development of computing (hardware and software) in the last decades has impacted scientific research in many fields including materials science, biology, chemistry and physics among many others. A new computational system for the accurate and fast simulation and 3D/VR visualization of nanostructures is presented here, using the open-source molecular dynamics (MD) computer program LAMMPS. This alternative computational method uses modern graphics processors, NVIDIA CUDA technology and specialized scientific codes to overcome processing speed barriers common to traditional computing methods. In conjunction with a virtual reality system used to model materials, this enhancement allows the addition of accelerated MD simulation capability. The motivation is to provide a novel research environment which simultaneously allows visualization, simulation, modeling and analysis. The research goal is to investigate the structure and properties of inorganic nanostructures (e.g., silica glass nanosprings) under different conditions using this innovative computational system. The work presented outlines a description of the 3D/VR Visualization System and basic components, an overview of important considerations such as the physical environment, details on the setup and use of the novel system, a general procedure for the accelerated MD enhancement, technical information, and relevant remarks. The impact of this work is the creation of a unique computational system combining nanoscale materials simulation, visualization and interactivity in a virtual environment, which is both a research and teaching instrument at UC Merced. PMID:25549300

Protein nanotechnology: what is it?

PubMed

Gerrard, Juliet A

2013-01-01

Protein nanotechnology is an emerging field that is still defining itself. It embraces the intersection of protein science, which exists naturally at the nanoscale, and the burgeoning field of nanotechnology. In this opening chapter, a select review is given of some of the exciting nanostructures that have already been created using proteins, and the sorts of applications that protein engineers are reaching towards in the nanotechnology space. This provides an introduction to the rest of the volume, which provides inspirational case studies, along with tips and tools to manipulate proteins into new forms and architectures, beyond Nature's original intentions.

Application of 1-aminocyclohexane carboxylic acid to protein nanostructure computer design

PubMed Central

Rodríguez-Ropero, Francisco; Zanuy, David; Casanovas, Jordi; Nussinov, Ruth; Alemán, Carlos

2009-01-01

Conformationally restricted amino acids are promising candidates to serve as basic pieces in redesigned protein motifs which constitute the basic modules in synthetic nanoconstructs. Here we study the ability of constrained cyclic amino acid 1-aminocyclohexane-1-carboxylic acid (Ac6c) to stabilize highly regular β-helical motifs excised from naturally occurring proteins. Calculations indicate that the conformational flexibility observed in both the ring and the main chain is significantly higher than that detected for other 1-aminocycloalkane-1-carboxylic acid (Acnc, where n refers to the size of the ring) with smaller cycles. Incorporation of Ac6c into the flexible loops of β-helical motifs indicates that the stability of such excised building blocks as well as the nano-assemblies derived from them is significantly enhanced. Thus, the intrinsic Ac6c tendency to adopt folded conformations combined with the low structural strain of the cyclohexane ring confers the ability to both self-adapt to the β-helix motif and to stabilize the overall structure by absorbing part of its conformational fluctuations. Comparison with other Acnc residues indicates that the ability to adapt to the targeted position improves considerably with the ring size, i.e. when the rigidity introduced by the strain of the ring decreases. PMID:18201062

Nanoscale superstructures assembled by polymerase chain reaction (PCR): programmable construction, structural diversity, and emerging applications.

PubMed

Kuang, Hua; Ma, Wei; Xu, Liguang; Wang, Libing; Xu, Chuanlai

2013-11-19

Polymerase chain reaction (PCR) is an essential tool in biotechnology laboratories and is becoming increasingly important in other areas of research. Extensive data obtained over the last 12 years has shown that the combination of PCR with nanoscale dispersions can resolve issues in the preparation DNA-based materials that include both inorganic and organic nanoscale components. Unlike conventional DNA hybridization and antibody-antigen complexes, PCR provides a new, effective assembly platform that both increases the yield of DNA-based nanomaterials and allows researchers to program and control assembly with predesigned parameters including those assisted and automated by computers. As a result, this method allows researchers to optimize to the combinatorial selection of the DNA strands for their nanoparticle conjugates. We have developed a PCR approach for producing various nanoscale assemblies including organic motifs such as small molecules, macromolecules, and inorganic building blocks, such as nanorods (NRs), metal, semiconductor, and magnetic nanoparticles (NPs). We start with a nanoscale primer and then modify that building block using the automated steps of PCR-based assembly including initialization, denaturation, annealing, extension, final elongation, and final hold. The intermediate steps of denaturation, annealing, and extension are cyclic, and we use computer control so that the assembled superstructures reach their predetermined complexity. The structures assembled using a small number of PCR cycles show a lower polydispersity than similar discrete structures obtained by direct hybridization between the nanoscale building blocks. Using different building blocks, we assembled the following structural motifs by PCR: (1) discrete nanostructures (NP dimers, NP multimers including trimers, pyramids, tetramers or hexamers, etc.), (2) branched NP superstructures and heterochains, (3) NP satellite-like superstructures, (4) Y-shaped nanostructures and DNA networks, (5) protein-DNA co-assembly structures, and (6) DNA block copolymers including trimers and pentamers. These results affirm that this method can produce a variety of chemical structures and in yields that are tunable. Using PCR-based preparation of DNA-bridged nanostructures, we can program the assembly of the nanoscale blocks through the adjustment of the primer intensity on the assembled units, the number of PCR cycles, or both. The resulting structures are highly complex and diverse and have interesting dynamics and collective properties. Potential applications of these materials include chirooptical materials, probe fabrication, and environmental and biomedical sensors.

Induced synthesis of toroid-like lead sulfide nanocomposites in ethanol solution through a protein templating route

NASA Astrophysics Data System (ADS)

Zhang, Li; Qin, Dezhi; Yang, Guangrui; Du, Xian; Zhang, Qiuxia; Li, Feng

2015-09-01

The toroid-like PbS nanocrystals have been prepared in zein ethanol solution based on self-assembly template of protein molecules. From transmission electron microscopy observation, the obtained samples were monodispersed with an average size of about 47 nm. The chemical composition and crystal structure of nanocomposites were determined by X-ray diffraction and energy-dispersive X-ray spectrum measurements. The interaction between PbS and zein was investigated through Fourier transform infrared, photoluminescence, circular dichroism (CD) spectra, and thermogravimetric analysis. The PbS nanocrystals could react with nitrogen and oxygen atoms of zein molecules through coordination and electrostatic force. The CD spectra results suggested that PbS nanocrystals induced the conformational transition of protein from α-helix to β-sheet and then self-assembled into ring or toroid nanostructure. The quenching of zein fluorescence induced by PbS nanocrystals also showed the change in the chemical microenvironments of the fluorescent amino acid residues in the protein structure. The key step of this facile, biomimetic route was the formation of self-assembly nanostructure of zein, which could regulate the nucleation and growth of toroid-like PbS nanocrystals.

Addressing the instability of DNA nanostructures in tissue culture.

PubMed

Hahn, Jaeseung; Wickham, Shelley F J; Shih, William M; Perrault, Steven D

2014-09-23

DNA nanotechnology is an advanced technique that could contribute diagnostic, therapeutic, and biomedical research devices to nanomedicine. Although such devices are often developed and demonstrated using in vitro tissue culture models, these conditions may not be compatible with DNA nanostructure integrity and function. The purpose of this study was to characterize the sensitivity of 3D DNA nanostructures produced via the origami method to the in vitro tissue culture environment and identify solutions to prevent loss of nanostructure integrity. We examined whether the physiological cation concentrations of cell culture medium and the nucleases present in fetal bovine serum (FBS) used as a medium supplement result in denaturation and digestion, respectively. DNA nanostructure denaturation due to cation depletion was design- and time-dependent, with one of four tested designs remaining intact after 24 h at 37 °C. Adjustment of medium by addition of MgSO4 prevented denaturation. Digestion of nanostructures by FBS nucleases in Mg(2+)-adjusted medium did not appear design-dependent and became significant within 24 h and when medium was supplemented with greater than 5% FBS. We estimated that medium supplemented with 10% FBS contains greater than 256 U/L equivalent of DNase I activity in digestion of DNA nanostructures. Heat inactivation at 75 °C and inclusion of actin protein in medium inactivated and inhibited nuclease activity, respectively. We examined the impact of medium adjustments on cell growth, viability, and phenotype. Adjustment of Mg(2+) to 6 mM did not appear to have a detrimental impact on cells. Heat inactivation was found to be incompatible with in vitro tissue culture, whereas inclusion of actin had no observable effect on growth and viability. In two in vitro assays, immune cell activation and nanoparticle endocytosis, we show that using conditions compatible with cell phenotype and nanostructure integrity is critical for obtaining reliable experimental data. Our study thus describes considerations that are vital for researchers undertaking in vitro tissue culture studies with DNA nanostructures and some potential solutions for ensuring that nanostructure integrity and functions are maintained during experiments.

Protein functionalization of ZnO nanostructure exhibits selective and enhanced toxicity to breast cancer cells through oxidative stress-based cell death mechanism.

PubMed

Mahanta, Sailendra; Prathap, S; Ban, Deependra Kumar; Paul, Subhankar

2017-08-01

Zinc oxide nanostructure (ZnONS) was chemically synthesized and functionalized (FZnONS BLA ) with a small protein bovine α-lactalbumin (BLA) by chemical cross-linking methods. Both nano-structures were characterized using various techniques such as electron microscopy, dynamic light scattering (DLS), UV-Vis spectroscopy, FT-IR, photo-luminescence and X-ray diffraction. Electron microscopy and DLS analysis revealed their (ZnONS and FZnONS BLA ) average size of 200nm and 450nm, respectively. When cytotoxicity of both the nanostructures were assessed in breast cancer cells MCF-7 and MDAMB231 by MTT assay and PI/Annexin V staining (FACS), FZnONS BLA demonstrated higher cell death than ZnONS primarily due to generation of intracellular reactive oxygen species (ROS). Our experimental results also suggested that such enhanced toxicity was due to the lethal structural variant of BLA in FZnONS BLA as well as higher cellular uptake than ZnONS by cancer cells. The death kinetics study with time in cancer cells further proved that FZnONS BLA caused toxicity much faster than ZnONS, thus suggested a strong role of lethal variant of BLA in FZnONS BLA as a cytotoxic agent in cancer cells. Furthermore, FZnONS BLA demonstrated excellent cytocompatibility (normal cells) and hemocompatibility compared to ZnONS. Hence, considering the biodegradable nature of ZnO nonmaterial, our results demonstrated that BLA functionalized ZnONS could be used to develop a suitable therapeutic strategy in cancer. Copyright © 2017. Published by Elsevier B.V.

Molecular Design of Bioinspired Nanostructures for Biomedical Applications: Synthesis, Self-Assembly and Functional Properties

NASA Astrophysics Data System (ADS)

Xu, Hesheng Victor; Zheng, Xin Ting; Mok, Beverly Yin Leng; Ibrahim, Salwa Ali; Yu, Yong; Tan, Yen Nee

2016-08-01

Biomolecules are the nanoscale building blocks of cells, which play multifaceted roles in the critical biological processes such as biomineralization in a living organism. In these processes, the biological molecules such as protein and nucleic acids use their exclusive biorecognition properties enabled from their unique chemical composition, shape and function to initiate a cascade of cellular events. The exceptional features of these biomolecules, coupled with the recent advancement in nanotechnology, have led to the emergence of a new research field that focuses on the molecular design of bioinspired nanostructures that inherit the extraordinary function of natural biomaterials. These “bioinspired” nanostructures could be formulated by biomimetic approaches through either self-assembling of biomolecules or acting as a biomolecular template/precursor to direct the synthesis of nanocomposite. In either situation, the resulting nanomaterials exhibit phenomenal biocompatibility, superb aqueous solubility and excellent colloidal stability, branding them exceptionally desirable for both in vitro and in vivo biomedical applications. In this review, we will present the recent developments in the preparation of “bioinspired” nanostructures through biomimetic self-assembly and biotemplating synthesis, as well as highlight their functional properties and potential applications in biomedical diagnostics and therapeutic delivery. Lastly, we will conclude this topic with some personal perspective on the challenges and future outlooks of the “bioinspired” nanostructures for nanomedicine.

Affibody Modified and Radiolabeled Gold-Iron Oxide Hetero-nanostructures for Tumor PET, Optical and MR Imaging

PubMed Central

Yang, Meng; Cheng, Kai; Qi, Shibo; Liu, Hongguang; Jiang, Yuxin; Jiang, Han; Li, Jinbo; Chen, Kai; Zhang, Huimao; Cheng, Zhen

2013-01-01

A highly monodispersed hetero-nanostructure with two different functional nanomaterials (gold (Au) and iron oxide (Fe3O4, IO)) within one structure was successfully developed as Affibody based trimodality nanoprobe (positron emission tomography, PET; optical imaging; and magnetic resonance imaging, MRI) for imaging of epidermal growth factor receptor (EGFR) positive tumors. Unlike other regular nanostructures with a single component, the Au-IO hetero-nanostructures (Au-IONPs) with unique chemical and physical properties have capability to combine several imaging modalities together to provide complementary information. The IO component within hetero-nanostructures serve as a T2 reporter for MRI; and gold component serve as both optical and PET reporters. Moreover, such hetero-nanoprobes could provide a robust nano-platform for surface-specific modification with both targeting molecules (anti-EGFR Affibody protein) and PET imaging reporters (radiometal 64Cu chelators) in highly efficient and reliable manner. In vitro and in vivo study showed that the resultant nanoprobe provided high specificity, sensitivity, and excellent tumor contrast for both PET and MRI imaging in the human EGFR-expressing cells and tumors. Our study data also highlighted the EGFR targeting efficiency of hetero-nanoparticles and the feasibility for their further theranostic applications. PMID:23343632

Stability of DNA Origami Nanoarrays in Cell Lysate

PubMed Central

Mei, Qian; Wei, Xixi; Su, Fengyu; Liu, Yan; Youngbull, Cody; Johnson, Roger; Lindsay, Stuart; Yan, Hao; Meldrum, Deirdre

2012-01-01

Scaffolded DNA origami, a method to create self-assembled nanostructures with spatially addressable features, has recently been used to develop water-soluble molecular chips for label-free RNA detection, platforms for deterministic protein positioning, and single molecule reaction observatories. These applications highlight the possibility of exploiting the unique properties and biocompatibility of DNA nanostructures in live, cellular systems. Herein, we assembled several DNA origami nanostructures of differing shape, size and probes, and investigated their interaction with lysate obtained from various normal and cancerous cell lines. We separated and analyzed the origami–lysate mixtures using agarose gel electrophoresis and recovered the DNA structures for functional assay and subsequent microscopic examination. Our results demonstrate that DNA origami nanostructures are stable in cell lysate and can be easily separated from lysate mixtures, in contrast to natural, single- and double-stranded DNA. Atomic force microscope (AFM) and transmission electron microscope (TEM) images show that the DNA origami structures are fully intact after separation from cell lysates and hybridize to their targets, verifying the superior structural integrity and functionality of self-assembled DNA origami nanostructures relative to conventional oligonucleotides. The stability and functionality of DNA origami structures in cell lysate validate their use for biological applications, for example, as programmable molecular rafts or disease detection platforms. PMID:21366226

Nanostructured Polyaniline Coating on ITO Glass Promotes the Neurite Outgrowth of PC 12 Cells by Electrical Stimulation.

PubMed

Wang, Liping; Huang, Qianwei; Wang, Jin-Ye

2015-11-10

A conducting polymer polyaniline (PANI) with nanostructure was synthesized on indium tin oxide (ITO) glass. The effect of electrical stimulation on the proliferation and the length of neurites of PC 12 cells was investigated. The dynamic protein adsorption on PANI and ITO surfaces in a cell culture medium was also compared with and without electrical stimulation. The adsorbed proteins were characterized using SDS-PAGE. A PANI coating on ITO surface was shown with 30-50 nm spherical nanostructure. The number of PC 12 cells was significantly greater on the PANI/ITO surface than on ITO and plate surfaces after cell seeding for 24 and 36 h. This result confirmed that the PANI coating is nontoxic to PC 12 cells. The electrical stimulation for 1, 2, and 4 h significantly enhanced the cell numbers for both PANI and ITO conducting surfaces. Moreover, the application of electrical stimulation also improved the neurite outgrowth of PC 12 cells, and the number of PC 12 cells with longer neurite lengths increased obviously under electrical stimulation for the PANI surface. From the mechanism, the adsorption of DMEM proteins was found to be enhanced by electrical stimulation for both PANI/ITO and ITO surfaces. A new band 2 (around 37 kDa) was observed from the collected adsorbed proteins when PC 12 cells were cultured on these surfaces, and culturing PC 12 cells also seemed to increase the amount of band 1 (around 90 kDa). When immersing PANI/ITO and ITO surfaces in a DMEM medium without a cell culture, the number of band 3 (around 70 kDa) and band 4 (around 45 kDa) proteins decreased compared to that of PC 12 cell cultured surfaces. These results are valuable for the design and improvement of the material performance for neural regeneration.

A study of the vibrational modes of a nanostructure with picosecond ultrasonics

NASA Astrophysics Data System (ADS)

Antonelli, G. Andrew; Maris, Humphrey J.; Malhotra, Sandra G.; Harper, James M. E.

2002-05-01

We describe experiments in which a sub-picosecond pump light pulse is used to excite vibrations in a nanostructure. The sample consists of a periodic array of copper wires embedded in a glass matrix on a silicon substrate. The motion of the wires after excitation is detected using a time-delayed probe light pulse. From the data, it is possible to determine the frequencies νn and damping rates Γn of a number of the normal modes of the structure. These modes have frequencies lying in the range 1-30 GHz. By comparison of the measured νn and Γn with the frequencies and damping rates calculated from a computer simulation of the vibrations of the nanostructure, we have been able to identify the different normal modes and deduce their vibration patterns.

Through-space transfer of chiral information mediated by a plasmonic nanomaterial

NASA Astrophysics Data System (ADS)

Ostovar Pour, Saeideh; Rocks, Louise; Faulds, Karen; Graham, Duncan; Parchaňský, Václav; Bouř, Petr; Blanch, Ewan W.

2015-07-01

The ability to detect chirality gives stereochemically attuned nanosensors the potential to revolutionize the study of biomolecular processes. Such devices may structurally characterize the mechanisms of protein-ligand binding, the intermediates of amyloidogenic diseases and the effects of phosphorylation and glycosylation. We demonstrate that single nanoparticle plasmonic reporters, or nanotags, can enable a stereochemical response to be transmitted from a chiral analyte to an achiral benzotriazole dye molecule in the vicinity of a plasmon resonance from an achiral metallic nanostructure. The transfer of chirality was verified by the measurement of mirror image surface enhanced resonance Raman optical activity spectra for the two enantiomers of both ribose and tryptophan. Computational modelling confirms these observations and reveals the novel chirality transfer mechanism responsible. This is the first report of colloidal metal nanoparticles in the form of single plasmonic substrates displaying an intrinsic chiral sensitivity once attached to a chiral molecule.

Scaling behaviour for the water transport in nanoconfined geometries

PubMed Central

Chiavazzo, Eliodoro; Fasano, Matteo; Asinari, Pietro; Decuzzi, Paolo

2014-01-01

The transport of water in nanoconfined geometries is different from bulk phase and has tremendous implications in nanotechnology and biotechnology. Here molecular dynamics is used to compute the self-diffusion coefficient D of water within nanopores, around nanoparticles, carbon nanotubes and proteins. For almost 60 different cases, D is found to scale linearly with the sole parameter θ as D(θ)=DB[1+(DC/DB−1)θ], with DB and DC the bulk and totally confined diffusion of water, respectively. The parameter θ is primarily influenced by geometry and represents the ratio between the confined and total water volumes. The D(θ) relationship is interpreted within the thermodynamics of supercooled water. As an example, such relationship is shown to accurately predict the relaxometric response of contrast agents for magnetic resonance imaging. The D(θ) relationship can help in interpreting the transport of water molecules under nanoconfined conditions and tailoring nanostructures with precise modulation of water mobility. PMID:24699509

Investigating bioconjugation by atomic force microscopy

PubMed Central

2013-01-01

Nanotechnological applications increasingly exploit the selectivity and processivity of biological molecules. Integration of biomolecules such as proteins or DNA into nano-systems typically requires their conjugation to surfaces, for example of carbon-nanotubes or fluorescent quantum dots. The bioconjugated nanostructures exploit the unique strengths of both their biological and nanoparticle components and are used in diverse, future oriented research areas ranging from nanoelectronics to biosensing and nanomedicine. Atomic force microscopy imaging provides valuable, direct insight for the evaluation of different conjugation approaches at the level of the individual molecules. Recent technical advances have enabled high speed imaging by AFM supporting time resolutions sufficient to follow conformational changes of intricately assembled nanostructures in solution. In addition, integration of AFM with different spectroscopic and imaging approaches provides an enhanced level of information on the investigated sample. Furthermore, the AFM itself can serve as an active tool for the assembly of nanostructures based on bioconjugation. AFM is hence a major workhorse in nanotechnology; it is a powerful tool for the structural investigation of bioconjugation and bioconjugation-induced effects as well as the simultaneous active assembly and analysis of bioconjugation-based nanostructures. PMID:23855448

Investigating bioconjugation by atomic force microscopy.

PubMed

Tessmer, Ingrid; Kaur, Parminder; Lin, Jiangguo; Wang, Hong

2013-07-15

Nanotechnological applications increasingly exploit the selectivity and processivity of biological molecules. Integration of biomolecules such as proteins or DNA into nano-systems typically requires their conjugation to surfaces, for example of carbon-nanotubes or fluorescent quantum dots. The bioconjugated nanostructures exploit the unique strengths of both their biological and nanoparticle components and are used in diverse, future oriented research areas ranging from nanoelectronics to biosensing and nanomedicine. Atomic force microscopy imaging provides valuable, direct insight for the evaluation of different conjugation approaches at the level of the individual molecules. Recent technical advances have enabled high speed imaging by AFM supporting time resolutions sufficient to follow conformational changes of intricately assembled nanostructures in solution. In addition, integration of AFM with different spectroscopic and imaging approaches provides an enhanced level of information on the investigated sample. Furthermore, the AFM itself can serve as an active tool for the assembly of nanostructures based on bioconjugation. AFM is hence a major workhorse in nanotechnology; it is a powerful tool for the structural investigation of bioconjugation and bioconjugation-induced effects as well as the simultaneous active assembly and analysis of bioconjugation-based nanostructures.

Gold/silver/gold trilayer films on nanostructured polycarbonate substrates for direct and label-free nanoplasmonic biosensing.

PubMed

López-Muñoz, Gerardo A; Estévez, M-Carmen; Vázquez-García, Marc; Berenguel-Alonso, Miguel; Alonso-Chamarro, Julián; Homs-Corbera, Antoni; Lechuga, Laura M

2018-05-01

Ultrasmooth gold/silver/gold trilayer nanostructured plasmonic sensors were obtained using commercial Blu-ray optical discs as nanoslits-based flexible polymer substrates. A thin gold film was used as an adhesion and nucleation layer to improve the chemical stability and reduce the surface roughness of the overlying silver film, without increasing ohmic plasmon losses. The structures were physically and optically characterized and compared with nanostructures of single gold layer. Ultrasmooth and chemically stable trilayer nanostructures with a surface roughness <0.5 nm were obtained following a simple and reproducible fabrication process. They showed a figure of merit (FOM) value up to 69.2 RIU -1 which is significantly higher (more than 95%) than the gold monolayer counterpart. Their potential for biosensing was demonstrated by employing the trilayer sensor for the direct and refractometric (label-free) detection of C-reactive protein (CRP) biomarker in undiluted urine achieving a Limit of Detection (LOD) in the pM order. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Probing the effects of the ester functional group, alkyl side chain length and anions on the bulk nanostructure of ionic liquids: a computational study.

PubMed

Fakhraee, Mostafa; Gholami, Mohammad Reza

2016-04-14

The effects of ester addition on nanostructural properties of biodegradable ILs composed of 1-alkoxycarbonyl-3-alkyl-imidazolium cations ([C1COOCnC1im](+), n = 1, 2, 4) combined with [Br](-), [NO3](-), [BF4](-), [PF6](-), [TfO](-), and [Tf2N](-) were explored by using the molecular dynamics (MD) simulations and quantum theory of atoms in molecules (QTAIM) analysis at 400 K. Various thermodynamic properties of these ILs were extensively computed in our earlier work (Ind. Eng. Chem. Res., 2015, 54, 11678-11700). Nano-scale segregation analysis demonstrates the formation of a small spherical island-like hydrocarbon within the continuous ionic domain for ILs with short alkyl side chain ([C1COOC1C1im]), and a sponge-like nanostructure for the compound with long alkyl side chain ([C1COOC4C1im]). Ester-functionalized ILs with ethyl side chain ([C1COOC2C1im]) are the turning point between two different morphologies. Non-polar channels were observed for [C1COOC4C1im] ILs composed of smaller anions such as [Br] and [NO3], whereas clustering organization was found for the other anions. Formation of the spherical micelle-like nanostructure was seen for lengthened cations. Finally, the incorporation of an ester group into the alkyl side chain of the cation leads to stronger segregation between charged and uncharged networks, which consequently increased the possibility of self-assembly and micelle formation.

Engineering Near-Field Transport of Energy using Nanostructured Materials

DTIC Science & Technology

2015-12-12

increasingly important for a wide range of nanotechnology applications. Recent computational studies on near- field radiative heat transfer (NFRHT) suggest...SECURITY CLASSIFICATION OF: The transport of heat at the nanometer scale is becoming increasingly important for a wide range of nanotechnology...applications. Recent computational studies on near- field radiative heat transfer (NFRHT) suggest that radiative energy transport between suitably chosen

Spectroscopy on the wing: naturally inspired SERS substrates for biochemical analysis.

PubMed

Garrett, Natalie L; Vukusic, Peter; Ogrin, Feodor; Sirotkin, Evgeny; Winlove, C Peter; Moger, Julian

2009-03-01

We show that naturally occurring chitinous nanostructures found on the wings of the Graphium butterfly can be used as substrates for surface-enhanced Raman scattering when coated with a thin film of gold or silver. The substrates were found to exhibit excellent biocompatibility and sensitivity, making them ideal for protein assaying. An assay using avidin/biotin binding showed that the substrates could be used to quantify protein binding directly from changes in the surface-enhanced Raman scattering (SERS) spectra and were sensitive over a concentration range comparable with a typical enzyme-linked immunosorbent assays (ELISA) assay. A biomimetic version of the wing nanostructures produced using a highly reproducible, large-scale fabrication process, yielded comparable enhancement factors and biocompatibility. The excellent biocompatibility of the wings and biomimetic substrates is unparalleled by other lithographically produced substrates, and this could pave the way for widespread application of ultrasensitive SERS-based bioassays.

Regulation of Hematopoietic Stem Cell Behavior by the Nanostructured Presentation of Extracellular Matrix Components

PubMed Central

Muth, Christine Anna; Steinl, Carolin; Klein, Gerd; Lee-Thedieck, Cornelia

2013-01-01

Hematopoietic stem cells (HSCs) are maintained in stem cell niches, which regulate stem cell fate. Extracellular matrix (ECM) molecules, which are an essential part of these niches, can actively modulate cell functions. However, only little is known on the impact of ECM ligands on HSCs in a biomimetic environment defined on the nanometer-scale level. Here, we show that human hematopoietic stem and progenitor cell (HSPC) adhesion depends on the type of ligand, i.e., the type of ECM molecule, and the lateral, nanometer-scaled distance between the ligands (while the ligand type influenced the dependency on the latter). For small fibronectin (FN)–derived peptide ligands such as RGD and LDV the critical adhesive interligand distance for HSPCs was below 45 nm. FN-derived (FN type III 7–10) and osteopontin-derived protein domains also supported cell adhesion at greater distances. We found that the expression of the ECM protein thrombospondin-2 (THBS2) in HSPCs depends on the presence of the ligand type and its nanostructured presentation. Functionally, THBS2 proved to mediate adhesion of HSPCs. In conclusion, the present study shows that HSPCs are sensitive to the nanostructure of their microenvironment and that they are able to actively modulate their environment by secreting ECM factors. PMID:23405094

Black silicon solar cell: analysis optimization and evolution towards a thinner and flexible future.

PubMed

Roy, Arijit Bardhan; Dhar, Arup; Choudhuri, Mrinmoyee; Das, Sonali; Hossain, S Minhaz; Kundu, Avra

2016-07-29

Analysis and optimization of silicon nano-structured geometry (black silicon) for photovoltaic applications has been reported. It is seen that a unique class of geometry: micro-nanostructure has the potential to find a balance between the conflicting interests of reduced reflection for wide angles of incidence, reduced surface area enhancement due to the nano-structuring of the substrate and reduced material wastage due to the etching of the silicon substrate to realize the geometry itself. It is established that even optimally designed micro-nanostructures would not be useful for conventional wafer based approaches. The work presents computational studies on how such micro-nanostructures are more potent for future ultra-thin monocrystalline silicon absorbers. For such ultra-thin absorbers, the optimally designed micro-nanostructures provide additional advantages of advanced light management capabilities as it behaves as a lossy 2D photonic crystal making the physically thin absorber optically thick along with the ability to collect photo-generated carriers orthogonal to the direction of light (radial junction) for unified photon-electron harvesting. Most significantly, the work answers the key question on how thin the monocrystalline solar absorber should be so that optimum micro-nanostructure would be able to harness the incident photons ensuring proper collection so as to reach the well-known Shockley-Queisser limit of solar cells. Flexible ultra-thin monocrystalline silicon solar cells have been fabricated using nanosphere lithography and MacEtch technique along with a synergistic association of crystalline and amorphous silicon technologies to demonstrate its physical and technological flexibilities. The outcomes are relevant so that nanotechnology may be seamlessly integrated into the technology roadmap of monocrystalline silicon solar cells as the silicon thickness should be significantly reduced without compromising the efficiency within the next decade.

Synthesis of tubular nanostructures from wheat bran albumins during proteolysis with V8 protease in the presence of calcium ions.

PubMed

Chaquilla-Quilca, G; Balandrán-Quintana, R R; Azamar-Barrios, J A; Ramos-Clamont Montfort, G; Mendoza-Wilson, A M; Mercado-Ruiz, J N; Madera-Santana, T J; López-Franco, Y L; Luna-Valdez, J G

2016-06-01

There are very few reports on the self-assembly of peptides derived from proteins of agro industrial byproducts origin. Although it has been claimed that purity is a determining factor in peptide self-assembly, whether proteins extracted using water along with other components also form self-assembled structures is not known. The results of this work prove that albumins from wheat bran, a byproduct obtained from the milling industry, can form tubular nanostructures during their hydrolysis with the V8 protease in the presence of Ca(2+). Electron microscopy of the hydrolysate revealed that under specific conditions, long filaments are formed, which are nanotubes of several microns in length, with inner and outer diameters of 100 and 200 nm, respectively. The infrared analysis of the hydrolysate identified (-)OOC-Ca(2+) interactions and changes in beta sheet content in response to variations in protein/V8/Ca(2+) molar ratios. A model that explains the probable mechanism of the observed self-assembly is discussed. Copyright © 2016 Elsevier Ltd. All rights reserved.

Design of Nanostructured Biological Materials Through Self-Assembly of Peptides and Proteins

DTIC Science & Technology

2002-01-01

of applications, including scaffolding for tissue repair in regenerative medicine, drug delivery and biological surface engineering. Tirrell and...colleagues [2] designed artificial proteins that undergo self-assembly to form hydrogels responsive to pH and other environmental changes. Ghadiri and...showed that other β-sheet peptide systems can also undergo self-assembly into regular nanofiber structures. Although they share no sequence

Innovative Microsystems: Novel Nanostructures to Capture Circulating Breast Cancer Cells

DTIC Science & Technology

2009-05-01

temperature to promote a Schiff-base reaction. Recombinant protein G from E . coli (Zymed Lab Inc.) 50 μg/ml in Ca- and Mg-free phosphate-buffered...recombinant protein G from E . coli (Zymed Lab Inc.), at a concentration of 50 mg ml1 in 1 PBS, is incubated on the activated surface overnight at 4 C...reaction. Recombinant protein G from E . coli (Zymed Lab Inc.) 50 μg/ml in Ca- and Mg-free phosphate-buffered saline (CMF-PBS), is incubated on the

Programming a topologically constrained DNA nanostructure into a sensor

NASA Astrophysics Data System (ADS)

Liu, Meng; Zhang, Qiang; Li, Zhongping; Gu, Jimmy; Brennan, John D.; Li, Yingfu

2016-06-01

Many rationally engineered DNA nanostructures use mechanically interlocked topologies to connect individual DNA components, and their physical connectivity is achieved through the formation of a strong linking duplex. The existence of such a structural element also poses a significant topological constraint on functions of component rings. Herein, we hypothesize and confirm that DNA catenanes with a strong linking duplex prevent component rings from acting as the template for rolling circle amplification (RCA). However, by using an RNA-containing DNA [2] catenane with a strong linking duplex, we show that a stimuli-responsive RNA-cleaving DNAzyme can linearize one component ring, and thus enable RCA, producing an ultra-sensitive biosensing system. As an example, a DNA catenane biosensor is engineered to detect the model bacterial pathogen Escherichia coli through binding of a secreted protein, with a detection limit of 10 cells ml-1, thus establishing a new platform for further applications of mechanically interlocked DNA nanostructures.

Programming a topologically constrained DNA nanostructure into a sensor

PubMed Central

Liu, Meng; Zhang, Qiang; Li, Zhongping; Gu, Jimmy; Brennan, John D.; Li, Yingfu

2016-01-01

Many rationally engineered DNA nanostructures use mechanically interlocked topologies to connect individual DNA components, and their physical connectivity is achieved through the formation of a strong linking duplex. The existence of such a structural element also poses a significant topological constraint on functions of component rings. Herein, we hypothesize and confirm that DNA catenanes with a strong linking duplex prevent component rings from acting as the template for rolling circle amplification (RCA). However, by using an RNA-containing DNA [2] catenane with a strong linking duplex, we show that a stimuli-responsive RNA-cleaving DNAzyme can linearize one component ring, and thus enable RCA, producing an ultra-sensitive biosensing system. As an example, a DNA catenane biosensor is engineered to detect the model bacterial pathogen Escherichia coli through binding of a secreted protein, with a detection limit of 10 cells ml−1, thus establishing a new platform for further applications of mechanically interlocked DNA nanostructures. PMID:27337657

Cation-Induced Stabilization and Denaturation of DNA Origami Nanostructures in Urea and Guanidinium Chloride.

PubMed

Ramakrishnan, Saminathan; Krainer, Georg; Grundmeier, Guido; Schlierf, Michael; Keller, Adrian

2017-11-01

The stability of DNA origami nanostructures under various environmental conditions constitutes an important issue in numerous applications, including drug delivery, molecular sensing, and single-molecule biophysics. Here, the effect of Na + and Mg 2+ concentrations on DNA origami stability is investigated in the presence of urea and guanidinium chloride (GdmCl), two strong denaturants commonly employed in protein folding studies. While increasing concentrations of both cations stabilize the DNA origami nanostructures against urea denaturation, they are found to promote DNA origami denaturation by GdmCl. These inverse behaviors are rationalized by a salting-out of Gdm + to the hydrophobic DNA base stack. The effect of cation-induced DNA origami denaturation by GdmCl deserves consideration in the design of single-molecule studies and may potentially be exploited in future applications such as selective denaturation for purification purposes. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Designer xylanosomes: protein nanostructures for enhanced xylan hydrolysis

USDA-ARS?s Scientific Manuscript database

This work is the first report of the successful design, construction, and application of multi-functional, self-assembling biocatalysts for targeted xylan hydrolysis, termed xylanosomes. Using the architecture of cellulosomes found in some anaerobic cellulolytic microbes, four different xylanosomes...

Exploitation of stable nanostructures based on the mouse polyomavirus for development of a recombinant vaccine against porcine circovirus 2

PubMed Central

Fraiberk, Martin; Hájková, Michaela; Krulová, Magdaléna; Kojzarová, Martina; Drda Morávková, Alena; Pšikal, Ivan

2017-01-01

The aim of this study was to develop a suitable vaccine antigen against porcine circovirus 2 (PCV2), the causative agent of post-weaning multi-systemic wasting syndrome, which causes significant economic losses in swine breeding. Chimeric antigens containing PCV2b Cap protein sequences based on the mouse polyomavirus (MPyV) nanostructures were developed. First, universal vectors for baculovirus-directed production of chimeric MPyV VLPs or pentamers of the major capsid protein, VP1, were designed for their exploitation as vaccines against other pathogens. Various strategies were employed based on: A) exposure of selected immunogenic epitopes on the surface of MPyV VLPs by insertion into a surface loop of the VP1 protein, B) insertion of foreign protein molecules inside the VLPs, or C) fusion of a foreign protein or its part with the C-terminus of VP1 protein, to form giant pentamers of a chimeric protein. We evaluated these strategies by developing a recombinant vaccine against porcine circovirus 2. All candidate vaccines induced the production of antibodies against the capsid protein of porcine circovirus after immunization of mice. The candidate vaccine, Var C, based on fusion of mouse polyomavirus and porcine circovirus capsid proteins, could induce the production of antibodies with the highest PCV2 neutralizing capacity. Its ability to induce the production of neutralization antibodies was verified after immunization of pigs. The advantage of this vaccine, apart from its efficient production in insect cells and easy purification, is that it represents a DIVA (differentiating infected from vaccinated animals) vaccine, which also induces an immune response against the mouse polyoma VP1 protein and is thus able to distinguish between vaccinated and naturally infected animals. PMID:28922413

Skyrmion states in thin confined polygonal nanostructures

NASA Astrophysics Data System (ADS)

Pepper, Ryan Alexander; Beg, Marijan; Cortés-Ortuño, David; Kluyver, Thomas; Bisotti, Marc-Antonio; Carey, Rebecca; Vousden, Mark; Albert, Maximilian; Wang, Weiwei; Hovorka, Ondrej; Fangohr, Hans

2018-03-01

Recent studies have demonstrated that skyrmionic states can be the ground state in thin-film FeGe disk nanostructures in the absence of a stabilising applied magnetic field. In this work, we advance this understanding by investigating to what extent this stabilisation of skyrmionic structures through confinement exists in geometries that do not match the cylindrical symmetry of the skyrmion—such as squares and triangles. Using simulation, we show that skyrmionic states can form the ground state for a range of system sizes in both triangular and square-shaped FeGe nanostructures of 10 nm thickness in the absence of an applied field. We further provide data to assist in the experimental verification of our prediction; to imitate an experiment where the system is saturated with a strong applied field before the field is removed, we compute the time evolution and show the final equilibrium configuration of magnetization fields, starting from a uniform alignment.

Barcode extension for analysis and reconstruction of structures

NASA Astrophysics Data System (ADS)

Myhrvold, Cameron; Baym, Michael; Hanikel, Nikita; Ong, Luvena L.; Gootenberg, Jonathan S.; Yin, Peng

2017-03-01

Collections of DNA sequences can be rationally designed to self-assemble into predictable three-dimensional structures. The geometric and functional diversity of DNA nanostructures created to date has been enhanced by improvements in DNA synthesis and computational design. However, existing methods for structure characterization typically image the final product or laboriously determine the presence of individual, labelled strands using gel electrophoresis. Here we introduce a new method of structure characterization that uses barcode extension and next-generation DNA sequencing to quantitatively measure the incorporation of every strand into a DNA nanostructure. By quantifying the relative abundances of distinct DNA species in product and monomer bands, we can study the influence of geometry and sequence on assembly. We have tested our method using 2D and 3D DNA brick and DNA origami structures. Our method is general and should be extensible to a wide variety of DNA nanostructures.

Barcode extension for analysis and reconstruction of structures.

PubMed

Myhrvold, Cameron; Baym, Michael; Hanikel, Nikita; Ong, Luvena L; Gootenberg, Jonathan S; Yin, Peng

2017-03-13

Collections of DNA sequences can be rationally designed to self-assemble into predictable three-dimensional structures. The geometric and functional diversity of DNA nanostructures created to date has been enhanced by improvements in DNA synthesis and computational design. However, existing methods for structure characterization typically image the final product or laboriously determine the presence of individual, labelled strands using gel electrophoresis. Here we introduce a new method of structure characterization that uses barcode extension and next-generation DNA sequencing to quantitatively measure the incorporation of every strand into a DNA nanostructure. By quantifying the relative abundances of distinct DNA species in product and monomer bands, we can study the influence of geometry and sequence on assembly. We have tested our method using 2D and 3D DNA brick and DNA origami structures. Our method is general and should be extensible to a wide variety of DNA nanostructures.

Barcode extension for analysis and reconstruction of structures

PubMed Central

Myhrvold, Cameron; Baym, Michael; Hanikel, Nikita; Ong, Luvena L; Gootenberg, Jonathan S; Yin, Peng

2017-01-01

Collections of DNA sequences can be rationally designed to self-assemble into predictable three-dimensional structures. The geometric and functional diversity of DNA nanostructures created to date has been enhanced by improvements in DNA synthesis and computational design. However, existing methods for structure characterization typically image the final product or laboriously determine the presence of individual, labelled strands using gel electrophoresis. Here we introduce a new method of structure characterization that uses barcode extension and next-generation DNA sequencing to quantitatively measure the incorporation of every strand into a DNA nanostructure. By quantifying the relative abundances of distinct DNA species in product and monomer bands, we can study the influence of geometry and sequence on assembly. We have tested our method using 2D and 3D DNA brick and DNA origami structures. Our method is general and should be extensible to a wide variety of DNA nanostructures. PMID:28287117

Nano and Microparticle-Enhanced Immunosensor Approaches for the Detection of Cancer Biomarker Proteins

NASA Astrophysics Data System (ADS)

Mani, Vigneshwaran

Accurate, sensitive, point-of-care multiplexed protein measurements are critical for early disease detection and monitoring, impacting biomarker and drug discovery, and personalized medicine. Significant application involves monitoring panels of proteins in the blood that are biomarkers for diagnosing cancer. However, measurements of biomarker panels in blood or other bodily fluids have been slow to integrate into current practice of cancer diagnostics partly due to the lack of technically simple, low-cost, sensitive, point-of-care multiplexed measurement devices, as well as the lack of rigorously validated protein panels. The present thesis in part addresses these limitations by the development of electrochemical and surface plasmon resonance (SPR) immunosensors utilizing 1mum superparamagnetic labels for accurate detection of prostate cancer biomarker proteins in patient serum samples. Electrochemical discrete immunosensors featuring nanostructured surface with densely packed 5 nm glutathione-coated gold nanoparticles coupled with multi-enzyme magnetic particle (MP) labels enabled measurement of prostate specific antigen (PSA) with a detection limit (DL) of 0.5 pg mL-1 in undiluted serum. Such low DLs are attributed to high surface area, conductivity of nanostructured surface, and multi-enzyme signal amplification. DLs are further improved by utilizing MP bioconjugated with more than 100,000 antibody labels to offline capture proteins from the serum sample matrix, minimizing nonspecific binding of interfering proteins on sensor surface before detection. This approach provided an unprecedented 10 fg DL mL-1 for PSA in undiluted serum using a flow SPR biosensor. Finally electrochemical microfluidic immunoarrays featuring nanostructured surface and offline protein capture by multi-label MPs enabled multiplexed detection of prostate cancer biomarkers PSA and interleukin-6 (IL-6). These approaches provided up to 1000-fold lower DLs compared to commercial bead based assays. The high sensitivity of these approaches will allow monitoring of biomarker levels in diseases states where proteins are in sub pg mL -1 concentrations that are normally challenging to detect using traditional methods such as enzyme linked immunosorbent assays (ELISA). Further emphases will be on SPR-based fundamental studies on binding affinity enhancement of MP conjugates to protein surfaces. In addition, this thesis describes the assembly of glucose/O2 enzymatic biofuel cells for power generation utilizing layer-by-layer films of osmium redox polymers and enzymes. Towards the end, the present thesis describes a simple, low-cost and accurate paper-based electrochemical device fabrication methods and its applications towards monitoring genotoxic activities in the environmental samples.

Computer aided design of nano-structured materials with tailored ionic conductivities.

PubMed

Sayle, Dean C; Doig, James A; Parker, Stephen C; Watson, Graeme W; Sayle, Thi X T

2005-01-07

We show, using simulation techniques, that the high ionic conductivity in BaF2/CaF2 heterolayers is because the interfaces reduce the activation energy barriers to mobility and increase the number of charge carriers.

Study of structural colour of Hebomoia glaucippe butterfly wing scales

NASA Astrophysics Data System (ADS)

Shur, V. Ya; Kuznetsov, D. K.; Pryakhina, V. I.; Kosobokov, M. S.; Zubarev, I. V.; Boymuradova, S. K.; Volchetskaya, K. V.

2017-10-01

Structural colours of Hebomoia glaucippe butterfly wing scales have been studied experimentally using high resolution scanning electron microscopy. Visualization of scales structures and computer simulation allowed distinguishing correlation between nanostructures on the scales and their colour.

Improving Osteoblast Response In Vitro by a Nanostructured Thin Film with Titanium Carbide and Titanium Oxides Clustered around Graphitic Carbon.

PubMed

Longo, Giovanni; Ioannidu, Caterina Alexandra; Scotto d'Abusco, Anna; Superti, Fabiana; Misiano, Carlo; Zanoni, Robertino; Politi, Laura; Mazzola, Luca; Iosi, Francesca; Mura, Francesco; Scandurra, Roberto

2016-01-01

Recently, we introduced a new deposition method, based on Ion Plating Plasma Assisted technology, to coat titanium implants with a thin but hard nanostructured layer composed of titanium carbide and titanium oxides, clustered around graphitic carbon. The nanostructured layer has a double effect: protects the bulk titanium against the harsh conditions of biological tissues and in the same time has a stimulating action on osteoblasts. The aim of this work is to describe the biological effects of this layer on osteoblasts cultured in vitro. We demonstrate that the nanostructured layer causes an overexpression of many early genes correlated to proteins involved in bone turnover and an increase in the number of surface receptors for α3β1 integrin, talin, paxillin. Analyses at single-cell level, by scanning electron microscopy, atomic force microscopy, and single cell force spectroscopy, show how the proliferation, adhesion and spreading of cells cultured on coated titanium samples are higher than on uncoated titanium ones. Finally, the chemistry of the layer induces a better formation of blood clots and a higher number of adhered platelets, compared to the uncoated cases, and these are useful features to improve the speed of implant osseointegration. In summary, the nanostructured TiC film, due to its physical and chemical properties, can be used to protect the implants and to improve their acceptance by the bone.

Magnetic nanostructuring and overcoming Brown's paradox to realize extraordinary high-temperature energy products

NASA Astrophysics Data System (ADS)

Balasubramanian, Balamurugan; Mukherjee, Pinaki; Skomski, Ralph; Manchanda, Priyanka; Das, Bhaskar; Sellmyer, David J.

2014-09-01

Nanoscience has been one of the outstanding driving forces in technology recently, arguably more so in magnetism than in any other branch of science and technology. Due to nanoscale bit size, a single computer hard disk is now able to store the text of 3,000,000 average-size books, and today's high-performance permanent magnets--found in hybrid cars, wind turbines, and disk drives--are nanostructured to a large degree. The nanostructures ideally are designed from Co- and Fe-rich building blocks without critical rare-earth elements, and often are required to exhibit high coercivity and magnetization at elevated temperatures of typically up to 180 °C for many important permanent-magnet applications. Here we achieve this goal in exchange-coupled hard-soft composite films by effective nanostructuring of high-anisotropy HfCo7 nanoparticles with a high-magnetization Fe65Co35 phase. An analysis based on a model structure shows that the soft-phase addition improves the performance of the hard-magnetic material by mitigating Brown's paradox in magnetism, a substantial reduction of coercivity from the anisotropy field. The nanostructures exhibit a high room-temperature energy product of about 20.3 MGOe (161.5 kJ/m3), which is a record for a rare earth- or Pt-free magnetic material and retain values as high as 17.1 MGOe (136.1 kJ/m3) at 180°C.

Computer Code for Nanostructure Simulation

NASA Technical Reports Server (NTRS)

Filikhin, Igor; Vlahovic, Branislav

2009-01-01

Due to their small size, nanostructures can have stress and thermal gradients that are larger than any macroscopic analogue. These gradients can lead to specific regions that are susceptible to failure via processes such as plastic deformation by dislocation emission, chemical debonding, and interfacial alloying. A program has been developed that rigorously simulates and predicts optoelectronic properties of nanostructures of virtually any geometrical complexity and material composition. It can be used in simulations of energy level structure, wave functions, density of states of spatially configured phonon-coupled electrons, excitons in quantum dots, quantum rings, quantum ring complexes, and more. The code can be used to calculate stress distributions and thermal transport properties for a variety of nanostructures and interfaces, transport and scattering at nanoscale interfaces and surfaces under various stress states, and alloy compositional gradients. The code allows users to perform modeling of charge transport processes through quantum-dot (QD) arrays as functions of inter-dot distance, array order versus disorder, QD orientation, shape, size, and chemical composition for applications in photovoltaics and physical properties of QD-based biochemical sensors. The code can be used to study the hot exciton formation/relation dynamics in arrays of QDs of different shapes and sizes at different temperatures. It also can be used to understand the relation among the deposition parameters and inherent stresses, strain deformation, heat flow, and failure of nanostructures.

Protein extraction into the bicontinuous microemulsion phase of a Water/SDS/pentanol/dodecane winsor-III system: Effect on nanostructure and protein conformation

DOE PAGES

Hayes, Douglas G.; Ye, Ran; Dunlap, Rachel N.; ...

2017-09-07

Bicontinuous microemulsions (BμEs), consisting of water and oil nanodomains separated by surfactant monolayers of near-zero curvature, are potentially valuable systems for purification and delivery of biomolecules, for hosting multiphasic biochemical reactions, and as templating media for preparing nanomaterials. We formed Winsor-III systems by mixing aqueous protein and sodium dodecyl sulfate (SDS) solutions with dodecane and 1-pentanol (cosurfactant) to efficiently extract proteins into the middle (BμE) phase. Bovine serum albumin (BSA) and cytochrome c partitioned to the BμE phase at 64% and 81% efficiency, respectively, producing highly concentrated protein solutions (32 and 44 g L –1, respectively), through release of watermore » and oil from the BμEs. Circular dichroism spectroscopic analysis demonstrated that BSA underwent minor secondary structural changes upon incorporation into BμEs, while the secondary structure of cytochrome c and pepsin underwent major changes. Small-angle x-ray scattering (SAXS) results show that proteins promoted an increase of the interfacial fluidity and surface area per volume for the BμE surfactant monolayers, and that each protein uniquely altered self-assembly in the Winsor-III systems. Cytochrome c partitioned via electrostatic attractions between SDS and the protein’s positively-charged groups, residing near the surfactant head groups of BμE monolayers, where it decreased surfactant packing efficiency. BSA partitioned through formation of SDS-BSA complexes via hydrophobic and electrostatic attractive interactions. As the BSA-SDS ratio increased, complexes’ partitioning favored BμEs over the oil excess phase due to the increased hydrophilicity of the complexes. In conclusion, this study demonstrates the potential utility of BμEs to purify proteins and prepare nanostructured fluids possessing high protein concentration.« less

Protein extraction into the bicontinuous microemulsion phase of a Water/SDS/pentanol/dodecane winsor-III system: Effect on nanostructure and protein conformation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hayes, Douglas G.; Ye, Ran; Dunlap, Rachel N.

Bicontinuous microemulsions (BμEs), consisting of water and oil nanodomains separated by surfactant monolayers of near-zero curvature, are potentially valuable systems for purification and delivery of biomolecules, for hosting multiphasic biochemical reactions, and as templating media for preparing nanomaterials. We formed Winsor-III systems by mixing aqueous protein and sodium dodecyl sulfate (SDS) solutions with dodecane and 1-pentanol (cosurfactant) to efficiently extract proteins into the middle (BμE) phase. Bovine serum albumin (BSA) and cytochrome c partitioned to the BμE phase at 64% and 81% efficiency, respectively, producing highly concentrated protein solutions (32 and 44 g L –1, respectively), through release of watermore » and oil from the BμEs. Circular dichroism spectroscopic analysis demonstrated that BSA underwent minor secondary structural changes upon incorporation into BμEs, while the secondary structure of cytochrome c and pepsin underwent major changes. Small-angle x-ray scattering (SAXS) results show that proteins promoted an increase of the interfacial fluidity and surface area per volume for the BμE surfactant monolayers, and that each protein uniquely altered self-assembly in the Winsor-III systems. Cytochrome c partitioned via electrostatic attractions between SDS and the protein’s positively-charged groups, residing near the surfactant head groups of BμE monolayers, where it decreased surfactant packing efficiency. BSA partitioned through formation of SDS-BSA complexes via hydrophobic and electrostatic attractive interactions. As the BSA-SDS ratio increased, complexes’ partitioning favored BμEs over the oil excess phase due to the increased hydrophilicity of the complexes. In conclusion, this study demonstrates the potential utility of BμEs to purify proteins and prepare nanostructured fluids possessing high protein concentration.« less

Characterization of gas tunnel type plasma sprayed hydroxyapatite-nanostructure titania composite coatings

NASA Astrophysics Data System (ADS)

Yugeswaran, S.; Kobayashi, A.; Ucisik, A. Hikmet; Subramanian, B.

2015-08-01

Hydroxyapatite (HA) can be coated onto metal implants as a ceramic biocompatible coating to bridge the growth between implants and human tissue. Meanwhile many efforts have been made to improve the mechanical properties of the HA coatings without affecting its bioactivity. In the present study, nanostructure titania (TiO2) was mixed with HA powder and HA-nanostructure TiO2 composite coatings were produced by gas tunnel type plasma spraying torch under optimized spraying conditions. For this purpose, composition of 10 wt% TiO2 + 90 wt% HA, 20 wt% TiO2 + 80 wt% HA and 30 wt% TiO2 + 70 wt% HA were selected as the feedstock materials. The phase, microstructure and mechanical properties of the coatings were characterized. The obtained results validated that the increase in weight percentage of nanostructure TiO2 in HA coating significantly increased the microhardness, adhesive strength and wear resistance of the coatings. Analysis of the in vitro bioactivity and cytocompatibility of the coatings were done using conventional simulated body fluid (c-SBF) solution and cultured green fluorescent protein (GFP) labeled marrow stromal cells (MSCs) respectively. The bioactivity results revealed that the composite coating has bio-active surface with good cytocompatibility.

Nucleic acid-based nanoengineering: novel structures for biomedical applications

PubMed Central

Li, Hanying; LaBean, Thomas H.; Leong, Kam W.

2011-01-01

Nanoengineering exploits the interactions of materials at the nanometre scale to create functional nanostructures. It relies on the precise organization of nanomaterials to achieve unique functionality. There are no interactions more elegant than those governing nucleic acids via Watson–Crick base-pairing rules. The infinite combinations of DNA/RNA base pairs and their remarkable molecular recognition capability can give rise to interesting nanostructures that are only limited by our imagination. Over the past years, creative assembly of nucleic acids has fashioned a plethora of two-dimensional and three-dimensional nanostructures with precisely controlled size, shape and spatial functionalization. These nanostructures have been precisely patterned with molecules, proteins and gold nanoparticles for the observation of chemical reactions at the single molecule level, activation of enzymatic cascade and novel modality of photonic detection, respectively. Recently, they have also been engineered to encapsulate and release bioactive agents in a stimulus-responsive manner for therapeutic applications. The future of nucleic acid-based nanoengineering is bright and exciting. In this review, we will discuss the strategies to control the assembly of nucleic acids and highlight the recent efforts to build functional nucleic acid nanodevices for nanomedicine. PMID:23050076

Computational Features of Flow Modeling in Nanostructured Sensors

NASA Astrophysics Data System (ADS)

Ionescu, Adela; Savu, Dan; Savu, Sorin; Coman, Daniela

2009-04-01

Nowadays the productivity of the welding processes represents an important factor in economy concepts. The technologies which are developed by the researchers are oriented to the increasing of the welding processes' productivity and to the improvement of the products' quality.

Domain alignment within ferroelectric/dielectric PbTiO 3 /SrTiO 3 superlattice nanostructures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Park, Joonkyu; Mangeri, John; Zhang, Qingteng

The ferroelectric domain pattern within lithographically defined PbTiO 3/SrTiO 3 ferroelectric/dielectric heteroepitaxial superlattice nanostructures is strongly influenced by the edges of the structures. Synchrotron X-ray nanobeam diffraction reveals that the spontaneously formed 180° ferroelectric stripe domains exhibited by such superlattices adopt a configuration in rectangular nanostructures in which domain walls are aligned with long patterned edges. The angular distribution of X-ray diffuse scattering intensity from nanodomains indicates that domains are aligned within an angular range of approximately 20° with respect to the edges. Computational studies based on a time-dependent Landau–Ginzburg–Devonshire model show that the preferred direction of the alignment resultsmore » from lowering of the bulk and electrostrictive contributions to the free energy of the system due to the release of the lateral mechanical constraint. This unexpected alignment appears to be intrinsic and not a result of distortions or defects caused by the patterning process. Thus, our work demonstrates how nanostructuring and patterning of heteroepitaxial superlattices allow for pathways to create and control ferroelectric structures that may appear counterintuitive.« less

Effects of antibacterial nanostructured composite films on vascular stents: hemodynamic behaviors, microstructural characteristics, and biomechanical properties.

PubMed

Cheng, Han-Yi; Hsiao, Wen-Tien; Lin, Li-Hsiang; Hsu, Ya-Ju; Sinrang, Andi Wardihan; Ou, Keng-Liang

2015-01-01

The purpose of this research was to investigate stresses resulting from different thicknesses and compositions of hydrogenated Cu-incorporated diamond-like carbon (a-C:H/Cu) films at the interface between vascular stent and the artery using three-dimensional reversed finite element models (FEMs). Blood flow velocity variation in vessels with plaques was examined by angiography, and the a-C:H/Cu films were characterized by transmission electron microscopy to analyze surface morphology. FEMs were constructed using a computer-aided reverse design system, and the effects of antibacterial nanostructured composite films in the stress field were investigated. The maximum stress in the vascular stent occurred at the intersections of net-like structures. Data analysis indicated that the stress decreased by 15% in vascular stents with antibacterial nanostructured composite films compared to the control group, and the stress decreased with increasing film thickness. The present results confirmed that antibacterial nanostructured composite films improve the biomechanical properties of vascular stents and release abnormal stress to prevent restenosis. The results of the present study offer the clinical benefit of inducing superior biomechanical behavior in vascular stents. © 2014 Wiley Periodicals, Inc.

Domain alignment within ferroelectric/dielectric PbTiO 3 /SrTiO 3 superlattice nanostructures

DOE PAGES

Park, Joonkyu; Mangeri, John; Zhang, Qingteng; ...

2018-01-22

The ferroelectric domain pattern within lithographically defined PbTiO 3/SrTiO 3 ferroelectric/dielectric heteroepitaxial superlattice nanostructures is strongly influenced by the edges of the structures. Synchrotron X-ray nanobeam diffraction reveals that the spontaneously formed 180° ferroelectric stripe domains exhibited by such superlattices adopt a configuration in rectangular nanostructures in which domain walls are aligned with long patterned edges. The angular distribution of X-ray diffuse scattering intensity from nanodomains indicates that domains are aligned within an angular range of approximately 20° with respect to the edges. Computational studies based on a time-dependent Landau–Ginzburg–Devonshire model show that the preferred direction of the alignment resultsmore » from lowering of the bulk and electrostrictive contributions to the free energy of the system due to the release of the lateral mechanical constraint. This unexpected alignment appears to be intrinsic and not a result of distortions or defects caused by the patterning process. Thus, our work demonstrates how nanostructuring and patterning of heteroepitaxial superlattices allow for pathways to create and control ferroelectric structures that may appear counterintuitive.« less

Investigation of deformation mechanisms of staggered nanocomposites using molecular dynamics

NASA Astrophysics Data System (ADS)

Mathiazhagan, S.; Anup, S.

2016-08-01

Biological materials with nanostructure of regularly or stair-wise staggered arrangements of hard platelets reinforced in a soft protein matrix have superior mechanical properties. Applications of these nanostructures to ceramic matrix composites could enhance their toughness. Using molecular dynamics simulations, mechanical behaviour of the bio-inspired nanocomposites is studied. Regularly staggered model shows better flow behaviour compared to stair-wise staggered model due to the symmetrical crack propagation along the interface. Though higher stiffness and strength are obtained for stair-wise staggered models, rapid crack propagation reduces the toughness. Arresting this crack propagation could lead to superior mechanical properties in stair-wise staggered models.

Fabrication of circular assemblies with DNA tetrahedrons: from static structures to a dynamic rotary motor

PubMed Central

Wang, Liying; Meng, Zhenyu; Martina, Felicia; Shao, Huilin

2017-01-01

Abstract DNA tetrahedron as the simplest 3D DNA nanostructure has been applied widely in biomedicine and biosensing. Herein, we design and fabricate a series of circular assemblies of DNA tetrahedron with high purity and decent yields. These circular nanostructures are confirmed by endonuclease digestion, gel electrophoresis and atomic force microscopy. Inspired by rotary protein motor, we demonstrate these circular architectures can serve as a stator for a rotary DNA motor to achieve the circular rotation. The DNA motor can rotate on the stators for several cycles, and the locomotion of the motor is monitored by the real-time fluorescent measurements. PMID:29126166

pH-directed self-assembling helical peptide conformation

USDA-ARS?s Scientific Manuscript database

The beta-sheet and alpha-helix peptide conformation are two of the most fundamentally ordered secondary structures found in proteins and peptides. They also give rise to self-assembling motifs that form macromolecular channels and nanostructures. Through design these conformations can yield enhance...

Numerical Study of Plasmonic Efficiency of Gold Nanostripes for Molecule Detection

PubMed Central

2015-01-01

In plasmonics, the accurate computation of the electromagnetic field enhancement is necessary in determining the amplitude and the spatial extension of the field around nanostructures. Here, the problem of the interaction between an electromagnetic excitation and gold nanostripes is solved. An optimization scheme, including an adaptive remeshing process with error estimator, is used to solve the problem through a finite element method. The variations of the electromagnetic field amplitude and the plasmonic active zones around nanostructures for molecule detection are studied in this paper taking into account the physical and geometrical parameters of the nanostripes. The evolution between the sizes and number of nanostripes is shown. PMID:25734184

Visualization of Individual Images in Patterned Organic-Inorganic Multilayers Using GISAXS-CT.

PubMed

Ogawa, Hiroki; Nishikawa, Yukihiro; Takenaka, Mikihito; Fujiwara, Akihiko; Nakanishi, Yohei; Tsujii, Yoshinobu; Takata, Masaki; Kanaya, Toshiji

2017-05-16

Using grazing-incidence small-angle scattering (GISAXS) with computed tomography (CT), we have individually reconstructed the spatial distribution of a thin gold (Au) layer buried under a thin poly(styrene-b-2-vinylpyridine) (PS-b-P2VP) layer. Owing to the difference between total reflection angles of Au and PS-b-P2VP, the scattering profiles for Au nanoparticles and self-assembled nanostructures of PS-b-P2VP could be independently obtained by changing the X-ray angle of incidence. Reconstruction of scattering profiles allows one to separately characterize spatial distributions in Au and PS-b-P2VP nanostructures.

Large scale atomistic approaches to thermal transport and phonon scattering in nanostructured materials

NASA Astrophysics Data System (ADS)

Savic, Ivana

2012-02-01

Decreasing the thermal conductivity of bulk materials by nanostructuring and dimensionality reduction, or by introducing some amount of disorder represents a promising strategy in the search for efficient thermoelectric materials [1]. For example, considerable improvements of the thermoelectric efficiency in nanowires with surface roughness [2], superlattices [3] and nanocomposites [4] have been attributed to a significantly reduced thermal conductivity. In order to accurately describe thermal transport processes in complex nanostructured materials and directly compare with experiments, the development of theoretical and computational approaches that can account for both anharmonic and disorder effects in large samples is highly desirable. We will first summarize the strengths and weaknesses of the standard atomistic approaches to thermal transport (molecular dynamics [5], Boltzmann transport equation [6] and Green's function approach [7]) . We will then focus on the methods based on the solution of the Boltzmann transport equation, that are computationally too demanding, at present, to treat large scale systems and thus to investigate realistic materials. We will present a Monte Carlo method [8] to solve the Boltzmann transport equation in the relaxation time approximation [9], that enables computation of the thermal conductivity of ordered and disordered systems with a number of atoms up to an order of magnitude larger than feasible with straightforward integration. We will present a comparison between exact and Monte Carlo Boltzmann transport results for small SiGe nanostructures and then use the Monte Carlo method to analyze the thermal properties of realistic SiGe nanostructured materials. This work is done in collaboration with Davide Donadio, Francois Gygi, and Giulia Galli from UC Davis.[4pt] [1] See e.g. A. J. Minnich, M. S. Dresselhaus, Z. F. Ren, and G. Chen, Energy Environ. Sci. 2, 466 (2009).[0pt] [2] A. I. Hochbaum et al, Nature 451, 163 (2008).[0pt] [3] R. Venkatasubramanian, E. Siivola, T. Colpitts, and B. O'Quinn, Nature 413, 597 (2001).[0pt] [4] B. Poudel et al, Science 320, 634 (2008).[0pt] [5] See e.g. Y. He, D. Donadio, and G. Galli, Nano Lett. 11, 3608 (2011).[0pt] [6] See e.g. A. Ward and D. A. Broido, Phys. Rev. B 81, 085205 (2010).[0pt] [7] See e.g. I. Savic, N. Mingo, and D. A. Stewart, Phys. Rev. Lett. 101, 165502 (2008).[0pt] [8] I. Savic, D.Donadio, F.Gygi, and G.Galli (in preparation).[0pt] [9] See e.g. J. E. Turney, E. S. Landry, A. J. H. McGaughey, and C. H. Amon, Phys. Rev. B, 79, 064301 (2009).

Nanochemistry of Protein-Based Delivery Agents

PubMed Central

Rajendran, Subin R. C. K.; Udenigwe, Chibuike C.; Yada, Rickey Y.

2016-01-01

The past decade has seen an increased interest in the conversion of food proteins into functional biomaterials, including their use for loading and delivery of physiologically active compounds such as nutraceuticals and pharmaceuticals. Proteins possess a competitive advantage over other platforms for the development of nanodelivery systems since they are biocompatible, amphipathic, and widely available. Proteins also have unique molecular structures and diverse functional groups that can be selectively modified to alter encapsulation and release properties. A number of physical and chemical methods have been used for preparing protein nanoformulations, each based on different underlying protein chemistry. This review focuses on the chemistry of the reorganization and/or modification of proteins into functional nanostructures for delivery, from the perspective of their preparation, functionality, stability and physiological behavior. PMID:27489854

Nanochemistry of protein-based delivery agents

NASA Astrophysics Data System (ADS)

Rajendran, Subin; Udenigwe, Chibuike; Yada, Rickey

2016-07-01

The past decade has seen an increased interest in the conversion of food proteins into functional biomaterials, including their use for loading and delivery of physiologically active compounds such as nutraceuticals and pharmaceuticals. Proteins possess a competitive advantage over other platforms for the development of nanodelivery systems since they are biocompatible, amphipathic, and widely available. Proteins also have unique molecular structures and diverse functional groups that can be selectively modified to alter encapsulation and release properties. A number of physical and chemical methods have been used for preparing protein nanoformulations, each based on different underlying protein chemistry. This review focuses on the chemistry of the reorganization and/or modification of proteins into functional nanostructures for delivery, from the perspective of their preparation, functionality, stability and physiological behavior.

Engineering building blocks for self-assembling protein nanoparticles

PubMed Central

2010-01-01

Like natural viruses, manmade protein cages for drug delivery are to be ideally formed by repetitive subunits with self-assembling properties, mimicking viral functions and molecular organization. Naturally formed nanostructures (such as viruses, flagella or simpler protein oligomers) can be engineered to acquire specific traits of interest in biomedicine, for instance through the addition of cell targeting agents for desired biodistribution and specific delivery of associated drugs. However, fully artificial constructs would be highly desirable regarding finest tuning and adaptation to precise therapeutic purposes. Although engineering of protein assembling is still in its infancy, arising principles and promising strategies of protein manipulation point out the rational construction of nanoscale protein cages as a feasible concept, reachable through conventional recombinant DNA technologies and microbial protein production. PMID:21192790

Robust optimization of a tandem grating solar thermal absorber

NASA Astrophysics Data System (ADS)

Choi, Jongin; Kim, Mingeon; Kang, Kyeonghwan; Lee, Ikjin; Lee, Bong Jae

2018-04-01

Ideal solar thermal absorbers need to have a high value of the spectral absorptance in the broad solar spectrum to utilize the solar radiation effectively. Majority of recent studies about solar thermal absorbers focus on achieving nearly perfect absorption using nanostructures, whose characteristic dimension is smaller than the wavelength of sunlight. However, precise fabrication of such nanostructures is not easy in reality; that is, unavoidable errors always occur to some extent in the dimension of fabricated nanostructures, causing an undesirable deviation of the absorption performance between the designed structure and the actually fabricated one. In order to minimize the variation in the solar absorptance due to the fabrication error, the robust optimization can be performed during the design process. However, the optimization of solar thermal absorber considering all design variables often requires tremendous computational costs to find an optimum combination of design variables with the robustness as well as the high performance. To achieve this goal, we apply the robust optimization using the Kriging method and the genetic algorithm for designing a tandem grating solar absorber. By constructing a surrogate model through the Kriging method, computational cost can be substantially reduced because exact calculation of the performance for every combination of variables is not necessary. Using the surrogate model and the genetic algorithm, we successfully design an effective solar thermal absorber exhibiting a low-level of performance degradation due to the fabrication uncertainty of design variables.

Computational Analysis of the Optical and Charge Transport Properties of Ultrasonic Spray Pyrolysis-Grown Zinc Oxide/Graphene Hybrid Structures.

PubMed

Ali, Amgad Ahmed; Hashim, Abdul Manaf

2016-12-01

We demonstrate a systematic computational analysis of the measured optical and charge transport properties of the spray pyrolysis-grown ZnO nanostructures, i.e. nanosphere clusters (NSCs), nanorods (NRs) and nanowires (NWs) for the first time. The calculated absorbance spectra based on the time-dependent density functional theory (TD-DFT) shows very close similarity with the measured behaviours under UV light. The atomic models and energy level diagrams for the grown nanostructures were developed and discussed to explain the structural defects and band gap. The induced stresses in the lattices of ZnO NSCs that formed during the pyrolysis process seem to cause the narrowing of the gap between the energy levels. ZnO NWs and NRs show homogeneous distribution of the LUMO and HOMO orbitals all over the entire heterostructure. Such distribution contributes to the reduction of the band gap down to 2.8 eV, which has been confirmed to be in a good agreement with the experimental results. ZnO NWs and NRs exhibited better emission behaviours under the UV excitation as compared to ZnO NSCs and thin film as their visible range emissions are strongly quenched. Based on the electrochemical impedance measurement, the electrical models and electrostatic potential maps were developed to calculate the electron lifetime and to explain the mobility or diffusion behaviours in the grown nanostructure, respectively.

Computational Analysis of the Optical and Charge Transport Properties of Ultrasonic Spray Pyrolysis-Grown Zinc Oxide/Graphene Hybrid Structures

NASA Astrophysics Data System (ADS)

Ali, Amgad Ahmed; Hashim, Abdul Manaf

2016-05-01

We demonstrate a systematic computational analysis of the measured optical and charge transport properties of the spray pyrolysis-grown ZnO nanostructures, i.e. nanosphere clusters (NSCs), nanorods (NRs) and nanowires (NWs) for the first time. The calculated absorbance spectra based on the time-dependent density functional theory (TD-DFT) shows very close similarity with the measured behaviours under UV light. The atomic models and energy level diagrams for the grown nanostructures were developed and discussed to explain the structural defects and band gap. The induced stresses in the lattices of ZnO NSCs that formed during the pyrolysis process seem to cause the narrowing of the gap between the energy levels. ZnO NWs and NRs show homogeneous distribution of the LUMO and HOMO orbitals all over the entire heterostructure. Such distribution contributes to the reduction of the band gap down to 2.8 eV, which has been confirmed to be in a good agreement with the experimental results. ZnO NWs and NRs exhibited better emission behaviours under the UV excitation as compared to ZnO NSCs and thin film as their visible range emissions are strongly quenched. Based on the electrochemical impedance measurement, the electrical models and electrostatic potential maps were developed to calculate the electron lifetime and to explain the mobility or diffusion behaviours in the grown nanostructure, respectively.

Alpha-Helical Protein Domains Unify Strength and Robustness through Hierarchical Nanostructures

DTIC Science & Technology

2009-01-23

backbone atom (hydrogen donor) of peptide i + 4 in the polypeptide chain. Consequently, at each convolution , 3.5 H- bonds are found in a parallel...signaling and deformation behavior of cytoskeletal protein networks in cells (e.g. intermediate filaments vimentin and lamin as well as actin [7, 8... convolution . The Hierarchical Bell model enables one to predict the strength of different hierarchical bond arrangements as a function of the

RNA and RNP as Building Blocks for Nanotechnology and Synthetic Biology.

PubMed

Ohno, Hirohisa; Saito, Hirohide

2016-01-01

Recent technologies that aimed to elucidate cellular function have revealed essential roles for RNA molecules in living systems. Our knowledge concerning functional and structural information of naturally occurring RNA and RNA-protein (RNP) complexes is increasing rapidly. RNA and RNP interaction motifs are structural units that function as building blocks to constitute variety of complex structures. RNA-central synthetic biology and nanotechnology are constructive approaches that employ the accumulated information and build synthetic RNA (RNP)-based circuits and nanostructures. Here, we describe how to design and construct synthetic RNA (RNP)-based devices and structures at the nanometer-scale for biological and future therapeutic applications. RNA/RNP nanostructures can also be utilized as the molecular scaffold to control the localization or interactions of target molecule(s). Moreover, RNA motifs recognized by RNA-binding proteins can be applied to make protein-responsive translational "switches" that can turn gene expression "on" or "off" depending on the intracellular environment. This "synthetic RNA and RNP world" will expand tools for nanotechnology and synthetic biology. In addition, these reconstructive approaches would lead to a greater understanding of building principle in naturally occurring RNA/RNP molecules and systems. Copyright © 2016 Elsevier Inc. All rights reserved.

Highly sensitive protein detection using a plasmonic field effect transistor (Conference Presentation)

NASA Astrophysics Data System (ADS)

Shokri-Kojori, Hossein; Ji, Yiwen; Han, Xu; Paik, Younghun; Braunschweig, Adam; Kim, Sung Jin

2016-03-01

Localized surface Plasmon Resonance (LSPR) is a nanoscale phenomenon which presents strong resonance associated with noble metal nanostructures. This plasmon resonance based technology enables highly sensitive detection for chemical and biological applications. Recently, we have developed a plasmon field effect transistor (FET) that enables direct plasmonic-to-electric signal conversion with signal amplification. The plasmon FET consists of back-gated field effect transistor incorporated with gold nanoparticles on top of the FET channel. The gold nanostructures are physically separated from transistor electrodes and can be functionalized for a specific biological application. In this presentation, we report a successful demonstration of a model system to detect Con A proteins using Carbohydrate linkers as a capture molecule. The plasmon FET detected a very low concentration of Con A (0.006 mg/L) while it offers a wide dynamic range of 0.006-50 mg/L. In this demonstration, we used two-color light sources instead of a bulky spectrometer to achieve high sensitivity and wide dynamic range. The details of two-color based differential measurement method will be discussed. This novel protein-based sensor has several advantages such as extremely small size for point-of-care system, multiplexing capability, no need of complex optical geometry.

Spin Dependent Transport Properties of Metallic and Semiconducting Nanostructures

NASA Astrophysics Data System (ADS)

Sapkota, Keshab R.

Present computing and communication devices rely on two different classes of technologies; information processing devices are based on electrical charge transport in semiconducting materials while information storage devices are based on orientation of electron spins in magnetic materials. A realization of a hybrid-type device that is based on charge as well as spin properties of electrons would perform both of these actions thereby enhancing computation power to many folds and reducing power consumptions. This dissertation focuses on the fabrication of such spin-devices based on metallic and semiconducting nanostructures which can utilize spin as well as charge properties of electrons. A simplified design of the spin-device consists of a spin injector, a semiconducting or metallic channel, and a spin detector. The channel is the carrier of the spin signal from the injector to the detector and therefore plays a crucial role in the manipulation of spin properties in the device. In this work, nanostructures like nanowires and nanostripes are used to function the channel in the spin-device. Methods like electrospinning, hydrothermal, and wet chemical were used to synthesize nanowires while physical vapor deposition followed by heat treatment in controlled environment was used to synthesis nanostripes. Spin-devices fabrication of the synthesized nanostructures were carried out by electron beam lithography process. The details of synthesis of nanostructures, device fabrication procedures and measurement techniques will be discussed in the thesis. We have successfully fabricated the spin-devices of tellurium nanowire, indium nanostripe, and indium oxide nanostripe and studied their spin transport properties for the first time. These spin-devices show large spin relaxation length compared to normal metals like copper and offer potentials for the future technologies. Further, Heusler alloys nanowires like nanowires of Co 2FeAl were synthesized and studied for electrical transport properties since such systems are halfmetallic in nature and promise the possibilities of spin injection and detection. The study was extended to dilute magnetic semiconducting nanowire system of Cd1-xMnxTe which possess both magnetic and semiconducting properties. In summary, the studies made in this thesis will offer a new understanding of spin transport behavior for future technology.

A computational microscopy study of nanostructural evolution in irradiated pressure vessel steels

NASA Astrophysics Data System (ADS)

Odette, G. R.; Wirth, B. D.

1997-11-01

Nanostructural features that form in reactor pressure vessel steels under neutron irradiation at around 300°C lead to significant hardening and embrittlement. Continuum thermodynamic-kinetic based rate theories have been very successful in modeling the general characteristics of the copper and manganese nickel rich precipitate evolution, often the dominant source of embrittlement. However, a more detailed atomic scale understanding of these features is needed to interpret experimental measurements and better underpin predictive embrittlement models. Further, other embrittling features, believed to be subnanometer defect (vacancy)-solute complexes and small regions of modest enrichment of solutes are not well understood. A general approach to modeling embrittlement nanostructures, based on the concept of a computational microscope, is described. The objective of the computational microscope is to self-consistently integrate atomic scale simulations with other sources of information, including a wide range of experiments. In this work, lattice Monte Carlo (LMC) simulations are used to resolve the chemically and structurally complex nature of CuMnNiSi precipitates. The LMC simulations unify various nanoscale analytical characterization methods and basic thermodynamics. The LMC simulations also reveal that significant coupled vacancy and solute clustering takes place during cascade aging. The cascade clustering produces the metastable vacancy-cluster solute complexes that mediate flux effects. Cascade solute clustering may also play a role in the formation of dilute atmospheres of solute enrichment and enhance the nucleation of manganese-nickel rich precipitates at low Cu levels. Further, the simulations suggest that complex, highly correlated processes (e.g. cluster diffusion, formation of favored vacancy diffusion paths and solute scavenging vacancy cluster complexes) may lead to anomalous fast thermal aging kinetics at temperatures below about 450°C. The potential technical significance of these phenomena is described.

The presence of carbon nanostructures in bakery products induces metabolic stress in human mesenchymal stem cells through CYP1A and p53 gene expression.

PubMed

Al-Hadi, Ahmed M; Periasamy, Vaiyapuri Subbarayan; Athinarayanan, Jegan; Alshatwi, Ali A

2016-01-01

Ingredients commonly present in processed foods are excellent substrates for chemical reactions during modern thermal cooking or processing, which could possibly result in deteriorative carbonization changes mediated by a variety of thermal reactions. Spontaneous self-assembling complexation or polymerization of partially combusted lipids, proteins, and other food macromolecules with synthetic food additives during high temperature food processing or baking (200-250 °C) would result in the formation of carbon nanostructures (CNs). These unknown nanostructures may produce adverse physiological effects or potential health risks. The present work aimed to identify and characterize the nanostructures from the crusts of bread. Furthermore, a toxicological risk assessment of these nanostructures was conducted using human mesenchymal stem cells (hMSCs) as a model for cellular uptake and metabolic oxidative stress, with special reference to induced adipogenesis. CNs isolated from bread crusts were characterized using transmission electron microscopy. The in vitro risk assessment of the CNs was carried out in hMSCs using an MTT assay, cell morphological assessment, a reactive oxygen species assay, a mitochondrial trans-membrane potential assay, cell cycle progression assessment and gene expression analysis. Our results revealed that bread crusts contain CNs, which may form during the bread-making process. The in vitro results indicate that carbon nanostructures have moderately toxic effects in the hMSCs at a high dose (400 μg/mL). The mitochondrial trans-membrane potentials and intracellular ROS levels of the hMSCs were altered at this dose. The levels of the mRNA transcripts of metabolic stress-responsive genes such as CAT, GSR, GSTA4, CYP1A and p53 were significantly altered in response to CNs. Copyright © 2015 Elsevier B.V. All rights reserved.

SERS+MEF of the anti-tumoral drug emodin adsorbed on silver nanoparticles

NASA Astrophysics Data System (ADS)

Sevilla, Paz; De Llanos, Raquel; Domingo, Concepción; Sánchez-Cortés, Santiago; García-Ramos, José V.

2010-02-01

Metal nanostructures are known to amplify the spontaneous emission of fluorescent molecules by resonant coupling to external electromagnetic fields. We have used spectroscopy to characterize the structural properties of emodin molecules, a natural anthraquinone dye, and bovine serum albumin, the most abundant protein in plasma, in the presence of silver nanoparticles. Aggregation of emodin at pH=10 and pH=6 gives rise to SERS and MEF effects in silver colloid. We have obtained MEF spectra at acidic pH=2.9 using two different silver nanostructures. We have also studied the change in the secondary structure of bovine serum albumin adsorbed on metal nanoparticles surface. Circular dichroism, fluorescence emission and fluorescence lifetime measurements indicate an increase in the alfa-helical content of the protein and a change in the environment of the tryptophan residues that bury in the interior of the biomolecule. This variation on the secondary structure could have further influence in the binding of the drug to form transport and regulatory complexes.

Cracks growth behaviors of commercial pure titanium under nanosecond laser irradiation for formation of nanostructure-covered microstructures (with sub-5-μm)

NASA Astrophysics Data System (ADS)

Pan, A. F.; Wang, W. J.; Mei, X. S.; Zheng, B. X.; Yan, Z. X.

2016-11-01

This study reported on the formation of sub-5-μm microstructures covered on titanium by cracks growth under 10-ns laser radiation at the wavelength of 532 nm and its induced light modification for production of nanostructures. The electric field intensity and laser power density absorbed by commercial pure titanium were computed to investigate the self-trapping introduced by cracks and the effect of surface morphology on laser propagation characteristics. It is found that nanostructures can form at the surface with the curvature radius below 20 μm. Meanwhile, variable laser fluences were applied to explore the evolution of cracks on commercial pure titanium with or without melt as spot overlap number increased. Experimental study was first performed at the peak laser fluence of 1.063 J/cm2 to investigate the microstructures induced only by cracks growth. The results demonstrated that angular microstructures with size between 1.68 μm and 4.74 μm was obtained and no nanostructure covered. Then, at the peak laser fluence of 2.126 J/cm2, there were some nanostructures covered on the melt-induced curved microstructured surface. However, surface molten material submerged in the most of cracks at the spot overlap number of 744, where the old cracks disappeared. The results indicated that there was too much molten material and melting time at the peak laser fluence of 2.126 J/cm2, which was not suitable for obtainment of perfect micro-nano structures. On this basis, peak laser fluence was reduced down to 1.595 J/cm2 and the sharp sub-5 μm microstructures with nanostructures covered was obtained at spot overlap number of 3720.

Fabrication and characterization of ordered arrays of nanostructures

NASA Astrophysics Data System (ADS)

Larson, Preston

2005-11-01

Nanostructures are currently of great interest because of their unique properties and potential applications in a wide range of areas such as opto-electronic and biomedical devices. Current research in nanotechnology involves fabrication and characterization of these structures, as well as theoretical and experimental studies to explore their unique and novel properties. Not only do nanostructures have the potential to be both evolutionary (state-of-the-art ICs have more and more features on the nanoscale) but revolutionary (quantum computing) as well. In this thesis, a combination of bottom-up and top-down approaches is explored to fabricate ordered arrays of nanostrucutures. The bottom-up approach involves the growth of self-organized porous anodic aluminum oxide (AAO) films. AAO films consist of a well ordered hexagonal array of close-packed pores with diameters and spacings ranging from around 5 to 500 nm. Via a top-down approach, these AAO films are then used as masks or templates to fabricate ordered arrays of nanostructures (i.e. dots, holes, meshes, pillars, rings, etc.) of various materials using conventional deposition and/or etching techniques. Using AAO films as masks allows a simple and economical method to fabricate arrays of structures with nano-scale dimensions. Furthermore, they allow the fabrication of large areas (many millimeters on a side) of highly uniform and well-ordered arrays of nanostructures, a crucial requirement for most characterization techniques and applications. Characterization of these nanostructures using various techniques (electron microscopy, atomic force microscopy, UV-Vis absorption spectroscopy, photoluminescence, capacitance-voltage measurements, magnetization hysteresis curves, etc.) will be presented. Finally, these structures provide a unique opportunity to determine the single and collective properties of nanostructure arrays and will have various future applications including but not limited to: data storage, light emitting or sensing devices, nano-tribological coatings for surfaces, bio-sensors, filters, and more.

Bacterium Escherichia coli- and phage P22-templated synthesis of semiconductor nanostructures

NASA Astrophysics Data System (ADS)

Shen, Liming

The properties of inorganic materials in the nanoscale are found to be size- and shape-dependent due to quantum confinement effects, and thereby nanomaterials possess properties very different from those of single molecules as well as those of bulk materials. Assembling monodispersed nanoparticles into highly ordered hierarchical architectures is expected to generate novel collective properties for potential applications in catalysis, energy, biomedicine, etc. The major challenge in the assembly of nanoparticles lies in the development of controllable synthetic strategies that enable the growth and assembly of nanoparticles with high selectivity and good controllability. Biological matter possesses robust and precisely ordered structures that exist in a large variety of shapes and sizes, providing an ideal platform for synthesizing high-performance nanostructures. The primary goal of this thesis work has been to develop rational synthetic strategies for high-performance nanostructured materials using biological templates, which are difficult to achieve through traditional chemical synthetic methods. These approaches can serve as general bio-inspired approaches for synthesizing nanoparticle assemblies with desired components and architectures. CdS- and TiO2-binding peptides have been identified using phage display biopanning technique and the mechanism behind the specific affinity between the selected peptides and inorganic substrates are analyzed. The ZnS- and CdS-binding peptides, identified by the phage display biopanning, are utilized for the selective nucleation and growth of sulfides over self-assembled genetically engineered P22 coat proteins, resulting in ordered nanostructures of sulfide nanocrystal assemblies. The synthetic strategy can be extended to the fabrication of a variety of other nanostructures. A simple sonochemical route for the synthesis and assembly of CdS nanostructures with high yield under ambient conditions has been developed by exploiting the chemical characteristics and structure of permeabilized E. coli bacteria. The crystal phase, morphology, micro/nanostructure, optical absorption, and photocatalytic properties of the CdS nanostructures are tailored over a wide range by merely changing the synthetic conditions. Photoanodes fabricated using the nanoporous hollow CdS microrods exhibit excellent performance for the photocatalytic hydrogen production. This facile approach has been extended to the synthesis and assembly of other semiconducting sulfides, including PbS, ZnS, and HgS.

Improving Osteoblast Response In Vitro by a Nanostructured Thin Film with Titanium Carbide and Titanium Oxides Clustered around Graphitic Carbon

PubMed Central

Longo, Giovanni; Ioannidu, Caterina Alexandra; Scotto d’Abusco, Anna; Superti, Fabiana; Misiano, Carlo; Zanoni, Robertino; Politi, Laura; Mazzola, Luca; Iosi, Francesca; Mura, Francesco; Scandurra, Roberto

2016-01-01

Introduction Recently, we introduced a new deposition method, based on Ion Plating Plasma Assisted technology, to coat titanium implants with a thin but hard nanostructured layer composed of titanium carbide and titanium oxides, clustered around graphitic carbon. The nanostructured layer has a double effect: protects the bulk titanium against the harsh conditions of biological tissues and in the same time has a stimulating action on osteoblasts. Results The aim of this work is to describe the biological effects of this layer on osteoblasts cultured in vitro. We demonstrate that the nanostructured layer causes an overexpression of many early genes correlated to proteins involved in bone turnover and an increase in the number of surface receptors for α3β1 integrin, talin, paxillin. Analyses at single-cell level, by scanning electron microscopy, atomic force microscopy, and single cell force spectroscopy, show how the proliferation, adhesion and spreading of cells cultured on coated titanium samples are higher than on uncoated titanium ones. Finally, the chemistry of the layer induces a better formation of blood clots and a higher number of adhered platelets, compared to the uncoated cases, and these are useful features to improve the speed of implant osseointegration. Conclusion In summary, the nanostructured TiC film, due to its physical and chemical properties, can be used to protect the implants and to improve their acceptance by the bone. PMID:27031101

Computational strategies for the automated design of RNA nanoscale structures from building blocks using NanoTiler.

PubMed

Bindewald, Eckart; Grunewald, Calvin; Boyle, Brett; O'Connor, Mary; Shapiro, Bruce A

2008-10-01

One approach to designing RNA nanoscale structures is to use known RNA structural motifs such as junctions, kissing loops or bulges and to construct a molecular model by connecting these building blocks with helical struts. We previously developed an algorithm for detecting internal loops, junctions and kissing loops in RNA structures. Here we present algorithms for automating or assisting many of the steps that are involved in creating RNA structures from building blocks: (1) assembling building blocks into nanostructures using either a combinatorial search or constraint satisfaction; (2) optimizing RNA 3D ring structures to improve ring closure; (3) sequence optimisation; (4) creating a unique non-degenerate RNA topology descriptor. This effectively creates a computational pipeline for generating molecular models of RNA nanostructures and more specifically RNA ring structures with optimized sequences from RNA building blocks. We show several examples of how the algorithms can be utilized to generate RNA tecto-shapes.

Final Technical Report [Scalable methods for electronic excitations and optical responses of nanostructures: mathematics to algorithms to observables

DOE Office of Scientific and Technical Information (OSTI.GOV)

Saad, Yousef

2014-03-19

The master project under which this work is funded had as its main objective to develop computational methods for modeling electronic excited-state and optical properties of various nanostructures. The specific goals of the computer science group were primarily to develop effective numerical algorithms in Density Functional Theory (DFT) and Time Dependent Density Functional Theory (TDDFT). There were essentially four distinct stated objectives. The first objective was to study and develop effective numerical algorithms for solving large eigenvalue problems such as those that arise in Density Functional Theory (DFT) methods. The second objective was to explore so-called linear scaling methods ormore » Methods that avoid diagonalization. The third was to develop effective approaches for Time-Dependent DFT (TDDFT). Our fourth and final objective was to examine effective solution strategies for other problems in electronic excitations, such as the GW/Bethe-Salpeter method, and quantum transport problems.« less

Computational strategies for the automated design of RNA nanoscale structures from building blocks using NanoTiler☆

PubMed Central

Bindewald, Eckart; Grunewald, Calvin; Boyle, Brett; O’Connor, Mary; Shapiro, Bruce A.

2013-01-01

One approach to designing RNA nanoscale structures is to use known RNA structural motifs such as junctions, kissing loops or bulges and to construct a molecular model by connecting these building blocks with helical struts. We previously developed an algorithm for detecting internal loops, junctions and kissing loops in RNA structures. Here we present algorithms for automating or assisting many of the steps that are involved in creating RNA structures from building blocks: (1) assembling building blocks into nanostructures using either a combinatorial search or constraint satisfaction; (2) optimizing RNA 3D ring structures to improve ring closure; (3) sequence optimisation; (4) creating a unique non-degenerate RNA topology descriptor. This effectively creates a computational pipeline for generating molecular models of RNA nanostructures and more specifically RNA ring structures with optimized sequences from RNA building blocks. We show several examples of how the algorithms can be utilized to generate RNA tecto-shapes. PMID:18838281

Lipoprotein-biomimetic nanostructure enables efficient targeting delivery of siRNA to Ras-activated glioblastoma cells via macropinocytosis

NASA Astrophysics Data System (ADS)

Huang, Jia-Lin; Jiang, Gan; Song, Qing-Xiang; Gu, Xiao; Hu, Meng; Wang, Xiao-Lin; Song, Hua-Hua; Chen, Le-Pei; Lin, Ying-Ying; Jiang, Di; Chen, Jun; Feng, Jun-Feng; Qiu, Yong-Ming; Jiang, Ji-Yao; Jiang, Xin-Guo; Chen, Hong-Zhuan; Gao, Xiao-Ling

2017-05-01

Hyperactivated Ras regulates many oncogenic pathways in several malignant human cancers including glioblastoma and it is an attractive target for cancer therapies. Ras activation in cancer cells drives protein internalization via macropinocytosis as a key nutrient-gaining process. By utilizing this unique endocytosis pathway, here we create a biologically inspired nanostructure that can induce cancer cells to `drink drugs' for targeting activating transcription factor-5 (ATF5), an overexpressed anti-apoptotic transcription factor in glioblastoma. Apolipoprotein E3-reconstituted high-density lipoprotein is used to encapsulate the siRNA-loaded calcium phosphate core and facilitate it to penetrate the blood-brain barrier, thus targeting the glioblastoma cells in a macropinocytosis-dependent manner. The nanostructure carrying ATF5 siRNA exerts remarkable RNA-interfering efficiency, increases glioblastoma cell apoptosis and inhibits tumour cell growth both in vitro and in xenograft tumour models. This strategy of targeting the macropinocytosis caused by Ras activation provides a nanoparticle-based approach for precision therapy in glioblastoma and other Ras-activated cancers.

Silver nanoparticles with gelatin nanoshells: photochemical facile green synthesis and their antimicrobial activity

NASA Astrophysics Data System (ADS)

Pourjavadi, Ali; Soleyman, Rouhollah

2011-10-01

In the current study, a facile green synthesis of silver-gelatin core-shell nanostructures (spherical, spherical/cubic hybrid, and cubic, DLS diameter: 4.1-6.9 nm) is reported via the wet chemical synthesis procedure. Sunlight-UV as an available reducing agent cause mild reduction of silver ions into the silver nanoparticles (Ag-NPs). Gelatin protein, as an effective capping/shaping agent, was used in the reaction to self-assemble silver nanostructures. The formation of silver nanostructures and their self-assembly pattern was confirmed by SEM, AFM, and TEM techniques. Further investigations were carried out using zeta-potential, UV-Vis, FTIR, GPC, and TGA/DTG/DTA data. The prepared Ag-NPs showed proper and acceptable antimicrobial activity against three classes of microorganisms ( Escherichia coli Gram-negative bacteria, Staphylococcus aureus Gram-positive bacteria, and Candida albicans fungus). The antibacterial and antifungal Ag-NPs exhibit good stability in solution and can be considered as promising candidates for a wide range of biomedical applications.

Spatially-Interactive Biomolecular Networks Organized by Nucleic Acid Nanostructures

PubMed Central

Fu, Jinglin; Liu, Minghui; Liu, Yan; Yan, Hao

2013-01-01

Conspectus Living systems have evolved a variety of nanostructures to control the molecular interactions that mediate many functions including the recognition of targets by receptors, the binding of enzymes to substrates, and the regulation of enzymatic activity. Mimicking these structures outside of the cell requires methods that offer nanoscale control over the organization of individual network components. Advances in DNA nanotechnology have enabled the design and fabrication of sophisticated one-, two- and three-dimensional (1D, 2D and 3D) nanostructures that utilize spontaneous and sequence specific DNA hybridization. Compared to other self-assembling biopolymers, DNA nanostructures offer predictable and programmable interactions, and surface features to which other nanoparticles and bio-molecules can be precisely positioned. The ability to control the spatial arrangement of the components while constructing highly-organized networks will lead to various applications of these systems. For example, DNA nanoarrays with surface displays of molecular probes can sense noncovalent hybridization interactions with DNA, RNA, and proteins and covalent chemical reactions. DNA nanostructures can also align external molecules into well-defined arrays, which may improve the resolution of many structural determination methods, such as X-ray diffraction, cryo-EM, NMR, and super-resolution fluorescence. Moreover, by constraining target entities to specific conformations, self-assembled DNA nanostructures can serve as molecular rulers to evaluate conformation-dependent activities. This Account describes the most recent advances in the DNA nanostructure directed assembly of biomolecular networks and explores the possibility of applying this technology to other fields of study. Recently, several reports have demonstrated the DNA nanostructure directed assembly of spatially-interactive biomolecular networks. For example, researchers have constructed synthetic multi-enzyme cascades by organizing the position of the components using DNA nanoscaffolds in vitro, or by utilizing RNA matrices in vivo. These structures display enhanced efficiency compared to the corresponding unstructured enzyme mixtures. Such systems are designed to mimic cellular function, where substrate diffusion between enzymes is facilitated and reactions are catalyzed with high efficiency and specificity. In addition, researchers have assembled multiple choromophores into arrays using a DNA nanoscaffold that optimizes the relative distance between the dyes and their spatial organization. The resulting artificial light harvesting system exhibits efficient cascading energy transfers. Finally, DNA nanostructures have been used as assembly templates to construct nanodevices that execute rationally-designed behaviors, including cargo loading, transportation and route control. PMID:22642503

Circular Permutation of a Chaperonin Protein: Biophysics and Application to Nanotechnology

NASA Technical Reports Server (NTRS)

Paavola, Chad; Chan, Suzanne; Li, Yi-Fen; McMillan, R. Andrew; Trent, Jonathan

2004-01-01

We have designed five circular permutants of a chaperonin protein derived from the hyperthermophilic organism Sulfolobus shibatae. These permuted proteins were expressed in E. coli and are well-folded. Furthermore, all the permutants assemble into 18-mer double rings of the same form as the wild-type protein. We characterized the thermodynamics of folding for each permutant by both guanidine denaturation and differential scanning calorimetry. We also examined the assembly of chaperonin rings into higher order structures that may be used as nanoscale templates. The results show that circular permutation can be used to tune the thermodynamic properties of a protein template as well as facilitating the fusion of peptides, binding proteins or enzymes onto nanostructured templates.

Design of beta-domain swapping, alpha/beta-protein, environmentally sensitive coiled coil and peptide functionalized titania materials

NASA Astrophysics Data System (ADS)

Nagarkar, Radhika P.

2009-12-01

The objective of this dissertation is to apply rational peptide design to fabricate nanomaterials via self-assembly. This has been demonstrated in structurally diverse systems with an aim of deciphering the underlying principles governing how sequence affects the peptide's ability to adopt a specific secondary structure and ultimate material properties that are realized from the association of these secondary structural elements. Several amyloidogenic proteins have been shown to self-assemble into fibrils using a mechanism known as domain swapping. Here, discreet units of secondary structure are exchanged among discreet proteins during self-assembly to form extended networks with precise three dimensional organization. The possibility of using these mechanisms to design peptides capable of controlled assembly and fibril formation leading to materials with targeted properties is explored. By altering the placement of a beta-turn sequence that varies the size and location of the exchanged strand, twisting, non-twisting and laminated fibrillar nanostructures are obtained. Hydrogels prepared from these strand swapping beta-hairpins have varied rheological properties due to differences in their fibrillar nanostructures. In a second distinct design, alpha/beta-proteins are used to prepare environmentally sensitive hydrogels. Here, multiple distinct motifs for structural integrity and dynamic response within a single self-assembling peptide allow the amyloid-like fibrils formed to controllably alter their nano-topography in response to an external stimulus such as temperature. The development of these self-assembling alpha/beta-protein motifs also necessitated the design of pH sensitive antiparallel coiled coils. Exploring the basic principles responsible for pH dependent conformational changes in coiled coils can lead to new insights in the control of protein structure and function. Lastly, this dissertation discusses the interface between biomolecules and inorganic materials. Here, a new methodology of functionalizing titania nanoparticles with peptides is developed. In all of these different material forming systems, extensive biophysical characterization by circular dichroism spectroscopy, fourier transform infrared spectroscopy, X-ray diffraction and analytical ultracentrifugation is performed to understand peptide folding and self-assembly. Careful nanostructural characterization by electron and force microscopies is performed to elucidate self-assembly mechanisms and has proved to be vital in applying the iterative design process to develop responsive nanomaterials.

Interlocked DNA nanostructures controlled by a reversible logic circuit.

PubMed

Li, Tao; Lohmann, Finn; Famulok, Michael

2014-09-17

DNA nanostructures constitute attractive devices for logic computing and nanomechanics. An emerging interest is to integrate these two fields and devise intelligent DNA nanorobots. Here we report a reversible logic circuit built on the programmable assembly of a double-stranded (ds) DNA [3]pseudocatenane that serves as a rigid scaffold to position two separate branched-out head-motifs, a bimolecular i-motif and a G-quadruplex. The G-quadruplex only forms when preceded by the assembly of the i-motif. The formation of the latter, in turn, requires acidic pH and unhindered mobility of the head-motif containing dsDNA nanorings with respect to the central ring to which they are interlocked, triggered by release oligodeoxynucleotides. We employ these features to convert the structural changes into Boolean operations with fluorescence labelling. The nanostructure behaves as a reversible logic circuit consisting of tandem YES and AND gates. Such reversible logic circuits integrated into functional nanodevices may guide future intelligent DNA nanorobots to manipulate cascade reactions in biological systems.

Interlocked DNA nanostructures controlled by a reversible logic circuit

PubMed Central

Li, Tao; Lohmann, Finn; Famulok, Michael

2014-01-01

DNA nanostructures constitute attractive devices for logic computing and nanomechanics. An emerging interest is to integrate these two fields and devise intelligent DNA nanorobots. Here we report a reversible logic circuit built on the programmable assembly of a double-stranded (ds) DNA [3]pseudocatenane that serves as a rigid scaffold to position two separate branched-out head-motifs, a bimolecular i-motif and a G-quadruplex. The G-quadruplex only forms when preceded by the assembly of the i-motif. The formation of the latter, in turn, requires acidic pH and unhindered mobility of the head-motif containing dsDNA nanorings with respect to the central ring to which they are interlocked, triggered by release oligodeoxynucleotides. We employ these features to convert the structural changes into Boolean operations with fluorescence labelling. The nanostructure behaves as a reversible logic circuit consisting of tandem YES and AND gates. Such reversible logic circuits integrated into functional nanodevices may guide future intelligent DNA nanorobots to manipulate cascade reactions in biological systems. PMID:25229207

X-ray standing wave analysis of nanostructures using partially coherent radiation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tiwari, M. K., E-mail: mktiwari@rrcat.gov.in; Das, Gangadhar; Bedzyk, M. J.

2015-09-07

The effect of longitudinal (or temporal) coherence on total reflection assisted x-ray standing wave (TR-XSW) analysis of nanoscale materials is quantitatively demonstrated by showing how the XSW fringe visibility can be strongly damped by decreasing the spectral resolution of the incident x-ray beam. The correction for nonzero wavelength dispersion (δλ ≠ 0) of the incident x-ray wave field is accounted for in the model computations of TR-XSW assisted angle dependent fluorescence yields of the nanostructure coatings on x-ray mirror surfaces. Given examples include 90 nm diameter Au nanospheres deposited on a Si(100) surface and a 3 nm thick Zn layer trapped on top amore » 100 nm Langmuir-Blodgett film coating on a Au mirror surface. Present method opens up important applications, such as enabling XSW studies of large dimensioned nanostructures using conventional laboratory based partially coherent x-ray sources.« less

Mechanical behavior of nanostructured and ultrafine-grained materials under shock wave loadings. experimental data and results of computer simulation

NASA Astrophysics Data System (ADS)

Skripnyak, Vladimir

2012-03-01

Features of mechanical behavior of nanostructured and ultrafine-grained metals under quasistatic and shock wave loadings are discussed. Features of mechanical behavior of nanostructured and ultrafine grained metals over a wide range of strain rates are discussed. A constitutive model for mechanical behavior of metal alloys under shock wave loading including a grain size distribution, a precipitate hardening, and physical mechanisms of shear stress relaxation is presented. Strain rate sensitivity of the yield stress of face-centered-cubic, hexagonal close-packed metal alloys depends on grain size, whereas the Hugoniot elastic limits of ultrafine-grained copper, aluminum, and titanium alloys are close to values of coarse-grained counterparts. At quasi-static loading the yield strength and the tensile strength of titanium alloys with grain size from 300 to 500 nm are twice higher than at coarse-grained counterparts. But the spall strength of the UFG titanium alloys exceeds the value of coarse-grained counterparts only for 10 percents.

Nanomanufacturing : nano-structured materials made layer-by-layer.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cox, James V.; Cheng, Shengfeng; Grest, Gary Stephen

Large-scale, high-throughput production of nano-structured materials (i.e. nanomanufacturing) is a strategic area in manufacturing, with markets projected to exceed $1T by 2015. Nanomanufacturing is still in its infancy; process/product developments are costly and only touch on potential opportunities enabled by growing nanoscience discoveries. The greatest promise for high-volume manufacturing lies in age-old coating and imprinting operations. For materials with tailored nm-scale structure, imprinting/embossing must be achieved at high speeds (roll-to-roll) and/or over large areas (batch operation) with feature sizes less than 100 nm. Dispersion coatings with nanoparticles can also tailor structure through self- or directed-assembly. Layering films structured with thesemore » processes have tremendous potential for efficient manufacturing of microelectronics, photovoltaics and other topical nano-structured devices. This project is designed to perform the requisite R and D to bring Sandia's technology base in computational mechanics to bear on this scale-up problem. Project focus is enforced by addressing a promising imprinting process currently being commercialized.« less

Atomically flat single-crystalline gold nanostructures for plasmonic nanocircuitry.

PubMed

Huang, Jer-Shing; Callegari, Victor; Geisler, Peter; Brüning, Christoph; Kern, Johannes; Prangsma, Jord C; Wu, Xiaofei; Feichtner, Thorsten; Ziegler, Johannes; Weinmann, Pia; Kamp, Martin; Forchel, Alfred; Biagioni, Paolo; Sennhauser, Urs; Hecht, Bert

2010-01-01

Deep subwavelength integration of high-definition plasmonic nanostructures is of key importance in the development of future optical nanocircuitry for high-speed communication, quantum computation and lab-on-a-chip applications. To date, the experimental realization of proposed extended plasmonic networks consisting of multiple functional elements remains challenging, mainly because of the multi-crystallinity of commonly used thermally evaporated gold layers. This can produce structural imperfections in individual circuit elements that drastically reduce the yield of functional integrated nanocircuits. In this paper we demonstrate the use of large (>100 μm(2)) but thin (<80 nm) chemically grown single-crystalline gold flakes that, after immobilization, serve as an ideal basis for focused ion beam milling and other top-down nanofabrication techniques on any desired substrate. Using this methodology we obtain high-definition ultrasmooth gold nanostructures with superior optical properties and reproducible nano-sized features over micrometre-length scales. Our approach provides a possible solution to overcome the current fabrication bottleneck and realize high-definition plasmonic nanocircuitry.

Effects of oxidation on the plasmonic properties of aluminum nanoclusters.

PubMed

Douglas-Gallardo, Oscar A; Soldano, Germán J; Mariscal, Marcelo M; Sánchez, Cristián Gabriel

2017-11-16

The scouting of alternative plasmonic materials able to enhance and extend the optical properties of noble metal nanostructures is on the rise. Aluminum is endowed with a set of interesting properties which turn it into an attractive plasmonic material. Here we present the optical and electronic features of different aluminum nanostructures stemming from a multilevel computational study. Molecular Dynamics (MD) simulations using a reactive force field (ReaxFF), carefully validated with Density Functional Theory (DFT), were employed to mimic the oxidation of icosahedral aluminum nanoclusters. Resulting structures with different oxidation degrees were then studied through the Time-Dependent Density Functional Tight Binding (TD-DFTB) method. A similar approach was used in aluminum nanoclusters with a disordered structure to study how the loss of crystallinity affects the optical properties. To the best of our knowledge, this is the first report that addresses this issue from the fully atomistic time-dependent approach by means of two different and powerful simulation tools able to describe quantum and physicochemical properties associated with nanostructured particles.

Electron Microscopic Visualization of Protein Assemblies on Flattened DNA Origami.

PubMed

Mallik, Leena; Dhakal, Soma; Nichols, Joseph; Mahoney, Jacob; Dosey, Anne M; Jiang, Shuoxing; Sunahara, Roger K; Skiniotis, Georgios; Walter, Nils G

2015-07-28

DNA provides an ideal substrate for the engineering of versatile nanostructures due to its reliable Watson-Crick base pairing and well-characterized conformation. One of the most promising applications of DNA nanostructures arises from the site-directed spatial arrangement with nanometer precision of guest components such as proteins, metal nanoparticles, and small molecules. Two-dimensional DNA origami architectures, in particular, offer a simple design, high yield of assembly, and large surface area for use as a nanoplatform. However, such single-layer DNA origami were recently found to be structurally polymorphous due to their high flexibility, leading to the development of conformationally restrained multilayered origami that lack some of the advantages of the single-layer designs. Here we monitored single-layer DNA origami by transmission electron microscopy (EM) and discovered that their conformational heterogeneity is dramatically reduced in the presence of a low concentration of dimethyl sulfoxide, allowing for an efficient flattening onto the carbon support of an EM grid. We further demonstrated that streptavidin and a biotinylated target protein (cocaine esterase, CocE) can be captured at predesignated sites on these flattened origami while maintaining their functional integrity. Our demonstration that protein assemblies can be constructed with high spatial precision (within ∼2 nm of their predicted position on the platforms) by using strategically flattened single-layer origami paves the way for exploiting well-defined guest molecule assemblies for biochemistry and nanotechnology applications.

DNA nanotechnology

NASA Astrophysics Data System (ADS)

Seeman, Nadrian C.; Sleiman, Hanadi F.

2018-01-01

DNA is the molecule that stores and transmits genetic information in biological systems. The field of DNA nanotechnology takes this molecule out of its biological context and uses its information to assemble structural motifs and then to connect them together. This field has had a remarkable impact on nanoscience and nanotechnology, and has been revolutionary in our ability to control molecular self-assembly. In this Review, we summarize the approaches used to assemble DNA nanostructures and examine their emerging applications in areas such as biophysics, diagnostics, nanoparticle and protein assembly, biomolecule structure determination, drug delivery and synthetic biology. The introduction of orthogonal interactions into DNA nanostructures is discussed, and finally, a perspective on the future directions of this field is presented.

A new approach to the deposition of nanostructured biocatalytic films

NASA Astrophysics Data System (ADS)

Troitsky, V. I.; Berzina, T. S.; Pastorino, L.; Bernasconi, E.; Nicolini, C.

2003-06-01

In the present work, monolayer engineering was used to fabricate biocatalytic nanostructured thin films based on the enzyme penicillin G acylase. The biocatalytic films with enhanced characteristics were produced by the deposition of alternate-layer assemblies with a predetermined structure using a combination of Langmuir-Blodgett and adsorption techniques. The value of enzyme activity and the level of protein detachment were measured in dependence on the variation of film composition and on the sequence of layer alternation. As a result, highly active and stable structures were found, which could be promising candidates for practical applications. The method of modification of the deposition method to provide continuous film formation on large-area supports is discussed.

NANOSTRUCTURED MATERIAL DESIGN FOR HG, AS, AND SE CAPTURE

EPA Science Inventory

The goal of this research project is to identify potential materials that can be used as multipollutant sorbents using a hierarchy of computational modeling approaches. Palladium (Pd) and gold (Au) alloys were investigated and the results show that the addition of a small amou...

Nanostructured Block Copolymer Solutions and Composites: Mechanical and Structural Properties

NASA Astrophysics Data System (ADS)

Walker, Lynn

2015-03-01

Self-assembled block copolymer templates are used to control the nanoscale structure of materials that would not otherwise order in solution. In this work, we have developed a technique to use close-packed cubic and cylindrical mesophases of a thermoreversible block copolymer (PEO-PPO-PEO) to impart spatial order on dispersed nanoparticles. The thermoreversible nature of the template allows for the dispersion of particles synthesized outside the template. This feature extends the applicability of this templating method to many particle-polymer systems, including proteins, and also permits a systematic evaluation of the impact of design parameters on the structure and mechanical properties of the nanocomposites. The criteria for forming co-crystals have been characterized using small-angle scatting and the mechanical properties of these soft crystals determined. Numerous crystal structures have been reported for the block copolymer system and we have taken advantage of several to generate soft co-crystals. The result of this templating is spatially ordered nanoparticle arrays embedded within the block copolymer nanostructure. These soft materials can be shear aligned into crystals with long range order and this shear alignment is discussed. Finally, the dynamics of nanoparticles within the nanostructured material are characterized with fluorescence recovery after photobleaching (FRAP). The applications and general behavior of these nanostructured hydrogels are outlined.

Computational characterization of ordered nanostructured surfaces

NASA Astrophysics Data System (ADS)

Mohieddin Abukhdeir, Nasser

2016-08-01

A vital and challenging task for materials researchers is to determine relationships between material characteristics and desired properties. While the measurement and assessment of material properties can be complex, quantitatively characterizing their structure is frequently a more challenging task. This issue is magnified for materials researchers in the areas of nanoscience and nanotechnology, where material structure is further complicated by phenomena such as self-assembly, collective behavior, and measurement uncertainty. Recent progress has been made in this area for both self-assembled and nanostructured surfaces due to increasing accessibility of imaging techniques at the nanoscale. In this context, recent advances in nanomaterial surface structure characterization are reviewed including the development of new theory and image processing methods.

RNA as a stable polymer to build controllable and defined nanostructures for material and biomedical applications

PubMed Central

Li, Hui; Lee, Taek; Dziubla, Thomas; Pi, Fengmei; Guo, Sijin; Xu, Jing; Li, Chan; Haque, Farzin; Liang, Xing-Jie; Guo, Peixuan

2015-01-01

Summary The value of polymers is manifested in their vital use as building blocks in material and life sciences. Ribonucleic acid (RNA) is a polynucleic acid, but its polymeric nature in materials and technological applications is often overlooked due to an impression that RNA is seemingly unstable. Recent findings that certain modifications can make RNA resistant to RNase degradation while retaining its authentic folding property and biological function, and the discovery of ultra-thermostable RNA motifs have adequately addressed the concerns of RNA unstability. RNA can serve as a unique polymeric material to build varieties of nanostructures including nanoparticles, polygons, arrays, bundles, membrane, and microsponges that have potential applications in biomedical and material sciences. Since 2005, more than a thousand publications on RNA nanostructures have been published in diverse fields, indicating a remarkable increase of interest in the emerging field of RNA nanotechnology. In this review, we aim to: delineate the physical and chemical properties of polymers that can be applied to RNA; introduce the unique properties of RNA as a polymer; review the current methods for the construction of RNA nanostructures; describe its applications in material, biomedical and computer sciences; and, discuss the challenges and future prospects in this field. PMID:26770259

Avian Nanostructured Tissues as Models for New Defensive Coatings and Photonic Crystal Fibers

DTIC Science & Technology

2012-03-31

promiscuous binding capacity of chitin , the chemical backbone of the arthropod cuticle (Kumar 2000). This polysaccharide binds many proteins and other...properties. The greater refractive index contrast between light and dark layers afforded by chitin may allow Arthropoda to attain brighter and more 71

DNA-Enabled Integrated Molecular Systems for Computation and Sensing

DTIC Science & Technology

2014-05-21

nanostructures to create nanophotonic networks that undergo nonradiative , near-field energy transfer. This process is known as resonance energy transfer (RET...promoting A to A*. The A* species can then decay nonradiatively or emit a photon of energy hν2.When chromophores are too far away, they cannot efficiently

Numerical Modelling of Mechanical Properties of C-Pd Film by Homogenization Technique and Finite Element Method

NASA Astrophysics Data System (ADS)

Rymarczyk, Joanna; Kowalczyk, Piotr; Czerwosz, Elzbieta; Bielski, Włodzimierz

2011-09-01

The nanomechanical properties of nanostructural carbonaceous-palladium films are studied. The nanoindentation experiments are numerically using the Finite Element Method. The homogenization theory is applied to compute the properties of the composite material used as the input data for nanoindentation calculations.

Nanostructure of DNA repair foci revealed by superresolution microscopy.

PubMed

Sisario, Dmitri; Memmel, Simon; Doose, Sören; Neubauer, Julia; Zimmermann, Heiko; Flentje, Michael; Djuzenova, Cholpon S; Sauer, Markus; Sukhorukov, Vladimir L

2018-06-12

Induction of DNA double-strand breaks (DSBs) by ionizing radiation leads to formation of micrometer-sized DNA-repair foci, whose organization on the nanometer-scale remains unknown because of the diffraction limit (∼200 nm) of conventional microscopy. Here, we applied diffraction-unlimited, direct stochastic optical-reconstruction microscopy ( dSTORM) with a lateral resolution of ∼20 nm to analyze the focal nanostructure of the DSB marker histone γH2AX and the DNA-repair protein kinase (DNA-PK) in irradiated glioblastoma multiforme cells. Although standard confocal microscopy revealed substantial colocalization of immunostained γH2AX and DNA-PK, in our dSTORM images, the 2 proteins showed very little (if any) colocalization despite their close spatial proximity. We also found that γH2AX foci consisted of distinct circular subunits ("nanofoci") with a diameter of ∼45 nm, whereas DNA-PK displayed a diffuse, intrafocal distribution. We conclude that γH2AX nanofoci represent the elementary, structural units of DSB repair foci, that is, individual γH2AX-containing nucleosomes. dSTORM-based γH2AX nanofoci counting and distance measurements between nanofoci provided quantitative information on the total amount of chromatin involved in DSB repair as well as on the number and longitudinal distribution of γH2AX-containing nucleosomes in a chromatin fiber. We thus estimate that a single focus involves between ∼0.6 and ∼1.1 Mbp of chromatin, depending on radiation treatment. Because of their ability to unravel the nanostructure of DSB-repair foci, dSTORM and related single-molecule localization nanoscopy methods will likely emerge as powerful tools in biology and medicine to elucidate the effects of DNA damaging agents in cells.-Sisario, D., Memmel, S., Doose, S., Neubauer, J., Zimmermann, H., Flentje, M., Djuzenova, C. S., Sauer, M., Sukhorukov, V. L. Nanostructure of DNA repair foci revealed by superresolution microscopy.

Microstructural, spectroscopic, and antibacterial properties of silver-based hybrid nanostructures biosynthesized using extracts of coriander leaves and seeds

PubMed Central

Luna, Carlos; Barriga-Castro, Enrique Díaz; Gómez-Treviño, Alberto; Núñez, Nuria O; Mendoza-Reséndez, Raquel

2016-01-01

Coriander leaves and seeds have been highly appreciated since ancient times, not only due to their pleasant flavors but also due to their inhibitory activity on food degradation and their beneficial properties for health, both ascribed to their strong antioxidant activity. Recently, it has been shown that coriander leaf extracts can mediate the synthesis of metallic nanoparticles through oxidation/reduction reactions. In the present study, extracts of coriander leaves and seeds have been used as reaction media for the wet chemical synthesis of ultrafine silver nanoparticles and nanoparticle clusters, with urchin- and tree-like shapes, coated by biomolecules (mainly, proteins and polyphenols). In this greener route of nanostructure preparation, the active biocompounds of coriander simultaneously play the roles of reducing and stabilizing agents. The morphological and microstructural studies of the resulting biosynthesized silver nanostructures revealed that the nanostructures prepared with a small concentration of the precursor Ag salt (AgNO3 =5 mM) exhibit an ultrafine size and a narrow size distribution, whereas particles synthesized with high concentrations of the precursor Ag salt (AgNO3 =0.5 M) are polydisperse and formation of supramolecular structures occurs. Fourier transform infrared and Raman spectroscopy studies indicated that the bioreduction of the Ag− ions takes place through their interactions with free amines, carboxylate ions, and hydroxyl groups. As a consequence of such interactions, residues of proteins and polyphenols cap the biosynthesized Ag nanoparticles providing them a hybrid core/shell structure. In addition, these biosynthesized Ag nanomaterials exhibited size-dependent plasmon extinction bands and enhanced bactericidal activities against both Gram-positive and Gram-negative bacteria, displaying minimal inhibitory Ag concentrations lower than typical values reported in the literature for Ag nanoparticles, probably due to the synergy of the bactericidal activities of the Ag nanoparticle cores and their capping ligands. PMID:27703347

Recent progress on fabrication and drug delivery applications of nanostructured hydroxyapatite.

PubMed

Mondal, Sudip; Dorozhkin, Sergy V; Pal, Umapada

2018-07-01

Through this brief review, we provide a comprehensive historical background of the development of nanostructured hydroxyapatite (nHAp), and its application potentials for controlled drug delivery, drug conjugation, and other biomedical treatments. Aspects associated with efficient utilization of hydroxyapatite (HAp) nanostructures such as their synthesis, interaction with drug molecules, and other concerns, which need to be resolved before they could be used as a potential drug carrier in body system, are discussed. This review focuses on the evolution of perceptions, practices, and accomplishments in providing improved delivery systems for drugs until date. The pioneering developments that have presaged today's fascinating state of the art drug delivery systems based on HAp and HAp-based composite nanostructures are also discussed. Special emphasis has been given to describe the application and effectiveness of modified HAp as drug carrier agent for different diseases such as bone-related disorders, carriers for antibiotics, anti-inflammatory, carcinogenic drugs, medical imaging, and protein delivery agents. As only a very few published works made comprehensive evaluation of HAp nanostructures for drug delivery applications, we try to cover the three major areas: concepts, practices and achievements, and applications, which have been consolidated and patented for their practical usage. The review covers a broad spectrum of nHAp and HAp modified inorganic drug carriers, emphasizing some of their specific aspects those needed to be considered for future drug delivery applications. This article is categorized under: Implantable Materials and Surgical Technologies > Nanomaterials and Implants Therapeutic Approaches and Drug Discovery > Nanomedicine for Respiratory Disease Nanotechnology Approaches to Biology > Cells at the Nanoscale. © 2017 Wiley Periodicals, Inc.

Fibrinogen and fibrin based micro and nano scaffolds incorporated with drugs, proteins, cells and genes for therapeutic biomedical applications

PubMed Central

Rajangam, Thanavel; An, Seong Soo A

2013-01-01

Over the past two decades, many types of natural and synthetic polymer-based micro- and nanocarriers, with exciting properties and applications, have been developed for application in various types of tissue regeneration, including bone, cartilage, nerve, blood vessels, and skin. The development of suitable polymers scaffold designs to aid the repair of specific cell types have created diverse and important potentials in tissue restoration. Fibrinogen (Fbg)- and fibrin (Fbn)-based micro- and nanostructures can provide suitable natural matrix environments. Since these primary materials are abundantly available in blood as the main coagulation proteins, they can easily interact with damaged tissues and cells through native biochemical interactions. Fbg- and Fbn-based micro and nanostructures can also be consecutively furnished/or encapsulated and specifically delivered, with multiple growth factors, proteins, and stem cells, in structures designed to aid in specific phases of the tissue regeneration process. The present review has been carried out to demonstrate the progress made with micro and nanoscaffold applications and features a number of applications of Fbg- and Fbn-based carriers in the field of biomaterials, including the delivery of drugs, active biomolecules, cells, and genes, that have been effectively used in tissue engineering and regenerative medicine. PMID:24106425

Nanoscale porosity in polymer films: fabrication and therapeutic applications

PubMed Central

Bernards, Daniel A.; Desai, Tejal A.

2011-01-01

This review focuses on current developments in the field of nanostructured bulk polymers and their application in bioengineering and therapeutic sciences. In contrast to well-established nanoscale materials, such as nanoparticles and nanofibers, bulk nanostructured polymers combine nanoscale structure in a macroscopic construct, which enables unique application of these materials. Contemporary fabrication and processing techniques capable of producing nanoporous polymer films are reviewed. Focus is placed on techniques capable of sub-100 nm features since this range approaches the size scale of biological components, such as proteins and viruses. The attributes of these techniques are compared, with an emphasis on the characteristic advantages and limitations of each method. Finally, application of these materials to biofiltration, immunoisolation, and drug delivery are reviewed. PMID:22140398

Fabrication of circular assemblies with DNA tetrahedrons: from static structures to a dynamic rotary motor.

PubMed

Wang, Liying; Meng, Zhenyu; Martina, Felicia; Shao, Huilin; Shao, Fangwei

2017-12-01

DNA tetrahedron as the simplest 3D DNA nanostructure has been applied widely in biomedicine and biosensing. Herein, we design and fabricate a series of circular assemblies of DNA tetrahedron with high purity and decent yields. These circular nanostructures are confirmed by endonuclease digestion, gel electrophoresis and atomic force microscopy. Inspired by rotary protein motor, we demonstrate these circular architectures can serve as a stator for a rotary DNA motor to achieve the circular rotation. The DNA motor can rotate on the stators for several cycles, and the locomotion of the motor is monitored by the real-time fluorescent measurements. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jee, S.S.; DiMasi, E.; Kasinath, R.K.

Bone is a hierarchically structured composite which imparts it with unique mechanical properties and bioresorptive potential. These properties are primarily influenced by the underlying nanostructure of bone, which consists of nanocrystals of hydroxyapatite embedded and uniaxially aligned within collagen fibrils. There is also a small fraction of non-collagenous proteins in bone, and these are thought to play an important role in bone's formation. In our in vitro model system of bone formation, polyanionic peptides are used to mimic the role of the non-collagenous proteins. In our prior studies, we have shown that intrafibrillar mineralization can be achieved in synthetic reconstitutedmore » collagen sponges using a polymer-induced liquid-precursor (PILP) mineralization process. This led to a nanostructured arrangement of hydroxyapatite crystals within the individual fibrils which closely mimics that of bone. This report demonstrates that biogenic collagen scaffolds obtained from turkey tendon, which consist of densely packed and oriented collagen fibrils, can also be mineralized by the PILP process. Synchrotron X-ray diffraction studies show that the mineralization process leads to a high degree of crystallographic orientation at the macroscale, thus emulating that found in the biological system of naturally mineralizing turkey tendon.« less

Records for conversion of laser energy to nuclear energy in exploding nanostructures

NASA Astrophysics Data System (ADS)

Jortner, Joshua; Last, Isidore

2017-09-01

Table-top nuclear fusion reactions in the chemical physics laboratory can be driven by high-energy dynamics of Coulomb exploding, multicharged, deuterium containing nanostructures generated by ultraintense, femtosecond, near-infrared laser pulses. Theoretical-computational studies of table-top laser-driven nuclear fusion of high-energy (up to 15 MeV) deuterons with 7Li, 6Li and D nuclei demonstrate the attainment of high fusion yields within a source-target reaction design, which constitutes the highest table-top fusion efficiencies obtained up to date. The conversion efficiency of laser energy to nuclear energy (0.1-1.0%) for table-top fusion is comparable to that for DT fusion currently accomplished for 'big science' inertial fusion setups.

Free energy calculation of permeant-membrane interactions using molecular dynamics simulations.

PubMed

Elvati, Paolo; Violi, Angela

2012-01-01

Nanotoxicology, the science concerned with the safe use of nanotechnology and nanostructure design for biological applications, is a field of research that has recently received great attention, as a result of the rapid growth in nanotechnology. Many nanostructures are of a scale and chemical composition similar to many biomolecular environments, and recent papers have reported evident toxicity of selected nanoparticles. Molecular simulations can help develop a mechanistic understanding of how structural properties affect bioactivity. In this chapter, we describe how to compute the free energy of interactions between cellular membranes and benzene, the main constituent of some toxic carbonaceous particles, with well-tempered metadynamics. This algorithm reconstructs the free energy surface and accelerates rare events in a coarse-grained representation of the system.

Transitioning Rationally Designed Catalytic Materials to Real 'Working' Catalysts Produced at Commercial Scale: Nanoparticle Materials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schaidle, Joshua A.; Habas, Susan E.; Baddour, Frederick G.

Catalyst design, from idea to commercialization, requires multi-disciplinary scientific and engineering research and development over 10-20 year time periods. Historically, the identification of new or improved catalyst materials has largely been an empirical trial-and-error process. However, advances in computational capabilities (new tools and increased processing power) coupled with new synthetic techniques have started to yield rationally-designed catalysts with controlled nano-structures and tailored properties. This technological advancement represents an opportunity to accelerate the catalyst development timeline and to deliver new materials that outperform existing industrial catalysts or enable new applications, once a number of unique challenges associated with the scale-up ofmore » nano-structured materials are overcome.« less

An Antibody-Immobilized Silica Inverse Opal Nanostructure for Label-Free Optical Biosensors.

PubMed

Lee, Wang Sik; Kang, Taejoon; Kim, Shin-Hyun; Jeong, Jinyoung

2018-01-20

Three-dimensional SiO₂-based inverse opal (SiO₂-IO) nanostructures were prepared for use as biosensors. SiO₂-IO was fabricated by vertical deposition and calcination processes. Antibodies were immobilized on the surface of SiO₂-IO using 3-aminopropyl trimethoxysilane (APTMS), a succinimidyl-[(N-maleimidopropionamido)-tetraethyleneglycol] ester (NHS-PEG₄-maleimide) cross-linker, and protein G. The highly accessible surface and porous structure of SiO₂-IO were beneficial for capturing influenza viruses on the antibody-immobilized surfaces. Moreover, as the binding leads to the redshift of the reflectance peak, the influenza virus could be detected by simply monitoring the change in the reflectance spectrum without labeling. SiO₂-IO showed high sensitivity in the range of 10³-10⁵ plaque forming unit (PFU) and high specificity to the influenza A (H1N1) virus. Due to its structural and optical properties, SiO₂-IO is a promising material for the detection of the influenza virus. Our study provides a generalized sensing platform for biohazards as various sensing strategies can be employed through the surface functionalization of three-dimensional nanostructures.

Nanostructured titanium-silver coatings with good antibacterial activity and cytocompatibility fabricated by one-step magnetron sputtering

NASA Astrophysics Data System (ADS)

Bai, Long; Hang, Ruiqiang; Gao, Ang; Zhang, Xiangyu; Huang, Xiaobo; Wang, Yueyue; Tang, Bin; Zhao, Lingzhou; Chu, Paul K.

2015-11-01

Bacterial infection and loosing are serious complications for biomedical implants in the orthopedic, dental, and other biomedical fields and the ideal implants should combine good antibacterial ability and bioactivity. In this study, nanostructured titanium-silver (Ti-Ag) coatings with different Ag contents (1.2 to 21.6 at%) are prepared on Ti substrates by magnetron sputtering. As the Ag concentration is increased, the coatings change from having dense columnar crystals to sparse ones and eventually no columnar structure. The Ti-Ag coatings can effectively kill Staphylococcus aureus during the first few days and remain moderately antibacterial after immersion for 75 days. Compared to pure Ti, the Ti-Ag coatings show good cytocompatibility as indicated by good osteoblast adhesion, proliferation, intracellular total protein synthesis, and alkaline phosphatase (ALP) activity. In addition, cell spreading, collagen secretion, and extracellular matrix mineralization are promoted on the coatings with the proper Ag contents due to the nanostructured morphological features. Our results indicate that favorable antibacterial activity and osseointegration ability can be simultaneously achieved by regulating the Ag contents in Ti-Ag coatings.

Advances in structural design of lipid-based nanoparticle carriers for delivery of macromolecular drugs, phytochemicals and anti-tumor agents.

PubMed

Angelova, Angelina; Garamus, Vasil M; Angelov, Borislav; Tian, Zhenfen; Li, Yawen; Zou, Aihua

2017-11-01

The present work highlights recent achievements in development of nanostructured dispersions and biocolloids for drug delivery applications. We emphasize the key role of biological small-angle X-ray scattering (BioSAXS) investigations for the nanomedicine design. A focus is given on controlled encapsulation of small molecular weight phytochemical drugs in lipid-based nanocarriers as well as on encapsulation of macromolecular siRNA, plasmid DNA, peptide and protein pharmaceuticals in nanostructured nanoparticles that may provide efficient intracellular delivery and triggered drug release. Selected examples of utilisation of the BioSAXS method for characterization of various types of liquid crystalline nanoorganizations (liposome, spongosome, cubosome, hexosome, and nanostructured lipid carriers) are discussed in view of the successful encapsulation and protection of phytochemicals and therapeutic biomolecules in the hydrophobic or the hydrophilic compartments of the nanocarriers. We conclude that the structural design of the nanoparticulate carriers is of crucial importance for the therapeutic outcome and the triggered drug release from biocolloids. Copyright © 2017 Elsevier B.V. All rights reserved.

Lyotropic liquid crystal engineering moving beyond binary compositional space - ordered nanostructured amphiphile self-assembly materials by design.

PubMed

van 't Hag, Leonie; Gras, Sally L; Conn, Charlotte E; Drummond, Calum J

2017-05-22

Ordered amphiphile self-assembly materials with a tunable three-dimensional (3D) nanostructure are of fundamental interest, and crucial for progressing several biological and biomedical applications, including in meso membrane protein crystallization, as drug and medical contrast agent delivery vehicles, and as biosensors and biofuel cells. In binary systems consisting of an amphiphile and a solvent, the ability to tune the 3D cubic phase nanostructure, lipid bilayer properties and the lipid mesophase is limited. A move beyond the binary compositional space is therefore required for efficient engineering of the required material properties. In this critical review, the phase transitions upon encapsulation of more than 130 amphiphilic and soluble additives into the bicontinuous lipidic cubic phase under excess hydration are summarized. The data are interpreted using geometric considerations, interfacial curvature, electrostatic interactions, partition coefficients and miscibility of the alkyl chains. The obtained lyotropic liquid crystal engineering design rules can be used to enhance the formulation of self-assembly materials and provides a large library of these materials for use in biomedical applications (242 references).

Digitally encoded DNA nanostructures for multiplexed, single-molecule protein sensing with nanopores

NASA Astrophysics Data System (ADS)

Bell, Nicholas A. W.; Keyser, Ulrich F.

2016-07-01

The simultaneous detection of a large number of different analytes is important in bionanotechnology research and in diagnostic applications. Nanopore sensing is an attractive method in this regard as the approach can be integrated into small, portable device architectures, and there is significant potential for detecting multiple sub-populations in a sample. Here, we show that highly multiplexed sensing of single molecules can be achieved with solid-state nanopores by using digitally encoded DNA nanostructures. Based on the principles of DNA origami, we designed a library of DNA nanostructures in which each member contains a unique barcode; each bit in the barcode is signalled by the presence or absence of multiple DNA dumbbell hairpins. We show that a 3-bit barcode can be assigned with 94% accuracy by electrophoretically driving the DNA structures through a solid-state nanopore. Select members of the library were then functionalized to detect a single, specific antibody through antigen presentation at designed positions on the DNA. This allows us to simultaneously detect four different antibodies of the same isotype at nanomolar concentration levels.

Digitally encoded DNA nanostructures for multiplexed, single-molecule protein sensing with nanopores.

PubMed

Bell, Nicholas A W; Keyser, Ulrich F

2016-07-01

The simultaneous detection of a large number of different analytes is important in bionanotechnology research and in diagnostic applications. Nanopore sensing is an attractive method in this regard as the approach can be integrated into small, portable device architectures, and there is significant potential for detecting multiple sub-populations in a sample. Here, we show that highly multiplexed sensing of single molecules can be achieved with solid-state nanopores by using digitally encoded DNA nanostructures. Based on the principles of DNA origami, we designed a library of DNA nanostructures in which each member contains a unique barcode; each bit in the barcode is signalled by the presence or absence of multiple DNA dumbbell hairpins. We show that a 3-bit barcode can be assigned with 94% accuracy by electrophoretically driving the DNA structures through a solid-state nanopore. Select members of the library were then functionalized to detect a single, specific antibody through antigen presentation at designed positions on the DNA. This allows us to simultaneously detect four different antibodies of the same isotype at nanomolar concentration levels.

Multi-enzyme complexes on DNA scaffolds capable of substrate channelling with an artificial swinging arm

NASA Astrophysics Data System (ADS)

Fu, Jinglin; Yang, Yuhe Renee; Johnson-Buck, Alexander; Liu, Minghui; Liu, Yan; Walter, Nils G.; Woodbury, Neal W.; Yan, Hao

2014-07-01

Swinging arms are a key functional component of multistep catalytic transformations in many naturally occurring multi-enzyme complexes. This arm is typically a prosthetic chemical group that is covalently attached to the enzyme complex via a flexible linker, allowing the direct transfer of substrate molecules between multiple active sites within the complex. Mimicking this method of substrate channelling outside the cellular environment requires precise control over the spatial parameters of the individual components within the assembled complex. DNA nanostructures can be used to organize functional molecules with nanoscale precision and can also provide nanomechanical control. Until now, protein-DNA assemblies have been used to organize cascades of enzymatic reactions by controlling the relative distance and orientation of enzymatic components or by facilitating the interface between enzymes/cofactors and electrode surfaces. Here, we show that a DNA nanostructure can be used to create a multi-enzyme complex in which an artificial swinging arm facilitates hydride transfer between two coupled dehydrogenases. By exploiting the programmability of DNA nanostructures, key parameters including position, stoichiometry and inter-enzyme distance can be manipulated for optimal activity.

Multi-enzyme complexes on DNA scaffolds capable of substrate channelling with an artificial swinging arm.

PubMed

Fu, Jinglin; Yang, Yuhe Renee; Johnson-Buck, Alexander; Liu, Minghui; Liu, Yan; Walter, Nils G; Woodbury, Neal W; Yan, Hao

2014-07-01

Swinging arms are a key functional component of multistep catalytic transformations in many naturally occurring multi-enzyme complexes. This arm is typically a prosthetic chemical group that is covalently attached to the enzyme complex via a flexible linker, allowing the direct transfer of substrate molecules between multiple active sites within the complex. Mimicking this method of substrate channelling outside the cellular environment requires precise control over the spatial parameters of the individual components within the assembled complex. DNA nanostructures can be used to organize functional molecules with nanoscale precision and can also provide nanomechanical control. Until now, protein-DNA assemblies have been used to organize cascades of enzymatic reactions by controlling the relative distance and orientation of enzymatic components or by facilitating the interface between enzymes/cofactors and electrode surfaces. Here, we show that a DNA nanostructure can be used to create a multi-enzyme complex in which an artificial swinging arm facilitates hydride transfer between two coupled dehydrogenases. By exploiting the programmability of DNA nanostructures, key parameters including position, stoichiometry and inter-enzyme distance can be manipulated for optimal activity.

Biomimetic structural engineering of P22 virus-like particles for catalysis and immune modulation

NASA Astrophysics Data System (ADS)

Schwarz, Benjamin

Within biology molecules are arranged in hierarchical structures that coordinate and control the many processes that allow for complex organisms to exist. Proteins and other functional macromolecules are often studied outside their natural nanostructural context because it remains difficult to create controlled arrangements of proteins at this size scale. Viruses are elegantly simple nano-systems that exist at the interface of living organisms and non-living biological machines. Studied and viewed primarily as pathogens to be combatted, viruses have emerged as models of structural efficiency at the nanoscale and have spurred the development of biomimetic nanoparticle systems. Virus-like particles (VLPs) are noninfectious protein cages derived from viruses or other cage-forming systems. VLPs provide incredibly regular scaffolds for building at the nanoscale. In this work I have utilized the VLP derived from the bacteriophage P22 as a platform for the organization of enzymes, antigens, and immune-stimulating proteins inside and outside the capsid through purely genetic means. In the case of enzymes, encapsulation of a two-enzyme pathway has led to the development of metabolic nanoparticle catalysts and an expanded understanding of the control that structure exerts on metabolic flux. These same structural elements applied to the delivery of protein subunit antigens directed at cytotoxic T cell immunity result in drastically enhanced antigen processing and lasting immunological memory. Lastly, presentation of immune-stimulating proteins from the Tumor Necrosis Factor Super Family on the surface of the P22 VLP enhances the cell signaling efficiency of these compounds 50-fold and provides strategies for the application of these proteins as immune modulatory oncology therapeutics. In all of these cases, the reintroduction of nanostructure to these protein systems, reminiscent of their natural environment, has led to both new technologies and a better understanding of the role of structure in biological processes.

Spectral and Spatial Coherent Emission of Thermal Radiation from Metal-Semiconductor Nanostructures

DTIC Science & Technology

2012-03-01

Coupled Wave Analysis (RCWA) numerical technique and Computer Simulation Technology (CST) electromagnetic modeling software, two structures were...Stephanie Gray, IR-VASE and modeling  Dr. Kevin Gross, FTIR  Mr. Richard Johnston, Cleanroom and Photolithography  Ms. Abbey Juhl, Nanoscribe...Appendix B. Supplemental IR-VASE Measurements and Modeling .............................114 Bibliography

Ab initio electronic transport and thermoelectric properties of solids from full and range-separated hybrid functionals

NASA Astrophysics Data System (ADS)

Sansone, Giuseppe; Ferretti, Andrea; Maschio, Lorenzo

2017-09-01

Within the semiclassical Boltzmann transport theory in the constant relaxation-time approximation, we perform an ab initio study of the transport properties of selected systems, including crystalline solids and nanostructures. A local (Gaussian) basis set is adopted and exploited to analytically evaluate band velocities as well as to access full and range-separated hybrid functionals (such as B3LYP, PBE0, or HSE06) at a moderate computational cost. As a consequence of the analytical derivative, our approach is computationally efficient and does not suffer from problems related to band crossings. We investigate and compare the performance of a variety of hybrid functionals in evaluating Boltzmann conductivity. Demonstrative examples include silicon and aluminum bulk crystals as well as two thermoelectric materials (CoSb3, Bi2Te3). We observe that hybrid functionals other than providing more realistic bandgaps—as expected—lead to larger bandwidths and hence allow for a better estimate of transport properties, also in metallic systems. As a nanostructure prototype, we also investigate conductivity in boron-nitride (BN) substituted graphene, in which nanoribbons (nanoroads) alternate with BN ones.

Engineered Nanostructures of Haptens Lead to Unexpected Formation of Membrane Nanotubes Connecting Rat Basophilic Leukemia Cells.

PubMed

Li, Jie-Ren; Ross, Shailise S; Liu, Yang; Liu, Ying X; Wang, Kang-Hsin; Chen, Huan-Yuan; Liu, Fu-Tong; Laurence, Ted A; Liu, Gang-Yu

2015-07-28

A recent finding reports that co-stimulation of the high-affinity immunoglobulin E (IgE) receptor (FcεRI) and the chemokine receptor 1 (CCR1) triggered formation of membrane nanotubes among bone-marrow-derived mast cells. The co-stimulation was attained using corresponding ligands: IgE binding antigen and macrophage inflammatory protein 1α (MIP1 α), respectively. However, this approach failed to trigger formation of nanotubes among rat basophilic leukemia (RBL) cells due to the lack of CCR1 on the cell surface (Int. Immunol. 2010, 22 (2), 113-128). RBL cells are frequently used as a model for mast cells and are best known for antibody-mediated activation via FcεRI. This work reports the successful formation of membrane nanotubes among RBLs using only one stimulus, a hapten of 2,4-dinitrophenyl (DNP) molecules, which are presented as nanostructures with our designed spatial arrangements. This observation underlines the significance of the local presentation of ligands in the context of impacting the cellular signaling cascades. In the case of RBL, certain DNP nanostructures suppress antigen-induced degranulation and facilitate the rearrangement of the cytoskeleton to form nanotubes. These results demonstrate an important scientific concept; engineered nanostructures enable cellular signaling cascades, where current technologies encounter great difficulties. More importantly, nanotechnology offers a new platform to selectively activate and/or inhibit desired cellular signaling cascades.

Giant magnetic anisotropy of heavy p-elements on high-symmetry substrates: a new paradigm for supported nanostructures

NASA Astrophysics Data System (ADS)

Pang, Rui; Deng, Bei; Shi, Xingqiang; Zheng, Xiaohong

2018-04-01

Nanostructures with giant magnetic anisotropy energies (MAEs) are desired in designing miniaturized magnetic storage and quantum computing devices. Previous works focused mainly on materials or elements with d electrons. Here, by taking Bi–X(X = In, Tl, Ge, Sn, Pb) adsorbed on nitrogenized divacancy of graphene and Bi atoms adsorbed on MgO(100) as examples, through ab initio and model calculations, we propose that special p-element dimers and single-adatoms on symmetry-matched substrates possess giant atomic MAEs of 72–200 meV, and has room temperature structural stability. The huge MAEs originate from the p-orbital degeneracy around the Fermi level in a symmetry-matched surface ligand field and the lifting of this degeneracy when spin–orbit interaction (SOI) is taken into account. Especially, we developed a simplified quantum mechanical model for the design principles of giant MAEs of supported magnetic adatoms and dimers. Thus, our discoveries and mechanisms provide a new paradigm to design giant atomic MAE of p electrons in supported nanostructures.

Computer Tomograph (CT) imaging of mandibular anatomical substrate in animal model restored with nanostructured hydroxyapatite compounds

PubMed Central

Ciuluvică, R; Grădinaru, S; Popescu, M; Piticescu, RM; Cergan, R

2015-01-01

Introduction: This study was meant to test a new type of bone graft on an animal model. This material was a nanostructured hydroxyapatite. Materials and Methods: the study was conducted according to Ethic Committee Regulation on animal model (Oryctolagus cuniculus – rabbit) between August and November 2014, at “Carol Davila” University of Medicine and Pharmacy, Bucharest. The animals were tested by using a CT at the level of the mandible before and after using the nanostructured hydroxyapatite. Results: The animals were CT scanned at 1, 2 and respectively 3 months, noticing a growth of the mandibular bone density. After 3 months, a bone density equal with the density of the healthy bone was noticed. Conclusions: The use of the bone graft could be a viable alternative to available materials. The advantage was that bone recovery had a density similar to the density of the healthy bone and the cost of production was low because it was made out of Calcium azotate and monobasic ammonium phosphate. PMID:25914749

Atomistic simulations of thermal transport in Si and SiGe based materials: From bulk to nanostructures

NASA Astrophysics Data System (ADS)

Savic, Ivana; Mingo, Natalio; Donadio, Davide; Galli, Giulia

2010-03-01

It has been recently proposed that Si and SiGe based nanostructured materials may exhibit low thermal conductivity and overall promising properties for thermoelectric applications. Hence there is a considerable interest in developing accurate theoretical and computational methods which can help interpret recent measurements, identify the physical origin of the reduced thermal conductivity, as well as shed light on the interplay between disorder and nanostructuring in determining a high figure of merit. In this work, we investigate the capability of an atomistic Green's function method [1] to describe phonon transport in several types of Si and SiGe based systems: amorphous Si, SiGe alloys, planar and nanodot Si/SiGe multilayers. We compare our results with experimental data [2,3], and with the findings of molecular dynamics simulations and calculations based on the Boltzmann transport equation. [1] I. Savic, N. Mingo, and D. A. Stewart, Phys. Rev. Lett. 101, 165502 (2008). [2] S.-M. Lee, D. G. Cahill, and R. Venkatasubramanian, Appl. Phys. Lett. 70, 2957 (1997). [3] G. Pernot et al., submitted.

Measurements Of The Effects Of Grain Boundary And Alloy Scattering On Spectral Phonon Mean Free Path Distributions.

NASA Astrophysics Data System (ADS)

Lubner, Sean; Khan, Md. Imran; Dames, Chris

In the electronics and clean energy fields, it is increasingly necessary to reliably model the dissipation of heat from micro and nanostructures or nanostructured materials such as in batteries, computer chips, and thermoelectrics. In these regimes where length scales are comparable to the mean free paths (MFPs) of energy carriers, the diffusion law of heat conduction begins to break down. In this talk, I present our recent results from using a time domain thermoreflectance (TDTR) technique with laser spot 1/e-squared radii less than 2 microns to measure sub-diffusion thermal transport in silicon, nanograined-silicon (ng-Si), and silicon germanium (SiGe) alloys. Our results experimentally demonstrate that alloy scattering skews phonon spectra toward longer MFPs, while nanostructuring skews phonon spectra toward shorter MFPs. As a consequence, we show that a significant fraction of the heat-carrying phonons in SiGe have MFPs greater than 10 microns at room temperature, and that the thermal conductivity of ng-Si overtakes that of SiGe after microstructuring. NSF.

Simulations of the synthesis of boron-nitride nanostructures in a hot, high pressure gas volume† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c8sc00667a

PubMed Central

Han, Longtao; Irle, Stephan; Nakai, Hiromi

2018-01-01

We performed nanosecond timescale computer simulations of clusterization and agglomeration processes of boron nitride (BN) nanostructures in hot, high pressure gas, starting from eleven different atomic and molecular precursor systems containing boron, nitrogen and hydrogen at various temperatures from 1500 to 6000 K. The synthesized BN nanostructures self-assemble in the form of cages, flakes, and tubes as well as amorphous structures. The simulations facilitate the analysis of chemical dynamics and we are able to predict the optimal conditions concerning temperature and chemical precursor composition for controlling the synthesis process in a high temperature gas volume, at high pressure. We identify the optimal precursor/temperature choices that lead to the nanostructures of highest quality with the highest rate of synthesis, using a novel parameter of the quality of the synthesis (PQS). Two distinct mechanisms of BN nanotube growth were found, neither of them based on the root-growth process. The simulations were performed using quantum-classical molecular dynamics (QCMD) based on the density-functional tight-binding (DFTB) quantum mechanics in conjunction with a divide-and-conquer (DC) linear scaling algorithm, as implemented in the DC-DFTB-K code, enabling the study of systems as large as 1300 atoms in canonical NVT ensembles for 1 ns time. PMID:29780513

Recent advances in protein and Peptide drug delivery: a special emphasis on polymeric nanoparticles.

PubMed

Patel, Ashaben; Patel, Mitesh; Yang, Xiaoyan; Mitra, Ashim K

2014-01-01

Proteins and peptides are widely indicated in many diseased states. Parenteral route is the most commonly em- ployed method of administration for therapeutic proteins and peptides. However, requirement of frequent injections due to short in vivo half-life results in poor patient compliance. Non-invasive drug delivery routes such as nasal, transdermal, pulmonary, and oral offer several advantages over parenteral administration. Intrinsic physicochemical properties and low permeability across biological membrane limit protein delivery via non-invasive routes. One of the strategies to improve protein and peptide absorption is by delivering through nanostructured delivery carriers. Among nanocarriers, polymeric nanoparticles (NPs) have demonstrated significant advantages over other delivery systems. This article summarizes the application of polymeric NPs for protein and peptide drug delivery following oral, nasal, pulmonary, parenteral, transder mal, and ocular administrations.

Recent Advances in Protein and Peptide Drug Delivery: A Special Emphasis on Polymeric Nanoparticles

PubMed Central

Patel, Ashaben; Patel, Mitesh; Yang, Xiaoyan; Mitra, Ashim K.

2015-01-01

Proteins and peptides are widely indicated in many diseased states. Parenteral route is the most commonly employed method of administration for therapeutic proteins and peptides. However, requirement of frequent injections due to short in vivo half-life results in poor patient compliance. Non-invasive drug delivery routes such as nasal, transdermal, pulmonary, and oral offer several advantages over parenteral administration. Intrinsic physicochemical properties and low permeability across biological membrane limit protein delivery via non-invasive routes. One of the strategies to improve protein and peptide absorption is by delivering through nanostructured delivery carriers. Among nanocarriers, polymeric nanoparticles (NPs) have demonstrated significant advantages over other delivery systems. This article summarizes the application of polymeric NPs for protein and peptide drug delivery following oral, nasal, pulmonary, parenteral, transdermal, and ocular administrations. PMID:25106908

Directing the assembly of nanostructured films with living cells

NASA Astrophysics Data System (ADS)

Brinker, C. Jeffrey

2007-03-01

This talk describes our recent discovery of the ability of living cells to organize extended nanostructures and nano-objects in a manner that creates a unique, highly biocompatible nano//bio interface (Science 313, 337-340, 2006). We find that, using short chain phospholipids to direct the formation of thin film silica mesophases during evaporation-induced self-assembly, the introduction of cells (so far yeast and bacteria) alters profoundly the inorganic self-assembly pathway. Cells actively organize around themselves an ordered, multilayered lipid-membrane that interfaces coherently with a lipid-templated silica mesophase. This bio/nano interface is unique in that it withstands drying (even evacuation) without cracking or the development of tensile stresses -- yet it maintains accessibility to molecules, proteins/antibodies, plasmids, etc - introduced into the 3D silica host. Additionally cell viability is preserved for weeks to months in the absence of buffer, making these constructs useful as standalone cell-based sensors. The bio/nano interfaces we describe do not form `passively' -- rather they are a consequence of the cell's ability to sense and actively respond to external stimuli. During EISA, solvent evaporation concentrates the extracellular environment in osmolytes. In response to this hyperosmotic stress, the cells release water, creating a gradient in pH, which is maintained within the adjoining nanostructured host and serves to localize lipids, proteins, plasmids, lipidized nanocrystals, and a variety of other components at the cellular surface. This active organization of the bio/nano interface can be accomplished during ink-jet printing or selective wetting -- processes allowing patterning of cellular arrays - and even spatially-defined genetic modification.

FeNi nanotubes: perspective tool for targeted delivery

NASA Astrophysics Data System (ADS)

Kaniukov, Egor; Shumskaya, Alena; Yakimchuk, Dzmitry; Kozlovskiy, Artem; Korolkov, Ilya; Ibragimova, Milana; Zdorovets, Maxim; Kadyrzhanov, Kairat; Rusakov, Vyacheslav; Fadeev, Maxim; Lobko, Eugenia; Saunina, Kristina; Nikolaevich, Larisa

2018-05-01

Targeted delivery of drugs and proteins by magnetic field is a promising method to treat cancer that reduces undesired systemic toxicity of drugs. In this method, the therapeutic agent is attached through links to functional groups with magnetic nanostructure and injected into the blood to be transported to the problem area. To provide a local effect of drug treatment, nanostructures are concentrated and fixed in the selected area by the external magnetic field (magnet). After the exposure, carriers are removed from the circulatory system by magnetic field. In this study, Fe20Ni80 nanotubes are considered as carriers for targeted delivery of drugs and proteins. A simple synthesis method is proposed to form these structures by electrodeposition in PET template pores, and structural and magnetic properties are studied in detail. Nanotubes have polycrystalline walls providing mechanical strength of carriers and magnetic anisotropy that allow controlling the nanostructure movement under the exposure of by magnetic field. Moreover, potential advantages of magnetic nanotubes are discussed in comparison with other carrier types. Most sufficient of them is predictable behavior in magnetic field due to the absence of magnetic core, low specific density that allows floating in biological media, and large specific surface area providing the attachment of a larger number of payloads for the targeted delivery. A method of coating nanotube surfaces with PMMA is proposed to exclude possible negative impact of the carrier material and to form functional bonds for the payload connection. Cytotoxicity studies of coated and uncoated nanotubes are carried out to understand their influence on the biological media.

DNA-assisted oligomerization of pore-forming toxin monomers into precisely-controlled protein channels

PubMed Central

Knechtel, Johann

2017-01-01

Abstract We have developed a novel approach for creating membrane-spanning protein-based pores. The construction principle is based on using well-defined, circular DNA nanostructures to arrange a precise number of pore-forming protein toxin monomers. We can thereby obtain, for the first time, protein pores with specifically set diameters. We demonstrate this principle by constructing artificial alpha-hemolysin (αHL) pores. The DNA/αHL hybrid nanopores composed of twelve, twenty or twenty-six monomers show stable insertions into lipid bilayers during electrical recordings, along with steady, pore size-dependent current levels. Our approach successfully advances the applicability of nanopores, in particular towards label-free studies of single molecules in large nanoscaled biological structures. PMID:29088457

Wide-Field Fluorescence Microscopy of Real-Time Bioconjugation Sensing

PubMed Central

Szalkowski, Marcin; Sulowska, Karolina; Grzelak, Justyna; Niedziółka-Jönsson, Joanna; Roźniecka, Ewa

2018-01-01

We apply wide-field fluorescence microscopy to measure real-time attachment of photosynthetic proteins to plasmonically active silver nanowires. The observation of this effect is enabled, on the one hand, by sensitive detection of fluorescence and, on the other hand, by plasmonic enhancement of protein fluorescence. We examined two sample configurations with substrates being a bare glass coverslip and a coverslip functionalized with a monolayer of streptavidin. The different preparation of the substrate changes the observed behavior as far as attachment of the protein is concerned as well as its subsequent photobleaching. For the latter substrate the conjugation process is measurably slower. The described method can be universally applied in studying protein-nanostructure interactions for real-time fluorescence-based sensing. PMID:29351211

Wide-Field Fluorescence Microscopy of Real-Time Bioconjugation Sensing.

PubMed

Szalkowski, Marcin; Sulowska, Karolina; Grzelak, Justyna; Niedziółka-Jönsson, Joanna; Roźniecka, Ewa; Kowalska, Dorota; Maćkowski, Sebastian

2018-01-19

We apply wide-field fluorescence microscopy to measure real-time attachment of photosynthetic proteins to plasmonically active silver nanowires. The observation of this effect is enabled, on the one hand, by sensitive detection of fluorescence and, on the other hand, by plasmonic enhancement of protein fluorescence. We examined two sample configurations with substrates being a bare glass coverslip and a coverslip functionalized with a monolayer of streptavidin. The different preparation of the substrate changes the observed behavior as far as attachment of the protein is concerned as well as its subsequent photobleaching. For the latter substrate the conjugation process is measurably slower. The described method can be universally applied in studying protein-nanostructure interactions for real-time fluorescence-based sensing.

Workshop on Measurement Needs for Local-Structure Determination in Inorganic Materials

PubMed Central

Levin, Igor; Vanderah, Terrell

2008-01-01

The functional responses (e.g., dielectric, magnetic, catalytic, etc.) of many industrially-relevant materials are controlled by their local structure—a term that refers to the atomic arrangements on a scale ranging from atomic (sub-nanometer) to several nanometers. Thus, accurate knowledge of local structure is central to understanding the properties of nanostructured materials, thereby placing the problem of determining atomic positions on the nanoscale—the so-called “nanostructure problem”—at the center of modern materials development. Today, multiple experimental techniques exist for probing local atomic arrangements; nonetheless, finding accurate comprehensive, and robust structural solutions for the nanostructured materials still remains a formidable challenge because any one of these methods yields only a partial view of the local structure. The primary goal of this 2-day NIST-sponsored workshop was to bring together experts in the key experimental and theoretical areas relevant to local-structure determination to devise a strategy for the collaborative effort required to develop a comprehensive measurement solution on the local scale. The participants unanimously agreed that solving the nanostructure problem—an ultimate frontier in materials characterization—necessitates a coordinated interdisciplinary effort that transcends the existing capabilities of any single institution, including national laboratories, centers, and user facilities. The discussions converged on an institute dedicated to local structure determination as the most viable organizational platform for successfully addressing the nanostructure problem. The proposed “institute” would provide an intellectual infrastructure for local structure determination by (1) developing and maintaining relevant computer software integrated in an open-source global optimization framework (Fig. 2), (2) connecting industrial and academic users with experts in measurement techniques, (3) developing and maintaining pertinent databases, and (4) providing necessary education and training. PMID:27096131

Materials taking a lesson from nature.

PubMed

Tian, Liangfei; Croisier, Emmanuel; Frauenrath, Holger

2013-01-01

Structural biomaterials with their often extraordinary properties and versatile functions are typically constructed from very limited sets of building blocks and types of supramolecular interactions. In this review we discuss how, inspired by nature's design principles for protein-based materials, oligopeptide-modified polymers can be used as a versatile toolbox to program nanostructure and hierarchical structure formation in synthetic materials.

Natural biopolymers : novel templates for the synthesis of nanostructures.

Treesearch

Sonal Padalkar; J.R. Capadona; S.J. Rowan; C. Weder; Yu-Ho Won; Lia A. Stanciu; Robert J. Moon

2010-01-01

Biological systems such as proteins, viruses, and DNA have been most often reported to be used as templates for the synthesis of functional nanomaterials, but the properties of widely available biopolymers, such as cellulose, have been much less exploited for this purpose. Here, we report for the first time that cellulose nanocrystals (CNC) have the capacity to assist...

75 FR 42377 - Application(s) for Duty-Free Entry of Scientific Instruments

Federal Register 2010, 2011, 2012, 2013, 2014

2010-07-21

... States. Comments must comply with 15 CFR 301.5(a)(3) and (4) of the regulations and be postmarked on or... Microscope. Manufacturer: FEI Company, Czech Republic. Intended Use: The instrument will be used to provide 3... the cells, proteins of the tissues and metallic nanostructures will be analyzed with the instrument...

Orthogonal chemical functionalization of patterned gold on silica surfaces

PubMed Central

Léonard, Didier; Le Mogne, Thierry; Zuttion, Francesca; Chevalier, Céline; Phaner-Goutorbe, Magali; Souteyrand, Éliane

2015-01-01

Summary Single-step orthogonal chemical functionalization procedures have been developed with patterned gold on silica surfaces. Different combinations of a silane and a thiol were simultaneously deposited on a gold/silica heterogeneous substrate. The orthogonality of the functionalization (i.e., selective grafting of the thiol on the gold areas and the silane on the silica) was demonstrated by X-ray photoelectron spectroscopy (XPS) as well as time-of-flight secondary ion mass spectrometry (ToF–SIMS) mapping. The orthogonal functionalization was used to immobilize proteins onto gold nanostructures on a silica substrate, as demonstrated by atomic force microscopy (AFM). These results are especially promising in the development of future biosensors where the selective anchoring of target molecules onto nanostructured transducers (e.g., nanoplasmonic biosensors) is a major challenge. PMID:26734519

Bacteriorhodopsin–ZnO hybrid as a potential sensing element for low-temperature detection of ethanol vapour

PubMed Central

Kumar, Saurav; Bagchi, Sudeshna; Prasad, Senthil; Sharma, Anupma; Kumar, Ritesh; Kaur, Rishemjit; Singh, Jagvir

2016-01-01

Summary Zinc oxide (ZnO) and bacteriorhodopsin (bR) hybrid nanostructures were fabricated by immobilizing bR on ZnO thin films and ZnO nanorods. The morphological and spectroscopic analysis of the hybrid structures confirmed the ZnO thin film/nanorod growth and functional properties of bR. The photoactivity results of the bR protein further corroborated the sustainability of its charge transport property and biological activity. When exposed to ethanol vapour (reducing gas) at low temperature (70 °C), the fabricated sensing elements showed a significant increase in resistivity, as opposed to the conventional n-type behaviour of bare ZnO nanostructures. This work opens up avenues towards the fabrication of low temperature, photoactivated, nanomaterial–biomolecule hybrid gas sensors. PMID:27335741

Helical plant viral nanoparticles-bioinspired synthesis of nanomaterials and nanostructures.

PubMed

Narayanan, Kannan Badri; Han, Sung Soo

2017-05-19

Viral nanotechnology is revolutionizing the biomimetic and bioinspired synthesis of novel nanomaterials. Bottom-up nanofabrication by self-assembly of individual molecular components of elongated viral nanoparticles (VNPs) and virus-like particles (VLPs) has resulted in the production of superior materials and structures in the nano(bio)technological fields. Viral capsids are attractive materials, because of their symmetry, monodispersity, and polyvalency. Helical VNPs/VLPs are unique prefabricated nanoscaffolds with large surface area to volume ratios and high aspect ratios, and enable the construction of exquisite supramolecular nanostructures. This review discusses the genetic and chemical modifications of outer, inner, and interface surfaces of a viral protein cage that will almost certainly lead to the development of superior next-generation targeted drug delivery and imaging systems, biosensors, energy storage and optoelectronic devices, therapeutics, and catalysts.

Graphene-polymer hybrid nanostructure-based bioenergy storage device for real-time control of biological motor activity.

PubMed

Byun, Kyung-Eun; Choi, Dong Shin; Kim, Eunji; Seo, David H; Yang, Heejun; Seo, Sunae; Hong, Seunghun

2011-11-22

We report a graphene-polymer hybrid nanostructure-based bioenergy storage device to turn on and off biomotor activity in real-time. In this strategy, graphene was functionalized with amine groups and utilized as a transparent electrode supporting the motility of biomotors. Conducting polymer patterns doped with adenosine triphosphate (ATP) were fabricated on the graphene and utilized for the fast release of ATP by electrical stimuli through the graphene. The controlled release of biomotor fuel, ATP, allowed us to control the actin filament transportation propelled by the biomotor in real-time. This strategy should enable the integrated nanodevices for the real-time control of biological motors, which can be a significant stepping stone toward hybrid nanomechanical systems based on motor proteins. © 2011 American Chemical Society

Manufacture and characterisation of EmDerm-novel hierarchically structured bio-active scaffolds for tissue regeneration.

PubMed

Lim, Xuxin; Potter, Matthew; Cui, Zhanfeng; Dye, Julian F

2018-06-05

There are significant challenges for using emulsion templating as a method of manufacturing macro-porous protein scaffolds. Issues include protein denaturation by adsorption at hydrophobic interfaces, emulsion instability, oil droplet and surfactant removal after protein gelation, and compatible cross-linking methods. We investigated an oil-in-water macro-emulsion stabilised with a surfactant blend, as a template for manufacturing protein-based nano-structured bio-intelligent scaffolds (EmDerm) with tuneable micro-scale porosity for tissue regeneration. Prototype EmDerm scaffolds were made using either collagen, through thermal gelation, fibrin, through enzymatic coagulation or collagen-fibrin composite. Pore size was controlled via surfactant-to-oil phase ratio. Scaffolds were crosslink-stabilised with EDC/NHS for varying durations. Scaffold micro-architecture and porosity were characterised with SEM, and mechanical properties by tensiometry. Hydrolytic and proteolytic degradation profiles were quantified by mass decrease over time. Human dermal fibroblasts, endothelial cells and bone marrow derived mesenchymal stem cells were used to investigate cytotoxicity and cell proliferation within each scaffold. EmDerm scaffolds showed nano-scale based hierarchical structures, with mean pore diameters ranging from 40-100 microns. The Young's modulus range was 1.1-2.9 MPa, and ultimate tensile strength was 4-16 MPa. Degradation rate was related to cross-linking duration. Each EmDerm scaffold supported excellent cell ingress and proliferation compared to the reference materials Integra™ and Matriderm™. Emulsion templating is a novel rapid method of fabricating nano-structured fibrous protein scaffolds with micro-scale pore dimensions. These scaffolds hold promising clinical potential for regeneration of the dermis and other soft tissues, e.g., for burns or chronic wound therapies.

Teaching the Growth, Ripening, and Agglomeration of Nanostructures in Computer Experiments

ERIC Educational Resources Information Center

Meyburg, Jan Philipp; Diesing, Detlef

2017-01-01

This article describes the implementation and application of a metal deposition and surface diffusion Monte Carlo simulation in a physical chemistry lab course. Here the self-diffusion of Ag atoms on a Ag(111) surface is modeled and compared to published experimental results. Both the thin-film homoepitaxial growth during adatom deposition onto a…

Application of Traditional and Nanostructure Materials for Medical Electron Beams Collimation: Numerical Simulation

NASA Astrophysics Data System (ADS)

Miloichikova, I. A.; Stuchebrov, S. G.; Zhaksybayeva, G. K.; Wagner, A. R.

2015-11-01

Nowadays, the commercial application of the electron accelerators grows in the industry, in the research investigations, in the medical diagnosis and treatment. In this regard, the electron beam profile modification in accordance with specific purposes is an actual task. In this paper the model of the TPU microtron extracted electron beam developed in the program “Computer Laboratory (PCLab)” is described. The internal beam divergence influence for the electron beam profile and depth dose distribution in the air is considered. The possibility of using the nanostructure materials for the electron beam formation was analyzed. The simulation data of the electron beam shape collimated by different materials (lead, corund- zirconia nanoceramic, gypsum) are shown. The collimator material influence for the electron beam profile and shape are analyzed.

Engineered Nanostructures of Haptens Lead to Unexpected Formation of Membrane Nanotubes Connecting Rat Basophilic Leukemia Cells

DOE PAGES

Li, Jie-Ren; Ross, Shailise S.; Liu, Yang; ...

2015-06-09

We report here on a recent finding that co-stimulation of the high-affinity immunoglobulin E (IgE) receptor (FcεRI) and the chemokine receptor 1 (CCR1) triggered formation of membrane nanotubes among bone-marrow-derived mast cells. The co-stimulation was attained using corresponding ligands: IgE binding antigen and macrophage inflammatory protein 1α (MIP1 α), respectively. However, this approach failed to trigger formation of nanotubes among rat basophilic leukemia (RBL) cells due to the lack of CCR1 on the cell surface (Int. Immunol. 2010, 22 (2), 113–128). RBL cells are frequently used as a model for mast cells and are best known for antibody-mediated activation viamore » FcεRI. This work reports the successful formation of membrane nanotubes among RBLs using only one stimulus, a hapten of 2,4-dinitrophenyl (DNP) molecules, which are presented as nanostructures with our designed spatial arrangements. This observation underlines the significance of the local presentation of ligands in the context of impacting the cellular signaling cascades. In the case of RBL, certain DNP nanostructures suppress antigen-induced degranulation and facilitate the rearrangement of the cytoskeleton to form nanotubes. We conclude that these results demonstrate an important scientific concept; engineered nanostructures enable cellular signaling cascades, where current technologies encounter great difficulties. More importantly, nanotechnology offers a new platform to selectively activate and/or inhibit desired cellular signaling cascades.« less

Dual Functional Core-Shell Fluorescent Ag2S@Carbon Nanostructure for Selective Assay of E. coli O157:H7 and Bactericidal Treatment.

PubMed

Wang, Ning; Wei, Xing; Zheng, An-Qi; Yang, Ting; Chen, Ming-Li; Wang, Jian-Hua

2017-03-24

A dual functional fluorescent core-shell Ag 2 S@Carbon nanostructure is prepared by a hydrothermally assisted multi-amino synthesis approach with folic acid (FA), polyethylenimine (PEI), and mannoses (Mans) as carbon and nitrogen sources (FA-PEI-Mans-Ag 2 S nanocomposite shortly as Ag 2 S@C). The nanostructure exhibits strong fluorescent emission at λ ex /λ em = 340/450 nm with a quantum yield of 12.57 ± 0.52%. Ag 2 S@C is bound to E. coli O157:H7 via strong interaction with the Mans moiety in Ag 2 S@C with FimH proteins on the fimbriae tip in E. coli O157:H7. Fluorescence emission from Ag 2 S@C/E. coli conjugate is closely related to the content of E. coli O157:H7. Thus, a novel procedure for fluorescence assay of E. coli O157:H7 is developed, offering a detection limit of 330 cfu mL -1 . Meanwhile, the Ag 2 S@C nanostructure exhibits excellent antibacterial performance against E. coli O157:H7. A 99.9% sterilization rate can be readily achieved for E. coli O157:H7 at a concentration of 10 6 -10 7 cfu mL -1 with 3.3 or 10 μg mL -1 of Ag 2 S@C with an interaction time of 5 or 0.5 min, respectively.

An Improved Ultrasensitive Enzyme-Linked Immunosorbent Assay Using Hydrangea-Like Antibody-Enzyme-Inorganic Three-in-One Nanocomposites.

PubMed

Wei, Tianxiang; Du, Dan; Zhu, Mei-Jun; Lin, Yuehe; Dai, Zhihui

2016-03-01

Protein-inorganic nanoflowers, composed of protein and copper(II) phosphate (Cu3(PO4)2), have recently grabbed people's attention. Because the synthetic method requires no organic solvent and because of the distinct hierarchical nanostructure, protein-inorganic nanoflowers display enhanced catalytic activity and stability and would be a promising tool in biocatalytical processes and biological and biomedical fields. In this work, we first coimmobilized the enzyme, antibody, and Cu3(PO4)2 into a three-in-one hybrid protein-inorganic nanoflower to enable it to possess dual functions: (1) the antibody portion retains the ability to specifically capture the corresponding antigen; (2) the nanoflower has enhanced enzymatic activity and stability to produce an amplified signal. The prepared antibody-enzyme-inorganic nanoflower was first applied in an enzyme-linked immunosorbent assay to serve as a novel enzyme-labeled antibody for Escherichia coli O157:H7 (E. coli O157:H7) determination. The detection limit is 60 CFU L(-1), which is far superior to commercial ELISA systems. The three-in-one antibody (anti-E. coli O157:H7 antibody)-enzyme (horseradish peroxidase)-inorganic (Cu3(PO4)2) nanoflower has some advantages over commercial enzyme-antibody conjugates. First, it is much easier to prepare and does not need any complex covalent modification. Second, it has fairly high capture capability and catalytic activity because it is presented as aggregates of abundant antibodies and enzymes. Third, it has enhanced enzymatic stability compared to the free form of enzyme due to the unique hierarchical nanostructure.

Nanostructure and molecular mechanics of spider dragline silk protein assemblies

PubMed Central

Keten, Sinan; Buehler, Markus J.

2010-01-01

Spider silk is a self-assembling biopolymer that outperforms most known materials in terms of its mechanical performance, despite its underlying weak chemical bonding based on H-bonds. While experimental studies have shown that the molecular structure of silk proteins has a direct influence on the stiffness, toughness and failure strength of silk, no molecular-level analysis of the nanostructure and associated mechanical properties of silk assemblies have been reported. Here, we report atomic-level structures of MaSp1 and MaSp2 proteins from the Nephila clavipes spider dragline silk sequence, obtained using replica exchange molecular dynamics, and subject these structures to mechanical loading for a detailed nanomechanical analysis. The structural analysis reveals that poly-alanine regions in silk predominantly form distinct and orderly beta-sheet crystal domains, while disorderly regions are formed by glycine-rich repeats that consist of 31-helix type structures and beta-turns. Our structural predictions are validated against experimental data based on dihedral angle pair calculations presented in Ramachandran plots, alpha-carbon atomic distances, as well as secondary structure content. Mechanical shearing simulations on selected structures illustrate that the nanoscale behaviour of silk protein assemblies is controlled by the distinctly different secondary structure content and hydrogen bonding in the crystalline and semi-amorphous regions. Both structural and mechanical characterization results show excellent agreement with available experimental evidence. Our findings set the stage for extensive atomistic investigations of silk, which may contribute towards an improved understanding of the source of the strength and toughness of this biological superfibre. PMID:20519206

Nanostructure and molecular mechanics of spider dragline silk protein assemblies.

PubMed

Keten, Sinan; Buehler, Markus J

2010-12-06

Spider silk is a self-assembling biopolymer that outperforms most known materials in terms of its mechanical performance, despite its underlying weak chemical bonding based on H-bonds. While experimental studies have shown that the molecular structure of silk proteins has a direct influence on the stiffness, toughness and failure strength of silk, no molecular-level analysis of the nanostructure and associated mechanical properties of silk assemblies have been reported. Here, we report atomic-level structures of MaSp1 and MaSp2 proteins from the Nephila clavipes spider dragline silk sequence, obtained using replica exchange molecular dynamics, and subject these structures to mechanical loading for a detailed nanomechanical analysis. The structural analysis reveals that poly-alanine regions in silk predominantly form distinct and orderly beta-sheet crystal domains, while disorderly regions are formed by glycine-rich repeats that consist of 3₁-helix type structures and beta-turns. Our structural predictions are validated against experimental data based on dihedral angle pair calculations presented in Ramachandran plots, alpha-carbon atomic distances, as well as secondary structure content. Mechanical shearing simulations on selected structures illustrate that the nanoscale behaviour of silk protein assemblies is controlled by the distinctly different secondary structure content and hydrogen bonding in the crystalline and semi-amorphous regions. Both structural and mechanical characterization results show excellent agreement with available experimental evidence. Our findings set the stage for extensive atomistic investigations of silk, which may contribute towards an improved understanding of the source of the strength and toughness of this biological superfibre.

Multiscale mechanisms of nutritionally induced property variation in spider silks.

PubMed

Blamires, Sean J; Nobbs, Madeleine; Martens, Penny J; Tso, I-Min; Chuang, Wei-Tsung; Chang, Chung-Kai; Sheu, Hwo-Shuenn

2018-01-01

Variability in spider major ampullate (MA) silk properties at different scales has proven difficult to determine and remains an obstacle to the development of synthetic fibers mimicking MA silk performance. A multitude of techniques may be used to measure multiscale aspects of silk properties. Here we fed five species of Araneoid spider solutions that either contained protein or were protein deprived and performed silk tensile tests, small and wide-angle X-ray scattering (SAXS/WAXS), amino acid composition analyses, and silk gene expression analyses, to resolve persistent questions about how nutrient deprivation induces variations in MA silk mechanical properties across scales. Our analyses found that the properties of each spider's silk varied differently in response to variations in their protein intake. We found changes in the crystalline and non-crystalline nanostructures to play specific roles in inducing the property variations we found. Across treatment MaSp expression patterns differed in each of the five species. We found that in most species MaSp expression and amino acid composition variations did not conform with our predictions based on a traditional MaSp expression model. In general, changes to the silk's alanine and proline compositions influenced the alignment of the proteins within the silk's amorphous region, which influenced silk extensibility and toughness. Variations in structural alignment in the crystalline and non-crystalline regions influenced ultimate strength independent of genetic expression. Our study provides the deepest insights thus far into the mechanisms of how MA silk properties vary from gene expression to nanostructure formations to fiber mechanics. Such knowledge is imperative for promoting the production of synthetic silk fibers.

Si/SiGe heterointerfaces in one-, two-, and three-dimensional nanostructures: their impact on SiGe light emission

NASA Astrophysics Data System (ADS)

Lockwood, David; Wu, Xiaohua; Baribeau, Jean-Marc; Mala, Selina; Wang, Xialou; Tsybeskov, Leonid

2016-03-01

Fast optical interconnects together with an associated light emitter that are both compatible with conventional Si-based complementary metal-oxide- semiconductor (CMOS) integrated circuit technology is an unavoidable requirement for the next-generation microprocessors and computers. Self-assembled Si/Si1-xGex nanostructures, which can emit light at wavelengths within the important optical communication wavelength range of 1.3 - 1.55 μm, are already compatible with standard CMOS practices. However, the expected long carrier radiative lifetimes observed to date in Si and Si/Si1-xGex nanostructures have prevented the attainment of efficient light-emitting devices including the desired lasers. Thus, the engineering of Si/Si1-xGex heterostructures having a controlled composition and sharp interfaces is crucial for producing the requisite fast and efficient photoluminescence (PL) at energies in the range 0.8-0.9 eV. In this paper we assess how the nature of the interfaces between SiGe nanostructures and Si in heterostructures strongly affects carrier mobility and recombination for physical confinement in three dimensions (corresponding to the case of quantum dots), two dimensions (corresponding to quantum wires), and one dimension (corresponding to quantum wells). The interface sharpness is influenced by many factors such as growth conditions, strain, and thermal processing, which in practice can make it difficult to attain the ideal structures required. This is certainly the case for nanostructure confinement in one dimension. However, we demonstrate that axial Si/Ge nanowire (NW) heterojunctions (HJs) with a Si/Ge NW diameter in the range 50 - 120 nm produce a clear PL signal associated with band-to-band electron-hole recombination at the NW HJ that is attributed to a specific interfacial SiGe alloy composition. For three-dimensional confinement, the experiments outlined here show that two quite different Si1-xGex nanostructures incorporated into a Si0.6Ge0.4 wavy superlattice structure display PL of high intensity while exhibiting a characteristic decay time that is up to 1000 times shorter than that found in conventional Si/SiGe nanostructures. The non-exponential PL decay found experimentally in Si/SiGe nanostructures can be interpreted as resulting from variations in the separation distance between electrons and holes at the Si/SiGe heterointerface. The results demonstrate that a sharp Si/SiGe heterointerface acts to reduce the carrier radiative recombination lifetime and increase the PL quantum

Fluorescence Intensity- and Lifetime-Based Glucose Sensing Using Glucose/Galactose-Binding Protein

PubMed Central

Pickup, John C.; Khan, Faaizah; Zhi, Zheng-Liang; Coulter, Jonathan; Birch, David J. S.

2013-01-01

We review progress in our laboratories toward developing in vivo glucose sensors for diabetes that are based on fluorescence labeling of glucose/galactose-binding protein. Measurement strategies have included both monitoring glucose-induced changes in fluorescence resonance energy transfer and labeling with the environmentally sensitive fluorophore, badan. Measuring fluorescence lifetime rather than intensity has particular potential advantages for in vivo sensing. A prototype fiber-optic-based glucose sensor using this technology is being tested.Fluorescence technique is one of the major solutions for achieving the continuous and noninvasive glucose sensor for diabetes. In this article, a highly sensitive nanostructured sensor is developed to detect extremely small amounts of aqueous glucose by applying fluorescence energy transfer (FRET). A one-pot method is applied to produce the dextran-fluorescein isothiocyanate (FITC)-conjugating mesoporous silica nanoparticles (MSNs), which afterward interact with the tetramethylrhodamine isothiocyanate (TRITC)-labeled concanavalin A (Con A) to form the FRET nanoparticles (FITC-dextran-Con A-TRITC@MSNs). The nanostructured glucose sensor is then formed via the self-assembly of the FRET nanoparticles on a transparent, flexible, and biocompatible substrate, e.g., poly(dimethylsiloxane). Our results indicate the diameter of the MSNs is 60 ± 5 nm. The difference in the images before and after adding 20 μl of glucose (0.10 mmol/liter) on the FRET sensor can be detected in less than 2 min by the laser confocal laser scanning microscope. The correlation between the ratio of fluorescence intensity, I(donor)/I(acceptor), of the FRET sensor and the concentration of aqueous glucose in the range of 0.04–4 mmol/liter has been investigated; a linear relationship is found. Furthermore, the durability of the nanostructured FRET sensor is evaluated for 5 days. In addition, the recorded images can be converted to digital images by obtaining the pixels from the resulting matrix using Matlab image processing functions. We have also studied the in vitro cytotoxicity of the device. The nanostructured FRET sensor may provide an alternative method to help patients manage the disease continuously. PMID:23439161

Modeling self-organization of novel organic materials

NASA Astrophysics Data System (ADS)

Sayar, Mehmet

In this thesis, the structural organization of oligomeric multi-block molecules is analyzed by computational analysis of coarse-grained models. These molecules form nanostructures with different dimensionalities, and the nanostructured nature of these materials leads to novel structural properties at different length scales. Previously, a number of oligomeric triblock rodcoil molecules have been shown to self-organize into mushroom shaped noncentrosymmetric nanostructures. Interestingly, thin films of these molecules contain polar domains and a finite macroscopic polarization. However, the fully polarized state is not the equilibrium state. In the first chapter, by solving a model with dipolar and Ising-like short range interactions, we show that polar domains are stable in films composed of aggregates as opposed to isolated molecules. Unlike classical molecular systems, these nanoaggregates have large intralayer spacings (a ≈ 6 nm), leading to a reduction in the repulsive dipolar interactions that oppose polar order within layers. This enables the formation of a striped pattern with polar domains of alternating directions. The energies of the possible structures at zero temperature are computed exactly and results of Monte Carlo simulations are provided at non-zero temperatures. In the second chapter, the macroscopic polarization of such nanostructured films is analyzed in the presence of a short range surface interaction. The surface interaction leads to a periodic domain structure where the balance between the up and down domains is broken, and therefore films of finite thickness have a net macroscopic polarization. The polarization per unit volume is a function of film thickness and strength of the surface interaction. Finally, in chapter three, self-organization of organic molecules into a network of one dimensional objects is analyzed. Multi-block organic dendron rodcoil molecules were found to self-organize into supramolecular nanoribbons (threads) and form gels at very low concentrations. Here, the formation and structural properties of these networks are studied with Monte Carlo simulations. The model gelators can form intra and inter-thread bonds, and the threads have a finite stiffness. The results suggest that the high persistence length is a result of the interplay of thread stiffness and inter-thread interactions. Furthermore, this high persistence length enables the formation of networks at low concentrations.

Fluorescence Microscopy of Nanochannel-Confined DNA.

PubMed

Westerlund, Fredrik; Persson, Fredrik; Fritzsche, Joachim; Beech, Jason P; Tegenfeldt, Jonas O

2018-01-01

Stretching of DNA in nanoscale confinement allows for several important studies. The genetic contents of the DNA can be visualized on the single DNA molecule level and both the polymer physics of confined DNA and also DNA/protein and other DNA/DNA-binding molecule interactions can be explored. This chapter describes the basic steps to fabricate the nanostructures, perform the experiments and analyze the data.

Self-Assembling Protein Nanostructures - Towards Active Functionality

DTIC Science & Technology

2011-04-22

the (alpha-beta)8 barrel. A model thermophilic enzyme , natively a tetramer, was engineered as a monomer, a dimer (submitted to Biochimica et...problem. Objective one successfully built high surface area nanoscaffolds from amyloid fibrils, and demonstrated that enzyme activity could be attached...quaternary structure, amyloid fibril, organophosphorous hydrolase, enzyme Juliet Gerrard University of Canterbury 20 Kirkwood Ave Ilam 8041 - REPORT

Pro-Apoptotic Breast Cancer Nanotherapeutics

DTIC Science & Technology

2013-07-01

Examples of nonspherical cell-penetrating particles existing in nature include the fila- mentous viruses such as the tobaccomosaic virus and the potato... virus X.4 Inspired by these examples from biology, Discher et al. have shown that cylindrical micelles have longer circulation times relative to...intended to create a protective corona around the assembled nanostructure, which would limit nonspecific adsorption of proteins and reduce proteolysis

Plasmonic hybrid nanostructure with controlled interaction strength

NASA Astrophysics Data System (ADS)

Grzelak, Justyna K.; Krajnik, Bartosz; Thoreson, Mark D.; Nyga, Piotr; Shalaev, Vladimir M.; Mackowski, Sebastian

2014-03-01

In this report we discuss the influence of plasmon excitations in a silver island film on the fluorescence of photosynthetic complex, peridinin-chlorophyll-protein (PCP). Control of the separation between these two components is obtained by fabricating a wedge layer of silica across the substrate, with a thickness from 0 to 46 nm. Continuous variation of the silica thickness allows for gradual change of interaction strength between plasmon excitations in the metallic film and the excited states of pigments comprising photosynthetic complexes. While the largest separation between the silver film and photosynthetic complexes results in fluorescence featuring a mono-exponential decay and relatively narrow distribution of intensities, the PCP complexes placed on thinner silica spacers show biexponential fluorescence decay and significantly broader distribution of total fluorescence intensities. This broad distribution is a signature of stronger sensitivity of fluorescence enhancement upon actual parameters of a hybrid nanostructure. By gradual change of the silica spacer thickness we are able to reproduce classical distance dependence of fluorescence intensity in plasmonic hybrid nanostructures on ensemble level. Experiments carried out for different excitation wavelengths indicate that the interaction is stronger for excitations resonant with plasmon absorption in the metallic layer.

DNA scaffold nanostructures for efficient and directional propagation of light harvesting cascades

NASA Astrophysics Data System (ADS)

Brown, Carl W.; Samanta, Anirban; Buckhout-White, Susan; Díaz, Sebastián. A.; Walper, Scott A.; Goldman, Ellen R.; Medintz, Igor L.

2017-08-01

The development of light harvesting systems for directed, efficient control of energy transfer at the biomolecular level has generated considerable interest in the past decade. Molecular fluorophores provide a straightforward mechanism for determining nanoscale distance changes through Förster resonance energy transfer (FRET), and many systems seek to build off of this simple yet powerful principle to provide additional functionality. The use of DNA-based integrated biomolecular devices offer many unique advantages towards this end. DNA itself is an excellent engineering material - it is innately biocompatible, quickly and cheaply synthesized, and complex structures can be readily designed in silico. It also provides an excellent scaffold for the precise patterning of various biomolecules. Here, we discuss the systems that have been recently developed which add to this toolbox, including nanostructural dye patterning, photonic wires, and the incorporation of alternative energy propagation modalities, such as semiconductor quantum dots (QD) and the bioluminescent protein luciferase. In particular, we explore the incorporation of luciferase into various nanostructural conformations, providing the capability to efficiently control energy flow directionality. We discuss the nature of this system, including unexpected spectral complexities, in the context of the field.

Plasmon-induced absorption of blind chlorophylls in photosynthetic proteins assembled on silver nanowires.

PubMed

Szalkowski, Marcin; Janna Olmos, Julian David; Buczyńska, Dorota; Maćkowski, Sebastian; Kowalska, Dorota; Kargul, Joanna

2017-07-27

We demonstrate that controlled assembly of eukaryotic photosystem I with its associated light harvesting antenna complex (PSI-LHCI) on plasmonically active silver nanowires (AgNWs) substantially improves the optical functionality of such a novel biohybrid nanostructure. By comparing fluorescence intensities measured for PSI-LHCI complex randomly oriented on AgNWs and the results obtained for the PSI-LHCI/cytochrome c 553 (cyt c 553 ) bioconjugate with AgNWs we conclude that the specific binding of photosynthetic complexes with defined uniform orientation yields selective excitation of a pool of chlorophyll (Chl) molecules that are otherwise almost non-absorbing. This is remarkable, as this study shows for the first time that plasmonic excitations in metallic nanostructures can not only be used to enhance native absorption of photosynthetic pigments, but also - by employing cyt c 553 as the conjugation cofactor - to activate the specific Chl pools as the absorbing sites only when the uniform and well-defined orientation of PSI-LHCI with respect to plasmonic nanostructures is achieved. As absorption of PSI alone is comparatively low, our approach lends itself as an innovative approach to outperform the reported-to-date biohybrid devices with respect to solar energy conversion.

An Antibody-Immobilized Silica Inverse Opal Nanostructure for Label-Free Optical Biosensors

PubMed Central

Lee, Wang Sik; Kim, Shin-Hyun

2018-01-01

Three-dimensional SiO2-based inverse opal (SiO2-IO) nanostructures were prepared for use as biosensors. SiO2-IO was fabricated by vertical deposition and calcination processes. Antibodies were immobilized on the surface of SiO2-IO using 3-aminopropyl trimethoxysilane (APTMS), a succinimidyl-[(N-maleimidopropionamido)-tetraethyleneglycol] ester (NHS-PEG4-maleimide) cross-linker, and protein G. The highly accessible surface and porous structure of SiO2-IO were beneficial for capturing influenza viruses on the antibody-immobilized surfaces. Moreover, as the binding leads to the redshift of the reflectance peak, the influenza virus could be detected by simply monitoring the change in the reflectance spectrum without labeling. SiO2-IO showed high sensitivity in the range of 103–105 plaque forming unit (PFU) and high specificity to the influenza A (H1N1) virus. Due to its structural and optical properties, SiO2-IO is a promising material for the detection of the influenza virus. Our study provides a generalized sensing platform for biohazards as various sensing strategies can be employed through the surface functionalization of three-dimensional nanostructures. PMID:29361683

Fabrication of Semiordered Nanopatterned Diamond-like Carbon and Titania Films for Blood Contacting Applications.

PubMed

Nandakumar, Deepika; Bendavid, Avi; Martin, Philip J; Harris, Kenneth D; Ruys, Andrew J; Lord, Megan S

2016-03-23

Biomaterials with the ability to interface with, but not activate, blood components are essential for a multitude of medical devices. Diamond-like carbon (DLC) and titania (TiO2) have shown promise for these applications; however, both support platelet adhesion and activation. This study explored the fabrication of nanostructured DLC and TiO2 thin film coatings using a block copolymer deposition technique that produced semiordered nanopatterns with low surface roughness (5-8 nm Rrms). These surfaces supported fibrinogen and plasma protein adsorption that predominantly adsorbed between the nanofeatures and reduced the overall surface roughness. The conformation of the adsorbed fibrinogen was altered on the nanopatterned surfaces as compared with the planar surfaces to reveal higher levels of the platelet binding region. Planar DLC and TiO2 coatings supported less platelet adhesion than nanopatterned DLC and TiO2. However, platelets on the nanopatterned DLC coatings were less spread indicating a lower level of platelet activation on the nanostructured DLC coatings compared with the planar DLC coatings. These data indicated that nanostructured DLC coatings may find application in blood contacting medical devices in the future.

Nanostructured magnesium has fewer detrimental effects on osteoblast function.

PubMed

Weng, Lucy; Webster, Thomas J

2013-01-01

Efforts have been made recently to implement nanoscale surface features on magnesium, a biodegradable metal, to increase bone formation. Compared with normal magnesium, nanostructured magnesium has unique characteristics, including increased grain boundary properties, surface to volume ratio, surface roughness, and surface energy, which may influence the initial adsorption of proteins known to promote the function of osteoblasts (bone-forming cells). Previous studies have shown that one way to increase nanosurface roughness on magnesium is to soak the metal in NaOH. However, it has not been determined if degradation of magnesium is altered by creating nanoscale features on its surface to influence osteoblast density. The aim of the present in vitro study was to determine the influence of degradation of nanostructured magnesium, created by soaking in NaOH, on osteoblast density. Our results showed a less detrimental effect of magnesium degradation on osteoblast density when magnesium was treated with NaOH to create nanoscale surface features. The detrimental degradation products of magnesium are of significant concern when considering use of magnesium as an orthopedic implant material, and this study identified a surface treatment, ie, soaking in NaOH to create nanoscale features for magnesium that can improve its use in numerous orthopedic applications.

Self-assembled DNA Structures for Nanoconstruction

NASA Astrophysics Data System (ADS)

Yan, Hao; Yin, Peng; Park, Sung Ha; Li, Hanying; Feng, Liping; Guan, Xiaoju; Liu, Dage; Reif, John H.; LaBean, Thomas H.

2004-09-01

In recent years, a number of research groups have begun developing nanofabrication methods based on DNA self-assembly. Here we review our recent experimental progress to utilize novel DNA nanostructures for self-assembly as well as for templates in the fabrication of functional nano-patterned materials. We have prototyped a new DNA nanostructure known as a cross structure. This nanostructure has a 4-fold symmetry which promotes its self-assembly into tetragonal 2D lattices. We have utilized the tetragonal 2D lattices as templates for highly conductive metallic nanowires and periodic 2D protein nano-arrays. We have constructed and characterized a DNA nanotube, a new self-assembling superstructure composed of DNA tiles. We have also demonstrated an aperiodic DNA lattice composed of DNA tiles assembled around a long scaffold strand; the system translates information encoded in the scaffold strand into a specific and reprogrammable barcode pattern. We have achieved metallic nanoparticle linear arrays templated on self-assembled 1D DNA arrays. We have designed and demonstrated a 2-state DNA lattice, which displays expand/contract motion switched by DNA nanoactuators. We have also achieved an autonomous DNA motor executing unidirectional motion along a linear DNA track.

Nanostructured magnesium has fewer detrimental effects on osteoblast function

PubMed Central

Weng, Lucy; Webster, Thomas J

2013-01-01

Efforts have been made recently to implement nanoscale surface features on magnesium, a biodegradable metal, to increase bone formation. Compared with normal magnesium, nanostructured magnesium has unique characteristics, including increased grain boundary properties, surface to volume ratio, surface roughness, and surface energy, which may influence the initial adsorption of proteins known to promote the function of osteoblasts (bone-forming cells). Previous studies have shown that one way to increase nanosurface roughness on magnesium is to soak the metal in NaOH. However, it has not been determined if degradation of magnesium is altered by creating nanoscale features on its surface to influence osteoblast density. The aim of the present in vitro study was to determine the influence of degradation of nanostructured magnesium, created by soaking in NaOH, on osteoblast density. Our results showed a less detrimental effect of magnesium degradation on osteoblast density when magnesium was treated with NaOH to create nanoscale surface features. The detrimental degradation products of magnesium are of significant concern when considering use of magnesium as an orthopedic implant material, and this study identified a surface treatment, ie, soaking in NaOH to create nanoscale features for magnesium that can improve its use in numerous orthopedic applications. PMID:23674891

Enzyme cascades activated on topologically programmed DNA scaffolds

NASA Astrophysics Data System (ADS)

Wilner, Ofer I.; Weizmann, Yossi; Gill, Ron; Lioubashevski, Oleg; Freeman, Ronit; Willner, Itamar

2009-04-01

The ability of DNA to self-assemble into one-, two- and three-dimensional nanostructures, combined with the precision that is now possible when positioning nanoparticles or proteins on DNA scaffolds, provide a promising approach for the self-organization of composite nanostructures. Predicting and controlling the functions that emerge in self-organized biomolecular nanostructures is a major challenge in systems biology, and although a number of innovative examples have been reported, the emergent properties of systems in which enzymes are coupled together have not been fully explored. Here, we report the self-assembly of a DNA scaffold made of DNA strips that include `hinges' to which biomolecules can be tethered. We attach either two enzymes or a cofactor-enzyme pair to the scaffold, and show that enzyme cascades or cofactor-mediated biocatalysis can proceed effectively; similar processes are not observed in diffusion-controlled homogeneous mixtures of the same components. Furthermore, because the relative position of the two enzymes or the cofactor-enzyme pair is determined by the topology of the DNA scaffold, it is possible to control the reactivity of the system through the design of the individual DNA strips. This method could lead to the self-organization of complex multi-enzyme cascades.

Electrophoretic deposition of biomaterials

PubMed Central

Boccaccini, A. R.; Keim, S.; Ma, R.; Li, Y.; Zhitomirsky, I.

2010-01-01

Electrophoretic deposition (EPD) is attracting increasing attention as an effective technique for the processing of biomaterials, specifically bioactive coatings and biomedical nanostructures. The well-known advantages of EPD for the production of a wide range of microstructures and nanostructures as well as unique and complex material combinations are being exploited, starting from well-dispersed suspensions of biomaterials in particulate form (microsized and nanoscale particles, nanotubes, nanoplatelets). EPD of biological entities such as enzymes, bacteria and cells is also being investigated. The review presents a comprehensive summary and discussion of relevant recent work on EPD describing the specific application of the technique in the processing of several biomaterials, focusing on (i) conventional bioactive (inorganic) coatings, e.g. hydroxyapatite or bioactive glass coatings on orthopaedic implants, and (ii) biomedical nanostructures, including biopolymer–ceramic nanocomposites, carbon nanotube coatings, tissue engineering scaffolds, deposition of proteins and other biological entities for sensors and advanced functional coatings. It is the intention to inform the reader on how EPD has become an important tool in advanced biomaterials processing, as a convenient alternative to conventional methods, and to present the potential of the technique to manipulate and control the deposition of a range of nanomaterials of interest in the biomedical and biotechnology fields. PMID:20504802

Integrative self-assembly of functional hybrid nanoconstructs by inorganic wrapping of single biomolecules, biomolecule arrays and organic supramolecular assemblies

NASA Astrophysics Data System (ADS)

Patil, Avinash J.; Li, Mei; Mann, Stephen

2013-07-01

Synthesis of functional hybrid nanoscale objects has been a core focus of the rapidly progressing field of nanomaterials science. In particular, there has been significant interest in the integration of evolutionally optimized biological systems such as proteins, DNA, virus particles and cells with functional inorganic building blocks to construct mesoscopic architectures and nanostructured materials. However, in many cases the fragile nature of the biomolecules seriously constrains their potential applications. As a consequence, there is an on-going quest for the development of novel strategies to modulate the thermal and chemical stabilities, and performance of biomolecules under adverse conditions. This feature article highlights new methods of ``inorganic molecular wrapping'' of single or multiple protein molecules, individual double-stranded DNA helices, lipid bilayer vesicles and self-assembled organic dye superstructures using inorganic building blocks to produce bio-inorganic nanoconstructs with core-shell type structures. We show that spatial isolation of the functional biological nanostructures as ``armour-plated'' enzyme molecules or polynucleotide strands not only maintains their intact structure and biochemical properties, but also enables the fabrication of novel hybrid nanomaterials for potential applications in diverse areas of bionanotechnology.

Integrative self-assembly of functional hybrid nanoconstructs by inorganic wrapping of single biomolecules, biomolecule arrays and organic supramolecular assemblies.

PubMed

Patil, Avinash J; Li, Mei; Mann, Stephen

2013-08-21

Synthesis of functional hybrid nanoscale objects has been a core focus of the rapidly progressing field of nanomaterials science. In particular, there has been significant interest in the integration of evolutionally optimized biological systems such as proteins, DNA, virus particles and cells with functional inorganic building blocks to construct mesoscopic architectures and nanostructured materials. However, in many cases the fragile nature of the biomolecules seriously constrains their potential applications. As a consequence, there is an on-going quest for the development of novel strategies to modulate the thermal and chemical stabilities, and performance of biomolecules under adverse conditions. This feature article highlights new methods of "inorganic molecular wrapping" of single or multiple protein molecules, individual double-stranded DNA helices, lipid bilayer vesicles and self-assembled organic dye superstructures using inorganic building blocks to produce bio-inorganic nanoconstructs with core-shell type structures. We show that spatial isolation of the functional biological nanostructures as "armour-plated" enzyme molecules or polynucleotide strands not only maintains their intact structure and biochemical properties, but also enables the fabrication of novel hybrid nanomaterials for potential applications in diverse areas of bionanotechnology.

Cytotoxicity of protein corona-graphene oxide nanoribbons on human epithelial cells

NASA Astrophysics Data System (ADS)

Mbeh, Doris A.; Akhavan, Omid; Javanbakht, Taraneh; Mahmoudi, Morteza; Yahia, L.'Hocine

2014-11-01

Graphene oxide nanoribbons (GONRs) were synthesized using an oxidative unzipping of multi-walled carbon nanotubes. The interactions of the GONRs with various concentrations of fetal bovine serum or human plasma serum indicated that the GONRs were functionalized substantially by the albumin originated from the two different protein sources. Then, concentration-dependent cytotoxicity of the protein-functionalized GONRs on human epithelial cells was studied. Although the GONRs with concentrations ≤50 μg/mL did not exhibit significant cytotoxicity on the cells (with the cell viability >85%), the concentration of 100 μg/mL exhibited significant cytotoxicity including prevention of cell proliferation and induction of cell apoptosis. These results can provide more in-depth understanding about cytotoxic effects of graphene nanostructures which can be functionalized by the proteins of media.

Free-Standing Metal Oxide Nanoparticle Superlattices Constructed with Engineered Protein Containers Show in Crystallo Catalytic Activity.

PubMed

Lach, Marcel; Künzle, Matthias; Beck, Tobias

2017-12-11

The construction of defined nanostructured catalysts is challenging. In previous work, we established a strategy to assemble binary nanoparticle superlattices with oppositely charged protein containers as building blocks. Here, we show that these free-standing nanoparticle superlattices are catalytically active. The metal oxide nanoparticles inside the protein scaffold are accessible for a range of substrates and show oxidase-like and peroxidase-like activity. The stable superlattices can be reused for several reaction cycles. In contrast to bulk nanoparticle-based catalysts, which are prone to aggregation and difficult to characterize, nanoparticle superlattices based on engineered protein containers provide an innovative synthetic route to structurally defined heterogeneous catalysts with control over nanoparticle size and composition. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Nucleation of Iron Oxide Nanoparticles Mediated by Mms6 Protein in Situ

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kashyap, Sanjay; Woehl, Taylor J; Liu, Xunpei

2014-09-23

Biomineralization proteins are widely used as templating agents in biomimetic synthesis of a variety of organic–inorganic nanostructures. However, the role of the protein in controlling the nucleation and growth of biomimetic particles is not well understood, because the mechanism of the bioinspired reaction is often deduced from ex situ analysis of the resultant nanoscale mineral phase. Here we report the direct visualization of biomimetic iron oxide nanoparticle nucleation mediated by an acidic bacterial recombinant protein, Mms6, during an in situ reaction induced by the controlled addition of sodium hydroxide to solution-phase Mms6 protein micelles incubated with ferric chloride. Using inmore » situ liquid cell scanning transmission electron microscopy we observe the liquid iron prenucleation phase and nascent amorphous nanoparticles forming preferentially on the surface of protein micelles. Our results provide insight into the early steps of protein-mediated biomimetic nucleation of iron oxide and point to the importance of an extended protein surface during nanoparticle formation.« less

3D filling simulation of micro- and nanostructures in comparison to iso- and variothermal injection moulding trials

NASA Astrophysics Data System (ADS)

Rytka, C.; Lungershausen, J.; Kristiansen, P. M.; Neyer, A.

2016-06-01

Flow simulations can cut down both costs and time for the development of injection moulded polymer parts with functional surfaces used in life science and optical applications. We simulated the polymer melt flow into 3D micro- and nanostructures with Moldflow and Comsol and compared the results to real iso- and variothermal injection moulding trials below, at and above the transition temperature of the polymer. By adjusting the heat transfer coefficient and the transition temperature in the simulation it was possible to achieve good correlation with experimental findings at different processing conditions (mould temperature, injection velocity) for two polymers, namely polymethylmethacrylate and amorphous polyamide. The macroscopic model can be scaled down in volume and number of elements to save computational time for microstructure simulation and to enable first and foremost the nanostructure simulation, as long as local boundary conditions such as flow front speed are transferred correctly. The heat transfer boundary condition used in Moldflow was further evaluated in Comsol. Results showed that the heat transfer coefficient needs to be increased compared to macroscopic moulding in order to represent interfacial polymer/mould effects correctly. The transition temperature is most important in the packing phase for variothermal injection moulding.

Electron Energy-Loss Spectroscopy (EELS)Calculation in Finite-Difference Time-Domain (FDTD) Package: EELS-FDTD

NASA Astrophysics Data System (ADS)

Large, Nicolas; Cao, Yang; Manjavacas, Alejandro; Nordlander, Peter

2015-03-01

Electron energy-loss spectroscopy (EELS) is a unique tool that is extensively used to investigate the plasmonic response of metallic nanostructures since the early works in the '50s. To be able to interpret and theoretically investigate EELS results, a myriad of different numerical techniques have been developed for EELS simulations (BEM, DDA, FEM, GDTD, Green dyadic functions). Although these techniques are able to predict and reproduce experimental results, they possess significant drawbacks and are often limited to highly symmetrical geometries, non-penetrating trajectories, small nanostructures, and free standing nanostructures. We present here a novel approach for EELS calculations using the Finite-difference time-domain (FDTD) method: EELS-FDTD. We benchmark our approach by direct comparison with results from the well-established boundary element method (BEM) and published experimental results. In particular, we compute EELS spectra for spherical nanoparticles, nanoparticle dimers, nanodisks supported by various substrates, and gold bowtie antennas on a silicon nitride substrate. Our EELS-FDTD implementation can be easily extended to more complex geometries and configurations and can be directly implemented within other numerical methods. Work funded by the Welch Foundation (C-1222, L-C-004), and the NSF (CNS-0821727, OCI-0959097).

Computational chemistry calculations of stability for bismuth nanotubes, fullerene-like structures and hydrogen-containing nanostructures.

PubMed

Kharissova, Oxana V; Osorio, Mario; Vázquez, Mario Sánchez; Kharisov, Boris I

2012-08-01

Using molecular mechanics (MM+), semi-empirical (PM6) and density functional theory (DFT) (B3LYP) methods we characterized bismuth nanotubes. In addition, we predicted the bismuth clusters {Bi(20)(C(5V)), Bi(24)(C(6v)), Bi(28)(C(1)), B(32)(D(3H)), Bi(60)(C(I))} and calculated their conductor properties.

Integrated Multiscale Modeling of Molecular Computing Devices. Final Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tim Schulze

2012-11-01

The general theme of this research has been to expand the capabilities of a simulation technique, Kinetic Monte Carlo (KMC) and apply it to study self-assembled nano-structures on epitaxial thin films. KMC simulates thin film growth and evolution by replacing the detailed dynamics of the system's evolution, which might otherwise be studied using molecular dynamics, with an appropriate stochastic process.

Quantum Computers

DTIC Science & Technology

2010-03-04

and their sensitivity to charge and flux fluctuations. The first type of superconducting qubit , the charge qubit , omits the inductance . There is no...nanostructured NbN superconducting nanowire detectors have achieved high efficiency and photon number resolution16,17. One approach to a high-efficiency single...resemble classical high- speed integrated circuits and can be readily fabricated using existing technologies. The basic physics behind superconducting qubits

Kentucky DOE EPSCoR Program

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grulke, Eric; Stencel, John

2011-09-13

The KY DOE EPSCoR Program supports two research clusters. The Materials Cluster uses unique equipment and computational methods that involve research expertise at the University of Kentucky and University of Louisville. This team determines the physical, chemical and mechanical properties of nanostructured materials and examines the dominant mechanisms involved in the formation of new self-assembled nanostructures. State-of-the-art parallel computational methods and algorithms are used to overcome current limitations of processing that otherwise are restricted to small system sizes and short times. The team also focuses on developing and applying advanced microtechnology fabrication techniques and the application of microelectrornechanical systems (MEMS)more » for creating new materials, novel microdevices, and integrated microsensors. The second research cluster concentrates on High Energy and Nuclear Physics. lt connects research and educational activities at the University of Kentucky, Eastern Kentucky University and national DOE research laboratories. Its vision is to establish world-class research status dedicated to experimental and theoretical investigations in strong interaction physics. The research provides a forum, facilities, and support for scientists to interact and collaborate in subatomic physics research. The program enables increased student involvement in fundamental physics research through the establishment of graduate fellowships and collaborative work.« less

Nanostructure-mediated drug delivery.

PubMed

Hughes, Gareth A

2005-03-01

Nanotechnology is expected to have an impact on all industries including semiconductors, manufacturing, and biotechnology. Tools that provide the capability to characterize and manipulate materials at the nanoscale level further elucidate nanoscale phenomena and equip researchers and developers with the ability to fabricate novel materials and structures. One of the most promising societal impacts of nanotechnology is in the area of nanomedicine. Personalized health care, rational drug design, and targeted drug delivery are some of the benefits of a nanomedicine-based approach to therapy. This review will focus on the development of nanoscale drug delivery mechanisms. Nanostructured drug carriers allow for the delivery of not only small-molecule drugs but also the delivery of nucleic acids and proteins. Delivery of these molecules to specific areas within the body can be achieved, which will reduce systemic side effects and allow for more efficient use of the drug.

M13 bacteriophage displaying DOPA on surfaces: fabrication of various nanostructured inorganic materials without time-consuming screening processes.

PubMed

Park, Joseph P; Do, Minjae; Jin, Hyo-Eon; Lee, Seung-Wuk; Lee, Haeshin

2014-01-01

M13 bacteriophage (phage) was engineered for the use as a versatile template for preparing various nanostructured materials via genetic engineering coupled to enzymatic chemical conversions. First, we engineered the M13 phage to display TyrGluGluGlu (YEEE) on the pVIII coat protein and then enzymatically converted the Tyr residue to 3,4-dihydroxyl-l-phenylalanine (DOPA). The DOPA-displayed M13 phage could perform two functions: assembly and nucleation. The engineered phage assembles various noble metals, metal oxides, and semiconducting nanoparticles into one-dimensional arrays. Furthermore, the DOPA-displayed phage triggered the nucleation and growth of gold, silver, platinum, bimetallic cobalt-platinum, and bimetallic iron-platinum nanowires. This versatile phage template enables rapid preparation of phage-based prototype devices by eliminating the screening process, thus reducing effort and time.

Nanofabrication and ion milling introduced effects on magnetic properties in magnetic recording

NASA Astrophysics Data System (ADS)

Sun, Zhenzhong

Perpendicular magnetic nanostructures have played an important role in magnetic recording technologies. In this dissertation, a systematic study on the CoPt magnetic nanostructures from fabrication, characterization to computer simulation has been performed. During the fabrication process, ion irradiation/bombardment in ion mill can cause physical damage to the magnetic nanostructures and degrade their magnetic properties. To study the effect of ion damage on CoPt nanostructures, different degrees of ion damage are introduced into CoPt nanopillars by varying the accelerating voltage in ion mill. The results demonstrate that the ion damage can reduce the coercivity by softening circumferential edge, and therefore changes the switching mechanism from coherent rotation to nucleation followed by rapid domain wall propagation. The SFD of CoPt nanostructures is independent of ion damage and is mainly determined by the intrinsic anisotropy distribution of the film rather than the nanostructure size distribution. Anisotropy-graded bit-patterned media are fabricated and studied based on high anisotropy L10-FePt material system. L10-FePt thin films with linearly and quadratically distributed anisotropy are achieved by varying substrate temperature during film growth. After patterning, the anisotropy-graded L10-FePt nanopillars display a reduced switching field and maintain a good thermal stability compared to the non-graded one. Experimental investigation and comparison further prove the concept of "anisotropy-graded" bit-patterned media and their potential application in the future magnetic recording. During magnetic write head fabrication, ion-beam damage may degrade the performance of the magnetic write pole. A surface sensitive MOKE is used to characterize the magnetic properties of these etched FeCo films. MOKE measurement shows a hard axis hysteresis loop with a high Mr in the high power etched film due to the ion beam introduced defects. The high power etched film also shows the highest RMS by AFM measurement. The geometric peaks at the top surface may have shape anisotropy and serve as the pinning sites. These magnetic pinning sites can prevent the nucleation center forming at the top surface during the switching process and lead to a high Mr in the top surface region.

Computational modeling and simulation study of electronic and thermal properties in semiconductor nanostructures

NASA Astrophysics Data System (ADS)

Paul, Abhijeet

2011-07-01

The technological progress in dimensional scaling has not only kept Silicon CMOS industry on Moore's law for the past five decades but has also benefited many other areas such as thermoelectricity, photo-voltaics, and energy storage. Extending CMOS beyond Si (More Moore, MM) and adding functional diversity to CMOS (More Than Moore, MTM) requires a thorough understanding of the basic electron and heat flow in semiconductors. Along with experiments computer modeling and simulation are playing an increasingly vital role in exploring the numerous possibilities in materials, devices and systems. With these aspects in mind the present work applies computational physics modeling and simulations to explore the, (i) electronic, (ii) thermal, and (iii) thermoelectric properties in nano-scale semiconductors. The electronic structure of zinc-blende and lead-chalcogenide nano-materials is calculated using an atomistic Tight-Binding model. The phonon dispersion in zinc-blende materials is obtained using the Modified Valence Force Field model. Electronic and thermal transport at the nano-scale is explored using Green's function method and Landauer's method. Thermoelectric properties of semiconductor nanostructures are calculated using Landauer's method. Using computer modeling and simulations the variation of the three physical properties (i-iii) are explored with varying size, transport orientation, shape, porosity, strain and alloying of nanostructures. The key findings are, (a) III-Vs and Ge with optimized strain and orientation can improve transistors' and thermoelectric performance, (b) porous Si nanowires provide a lucrative idea for enhancing the thermoelectric efficiency at room temperature, and (c) Si/Ge superlattice nanowires can be used for nano-scale tuning of lattice thermal conductivity by period control. The present work led to the development of two new interface trap density extraction methods in ultra-scaled FinFETs and correlation of the phonon shifts in Si nanowires to their shape, size and orientation benchmarked against experimental Raman spectroscopy data, thereby enabling nano-scale metrology. Contribution of two research and six educational tools on nanoHUB.org forms an integral part of the work for global dissemination of semiconductor knowledge. Atomic level manipulation holds the key to engineer material properties at the nano-scale. The findings of this work will hopefully open and guide new ways of engineering the electronic and thermal properties for better performance.

Self-assembly in the ferritin nano-cage protein superfamily.

PubMed

Zhang, Yu; Orner, Brendan P

2011-01-01

Protein self-assembly, through specific, high affinity, and geometrically constraining protein-protein interactions, can control and lead to complex cellular nano-structures. Establishing an understanding of the underlying principles that govern protein self-assembly is not only essential to appreciate the fundamental biological functions of these structures, but could also provide a basis for their enhancement for nano-material applications. The ferritins are a superfamily of well studied proteins that self-assemble into hollow cage-like structures which are ubiquitously found in both prokaryotes and eukaryotes. Structural studies have revealed that many members of the ferritin family can self-assemble into nano-cages of two types. Maxi-ferritins form hollow spheres with octahedral symmetry composed of twenty-four monomers. Mini-ferritins, on the other hand, are tetrahedrally symmetric, hollow assemblies composed of twelve monomers. This review will focus on the structure of members of the ferritin superfamily, the mechanism of ferritin self-assembly and the structure-function relations of these proteins.

Super-Resolution Microscopy Unveils Dynamic Heterogeneities in Nanoparticle Protein Corona.

PubMed

Feiner-Gracia, Natalia; Beck, Michaela; Pujals, Sílvia; Tosi, Sébastien; Mandal, Tamoghna; Buske, Christian; Linden, Mika; Albertazzi, Lorenzo

2017-11-01

The adsorption of serum proteins, leading to the formation of a biomolecular corona, is a key determinant of the biological identity of nanoparticles in vivo. Therefore, gaining knowledge on the formation, composition, and temporal evolution of the corona is of utmost importance for the development of nanoparticle-based therapies. Here, it is shown that the use of super-resolution optical microscopy enables the imaging of the protein corona on mesoporous silica nanoparticles with single protein sensitivity. Particle-by-particle quantification reveals a significant heterogeneity in protein absorption under native conditions. Moreover, the diversity of the corona evolves over time depending on the surface chemistry and degradability of the particles. This paper investigates the consequences of protein adsorption for specific cell targeting by antibody-functionalized nanoparticles providing a detailed understanding of corona-activity relations. The methodology is widely applicable to a variety of nanostructures and complements the existing ensemble approaches for protein corona study. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Apatite nano-crystalline surface modification of poly(lactide-co-glycolide) sintered microsphere scaffolds for bone tissue engineering: implications for protein adsorption.

PubMed

Jabbarzadeh, Ehsan; Nair, Lakshmi S; Khan, Yusuf M; Deng, Meng; Laurencin, Cato T

2007-01-01

A number of bone tissue engineering approaches are aimed at (i) increasing the osteconductivity and osteoinductivity of matrices, and (ii) incorporating bioactive molecules within the scaffolds. In this study we examined the growth of a nano-crystalline mineral layer on poly(lactide-co-glycolide) (PLAGA) sintered microsphere scaffolds for tissue engineering. In addition, the influence of the mineral precipitate layer on protein adsorption on the scaffolds was studied. Scaffolds were mineralized by incubation in simulated body fluid (SBF). Scanning electron microscopy (SEM) analysis revealed that mineralized scaffolds possess a rough surface with a plate-like nanostructure covering the surface of microspheres. The results of protein adsorption and release studies showed that while the protein release pattern was similar for PLAGA and mineralized PLAGA scaffolds, precipitation of the mineral layer on PLAGA led to enhanced protein adsorption and slower protein release. Mineralization of tissue-engineered surfaces provides a method for both imparting bioactivity and controlling levels of protein adsorption and release.

Mesoscale crystallization of calcium phosphate nanostructures in protein (casein) micelles.

PubMed

Thachepan, Surachai; Li, Mei; Mann, Stephen

2010-11-01

Aqueous micelles of the multi-protein calcium phosphate complex, casein, were treated at 60°C and pH 7 over several months. Although partial dissociation of the micelles into 12 nm sized amorphous calcium phosphate (ACP)/protein nanoparticles occurred within a period of 14 days, crystallization of the ACP nanoclusters into bundles of hydroxyapatite (HAP) nanofilaments was not observed until after 12 weeks. The HAP nanofilaments were formed specifically within the partially disrupted protein micelles suggesting a micelle-mediated pathway of mesoscale crystallization. Similar experiments using ACP-containing synthetic micelles prepared from ß-casein protein alone indicated that co-aligned bundles of HAP nanofilaments were produced within the protein micelle interior after 24 hours at temperatures as low as 35°C. The presence of Mg²(+) ions in the casein micelles, as well as a possible synergistic effect associated with the multi-protein nature of the native aggregates, could account for the marked inhibition in mesoscale crystallization observed in the casein micelles compared with the single-component b-casein constructs.

Intracellular targeting of CD44+ cells with self-assembling, protein only nanoparticles.

PubMed

Pesarrodona, Mireia; Ferrer-Miralles, Neus; Unzueta, Ugutz; Gener, Petra; Tatkiewicz, Witold; Abasolo, Ibane; Ratera, Imma; Veciana, Jaume; Schwartz, Simó; Villaverde, Antonio; Vazquez, Esther

2014-10-01

CD44 is a multifunctional cell surface protein involved in proliferation and differentiation, angiogenesis and signaling. The expression of CD44 is up-regulated in several types of human tumors and particularly in cancer stem cells, representing an appealing target for drug delivery in the treatment of cancer. We have explored here several protein ligands of CD44 for the construction of self-assembling modular proteins designed to bind and internalize target cells. Among five tested ligands, two of them (A5G27 and FNI/II/V) drive the formation of protein-only, ring-shaped nanoparticles of about 14 nm that efficiently bind and penetrate CD44(+) cells by an endosomal route. The potential of these newly designed nanoparticles is evaluated regarding the need of biocompatible nanostructured materials for drug delivery in CD44-linked conditions. Copyright © 2014 Elsevier B.V. All rights reserved.

Local Crystalline Structure in an Amorphous Protein Dense Phase

PubMed Central

Greene, Daniel G.; Modla, Shannon; Wagner, Norman J.; Sandler, Stanley I.; Lenhoff, Abraham M.

2015-01-01

Proteins exhibit a variety of dense phases ranging from gels, aggregates, and precipitates to crystalline phases and dense liquids. Although the structure of the crystalline phase is known in atomistic detail, little attention has been paid to noncrystalline protein dense phases, and in many cases the structures of these phases are assumed to be fully amorphous. In this work, we used small-angle neutron scattering, electron microscopy, and electron tomography to measure the structure of ovalbumin precipitate particles salted out with ammonium sulfate. We found that the ovalbumin phase-separates into core-shell particles with a core radius of ∼2 μm and shell thickness of ∼0.5 μm. Within this shell region, nanostructures comprised of crystallites of ovalbumin self-assemble into a well-defined bicontinuous network with branches ∼12 nm thick. These results demonstrate that the protein gel is comprised in part of nanocrystalline protein. PMID:26488663

Preparation, characterization, nanostructures and bio functional analysis of sonicated protein co-precipitates from brewers' spent grain and soybean flour.

PubMed

Alu'datt, Muhammad H; Gammoh, Sana; Rababah, Taha; Almomani, Mohammed; Alhamad, Mohammad N; Ereifej, Khalil; Almajwal, Ali; Tahat, Asma; Hussein, Neveen M; Nasser, Sura Abou

2018-02-01

This investigation was performed to assess the effects of sonication on the structure of protein, extractability of phenolics, and biological properties of isolated proteins and protein co-precipitates prepared from brewers' spent grain and soybean flour. Scanning electron micrographs revealed that the sonicated protein isolates and co-precipitates had different microstructures with fewer aggregates and smaller particles down to the nanometer scale compared to non-sonicated samples. However, the levels of free and bound phenolics extracted from non-sonicated protein isolates and protein co-precipitates increased compared to sonicated samples. The bound phenolics extracted after acid hydrolysis of sonicated protein co-precipitates showed improved ACE inhibitory activity and diminished antioxidant potency compared to non-sonicated samples. However, the free phenolics extracted from sonicated protein co-precipitates showed decreased ACE inhibitory activity and increased antioxidant activities compared to non-sonicated samples. The free and bound phenolics extracted from sonicated protein co-precipitates showed increased alpha-amylase inhibitory activity compared to non-sonicated samples. Copyright © 2017 Elsevier Ltd. All rights reserved.

Nanopillar arrays of amorphous carbon nitride

NASA Astrophysics Data System (ADS)

Sai Krishna, Katla; Pavan Kumar, B. V. V. S.; Eswaramoorthy, Muthusamy

2011-07-01

Nanopillar arrays of amorphous carbon nitride have been prepared using anodic aluminum oxide (AAO) membrane as a template. The amine groups present on the surface of these nanopillars were exploited for functionalization with oleic acid in order to stabilize the nanostructure at the aqueous-organic interface and also for the immobilization of metal nanoparticles and protein. These immobilised nanoparticles were found to have good catalytic activity.

Tailoring the Optical Properties of Silicon with Ion Beam Created Nanostructures for Advanced Photonics Applications

NASA Astrophysics Data System (ADS)

Akhter, Perveen

In today's fast life, energy consumption has increased more than ever and with that the demand for a renewable and cleaner energy source as a substitute for the fossil fuels has also increased. Solar radiations are the ultimate source of energy but harvesting this energy in a cost effective way is a challenging task. Si is the dominating material for microelectronics and photovoltaics. But owing to its indirect band gap, Si is an inefficient light absorber, thus requiring a thickness of solar cells beyond tens of microns which increases the cost of solar energy. Therefore, techniques to increase light absorption in thin film Si solar cells are of great importance and have been the focus of research for a few decades now. Another big issue of technology in this fast-paced world is the computing rate or data transfer rate between components of a chip in ultra-fast processors. Existing electronic interconnects suffering from the signal delays and heat generation issues are unable to handle high data rates. A possible solution to this problem is in replacing the electronic interconnects with optical interconnects which have large data carrying capacity. However, optical components are limited in size by the fundamental laws of diffraction to about half a wavelength of light and cannot be combined with nanoscale electronic components. Tremendous research efforts have been directed in search of an advanced technology which can bridge the size gap between electronic and photonic worlds. An emerging technology of "plasmonics'' which exploits the extraordinary optical properties of metal nanostructures to tailor the light at nanoscale has been considered a potential solution to both of the above-mentioned problems. Research conducted for this dissertation has an overall goal to investigate the optical properties of silicon with metal nanostructures for photovoltaics and advanced silicon photonics applications. The first part of the research focuses on achieving enhanced light trapping in poly-Si thin films using ion implantation induced surface texturing. In addition to surface texturing produced by H and Ar ion implantations, metal nanostructures are also added to the surface to further suppress light reflection at the plasmonic resonance of metal nanostructures. Remarkable suppression has been achieved resulting in reflection from the air/Si interface to below ˜5%. In the second part, optical properties of embedded metal nanostructures in silicon matrix gettered into the ion implantation created nanocavities are studied. Embedded nanostructures can have a huge impact in future photonics applications by replacing the existing electronic and photonic components such as interconnects, waveguides, modulators and amplifiers with their plasmonic counterparts. This new method of encapsulating metal nanostructures in silicon is cost-effective and compatible with silicon fabrication technology. Spectroscopic ellipsometry is used to study the dielectric properties of silicon with embedded silver nanostructures. High absorption regions around 900 nm, corresponding to plasmonic absorption of Ag nanoparticles in Si, have been observed and compared to theoretical calculations and simulation results. The possibility of modifying the dielectric function of Si with metal nanostructures can lay the foundation for functional base structures for advanced applications in silicon photonics, photovoltaics and plasmonics.

Protein-Nanoparticle Interactions: Improving Immobilized Lytic Enzyme Activity and Surface Energy Effects

NASA Astrophysics Data System (ADS)

Downs, Emily Elizabeth

Protein-nanostructure conjugates, particularly particles, are a subject of significant interest due to changes in their fundamental behavior compared to bulk surfaces. As the size scale of nano-structured materials and proteins are on the same order of magnitude, nanomaterial properties can heavily influence how proteins adsorb and conform to the surface. Previous work has demonstrated the ability of nanoscale surfaces to modulate protein activity, conformation, and retention by modifying the particle surface curvature, morphology, and surface charge. This work has improved our understanding of the protein material interactions, but a complete understanding is still lacking. The goal of this thesis is to investigate two missing areas of understanding using two distinct systems. The first system utilizes a particle with controlled surface energy to observe the impact of surface energy on protein-particle interactions, while the second system uses a modified Listeria-specific protein to determine how protein structure and flexibility affects protein adsorption and activity on particles. Spherical, amorphous, and uniformly doped Zn-silica particles with tailored surface energies were synthesized to understand the impact of surface energy on protein adsorption behavior. Particle surface energy increased with a decrease in particle size and greater dopant concentrations. Protein adsorption and structural loss increased with both particle size and particle surface energy. Higher surface energies promoted protein-particle association and increased protein unfolding. Particle curvature and protein steric hindrance effects limited adsorption and structural loss on smaller particles. Protein surface charge heterogeneity was also found to be linked to both protein adsorption and unfolding behavior on larger particles. Greater surface charge heterogeneity led to higher adsorption concentrations and multilayer formation. These multilayers transitioned from protein-particle interactions to protein-protein interactions and were thicker with greater surface energy, which resulted in the recovery of secondary structure in the outermost layer. To help understand the impact of protein structure on nano-bio conjugate interactions, a listeria specific protein was used. This system was chosen as it has applications in the food industry in preventing bacterial contamination. The insertion of an amino acid linker between the enzymatic and binding domain of the protein improved the flexibility between domains, leading to increased adsorption, and improved activity in both cell-wall and plating assays. Additionally, linker modified protein incorporated into the silica-polymer nanocomposite showed significant activity in a real-world example of contaminated lettuce. This thesis study has isolated the impact of surface energy and protein flexibility on protein adsorption and structure. Particle surface energy affects adsorbed protein concentration and conformation. Coupled with protein surface charge, surface energy was also found to dictate multilayer thickness. The conformational flexibility of the protein was shown to help in controlling not only protein adsorption concentration but also in retaining protein activity after immobilization. Also, a controllable synthesis method for particles with adjustable surface energy, an ideal platform for studying protein-particle interactions, has been established.

Visualization of Iron-Binding Micelles in Acidic Recombinant Biomineralization Protein, MamC

DOE PAGES

Kashyap, Sanjay; Woehl, Taylor; Valverde-Tercedor, Carmen; ...

2014-01-01

Biological macromolecules are utilized in low-temperature synthetic methods to exert precise control over nanoparticle nucleation and placement. They enable low-temperature formation of a variety of functional nanostructured materials with properties often not achieved via conventional synthetic techniques. Here we report on the in situ visualization of a novel acidic bacterial recombinant protein, MamC, commonly present in the magnetosome membrane of several magnetotactic bacteria, including Magnetococcus marinus , strain MC-1. Our findings provide an insight into the self-assembly of MamC and point to formation of the extended protein surface, which is assumed to play an important role in the formation ofmore » biotemplated inorganic nanoparticles. The self-organization of MamC is compared to the behavior of another acidic recombinant iron-binding protein, Mms6.« less

Visualization of Iron-Binding Micelles in Acidic Recombinant Biomineralization Protein, MamC

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kashyap, Sanjay; Woehl, Taylor; Valverde-Tercedor, Carmen

2014-03-07

Biological macromolecules are utilized in low-temperature synthetic methods to exert precise control over nanoparticle nucleation and placement. They enable low-temperature formation of a variety of functional nanostructured materials with properties often not achieved via conventional synthetic techniques. Here we report on the in situ visualization of a novel acidic bacterial recombinant protein, MamC, commonly present in the magnetosome membrane of several magnetotactic bacteria, including Magnetococcus marinus, strain MC-1. Our findings provide an insight into the self-assembly of MamC and point to formation of the extended protein surface, which is assumed to play an important role in the formation of biotemplatedmore » inorganic nanoparticles. The self-organization of MamC is compared to the behavior of another acidic recombinant iron-binding protein, Mms6.« less

Ultrasonic tissue characterization for monitoring nanostructured TiO2-induced bone growth

NASA Astrophysics Data System (ADS)

Rus, G.; García-Martínez, J.

2007-07-01

The use of bioactive nanostructured TiO2 has recently been proposed for improving orthopaedic implant adhesion due to its improved biocompatibility with bone, since it induces: (i) osteoblast function, (ii) apatite nucleation and (iii) protein adsorption. The present work focuses on a non-ionizing radiation emitting technique for quantifying in real time the improvement in terms of mechanical properties of the surrounding bone due to the presence of the nanostructured TiO2 prepared by controlled precipitation and acid ageing. The mechanical strength is the ultimate goal of a bone implant and is directly related to the elastic moduli. Ultrasonics are high frequency mechanical waves and are therefore suited for characterizing elastic moduli. As opposed to echographic techniques, which are not correlated to elastic properties and are not able to penetrate bone, a low frequency ultrasonic transmission test is proposed, in which a P-wave is transmitted through the specimen and recorded. The problem is posed as an inverse problem, in which the unknown is a set of parameters that describe the mechanical constants of the sequence of layers. A finite element numerical model that depends on these parameters is used to predict the transformation of the waveform and compare to the measurement. The parameters that best describe the real tissue are obtained by minimizing the discrepancy between the real and numerically predicted waveforms. A sensitivity study to the uncertainties of the model is performed for establishing the feasibility of using this technique to investigate the macroscopic effect on bone growth of nanostructured TiO2 and its beneficial effect on implant adhesion.

Electrochemical synthesis of nanostructured gold film for the study of carbohydrate–lectin interactions using localized surface plasmon resonance spectroscopy

PubMed Central

Bhattarai, Jay K.; Sharma, Abeera; Fujikawa, Kohki; Demchenko, Alexei V.; Stine, Keith J.

2014-01-01

Localized surface plasmon resonance (LSPR) spectroscopy is a label-free chemical and biological molecular sensing technique whose sensitivity depends upon development of nanostructured transducers. Herein, we report an electrodeposition method for fabricating nanostructured gold films (NGFs) that can be used as transducers in LSPR spectroscopy. The NGF was prepared by electrodepositing gold from potassium dicyanoaurate solution onto a flat gold surface using two sequential controlled potential steps. Imaging by scanning electron microscopy reveals a morphology consisting of randomly configured block-like nanostructures. The bulk refractive index sensitivity of the prepared NGF is 100 ± 2 nm RIU−1 and the initial peak in the reflectance spectrum is at 518 ± 1 nm under N2(g). The figure of merit is 1.7. In addition, we have studied the interaction between carbohydrate (mannose) and lectin (Concanavalin A) on the NGF surface using LSPR spectroscopy by measuring the interaction of 8-mercaptooctyl-α-D-mannopyranoside (αMan-C8-SH) with Concanavalin A by first immobilizing αMan-C8-SH in mixed SAMs with 3,6-dioxa-8-mercaptooctanol (TEG-SH) on the NGF surface. The interaction of Con A with the mixed SAMs is confirmed using electrochemical impedance spectroscopy. Finally, the NGF surface was regenerated to its original sensitivity by removing the SAM and the bound biomolecules. The results from these experiments contribute toward the development of inexpensive LSPR based sensors that could be useful for studying glycan–protein interactions and other bioanalytical purposes. PMID:25442712

Multiscale mechanisms of nutritionally induced property variation in spider silks

PubMed Central

Nobbs, Madeleine; Martens, Penny J.; Tso, I-Min; Chuang, Wei-Tsung; Chang, Chung-Kai; Sheu, Hwo-Shuenn

2018-01-01

Variability in spider major ampullate (MA) silk properties at different scales has proven difficult to determine and remains an obstacle to the development of synthetic fibers mimicking MA silk performance. A multitude of techniques may be used to measure multiscale aspects of silk properties. Here we fed five species of Araneoid spider solutions that either contained protein or were protein deprived and performed silk tensile tests, small and wide-angle X-ray scattering (SAXS/WAXS), amino acid composition analyses, and silk gene expression analyses, to resolve persistent questions about how nutrient deprivation induces variations in MA silk mechanical properties across scales. Our analyses found that the properties of each spider’s silk varied differently in response to variations in their protein intake. We found changes in the crystalline and non-crystalline nanostructures to play specific roles in inducing the property variations we found. Across treatment MaSp expression patterns differed in each of the five species. We found that in most species MaSp expression and amino acid composition variations did not conform with our predictions based on a traditional MaSp expression model. In general, changes to the silk’s alanine and proline compositions influenced the alignment of the proteins within the silk’s amorphous region, which influenced silk extensibility and toughness. Variations in structural alignment in the crystalline and non-crystalline regions influenced ultimate strength independent of genetic expression. Our study provides the deepest insights thus far into the mechanisms of how MA silk properties vary from gene expression to nanostructure formations to fiber mechanics. Such knowledge is imperative for promoting the production of synthetic silk fibers. PMID:29390013

Thermal transport characterization of stanene/silicene heterobilayer and stanene bilayer nanostructures

NASA Astrophysics Data System (ADS)

Noshin, Maliha; Intisar Khan, Asir; Subrina, Samia

2018-05-01

Recently, stanene and silicene based nanostructures with low thermal conductivity have incited noteworthy interest due to their prospect in thermoelectrics. Aiming at the possibility of extracting lower thermal conductivity, in this study, we have proposed and modeled stanene/silicene heterobilayer nanoribbons, a new heterostructure and subsequently characterized their thermal transport by using an equilibrium molecular dynamics simulation. In addition, the thermal transport in bilayer stanene is also studied and compared. We have computed the thermal conductivity of the stanene/silicene and bilayer stanene nanostructures to characterize their thermal transport phenomena. The studied nanostructures show good thermal stability within the temperature range of 100-600 K. The room temperature thermal conductivities of pristine 10 nm × 3 nm stanene/silicene hetero-bilayer and stanene bilayer are estimated to be 3.63 ± 0.27 W m-1 K-1 and 1.31 ± 0.34 W m-1 K-1, respectively, which are smaller than that of silicene, graphene and some other 2D monolayers as well as heterobilayers such as stanene/graphene and silicene/graphene. In the temperature range of 100-600 K, the thermal conductivity of our studied bilayer nanoribbons decreases with an increase in the temperature. Furthermore, we have investigated the dependence of our estimated thermal conductivity on the size of the considered nanoribbons. The thermal conductivities of both the nanoribbons are found to increase with an increase in the width of the structure. The thermal conductivity shows a similar increasing trend with the increase in the ribbon length, as well. Our results suggest that, the low thermal conductivity of our studied bilayer structures can be further decreased by nanostructuring. The significantly low thermal conductivity of the stanene/silicene heterobilayer and stanene bilayer nanoribbons realized in our study would provide a good insight and encouragement into their appealing prospect in the thermoelectric applications.

Nanoscale insights on one- and two-dimensional material structures

NASA Astrophysics Data System (ADS)

Floresca, Herman Carlo

The race for smaller, faster and more efficient devices has led researchers to explore the possibilities of utilizing nanostructures for scaling. These one-dimensional and two-dimensional materials have properties that are attractive for this purpose but are still not well controlled. Control comes with a complete understanding of the materials' electrical, thermal, optical and structural characteristics but is difficult to obtain due to their small scale. This work is intended to help researchers overcome the difficulty in studying nanostructures by providing techniques for analysis and insights of nanostructures that have not been previously available. Two nanostructures were studied: silicon nanowires and graphene. The nanowires were prepared for cross-section transmission electron microscopy (TEM) to discover the effects that controlled oxidation has on the dimensions and shape of the nanowires. Since cross-section TEM is not able to provide information about surface structure, a method for manipulating the wires with orientation control was developed. With this ability, all three orthogonal views of the nanowire were compiled for a comprehensive study on its structure in terms of shape and surface roughness. Graphene was used for a two-dimensional analytical technique that took advantage of customized computer programs for data acquisition, measurement and display. With the information provided, distinctions between grain boundary types in polycrystalline graphene were made and supported by statistical information from the software's output. It was also applied to a growth series of graphene samples in conjunction with scanning electron microscopy (SEM) images and electron backscatter diffraction (EBSD) maps. The results help point to origins of graphene's polycrystalline nature. This dissertation concludes with a thought towards the future by highlighting a method that can help analyze nanostructures, which may become incorporated into the structures of large devices. The fold-out method is a TEM sample preparation technique utilizing a focused ion beam (FIB) for site specific thinning across a large sample area. Its process is demonstrated along with advantages over conventional methods.

Thermal transport characterization of stanene/silicene heterobilayer and stanene bilayer nanostructures.

PubMed

Noshin, Maliha; Khan, Asir Intisar; Subrina, Samia

2018-05-04

Recently, stanene and silicene based nanostructures with low thermal conductivity have incited noteworthy interest due to their prospect in thermoelectrics. Aiming at the possibility of extracting lower thermal conductivity, in this study, we have proposed and modeled stanene/silicene heterobilayer nanoribbons, a new heterostructure and subsequently characterized their thermal transport by using an equilibrium molecular dynamics simulation. In addition, the thermal transport in bilayer stanene is also studied and compared. We have computed the thermal conductivity of the stanene/silicene and bilayer stanene nanostructures to characterize their thermal transport phenomena. The studied nanostructures show good thermal stability within the temperature range of 100-600 K. The room temperature thermal conductivities of pristine 10 nm × 3 nm stanene/silicene hetero-bilayer and stanene bilayer are estimated to be 3.63 ± 0.27 W m -1 K -1 and 1.31 ± 0.34 W m -1 K -1 , respectively, which are smaller than that of silicene, graphene and some other 2D monolayers as well as heterobilayers such as stanene/graphene and silicene/graphene. In the temperature range of 100-600 K, the thermal conductivity of our studied bilayer nanoribbons decreases with an increase in the temperature. Furthermore, we have investigated the dependence of our estimated thermal conductivity on the size of the considered nanoribbons. The thermal conductivities of both the nanoribbons are found to increase with an increase in the width of the structure. The thermal conductivity shows a similar increasing trend with the increase in the ribbon length, as well. Our results suggest that, the low thermal conductivity of our studied bilayer structures can be further decreased by nanostructuring. The significantly low thermal conductivity of the stanene/silicene heterobilayer and stanene bilayer nanoribbons realized in our study would provide a good insight and encouragement into their appealing prospect in the thermoelectric applications.

Nanostructured N-doped orthorhombic Nb2O5 as an efficient stable photocatalyst for hydrogen generation under visible light.

PubMed

Kulkarni, Aniruddha K; Praveen, C S; Sethi, Yogesh A; Panmand, Rajendra P; Arbuj, Sudhir S; Naik, Sonali D; Ghule, Anil V; Kale, Bharat B

2017-11-07

The synthesis of orthorhombic nitrogen-doped niobium oxide (Nb 2 O 5-x N x ) nanostructures was performed and a photocatalytic study carried out in their use in the conversion of toxic H 2 S and water into hydrogen under UV-Visible light. Nanostructured orthorhombic Nb 2 O 5-x N x was synthesized by a simple solid-state combustion reaction (SSCR). The nanostructural features of Nb 2 O 5-x N x were examined by FESEM and HRTEM, which showed they had a porous chain-like structure, with chains interlocked with each other and with nanoparticles sized less than 10 nm. Diffuse reflectance spectra depicted their extended absorbance in the visible region with a band gap of 2.4 eV. The substitution of nitrogen in place of oxygen atoms as well as Nb-N bond formation were confirmed by X-ray photoelectron spectroscopy (XPS) and Raman spectroscopy. A computational study (DFT) of Nb 2 O 5-x N x was also performed for investigation and conformation of the crystal and electronic structure. N-Substitution clearly showed a narrowing of the band gap due to N 2p bands cascading above the O 2p band. Considering the band gap in the visible region, Nb 2 O 5-x N x exhibited enhanced photocatalytic activity toward hydrogen evolution (3010 μmol h -1 g -1 ) for water splitting and (9358 μmol h -1 g -1 ) for H 2 S splitting under visible light. The enhanced photocatalytic activity of Nb 2 O 5-x N x was attributed to its extended absorbance in the visible region due to its electronic structure being modified upon doping, which in turn generates more electron-hole pairs, which are responsible for higher H 2 generation. More significantly, the mesoporous nanostructure accelerated the supression of electron and hole recombination, which also contributed to the enhancement of its activity.

Imparting biomolecules to a metal-organic framework material by controlled DNA tetrahedron encapsulation

PubMed Central

Jia, Yongmei; Wei, Benmei; Duan, Ruixue; Zhang, Ying; Wang, Boya; Hakeem, Abdul; Liu, Nannan; Ou, Xiaowen; Xu, Shaofang; Chen, Zhifei; Lou, Xiaoding; Xia, Fan

2014-01-01

Recently, the incorporation of biomolecules in Metal-organic frameworks (MOFs) attracts many attentions because of controlling the functions, properties and stability of trapped molecules. Although there are few reports on protein/MOFs composites and their applications, none of DNA/MOFs composite is reported, as far as we know. Here, we report a new composite material which is self-assembled from 3D DNA (guest) and pre-synthesized MOFs (host) by electrostatic interactions and hydrophilic interactions in a well-dispersed fashion. Its biophysical characterization is well analyzed by fluorescence spectroscopy, quartz crystal microbalance (QCM) and transmission electron microscopy (TEM). This new composite material keeps 3D DNA nanostructure more stable than only 3D DNA nanostructure in DI water at room temperature, and stores amounts of genetic information. It will make DNA as a guest for MOFs and MOFs become a new platform for the development of DNA nanotechnology. PMID:25090047

Actively addressed single pixel full-colour plasmonic display

NASA Astrophysics Data System (ADS)

Franklin, Daniel; Frank, Russell; Wu, Shin-Tson; Chanda, Debashis

2017-05-01

Dynamic, colour-changing surfaces have many applications including displays, wearables and active camouflage. Plasmonic nanostructures can fill this role by having the advantages of ultra-small pixels, high reflectivity and post-fabrication tuning through control of the surrounding media. However, previous reports of post-fabrication tuning have yet to cover a full red-green-blue (RGB) colour basis set with a single nanostructure of singular dimensions. Here, we report a method which greatly advances this tuning and demonstrates a liquid crystal-plasmonic system that covers the full RGB colour basis set, only as a function of voltage. This is accomplished through a surface morphology-induced, polarization-dependent plasmonic resonance and a combination of bulk and surface liquid crystal effects that manifest at different voltages. We further demonstrate the system's compatibility with existing LCD technology by integrating it with a commercially available thin-film-transistor array. The imprinted surface interfaces readily with computers to display images as well as video.

Electronic Detection of Lectins Using Carbohydrate Functionalized Nanostructures: Graphene versus Carbon Nanotubes

PubMed Central

Chen, Yanan; Vedala, Harindra; Kotchey, Gregg P.; Audfray, Aymeric; Cecioni, Samy; Imberty, Anne; Vidal, Sébastien; Star, Alexander

2012-01-01

Here we investigated the interactions between lectins and carbohydrates using field-effect transistor (FET) devices comprised of chemically converted graphene (CCG) and single-walled carbon nanotubes (SWNTs). Pyrene- and porphyrin-based glycoconjugates were functionalized noncovalently on the surface of CCG-FET and SWNT-FET devices, which were then treated with 2 µM of nonspecific and specific lectins. In particular, three different lectins (PA-IL, PA-IIL and ConA) and three carbohydrate epitopes (galactose, fucose and mannose) were tested. The responses of 36 different devices were compared and rationalized using computer-aided models of carbon nanostructure/glycoconjugate interactions. Glycoconjugates surface coverage in addition to one-dimensional structures of SWNTs resulted in optimal lectin detection. Additionally, lectin titration data of SWNT- and CCG-based biosensors were used to calculate lectin dissociation constants (Kd) and compare them to the values obtained from the isothermal titration microcalorimetry (ITC) technique. PMID:22136380

Polar order in nanostructured organic materials

NASA Astrophysics Data System (ADS)

Sayar, M.; Olvera de la Cruz, M.; Stupp, S. I.

2003-02-01

Achiral multi-block liquid crystals are not expected to form polar domains. Recently, however, films of nanoaggregates formed by multi-block rodcoil molecules were identified as the first example of achiral single-component materials with macroscopic polar properties. By solving an Ising-like model with dipolar and asymmetric short-range interactions, we show here that polar domains are stable in films composed of aggregates as opposed to isolated molecules. Unlike classical molecular systems, these nanoaggregates have large intralayer spacings (a approx 8 nm), leading to a reduction in the repulsive dipolar interactions which oppose polar order within layers. In finite-thickness films of nanostructures, this effect enables the formation of polar domains. We compute exactly the energies of the possible structures consistent with the experiments as a function of film thickness at zero temperature (T). We also provide Monte Carlo simulations at non-zero T for a disordered hexagonal lattice that resembles the smectic-like packing in these nanofilms.

Simulation Studies of Mechanical Properties of Novel Silica Nano-structures

NASA Astrophysics Data System (ADS)

Muralidharan, Krishna; Torras Costa, Joan; Trickey, Samuel B.

2006-03-01

Advances in nanotechnology and the importance of silica as a technological material continue to stimulate computational study of the properties of possible novel silica nanostructures. Thus we have done classical molecular dynamics (MD) and multi-scale quantum mechanical (QM/MD) simulation studies of the mechanical properties of single-wall and multi-wall silica nano-rods of varying dimensions. Such nano-rods have been predicted by Mallik et al. to be unusually strong in tensile failure. Here we compare failure mechanisms of such nano-rods under tension, compression, and bending. The concurrent multi-scale QM/MD studies use the general PUPIL system (Torras et al.). In this case, PUPIL provides automated interoperation of the MNDO Transfer Hamiltonian QM code (Taylor et al.) and a locally written MD code. Embedding of the QM-forces domain is via the scheme of Mallik et al. Work supported by NSF ITR award DMR-0325553.

Advances on the nanostructuration of magnetic molecules on surfaces: the case of single-molecule magnets (SMM).

PubMed

Gómez-Segura, Jordi; Veciana, Jaume; Ruiz-Molina, Daniel

2007-09-28

SMMs exhibit slow magnetization relaxation rates characteristic of nanodomain particles whose origin is however on individual molecules. For this reason, they have attracted much interest due to their potential applications in high-density information storage devices and quantum computing applications, where for instance, each molecule can be used as a magnetic bit of information. However, for this to become a reality, several basic studies such as their deposition on surfaces are still highly required. Here we will revise all the experimental approximations that have been so far reported for their addressing, nanostructuration and study on surfaces, from the use of stamps as templates to their anchorage to gold surface through the use of thiol-based ligands. It is also important to emphasize that the results and methodologies described along this review are applicable not only to SMMs but to any molecular material.

Effects of tissue fixation and dehydration on tendon collagen nanostructure.

PubMed

Turunen, Mikael J; Khayyeri, Hanifeh; Guizar-Sicairos, Manuel; Isaksson, Hanna

2017-09-01

Collagen is the most prominent protein in biological tissues. Tissue fixation is often required for preservation or sectioning of the tissue. This may affect collagen nanostructure and potentially provide incorrect information when analyzed after fixation. We aimed to unravel the effect of 1) ethanol and formalin fixation and 2) 24h air-dehydration on the organization and structure of collagen fibers at the nano-scale using small and wide angle X-ray scattering. Samples were divided into 4 groups: ethanol fixed, formalin fixed, and two untreated sample groups. Samples were allowed to air-dehydrate in handmade Kapton pockets during the measurements (24h) except for one untreated group. Ethanol fixation affected the collagen organization and nanostructure substantially and during 24h of dehydration dramatic changes were evident. Formalin fixation had minor effects on the collagen organization but after 12h of air-dehydration the spatial variation increased substantially, not evident in the untreated samples. Generally, collagen shrinkage and loss of alignment was evident in all samples during 24h of dehydration but the changes were subtle in all groups except the ethanol fixed samples. This study shows that tissue fixation needs to be chosen carefully in order to preserve the features of interest in the tissue. Copyright © 2017 Elsevier Inc. All rights reserved.

DNA origami as an in vivo drug delivery vehicle for cancer therapy.

PubMed

Zhang, Qian; Jiang, Qiao; Li, Na; Dai, Luru; Liu, Qing; Song, Linlin; Wang, Jinye; Li, Yaqian; Tian, Jie; Ding, Baoquan; Du, Yang

2014-07-22

Many chemotherapeutics used for cancer treatments encounter issues during delivery to tumors in vivo and may have high levels of systemic toxicity due to their nonspecific distribution. Various materials have been explored to fabricate nanoparticles as drug carriers to improve delivery efficiency. However, most of these materials suffer from multiple drawbacks, such as limited biocompatibility and inability to engineer spatially addressable surfaces that can be utilized for multifunctional activity. Here, we demonstrate that DNA origami possessed enhanced tumor passive targeting and long-lasting properties at the tumor region. Particularly, the triangle-shaped DNA origami exhibits optimal tumor passive targeting accumulation. The delivery of the known anticancer drug doxorubicin into tumors by self-assembled DNA origami nanostructures was performed, and this approach showed prominent therapeutic efficacy in vivo. The DNA origami carriers were prepared through the self-assembly of M13mp18 phage DNA and hundreds of complementary DNA helper strands; the doxorubicin was subsequently noncovalently intercalated into these nanostructures. After conducting fluorescence imaging and safety evaluation, the doxorubicin-containing DNA origami exhibited remarkable antitumor efficacy without observable systemic toxicity in nude mice bearing orthotopic breast tumors labeled with green fluorescent protein. Our results demonstrated the potential of DNA origami nanostructures as innovative platforms for the efficient and safe drug delivery of cancer therapeutics in vivo.

Silk protein nanowires patterned using electron beam lithography.

PubMed

Pal, Ramendra K; Yadavalli, Vamsi K

2018-08-17

Nanofabrication approaches to pattern proteins at the nanoscale are useful in applications ranging from organic bioelectronics to cellular engineering. Specifically, functional materials based on natural polymers offer sustainable and environment-friendly substitutes to synthetic polymers. Silk proteins (fibroin and sericin) have emerged as an important class of biomaterials for next generation applications owing to excellent optical and mechanical properties, inherent biocompatibility, and biodegradability. However, the ability to precisely control their spatial positioning at the nanoscale via high throughput tools continues to remain a challenge. In this study electron beam lithography (EBL) is used to provide nanoscale patterning using methacrylate conjugated silk proteins that are photoreactive 'photoresists' materials. Very low energy electron beam radiation can be used to pattern silk proteins at the nanoscale and over large areas, whereby such nanostructure fabrication can be performed without specialized EBL tools. Significantly, using conducting polymers in conjunction with these silk proteins, the formation of protein nanowires down to 100 nm is shown. These wires can be easily degraded using enzymatic degradation. Thus, proteins can be precisely and scalably patterned and doped with conducting polymers and enzymes to form degradable, organic bioelectronic devices.

Optimized Materials From First Principles Simulations: Are We There Yet?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Galli, G; Gygi, F

2005-07-26

In the past thirty years, the use of scientific computing has become pervasive in all disciplines: collection and interpretation of most experimental data is carried out using computers, and physical models in computable form, with various degrees of complexity and sophistication, are utilized in all fields of science. However, full prediction of physical and chemical phenomena based on the basic laws of Nature, using computer simulations, is a revolution still in the making, and it involves some formidable theoretical and computational challenges. We illustrate the progress and successes obtained in recent years in predicting fundamental properties of materials in condensedmore » phases and at the nanoscale, using ab-initio, quantum simulations. We also discuss open issues related to the validation of the approximate, first principles theories used in large scale simulations, and the resulting complex interplay between computation and experiment. Finally, we describe some applications, with focus on nanostructures and liquids, both at ambient and under extreme conditions.« less

Fabrication and characterization of a chemically oxidized-nanostructured porous silicon based biosensor implementing orienting protein A.

PubMed

Naveas, Nelson; Hernandez-Montelongo, Jacobo; Pulido, Ruth; Torres-Costa, Vicente; Villanueva-Guerrero, Raúl; Predestinación García Ruiz, Josefa; Manso-Silván, Miguel

2014-03-01

Nanostructured porous silicon (PSi) elicits as a very attractive material for future biosensing systems due to its high surface area, biocompatibility and well-established fabrication methods. In order to engineer its performance as a biosensor transducer platform, the density of immunoglobulins properly immobilized and oriented onto the surface needs to be optimized. In this work we fabricated and characterized a novel biosensing system focusing on the improvement of the biofunctionalization cascade. The system consists on a chemically oxidized PSi platform derivatized with 3-aminopropyltriethoxysilane (APTS) that is coupled to Staphylococcus protein A (SpA). The chemical oxidation has previously demonstrated to enhance the biofunctionalization process and here "by implementing SpA" a molecularly oriented immunosensor is achieved. The biosensor system is characterized in terms of its chemical composition, wettability and optical reflectance. Finally, this system is successfully exploited to develop a biosensor for detecting asymmetric dimethylarginine (ADMA), an endogenous molecule involved in cardiovascular diseases. Therefore, this work is relevant from the point of view of design and optimization of the biomolecular immobilization cascade on PSi surfaces with the added value of contribution to the development of new assays for detecting ADMA with a view on prevention of cardiovascular diseases. Copyright © 2013 Elsevier B.V. All rights reserved.

Box-Behnken study design for optimization of bicalutamide-loaded nanostructured lipid carrier: stability assessment.

PubMed

Kudarha, Ritu; Dhas, Namdev L; Pandey, Abhijeet; Belgamwar, Veena S; Ige, Pradum P

2015-01-01

Bicalutamide (BCM) is an anti-androgen drug used to treat prostate cancer. In this study, nanostructured lipid carriers (NLCs) were chosen as a carrier for delivery of BCM using Box-Behnken (BB) design for optimizing various quality attributes such as particle size and entrapment efficiency which is very critical for efficient drug delivery and high therapeutic efficacy. Stability of formulated NLCs was assessed with respect to storage stability, pH stability, hemolysis, protein stability, serum protein stability and accelerated stability. Hot high-pressure homogenizer was utilized for formulation of BCM-loaded NLCs. In BB response surface methodology, total lipid, % liquid lipid and % soya lecithin was selected as independent variable and particle size and %EE as dependent variables. Scanning electron microscopy (SEM) was done for morphological study of NLCs. Differential scanning calorimeter and X-ray diffraction study were used to study crystalline and amorphous behavior. Analysis of design space showed that process was robust with the particle size less than 200 nm and EE up to 78%. Results of stability studies showed stability of carrier in various storage conditions and in different pH condition. From all the above study, it can be concluded that NLCs may be suitable carrier for the delivery of BCM with respect to stability and quality attributes.

Nanostructured biosensor using bioluminescence quenching technique for glucose detection.

PubMed

Chen, Longyan; Chen, Longyi; Dotzert, Michelle; Melling, C W James; Zhang, Jin

2017-08-22

Most methods for monitoring glucose level require an external energy source which may limit their application, particularly in vivo test. Bioluminescence technique offers an alternative way to provide emission light without external energy source by using bioluminescent proteins found from firefly or marine vertebrates and invertebrates. For quick and non-invasive detection of glucose, we herein developed a nanostructured biosensor by applying the bioluminescence technique. Luciferase bioluminescence protein (Rluc) is conjugated with β-cyclodextrin (β-CD). The bioluminescence intensity of Rluc can be quenched by 8 ± 3 nm gold nanoparticles (Au NPs) when Au NPs covalently bind to β-CD. In the presence of glucose, Au NPs are replaced and leave far from Rluc through a competitive reaction, which results in the restored bioluminescence intensity of Rluc. A linear relationship is observed between the restored bioluminescence intensity and the logarithmic glucose concentration in the range of 1-100 µM. In addition, the selectivity of this designed sensor has been evaluated. The performance of the senor for determination of the concentration of glucose in the blood of diabetic rats is studied for comparison with that of the concentration of glucose in aqueous. This study demonstrates the design of a bioluminescence sensor for quickly detecting the concentration of glucose sensitively.

Multiscale modeling of nanostructured ZnO based devices for optoelectronic applications: Dynamically-coupled structural fields, charge, and thermal transport processes

NASA Astrophysics Data System (ADS)

Abdullah, Abdulmuin; Alqahtani, Saad; Nishat, Md Rezaul Karim; Ahmed, Shaikh; SIU Nanoelectronics Research Group Team

Recently, hybrid ZnO nanostructures (such as ZnO deposited on ZnO-alloys, Si, GaN, polymer, conducting oxides, and organic compounds) have attracted much attention for their possible applications in optoelectronic devices (such as solar cells, light emitting and laser diodes), as well as in spintronics (such as spin-based memory, and logic). However, efficiency and performance of these hybrid ZnO devices strongly depend on an intricate interplay of complex, nonlinear, highly stochastic and dynamically-coupled structural fields, charge, and thermal transport processes at different length and time scales, which have not yet been fully assessed experimentally. In this work, we study the effects of these coupled processes on the electronic and optical emission properties in nanostructured ZnO devices. The multiscale computational framework employs the atomistic valence force-field molecular mechanics, models for linear and non-linear polarization, the 8-band sp3s* tight-binding models, and coupling to a TCAD toolkit to determine the terminal properties of the device. A series of numerical experiments are performed (by varying different nanoscale parameters such as size, geometry, crystal cut, composition, and electrostatics) that mainly aim to improve the efficiency of these devices. Supported by the U.S. National Science Foundation Grant No. 1102192.

Nanostructures having high performance thermoelectric properties

DOEpatents

Yang, Peidong; Majumdar, Arunava; Hochbaum, Allon I.; Chen, Renkun; Delgado, Raul Diaz

2015-12-22

The invention provides for a nanostructure, or an array of such nanostructures, each comprising a rough surface, and a doped or undoped semiconductor. The nanostructure is an one-dimensional (1-D) nanostructure, such a nanowire, or a two-dimensional (2-D) nanostructure. The nanostructure can be placed between two electrodes and used for thermoelectric power generation or thermoelectric cooling.

Nanostructures having high performance thermoelectric properties

DOEpatents

Yang, Peidong; Majumdar, Arunava; Hochbaum, Allon I; Chen, Renkun; Delgado, Raul Diaz

2014-05-20

The invention provides for a nanostructure, or an array of such nanostructures, each comprising a rough surface, and a doped or undoped semiconductor. The nanostructure is an one-dimensional (1-D) nanostructure, such a nanowire, or a two-dimensional (2-D) nanostructure. The nanostructure can be placed between two electrodes and used for thermoelectric power generation or thermoelectric cooling.

Nanostructured layers of thermoelectric materials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Urban, Jeffrey J.; Lynch, Jared; Coates, Nelson

This disclosure provides systems, methods, and apparatus related to thermoelectric materials. In one aspect, a method includes providing a plurality of nanostructures. The plurality of nanostructures comprise a thermoelectric material, with each nanostructure of the plurality of nanostructures having first ligands disposed on a surface of the nanostructure. The plurality of nanostructures is mixed with a solution containing second ligands and a ligand exchange process occurs in which the first ligands disposed on the plurality of nanostructures are replaced with the second ligands. The plurality of nanostructures is deposited on a substrate to form a layer. The layer is thermallymore » annealed.« less

Gate-defined Quantum Confinement in Suspended Bilayer Graphene

NASA Astrophysics Data System (ADS)

Allen, Monica

2013-03-01

Quantum confined devices in carbon-based materials offer unique possibilities for applications ranging from quantum computation to sensing. In particular, nanostructured carbon is a promising candidate for spin-based quantum computation due to the ability to suppress hyperfine coupling to nuclear spins, a dominant source of spin decoherence. Yet graphene lacks an intrinsic bandgap, which poses a serious challenge for the creation of such devices. We present a novel approach to quantum confinement utilizing tunnel barriers defined by local electric fields that break sublattice symmetry in suspended bilayer graphene. This technique electrostatically confines charges via band structure control, thereby eliminating the edge and substrate disorder that hinders on-chip etched nanostructures to date. We report clean single electron tunneling through gate-defined quantum dots in two regimes: at zero magnetic field using the energy gap induced by a perpendicular electric field and at finite magnetic fields using Landau level confinement. The observed Coulomb blockade periodicity agrees with electrostatic simulations based on local top-gate geometry, a direct demonstration of local control over the band structure of graphene. This technology integrates quantum confinement with pristine device quality and access to vibrational modes, enabling wide applications from electromechanical sensors to quantum bits. More broadly, the ability to externally tailor the graphene bandgap over nanometer scales opens a new unexplored avenue for creating quantum devices.

Exploring time-resolved photoluminescence for nanowires using a three-dimensional computational transient model.

PubMed

Ren, Dingkun; Scofield, Adam C; Farrell, Alan C; Rong, Zixuan; Haddad, Michael A; Laghumavarapu, Ramesh B; Liang, Baolai; Huffaker, Diana L

2018-04-26

Time-resolved photoluminescence (TRPL) has been implemented experimentally to measure the carrier lifetime of semiconductors for decades. For the characterization of nanowires, the rich information embedded in TRPL curves has not been fully interpreted and meaningfully mapped to the respective material properties. This is because their three-dimensional (3-D) geometries result in more complicated mechanisms of carrier recombination than those in thin films and analytical solutions cannot be found for those nanostructures. In this work, we extend the intrinsic power of TRPL by developing a full 3-D transient model, which accounts for different material properties and drift-diffusion, to simulate TRPL curves for nanowires. To show the capability of the model, we perform TRPL measurements on a set of GaAs nanowire arrays grown on silicon substrates and then fit the measured data by tuning various material properties, including carrier mobility, Shockley-Read-Hall recombination lifetime, and surface recombination velocity at the GaAs-Si heterointerface. From the resultant TRPL simulations, we numerically identify the lifetime characteristics of those material properties. In addition, we computationally map the spatial and temporal electron distributions in nanowire segments and reveal the underlying carrier dynamics. We believe this study provides a theoretical foundation for interpretation of TRPL measurements to unveil the complex carrier recombination mechanisms in 3-D nanostructured materials.

Stacked mechanical nanogenerator comprising piezoelectric semiconducting nanostructures and Schottky conductive contacts

DOEpatents

Wang, Zhong L [Marietta, GA; Xu, Sheng [Atlanta, GA

2011-08-23

An electric power generator includes a first conductive layer, a plurality of semiconducting piezoelectric nanostructures, a second conductive layer and a plurality of conductive nanostructures. The first conductive layer has a first surface from which the semiconducting piezoelectric nanostructures extend. The second conductive layer has a second surface and is parallel to the first conductive layer so that the second surface faces the first surface of the first conductive layer. The conductive nanostructures depend downwardly therefrom. The second conductive layer is spaced apart from the first conductive layer at a distance so that when a force is applied, the semiconducting piezoelectric nanostructures engage the conductive nanostructures so that the piezoelectric nanostructures bend, thereby generating a potential difference across the at semiconducting piezoelectric nanostructures and also thereby forming a Schottky barrier between the semiconducting piezoelectric nanostructures and the conductive nanostructures.

Silicon-embedded copper nanostructure network for high energy storage

DOEpatents

Yu, Tianyue

2018-01-23

Provided herein are nanostructure networks having high energy storage, electrochemically active electrode materials including nanostructure networks having high energy storage, as well as electrodes and batteries including the nanostructure networks having high energy storage. According to various implementations, the nanostructure networks have high energy density as well as long cycle life. In some implementations, the nanostructure networks include a conductive network embedded with electrochemically active material. In some implementations, silicon is used as the electrochemically active material. The conductive network may be a metal network such as a copper nanostructure network. Methods of manufacturing the nanostructure networks and electrodes are provided. In some implementations, metal nanostructures can be synthesized in a solution that contains silicon powder to make a composite network structure that contains both. The metal nanostructure growth can nucleate in solution and on silicon nanostructure surfaces.

Silicon-embedded copper nanostructure network for high energy storage

DOEpatents

Yu, Tianyue

2016-03-15

Provided herein are nanostructure networks having high energy storage, electrochemically active electrode materials including nanostructure networks having high energy storage, as well as electrodes and batteries including the nanostructure networks having high energy storage. According to various implementations, the nanostructure networks have high energy density as well as long cycle life. In some implementations, the nanostructure networks include a conductive network embedded with electrochemically active material. In some implementations, silicon is used as the electrochemically active material. The conductive network may be a metal network such as a copper nanostructure network. Methods of manufacturing the nanostructure networks and electrodes are provided. In some implementations, metal nanostructures can be synthesized in a solution that contains silicon powder to make a composite network structure that contains both. The metal nanostructure growth can nucleate in solution and on silicon nanostructure surfaces.

Interaction study on bovine serum albumin physically binding to silver nanoparticles: Evolution from discrete conjugates to protein coronas

NASA Astrophysics Data System (ADS)

Guo, Jun; Zhong, Ruibo; Li, Wanrong; Liu, Yushuang; Bai, Zhijun; Yin, Jun; Liu, Jingran; Gong, Pei; Zhao, Xinmin; Zhang, Feng

2015-12-01

The nanostructures formed by inorganic nanoparticles together with organic molecules especially biomolecules have attracted increasing attention from both industries and researching fields due to their unique hybrid properties. In this paper, we systemically studied the interactions between amphiphilic polymer coated silver nanoparticles and bovine serum albumins by employing the fluorescence quenching approach in combination with the Stern-Volmer and Hill equations. The binding affinity was determined to 1.30 × 107 M-1 and the interaction was spontaneously driven by mainly the van der Waals force and hydrogen-bond mediated interactions, and negatively cooperative from the point of view of thermodynamics. With the non-uniform coating of amphiphilic polymer, the silver nanoparticles can form protein coronas which can become discrete protein-nanoparticle conjugates when controlling their molar ratios of mixing. The protein's conformational changes upon binding nanoparticles was also studied by using the three-dimensional fluorescence spectroscopy.

Streamlined Synthesis and Assembly of a Hybrid Sensing Architecture with Solid Binding Proteins and Click Chemistry.

PubMed

Swift, Brian J F; Shadish, Jared A; DeForest, Cole A; Baneyx, François

2017-03-22

Combining bioorthogonal chemistry with the use of proteins engineered with adhesive and morphogenetic solid-binding peptides is a promising route for synthesizing hybrid materials with the economy and efficiency of living systems. Using optical sensing of chloramphenicol as a proof of concept, we show here that a GFP variant engineered with zinc sulfide and silica-binding peptides on opposite sides of its β-barrel supports the fabrication of protein-capped ZnS:Mn nanocrystals that exhibit the combined emission signatures of organic and inorganic fluorophores. Conjugation of a chloramphenicol-specific DNA aptamer to the protein shell through strain-promoted azide-alkyne cycloaddition and spontaneous concentration of the resulting nanostructures onto SiO 2 particles mediated by the silica-binding sequence enables visual detection of environmentally and clinically relevant concentrations of chloramphenicol through analyte-mediated inner filtering of sub-330 nm excitation light.

Cobalt ferrite nanocrystals: out-performing magnetotactic bacteria.

PubMed

Prozorov, Tanya; Palo, Pierre; Wang, Lijun; Nilsen-Hamilton, Marit; Jones, DeAnna; Orr, Daniel; Mallapragada, Surya K; Narasimhan, Balaji; Canfield, Paul C; Prozorov, Ruslan

2007-10-01

Magnetotactic bacteria produce exquisitely ordered chains of uniform magnetite (Fe(3)O(4)) nanocrystals, and the use of the bacterial mms6 protein allows for the shape-selective synthesis of Fe(3)O(4) nanocrystals. Cobalt ferrite (CoFe(2)O(4)) nanoparticles, on the other hand, are not known to occur in living organisms. Here we report on the use of the recombinant mms6 protein in a templated synthesis of CoFe(2)O(4) nanocrystals in vitro. We have covalently attached the full-length mms6 protein and a synthetic C-terminal domain of mms6 protein to self-assembling polymers in order to template hierarchical CoFe(2)O(4) nanostructures. This new synthesis pathway enables facile room-temperature shape-specific synthesis of complex magnetic crystalline nanomaterials with particle sizes in the range of 40-100 nm that are difficult to produce using conventional techniques.

Emerging Nanophotonic Applications Explored with Advanced Scientific Parallel Computing

NASA Astrophysics Data System (ADS)

Meng, Xiang

The domain of nanoscale optical science and technology is a combination of the classical world of electromagnetics and the quantum mechanical regime of atoms and molecules. Recent advancements in fabrication technology allows the optical structures to be scaled down to nanoscale size or even to the atomic level, which are far smaller than the wavelength they are designed for. These nanostructures can have unique, controllable, and tunable optical properties and their interactions with quantum materials can have important near-field and far-field optical response. Undoubtedly, these optical properties can have many important applications, ranging from the efficient and tunable light sources, detectors, filters, modulators, high-speed all-optical switches; to the next-generation classical and quantum computation, and biophotonic medical sensors. This emerging research of nanoscience, known as nanophotonics, is a highly interdisciplinary field requiring expertise in materials science, physics, electrical engineering, and scientific computing, modeling and simulation. It has also become an important research field for investigating the science and engineering of light-matter interactions that take place on wavelength and subwavelength scales where the nature of the nanostructured matter controls the interactions. In addition, the fast advancements in the computing capabilities, such as parallel computing, also become as a critical element for investigating advanced nanophotonic devices. This role has taken on even greater urgency with the scale-down of device dimensions, and the design for these devices require extensive memory and extremely long core hours. Thus distributed computing platforms associated with parallel computing are required for faster designs processes. Scientific parallel computing constructs mathematical models and quantitative analysis techniques, and uses the computing machines to analyze and solve otherwise intractable scientific challenges. In particular, parallel computing are forms of computation operating on the principle that large problems can often be divided into smaller ones, which are then solved concurrently. In this dissertation, we report a series of new nanophotonic developments using the advanced parallel computing techniques. The applications include the structure optimizations at the nanoscale to control both the electromagnetic response of materials, and to manipulate nanoscale structures for enhanced field concentration, which enable breakthroughs in imaging, sensing systems (chapter 3 and 4) and improve the spatial-temporal resolutions of spectroscopies (chapter 5). We also report the investigations on the confinement study of optical-matter interactions at the quantum mechanical regime, where the size-dependent novel properties enhanced a wide range of technologies from the tunable and efficient light sources, detectors, to other nanophotonic elements with enhanced functionality (chapter 6 and 7).

Microtubule-based nanomaterials: Exploiting nature's dynamic biopolymers

DOE PAGES

Bachand, George D.; Stevens, Mark J.; Spoerke, Erik David

2015-04-09

For more than a decade now, biomolecular systems have served as an inspiration for the development of synthetic nanomaterials and systems that are capable of reproducing many of unique and emergent behaviors of living systems. In addition, one intriguing element of such systems may be found in a specialized class of proteins known as biomolecular motors that are capable of performing useful work across multiple length scales through the efficient conversion of chemical energy. Microtubule (MT) filaments may be considered within this context as their dynamic assembly and disassembly dissipate energy, and perform work within the cell. MTs are onemore » of three cytoskeletal filaments in eukaryotic cells, and play critical roles in a range of cellular processes including mitosis and vesicular trafficking. Based on their function, physical attributes, and unique dynamics, MTs also serve as a powerful archetype of a supramolecular filament that underlies and drives multiscale emergent behaviors. In this review, we briefly summarize recent efforts to generate hybrid and composite nanomaterials using MTs as biomolecular scaffolds, as well as computational and synthetic approaches to develop synthetic one-dimensional nanostructures that display the enviable attributes of the natural filaments.« less

Computational protein design-the next generation tool to expand synthetic biology applications.

PubMed

Gainza-Cirauqui, Pablo; Correia, Bruno Emanuel

2018-05-02

One powerful approach to engineer synthetic biology pathways is the assembly of proteins sourced from one or more natural organisms. However, synthetic pathways often require custom functions or biophysical properties not displayed by natural proteins, limitations that could be overcome through modern protein engineering techniques. Structure-based computational protein design is a powerful tool to engineer new functional capabilities in proteins, and it is beginning to have a profound impact in synthetic biology. Here, we review efforts to increase the capabilities of synthetic biology using computational protein design. We focus primarily on computationally designed proteins not only validated in vitro, but also shown to modulate different activities in living cells. Efforts made to validate computational designs in cells can illustrate both the challenges and opportunities in the intersection of protein design and synthetic biology. We also highlight protein design approaches, which although not validated as conveyors of new cellular function in situ, may have rapid and innovative applications in synthetic biology. We foresee that in the near-future, computational protein design will vastly expand the functional capabilities of synthetic cells. Copyright © 2018. Published by Elsevier Ltd.

Computationally efficient method for optical simulation of solar cells and their applications

NASA Astrophysics Data System (ADS)

Semenikhin, I.; Zanuccoli, M.; Fiegna, C.; Vyurkov, V.; Sangiorgi, E.

2013-01-01

This paper presents two novel implementations of the Differential method to solve the Maxwell equations in nanostructured optoelectronic solid state devices. The first proposed implementation is based on an improved and computationally efficient T-matrix formulation that adopts multiple-precision arithmetic to tackle the numerical instability problem which arises due to evanescent modes. The second implementation adopts the iterative approach that allows to achieve low computational complexity O(N logN) or better. The proposed algorithms may work with structures with arbitrary spatial variation of the permittivity. The developed two-dimensional numerical simulator is applied to analyze the dependence of the absorption characteristics of a thin silicon slab on the morphology of the front interface and on the angle of incidence of the radiation with respect to the device surface.

2008 ALCF annual report.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Drugan, C.

2009-12-07

The word 'breakthrough' aptly describes the transformational science and milestones achieved at the Argonne Leadership Computing Facility (ALCF) throughout 2008. The number of research endeavors undertaken at the ALCF through the U.S. Department of Energy's (DOE) Innovative and Novel Computational Impact on Theory and Experiment (INCITE) program grew from 9 in 2007 to 20 in 2008. The allocation of computer time awarded to researchers on the Blue Gene/P also spiked significantly - from nearly 10 million processor hours in 2007 to 111 million in 2008. To support this research, we expanded the capabilities of Intrepid, an IBM Blue Gene/P systemmore » at the ALCF, to 557 teraflops (TF) for production use. Furthermore, we enabled breakthrough levels of productivity and capability in visualization and data analysis with Eureka, a powerful installation of NVIDIA Quadro Plex S4 external graphics processing units. Eureka delivered a quantum leap in visual compute density, providing more than 111 TF and more than 3.2 terabytes of RAM. On April 21, 2008, the dedication of the ALCF realized DOE's vision to bring the power of the Department's high performance computing to open scientific research. In June, the IBM Blue Gene/P supercomputer at the ALCF debuted as the world's fastest for open science and third fastest overall. No question that the science benefited from this growth and system improvement. Four research projects spearheaded by Argonne National Laboratory computer scientists and ALCF users were named to the list of top ten scientific accomplishments supported by DOE's Advanced Scientific Computing Research (ASCR) program. Three of the top ten projects used extensive grants of computing time on the ALCF's Blue Gene/P to model the molecular basis of Parkinson's disease, design proteins at atomic scale, and create enzymes. As the year came to a close, the ALCF was recognized with several prestigious awards at SC08 in November. We provided resources for Linear Scaling Divide-and-Conquer Electronic Structure Calculations for Thousand Atom Nanostructures, a collaborative effort between Argonne, Lawrence Berkeley National Laboratory, and Oak Ridge National Laboratory that received the ACM Gordon Bell Prize Special Award for Algorithmic Innovation. The ALCF also was named a winner in two of the four categories in the HPC Challenge best performance benchmark competition.« less

Aqueous-Based Fabrication of Low-VOC Nanostructured Block Copolymer Films as Potential Marine Antifouling Coatings.

PubMed

Kim, Kris S; Gunari, Nikhil; MacNeil, Drew; Finlay, John; Callow, Maureen; Callow, James; Walker, Gilbert C

2016-08-10

The ability to fabricate nanostructured films by exploiting the phenomenon of microphase separation has made block copolymers an invaluable tool for a wide array of coating applications. Standard approaches to engineering nanodomains commonly involve the application of organic solvents, either through dissolution or annealing protocols, resulting in the release of volatile organic compounds (VOCs). In this paper, an aqueous-based method of fabricating low-VOC nanostructured block copolymer films is presented. The reported procedure allows for the phase transfer of water insoluble triblock copolymer, poly(styrene-block-2 vinylpyridine-block-ethylene oxide) (PS-b-P2VP-b-PEO), from a water immiscible phase to an aqueous environment with the assistance of a diblock copolymeric phase transfer agent, poly(styrene-block-ethylene oxide) (PS-b-PEO). Phase transfer into the aqueous phase results in self-assembly of PS-b-P2VP-b-PEO into core-shell-corona micelles, which are characterized by dynamic light scattering techniques. The films that result from coating the micellar solution onto Si/SiO2 surfaces exhibit nanoscale features that disrupt the ability of a model foulant, a zoospore of Ulva linza, to settle. The multilayered architecture consists of a pH-responsive P2VP-"shell" which can be stimulated to control the size of these features. The ability of these nanostructured thin films to resist protein adsorption and serve as potential marine antifouling coatings is supported through atomic force microscopy (AFM) and analysis of the settlement of Ulva linza zoospore. Field trials of the surfaces in a natural environment show the inhibition of macrofoulants for 1 month.

Intensity-based readout of resonant-waveguide grating biosensors: Systems and nanostructures

NASA Astrophysics Data System (ADS)

Paulsen, Moritz; Jahns, Sabrina; Gerken, Martina

2017-09-01

Resonant waveguide gratings (RWG) - also called photonic crystal slabs (PCS) - have been established as reliable optical transducers for label-free biochemical assays as well as for cell-based assays. Current readout systems are based on mechanical scanning and spectrometric measurements with system sizes suitable for laboratory equipment. Here, we review recent progress in compact intensity-based readout systems for point-of-care (POC) applications. We briefly introduce PCSs as sensitive optical transducers and introduce different approaches for intensity-based readout systems. Photometric measurements have been realized with a simple combination of a light source and a photodetector. Recently a 96-channel, intensity-based readout system for both biochemical interaction analyses as well as cellular assays was presented employing the intensity change of a near cut-off mode. As an alternative for multiparametric detection, a camera system for imaging detection has been implemented. A portable, camera-based system of size 13 cm × 4.9 cm × 3.5 cm with six detection areas on an RWG surface area of 11 mm × 7 mm has been demonstrated for the parallel detection of six protein binding kinetics. The signal-to-noise ratio of this system corresponds to a limit of detection of 168 M (24 ng/ml). To further improve the signal-to-noise ratio advanced nanostructure designs are investigated for RWGs. Here, results on multiperiodic and deterministic aperiodic nanostructures are presented. These advanced nanostructures allow for the design of the number and wavelengths of the RWG resonances. In the context of intensity-based readout systems they are particularly interesting for the realization of multi-LED systems. These recent trends suggest that compact point-of-care systems employing disposable test chips with RWG functional areas may reach market in the near future.

Efficient marginalization to compute protein posterior probabilities from shotgun mass spectrometry data

PubMed Central

Serang, Oliver; MacCoss, Michael J.; Noble, William Stafford

2010-01-01

The problem of identifying proteins from a shotgun proteomics experiment has not been definitively solved. Identifying the proteins in a sample requires ranking them, ideally with interpretable scores. In particular, “degenerate” peptides, which map to multiple proteins, have made such a ranking difficult to compute. The problem of computing posterior probabilities for the proteins, which can be interpreted as confidence in a protein’s presence, has been especially daunting. Previous approaches have either ignored the peptide degeneracy problem completely, addressed it by computing a heuristic set of proteins or heuristic posterior probabilities, or by estimating the posterior probabilities with sampling methods. We present a probabilistic model for protein identification in tandem mass spectrometry that recognizes peptide degeneracy. We then introduce graph-transforming algorithms that facilitate efficient computation of protein probabilities, even for large data sets. We evaluate our identification procedure on five different well-characterized data sets and demonstrate our ability to efficiently compute high-quality protein posteriors. PMID:20712337

Bio-industrial waste silk fibroin protein and carbon nanotube induced carbonized growth of one dimensional ZnO based bio-nanosheets and their enhanced optoelectronic properties.

PubMed

Saravanan, Adhimoorthy; Huang, Bohr-Ran; Kathiravan, Deepa

2018-06-01

High performance UV/visible photodetectors are successfully fabricated from ZnO/fibroin protein-carbon nanotube (ZFPCNT) composites using a simple hydrothermal method. The as-fabricated ZnO nanorods (ZnO NRs) and ZFPCNT nanostructures were measured under different light illuminations. The measurements showed the UV-light photoresponse of the as-fabricated ZFPCNT nanostructures (55,555) to be approximately 26454% higher than that of the as-prepared ZnO NRs (210). This photodetector can sense photons with energies considerably smaller (2.75 eV) than the band gap of ZnO (3.22 eV). It was observed that the finest distribution of fibroin and CNT into 1D ZnO resulted in rapid electron transportation and hole recombination via carbon/nitrogen dopants from the ZFPCNT. Carbon dopants create new energy levels on the conduction band of the ZFPCNT, which reduces the barrier height to allow for charge carrier transportation under light illumination. Moreover, the nitrogen dopants increase the adsorptivity and amount of oxygen vacancies in the ZFPCNT so that it exhibits fast response/recovery times both in the dark and under light illumination. The selectivity of UV light among the other types of illumination can be ascribed to the deep-level energy traps (ET) of the ZFPCNT. These significant features of ZFPCNT lead to the excellent optical properties and creation of new pathways for the production of low-cost semiconductors and bio-waste protein based UV/visible photodetectors. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Web building and silk properties functionally covary among species of wolf spider.

PubMed

Lacava, Mariángeles; Camargo, Arley; Garcia, Luis F; Benamú, Marco A; Santana, Martin; Fang, Jian; Wang, Xungai; Blamires, Sean J

2018-04-15

Although phylogenetic studies have shown covariation between the properties of spider major ampullate (MA) silk and web building, both spider webs and silks are highly plastic so we cannot be sure whether these traits functionally covary or just vary across environments that the spiders occupy. As MaSp2-like proteins provide MA silk with greater extensibility, their presence is considered necessary for spider webs to effectively capture prey. Wolf spiders (Lycosidae) are predominantly non-web building, but a select few species build webs. We accordingly collected MA silk from two web-building and six non-web-building species found in semirural ecosystems in Uruguay to test whether the presence of MaSp2-like proteins (indicated by amino acid composition, silk mechanical properties and silk nanostructures) was associated with web building across the group. The web-building and non-web-building species were from disparate subfamilies so we estimated a genetic phylogeny to perform appropriate comparisons. For all of the properties measured, we found differences between web-building and non-web-building species. A phylogenetic regression model confirmed that web building and not phylogenetic inertia influences silk properties. Our study definitively showed an ecological influence over spider silk properties. We expect that the presence of the MaSp2-like proteins and the subsequent nanostructures improves the mechanical performance of silks within the webs. Our study furthers our understanding of spider web and silk co-evolution and the ecological implications of spider silk properties. © 2018 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2018 European Society For Evolutionary Biology.

An investigation on the physicochemical properties of the nanostructured [(4-X)PMAT][N(CN)2] ion pairs as energetic and tunable aryl alkyl amino tetrazolium based ionic liquids

NASA Astrophysics Data System (ADS)

Khalili, Behzad; Rimaz, Mehdi

2017-06-01

In this study the different class of tunable and high nitrogen content ionic liquids termed TAMATILs (Tunable Aryl Methyl Amino Tetrazolium based Ionic Liquids) were designed. The physicochemical properties of the nanostructured TAMATILs composed of para substituted phenyl methyl amino tetrazolium cations [(4-X)PMAT]+ (X = H, Me, OCH3, OH, NH2, NO2, F, CN, CHO, CF3, COMe and CO2Me) and dicyanimide anion [N(CN)2]- were fully investigated using M06-2X functional in conjunction with the 6-311++G(2d,2p) basis set. For all of the studied nanostructured ILs the structural parameters, interaction energy, cation's enthalpy of formation, natural charges, charge transfer values and topological properties were calculated and discussed. The substituent effect on the interaction energy and physicochemical properties also is taking into account. The results showed that the strength of interaction has a linear correlation with electron content of the phenyl ring in a way the substituents with electron withdrawing effects lead to make more stable ion pairs with higher interaction energies. Some of the main physical properties of ILs such as surface tension, melting point, critical-point temperature, electrochemical stability and conductivity are discussed and estimated for studying ion pairs using quantum chemical computationally obtained thermochemical data. Finally the enthalpy and Gibbs free energy of formation for twelve nanostructured individual cations with the general formula of [(4-X)PMAT]+ (X = 4-H, 4-Me, 4-OMe, 4-OH, 4-NH2, 4-NO2, 4-F, 4-CN, 4-CHO, 4-CF3, 4-COMe and 4-CO2Me) are calculated.

A facile and cost-effective TEM grid approach to design gold nano-structured substrates for high throughput plasmonic sensitive detection of biomolecules.

PubMed

Jia, Kun; Bijeon, Jean Louis; Adam, Pierre Michel; Ionescu, Rodica Elena

2013-02-21

A commercial TEM grid was used as a mask for the creation of extremely well-organized gold micro-/nano-structures on a glass substrate via a high temperature annealing process at 500 °C. The structured substrate was (bio)functionalized and used for the high throughput LSPR immunosensing of different concentrations of a model protein named bovine serum albumin.

Protein and cell micropatterning and its integration with micro/nanoparticles assembly.

PubMed

Yap, F L; Zhang, Y

2007-01-15

Micropatterning of proteins and cells has become very popular over the past decade due to its importance in the development of biosensors, microarrays, tissue engineering and cellular studies. This article reviews the techniques developed for protein and cell micropatterning and its biomedical applications. The prospect of integrating micro and nanoparticles with protein and cell micropatterning is discussed. The micro/nanoparticles are assembled into patterns and form the substrate for proteins and cell attachment. The assembled particles create a micro or nanotopography, depending on the size of the particles employed. The nonplanar structure can increase the surface area for biomolecules attachment and therefore enhance the sensitivity for detection in biosensors. Furthermore, a nanostructured substrate can influence the conformation and functionality of protein attached to it, while cellular response in terms of morphology, adhesion, proliferation, differentiation, etc. can be affected by a surface expressing micro or nanoscale structures. Proteins and cells tend to lose their normal functions upon attachment to substrate. By recognizing the types of topography that are favourable for preserving proteins and cell behaviour, and integrating it with micropattering will lead to the development of functional protein and cell patterns.

Mechanical Behavior of Nanostructured and Ultrafine Grained Materials under Shock Wave Loadings. Experimental Data and Results of Computer Simulation.

NASA Astrophysics Data System (ADS)

Skripnyak, Vladimir

2011-06-01

Features of mechanical behavior of nanostructured (NS) and ultrafine grained (UFG) metal and ceramic materials under quasistatic and shock wave loadings are discussed in this report. Multilevel models developed within the approach of computational mechanics of materials were used for simulation mechanical behavior of UFG and NS metals and ceramics. Comparisons of simulation results with experimental data are presented. Models of mechanical behavior of nanostructured metal alloys takes into account a several structural factors influencing on the mechanical behavior of materials (type of a crystal lattice, density of dislocations, a size of dislocation substructures, concentration and size of phase precipitation, and distribution of grains sizes). Results show the strain rate sensitivity of the yield stress of UFG and polycrystalline alloys is various in a range from 103 up to 106 1/s. But the difference of the Hugoniot elastic limits of a UFG and coarse-grained alloys may be not considerable. The spall strength, the yield stress of UFG and NS alloys are depend not only on grains size, but a number of factors such as a distribution of grains sizes, a concentration and sizes of voids and cracks, a concentration and sizes of phase precipitation. Some titanium alloys with grain sizes from 300 to 500 nm have the quasi-static yield strength and the tensile strength twice higher than that of coarse grained counterparts. But the spall strength of the UFG titanium alloys is only 10 percents above than that of coarse grained alloys. At the same time it was found the spall strength of the bulk UFG aluminium and magnesium alloys with precipitation strengthening is essentially higher in comparison of coarse-grained counterparts. The considerable decreasing of the strain before failure of UFG alloys was predicted at high strain rates. The Hugoniot elastic limits of oxide nanoceramics depend not only on the porosity, but also on sizes and volume distribution of voids.

Nanostructuring of Palladium with Low-Temperature Helium Plasma

PubMed Central

Fiflis, P.; Christenson, M.P.; Connolly, N.; Ruzic, D.N.

2015-01-01

Impingement of high fluxes of helium ions upon metals at elevated temperatures has given rise to the growth of nanostructured layers on the surface of several metals, such as tungsten and molybdenum. These nanostructured layers grow from the bulk material and have greatly increased surface area over that of a not nanostructured surface. They are also superior to deposited nanostructures due to a lack of worries over adhesion and differences in material properties. Several palladium samples of varying thickness were biased and exposed to a helium helicon plasma. The nanostructures were characterized as a function of the thickness of the palladium layer and of temperature. Bubbles of ~100 nm in diameter appear to be integral to the nanostructuring process. Nanostructured palladium is also shown to have better catalytic activity than not nanostructured palladium. PMID:28347109

Nanostructuring of Palladium with Low-Temperature Helium Plasma.

PubMed

Fiflis, P; Christenson, M P; Connolly, N; Ruzic, D N

2015-11-25

Impingement of high fluxes of helium ions upon metals at elevated temperatures has given rise to the growth of nanostructured layers on the surface of several metals, such as tungsten and molybdenum. These nanostructured layers grow from the bulk material and have greatly increased surface area over that of a not nanostructured surface. They are also superior to deposited nanostructures due to a lack of worries over adhesion and differences in material properties. Several palladium samples of varying thickness were biased and exposed to a helium helicon plasma. The nanostructures were characterized as a function of the thickness of the palladium layer and of temperature. Bubbles of ~100 nm in diameter appear to be integral to the nanostructuring process. Nanostructured palladium is also shown to have better catalytic activity than not nanostructured palladium.

Structure-sequence based analysis for identification of conserved regions in proteins

DOEpatents

Zemla, Adam T; Zhou, Carol E; Lam, Marisa W; Smith, Jason R; Pardes, Elizabeth

2013-05-28

Disclosed are computational methods, and associated hardware and software products for scoring conservation in a protein structure based on a computationally identified family or cluster of protein structures. A method of computationally identifying a family or cluster of protein structures in also disclosed herein.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Jie-Ren; Ross, Shailise S.; Liu, Yang

We report here on a recent finding that co-stimulation of the high-affinity immunoglobulin E (IgE) receptor (FcεRI) and the chemokine receptor 1 (CCR1) triggered formation of membrane nanotubes among bone-marrow-derived mast cells. The co-stimulation was attained using corresponding ligands: IgE binding antigen and macrophage inflammatory protein 1α (MIP1 α), respectively. However, this approach failed to trigger formation of nanotubes among rat basophilic leukemia (RBL) cells due to the lack of CCR1 on the cell surface (Int. Immunol. 2010, 22 (2), 113–128). RBL cells are frequently used as a model for mast cells and are best known for antibody-mediated activation viamore » FcεRI. This work reports the successful formation of membrane nanotubes among RBLs using only one stimulus, a hapten of 2,4-dinitrophenyl (DNP) molecules, which are presented as nanostructures with our designed spatial arrangements. This observation underlines the significance of the local presentation of ligands in the context of impacting the cellular signaling cascades. In the case of RBL, certain DNP nanostructures suppress antigen-induced degranulation and facilitate the rearrangement of the cytoskeleton to form nanotubes. We conclude that these results demonstrate an important scientific concept; engineered nanostructures enable cellular signaling cascades, where current technologies encounter great difficulties. More importantly, nanotechnology offers a new platform to selectively activate and/or inhibit desired cellular signaling cascades.« less

Interaction entropy for protein-protein binding

NASA Astrophysics Data System (ADS)

Sun, Zhaoxi; Yan, Yu N.; Yang, Maoyou; Zhang, John Z. H.

2017-03-01

Protein-protein interactions are at the heart of signal transduction and are central to the function of protein machine in biology. The highly specific protein-protein binding is quantitatively characterized by the binding free energy whose accurate calculation from the first principle is a grand challenge in computational biology. In this paper, we show how the interaction entropy approach, which was recently proposed for protein-ligand binding free energy calculation, can be applied to computing the entropic contribution to the protein-protein binding free energy. Explicit theoretical derivation of the interaction entropy approach for protein-protein interaction system is given in detail from the basic definition. Extensive computational studies for a dozen realistic protein-protein interaction systems are carried out using the present approach and comparisons of the results for these protein-protein systems with those from the standard normal mode method are presented. Analysis of the present method for application in protein-protein binding as well as the limitation of the method in numerical computation is discussed. Our study and analysis of the results provided useful information for extracting correct entropic contribution in protein-protein binding from molecular dynamics simulations.

Interaction entropy for protein-protein binding.

PubMed

Sun, Zhaoxi; Yan, Yu N; Yang, Maoyou; Zhang, John Z H

2017-03-28

Protein-protein interactions are at the heart of signal transduction and are central to the function of protein machine in biology. The highly specific protein-protein binding is quantitatively characterized by the binding free energy whose accurate calculation from the first principle is a grand challenge in computational biology. In this paper, we show how the interactionentropy approach, which was recently proposed for protein-ligand binding free energy calculation, can be applied to computing the entropic contribution to the protein-protein binding free energy. Explicit theoretical derivation of the interactionentropy approach for protein-protein interaction system is given in detail from the basic definition. Extensive computational studies for a dozen realistic protein-protein interaction systems are carried out using the present approach and comparisons of the results for these protein-protein systems with those from the standard normal mode method are presented. Analysis of the present method for application in protein-protein binding as well as the limitation of the method in numerical computation is discussed. Our study and analysis of the results provided useful information for extracting correct entropic contribution in protein-protein binding from molecular dynamics simulations.

Energy transduction and signal averaging of fluctuating electric fields by a single protein ion channel.

PubMed

Verdia-Baguena, C; Gomez, V; Cervera, J; Ramirez, P; Mafe, S

2016-12-21

We demonstrate the electrical rectification and signal averaging of fluctuating signals using a biological nanostructure in aqueous solution: a single protein ion channel inserted in the lipid bilayer characteristic of cell membranes. The conversion of oscillating, zero time-average potentials into directional currents permits charging of a load capacitor to significant steady-state voltages within a few minutes in the case of the outer membrane porin F (OmpF) protein, a bacterial channel of Escherichia coli. The experiments and simulations show signal averaging effects at a more fundamental level than the traditional cell and tissue scales, which are characterized by ensembles of many ion channels operating simultaneously. The results also suggest signal transduction schemes with bio-electronic interfaces and ionic circuits where soft matter nanodiodes can be coupled to conventional electronic elements.

Manipulation of the response of human endothelial colony-forming cells by focal adhesion assembly using gradient nanopattern plates.

PubMed

Cui, Long-Hui; Joo, Hyung Joon; Kim, Dae Hwan; Seo, Ha-Rim; Kim, Jung Suk; Choi, Seung-Cheol; Huang, Li-Hua; Na, Ji Eun; Lim, I-Rang; Kim, Jong-Ho; Rhyu, Im Joo; Hong, Soon Jun; Lee, Kyu Back; Lim, Do-Sun

2018-01-01

Nanotopography plays a pivotal role in the regulation of cellular responses. Nonetheless, little is known about how the gradient size of nanostructural stimuli alters the responses of endothelial progenitor cells without chemical factors. Herein, the fabrication of gradient nanopattern plates intended to mimic microenvironment nanotopography is described. The gradient nanopattern plates consist of nanopillars of increasing diameter ranges [120-200 nm (GP 120/200), 200-280 nm (GP 200/280), and 280-360 nm (GP 280/360)] that were used to screen the responses of human endothelial colony-forming cells (hECFCs). Nanopillars with a smaller nanopillar diameter caused the cell area and perimeter of hECFCs to decrease and their filopodial outgrowth to increase. The structure of vinculin (a focal adhesion marker in hECFCs) was also modulated by nanostructural stimuli of the gradient nanopattern plates. Moreover, Rho-associated protein kinase (ROCK) gene expression was significantly higher in hECFCs cultured on GP 120/200 than in those on flat plates (no nanopillars), and ROCK suppression impaired the nanostructural-stimuli-induced vinculin assembly. These results suggest that the gradient nanopattern plates generate size-specific nanostructural stimuli suitable for manipulation of the response of hECFCs, in a process dependent on ROCK signaling. This is the first evidence of size-specific nanostructure-sensing behavior of hECFCs. Nano feature surfaces are of growing interest as materials for a controlled response of various cells. In this study, we successfully fabricated gradient nanopattern plates to manipulate the response of blood-derived hECFCs without any chemical stimulation. Interestingly, we find that the sensitive nanopillar size for manipulation of hECFCs is range between 120 nm and 200 nm, which decreased the area and increased the filopodial outgrowth of hECFCs. Furthermore, we only modulate the nanopillar size to increase ROCK expression can be an attractive method for modulating the cytoskeletal integrity and focal adhesion of hECFCs. Copyright © 2017 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Smart polymer brush nanostructures guide the self-assembly of pore-spanning lipid bilayers with integrated membrane proteins

NASA Astrophysics Data System (ADS)

Wilhelmina de Groot, G.; Demarche, Sophie; Santonicola, M. Gabriella; Tiefenauer, Louis; Vancso, G. Julius

2014-01-01

Nanopores in arrays on silicon chips are functionalized with pH-responsive poly(methacrylic acid) (PMAA) brushes and used as supports for pore-spanning lipid bilayers with integrated membrane proteins. Robust platforms are created by the covalent grafting of polymer brushes using surface-initiated atom transfer radical polymerization (ATRP), resulting in sensor chips that can be successfully reused over several assays. His-tagged proteins are selectively and reversibly bound to the nitrilotriacetic acid (NTA) functionalization of the PMAA brush, and consequently lipid bilayer membranes are formed. The enhanced membrane resistance as determined by electrochemical impedance spectroscopy and free diffusion of dyed lipids observed as fluorescence recovery after photobleaching confirmed the presence of lipid bilayers. Immobilization of the His-tagged membrane proteins on the NTA-modified PMAA brush near the pore edges is characterized by fluorescence microscopy. This system allows us to adjust the protein density in free-standing bilayers, which are stabilized by the polymer brush underneath. The potential application of the integrated platform for ion channel protein assays is demonstrated.

Deformation Behavior of Al/a-Si Core-shell Nanostructures

NASA Astrophysics Data System (ADS)

Fleming, Robert

Al/a-Si core-shell nanostructures (CSNs), consisting of a hemispherical Al core surrounded by a hard shell of a-Si, have been shown to display unusual mechanical behavior in response to compression loading. Most notably, these nanostructures exhibit substantial deformation recovery, even when loaded much beyond the elastic limit. Nanoindentation measurements revealed a unique mechanical response characterized by discontinuous signatures in the load-displacement data. In conjunction with the indentation signatures, nearly complete deformation recovery is observed. This behavior is attributed to dislocation nucleation and annihilation events enabled by the 3-dimensional confinement of the Al core. As the core confinement is reduced, either through an increase in confined core volume or a change in the geometrical confinement, the indentation signatures and deformation resistance are significantly reduced. Complimentary molecular dynamics simulations show that a substantial amount of dislocation egression occurs in the core of CSNs during unloading as dislocations annihilate at the core/shell interface. Smaller core diameters correlate with the development of a larger back-stress within the core during unloading, which further correlates with improved dislocation annihilation after unloading. Furthermore, dislocations nucleated in the core of core-shell nanorods are not as effectively removed as compared to CSNs. Nanostructure-textured surfaces (NSTSs) composed of Al/a-Si CSNs have improved tribological properties compared surfaces patterned with Al nanodots and a flat (100) Si surface. NSTSs have a coefficient of friction (COF) as low as 0.015, exhibit low adhesion with adhesion forces on the order of less than 1 microN, and are highly deformation resistant, with no apparent surface deformation after nanoscratch testing, even at contact forces up to 8000 microN. In comparison, (100) Si has substantially higher adhesion and COF ( 10 microN and 0.062, respectively), while the Al nanodots have both higher friction (COF 0.044) and are deformed when subjected to contact loads as low as 250 microN. This integrated experimental and computational study elucidates the mechanisms that contribute to the novel properties of Al/a-Si CSNs and characterizes the tribological properties of surface composed of these nanostructures, which provides a foundation for the rational design of novel technologies based on CSNs.

A new computational strategy for identifying essential proteins based on network topological properties and biological information.

PubMed

Qin, Chao; Sun, Yongqi; Dong, Yadong

2017-01-01

Essential proteins are the proteins that are indispensable to the survival and development of an organism. Deleting a single essential protein will cause lethality or infertility. Identifying and analysing essential proteins are key to understanding the molecular mechanisms of living cells. There are two types of methods for predicting essential proteins: experimental methods, which require considerable time and resources, and computational methods, which overcome the shortcomings of experimental methods. However, the prediction accuracy of computational methods for essential proteins requires further improvement. In this paper, we propose a new computational strategy named CoTB for identifying essential proteins based on a combination of topological properties, subcellular localization information and orthologous protein information. First, we introduce several topological properties of the protein-protein interaction (PPI) network. Second, we propose new methods for measuring orthologous information and subcellular localization and a new computational strategy that uses a random forest prediction model to obtain a probability score for the proteins being essential. Finally, we conduct experiments on four different Saccharomyces cerevisiae datasets. The experimental results demonstrate that our strategy for identifying essential proteins outperforms traditional computational methods and the most recently developed method, SON. In particular, our strategy improves the prediction accuracy to 89, 78, 79, and 85 percent on the YDIP, YMIPS, YMBD and YHQ datasets at the top 100 level, respectively.

New Functional Device using Bio Nano Process

DTIC Science & Technology

2011-09-20

anticipated that acid treatment of CNTs would reduce the electronic properties.2 In contrast, Pender et al. created a bifunctional peptide aptamer that has...of amino acids . Here we report that a novel bifunctional cage-shaped protein able to fabricate a SWNT-titanium nanocompound containing nano-porous...nanostructures.6-7 Two peptide aptamers, NHBP-1 (DYFSSPYYEQLF)8 and minTBP-1 (RKLPDA)9 were genetically fused at the Fig. 1 (a) Amino acid sequence of CDT1. The

Solving the nanostructure problem: exemplified on metallic alloy nanoparticles

NASA Astrophysics Data System (ADS)

Petkov, Valeri; Prasai, Binay; Ren, Yang; Shan, Shiyao; Luo, Jin; Joseph, Pharrah; Zhong, Chuan-Jian

2014-08-01

With current technology moving rapidly toward smaller scales nanometer-size materials, hereafter called nanometer-size particles (NPs), are being produced in increasing numbers and explored for various useful applications ranging from photonics and catalysis to detoxification of wastewater and cancer therapy. Nature also is a prolific producer of useful NPs. Evidence can be found in ores on the ocean floor, minerals and soils on land and in the human body that, when water is excluded, is mostly made of proteins that are 6-10 nm in size and globular in shape. Precise knowledge of the 3D atomic-scale structure, that is how atoms are arranged in space, is a crucial prerequisite for understanding and so gaining more control over the properties of any material, including NPs. In the case of bulk materials such knowledge is fairly easy to obtain by Bragg diffraction experiments. Determining the 3D atomic-scale structure of NPs is, however, still problematic spelling trouble for science and technology at the nanoscale. Here we explore this so-called ``nanostructure problem'' from a practical point of view arguing that it can be solved when its technical, that is the inapplicability of Bragg diffraction to NPs, and fundamental, that is the incompatibility of traditional crystallography with NPs, aspects are both addressed properly. As evidence we present a successful and broadly applicable, 6-step approach to determining the 3D atomic-scale structure of NPs based on a suitable combination of a few experimental and computational techniques. This approach is exemplified on 5 nm sized PdxNi100-x particles (x = 26, 56 and 88) explored for catalytic applications. Furthermore, we show how once an NP atomic structure is determined precisely, a strategy for improving NP structure-dependent properties of particular interest to science and technology can be designed rationally and not subjectively as frequently done now.With current technology moving rapidly toward smaller scales nanometer-size materials, hereafter called nanometer-size particles (NPs), are being produced in increasing numbers and explored for various useful applications ranging from photonics and catalysis to detoxification of wastewater and cancer therapy. Nature also is a prolific producer of useful NPs. Evidence can be found in ores on the ocean floor, minerals and soils on land and in the human body that, when water is excluded, is mostly made of proteins that are 6-10 nm in size and globular in shape. Precise knowledge of the 3D atomic-scale structure, that is how atoms are arranged in space, is a crucial prerequisite for understanding and so gaining more control over the properties of any material, including NPs. In the case of bulk materials such knowledge is fairly easy to obtain by Bragg diffraction experiments. Determining the 3D atomic-scale structure of NPs is, however, still problematic spelling trouble for science and technology at the nanoscale. Here we explore this so-called ``nanostructure problem'' from a practical point of view arguing that it can be solved when its technical, that is the inapplicability of Bragg diffraction to NPs, and fundamental, that is the incompatibility of traditional crystallography with NPs, aspects are both addressed properly. As evidence we present a successful and broadly applicable, 6-step approach to determining the 3D atomic-scale structure of NPs based on a suitable combination of a few experimental and computational techniques. This approach is exemplified on 5 nm sized PdxNi100-x particles (x = 26, 56 and 88) explored for catalytic applications. Furthermore, we show how once an NP atomic structure is determined precisely, a strategy for improving NP structure-dependent properties of particular interest to science and technology can be designed rationally and not subjectively as frequently done now. Electronic supplementary information (ESI) available: XRD patterns, TEM and 3D structure modeling results. See DOI: 10.1039/c4nr01633e

Selective chromogenic detection of thiol-containing biomolecules using carbonaceous nanospheres loaded with silver nanoparticles as carrier.

PubMed

Hu, Bo; Zhao, Yang; Zhu, Hai-Zhou; Yu, Shu-Hong

2011-04-26

Thiol-containing biomolecules show strong affinity with noble metal nanostructures and could not only stably protect them but also control the self-assembly process of these special nanostructures. A highly selective and sensitive chromogenic detection method has been designed for the low and high molecular weight thiol-containing biomolecules, including cysteine, glutathione, dithiothreitol, and bovine serum albumin, using a new type of carbonaceous nanospheres loaded with silver nanoparticles (Ag NPs) as carrier. This strategy relies upon the place-exchange process between the reporter dyes on the surface of Ag NPs and the thiol groups of thiol-containing biomolecules. The concentration of biomolecules can be determined by monitoring with the fluorescence intensity of reporter dyes dispersed in solution. This new chromogenic assay method could selectively detect these biomolecules in the presence of various other amino acids and monosaccharides and even sensitively detect the thiol-containing biomolecules with different molecular weight, even including proteins.

Technology Development of Miniaturized Far-Infrared Sources for Biomolecular Spectroscopy

NASA Technical Reports Server (NTRS)

Kono, Junichiro

2003-01-01

The objective of this project was to develop a purely solid-state based, thus miniaturized, far-infrared (FIR) (also known as terahertz (THz)) wave source using III-V semiconductor nanostructures for biomolecular detection and sensing. Many biomolecules, such as DNA and proteins, have distinct spectroscopic features in the FIR wavelength range as a result of vibration-rotation-tunneling motions and various inter- and intra-molecule collective motions. Spectroscopic characterization of such molecules requires narrow linewidth, sufficiently high power, tunable (in wavelength), and coherent FIR sources. Unfortunately, the FIR frequency is one of the least technologically developed ranges in the electromagnetic spectrum. Currently available FIR sources based on non-solid state technology are bulky, inefficient, and very often incoherent. In this project we investigated antimonide based compound semiconductor (ABCS) nanostructures as the active medium to generate FIR radiation. The final goal of this project was to demonstrate a semiconductor THz source integrated with a pumping diode laser module to achieve a compact system for biomolecular applications.

Self-assembly of nucleic acids, silk and hybrid materials thereof.

PubMed

Humenik, Martin; Scheibel, Thomas

2014-12-17

Top-down approaches based on etching techniques have almost reached their limits in terms of dimension. Therefore, novel assembly strategies and types of nanomaterials are required to allow technological advances. Self-assembly processes independent of external energy sources and unlimited in dimensional scaling have become a very promising approach. Here,we highlight recent developments in self-assembled DNA-polymer, silk-polymer and silk-DNA hybrids as promising materials with biotic and abiotic moieties for constructing complex hierarchical materials in ‘bottom-up’ approaches. DNA block copolymers assemble into nanostructures typically exposing a DNA corona which allows functionalization, labeling and higher levels of organization due to its specific addressable recognition properties. In contrast, self-assembly of natural silk proteins as well as their recombinant variants yields mechanically stable β-sheet rich nanostructures. The combination of silk with abiotic polymers gains hybrid materials with new functionalities. Together, the precision of DNA hybridization and robustness of silk fibrillar structures combine in novel conjugates enable processing of higher-order structures with nanoscale architecture and programmable functions.

Supercapacitors based on c-type cytochromes using conductive nanostructured networks of living bacteria.

PubMed

Malvankar, Nikhil S; Mester, Tünde; Tuominen, Mark T; Lovley, Derek R

2012-02-01

Supercapacitors have attracted interest in energy storage because they have the potential to complement or replace batteries. Here, we report that c-type cytochromes, naturally immersed in a living, electrically conductive microbial biofilm, greatly enhance the device capacitance by over two orders of magnitude. We employ genetic engineering, protein unfolding and Nernstian modeling for in vivo demonstration of charge storage capacity of c-type cytochromes and perform electrochemical impedance spectroscopy, cyclic voltammetry and charge-discharge cycling to confirm the pseudocapacitive, redox nature of biofilm capacitance. The biofilms also show low self-discharge and good charge/discharge reversibility. The superior electrochemical performance of the biofilm is related to its high abundance of cytochromes, providing large electron storage capacity, its nanostructured network with metallic-like conductivity, and its porous architecture with hydrous nature, offering prospects for future low cost and environmentally sustainable energy storage devices. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Self-assembly of nucleic acids, silk and hybrid materials thereof

NASA Astrophysics Data System (ADS)

Humenik, Martin; Scheibel, Thomas

2014-12-01

Top-down approaches based on etching techniques have almost reached their limits in terms of dimension. Therefore, novel assembly strategies and types of nanomaterials are required to allow technological advances. Self-assembly processes independent of external energy sources and unlimited in dimensional scaling have become a very promising approach. Here, we highlight recent developments in self-assembled DNA-polymer, silk-polymer and silk-DNA hybrids as promising materials with biotic and abiotic moieties for constructing complex hierarchical materials in ‘bottom-up’ approaches. DNA block copolymers assemble into nanostructures typically exposing a DNA corona which allows functionalization, labeling and higher levels of organization due to its specific addressable recognition properties. In contrast, self-assembly of natural silk proteins as well as their recombinant variants yields mechanically stable β-sheet rich nanostructures. The combination of silk with abiotic polymers gains hybrid materials with new functionalities. Together, the precision of DNA hybridization and robustness of silk fibrillar structures combine in novel conjugates enable processing of higher-order structures with nanoscale architecture and programmable functions.

Nanoplasmonic Biosensor Using Localized Surface Plasmon Resonance Spectroscopy for Biochemical Detection.

PubMed

Zhang, Diming; Zhang, Qian; Lu, Yanli; Yao, Yao; Li, Shuang; Liu, Qingjun

2017-01-01

Localized surface plasmon resonance (LSPR) associated with metal nanostructures has developed into a highly useful sensor technique. Optical LSPR spectroscopy of nanostructures often shows sharp absorption and scattering peaks, which can be used to probe several bio-molecular interactions. Here, we report nanoplasmonic biosensors using LSPR on nanocup arrays (nanoCA) to recognize bio-molecular binding for biochemical detection. These sensors can be modified to quantify binding of small molecules to proteins for odorant and explosive detections. Electrochemical LSPR biosensors can also be designed by coupling electrochemistry and LSPR spectroscopy measurements. Multiple sensing information can be obtained and electrochemical LSPR property can be investigated for biosensors. In some applications, the electrochemical LSPR biosensor can be used to quantify immunoreactions and enzymatic activity. The biosensors exhibit better performance than those of conventional optical LSPR measurements. With multi-transducers, the nanoplasmonic biosensor can provide a promising approach for bio-detection in environmental monitoring, healthcare diagnostics, and food quality control.

Novel biomaterials: plasma-enabled nanostructures and functions

NASA Astrophysics Data System (ADS)

Levchenko, Igor; Keidar, Michael; Cvelbar, Uroš; Mariotti, Davide; Mai-Prochnow, Anne; Fang, Jinghua; (Ken Ostrikov, Kostya

2016-07-01

Material processing techniques utilizing low-temperature plasmas as the main process tool feature many unique capabilities for the fabrication of various nanostructured materials. As compared with the neutral-gas based techniques and methods, the plasma-based approaches offer higher levels of energy and flux controllability, often leading to higher quality of the fabricated nanomaterials and sometimes to the synthesis of the hierarchical materials with interesting properties. Among others, nanoscale biomaterials attract significant attention due to their special properties towards the biological materials (proteins, enzymes), living cells and tissues. This review briefly examines various approaches based on the use of low-temperature plasma environments to fabricate nanoscale biomaterials exhibiting high biological activity, biological inertness for drug delivery system, and other features of the biomaterials make them highly attractive. In particular, we briefly discuss the plasma-assisted fabrication of gold and silicon nanoparticles for bio-applications; carbon nanoparticles for bioimaging and cancer therapy; carbon nanotube-based platforms for enzyme production and bacteria growth control, and other applications of low-temperature plasmas in the production of biologically-active materials.

Nanomanufacturing of titania interfaces with controlled structural and functional properties by supersonic cluster beam deposition

NASA Astrophysics Data System (ADS)

Podestà, Alessandro; Borghi, Francesca; Indrieri, Marco; Bovio, Simone; Piazzoni, Claudio; Milani, Paolo

2015-12-01

Great emphasis is placed on the development of integrated approaches for the synthesis and the characterization of ad hoc nanostructured platforms, to be used as templates with controlled morphology and chemical properties for the investigation of specific phenomena of great relevance in interdisciplinary fields such as biotechnology, medicine, and advanced materials. Here, we discuss the crucial role and the advantages of thin film deposition strategies based on cluster-assembling from supersonic cluster beams. We select cluster-assembled nanostructured titania (ns-TiO2) as a case study to demonstrate that accurate control over morphological parameters can be routinely achieved, and consequently, over several relevant interfacial properties and phenomena, like surface charging in a liquid electrolyte, and proteins and nanoparticles adsorption. In particular, we show that the very good control of nanoscale morphology is obtained by taking advantage of simple scaling laws governing the ballistic deposition regime of low-energy, mass-dispersed clusters with reduced surface mobility.

[New toxicological patterns of nanomaterials, nanostructures and nanoparticles].

PubMed

Mazzotta, M; Mazzotta, A D; Fernández, M; Tamborino, B; De Filippis, G

2012-01-01

Nanomaterials engineered as nanotubes, quantum-dots, dendrimers or hybrid systems are increasing themselves by an annual mean rate of 4-5%, with rapid spread in various sectors e.g. biomedical. The liposolubility through membranes and the hydrosolubility through active transport do not interfere with nanoparticles below a certain size, which without activation processes and carrier, transport through thanks to capillaries, to intracellular pores (60 - 70 nm) and fissures (4 - 6 nm) in the same membranes. Conversely, in the processes of pinocytosis/endocytosis energy and carrier are required and endocytosis clathrin/caveolae mediated,is respectively for nanoparticles higher or lower than 200 nm. In occupational hazard nanostructures ranging from a few nm up to 100 - 150 nm have the ability to affect several organs through inhalation, intestinal, parental or dermal route of access. New toxicological aspects are associated to the capacity of nanomaterials of being more or less biocompatible or hydrosoluble, of creating bonds with proteins or to determine accumulation in the cells due to an incomplete elimination process.

Nanomanufacturing of titania interfaces with controlled structural and functional properties by supersonic cluster beam deposition

DOE Office of Scientific and Technical Information (OSTI.GOV)

Podestà, Alessandro, E-mail: alessandro.podesta@mi.infn.it, E-mail: pmilani@mi.infn.it; Borghi, Francesca; Indrieri, Marco

Great emphasis is placed on the development of integrated approaches for the synthesis and the characterization of ad hoc nanostructured platforms, to be used as templates with controlled morphology and chemical properties for the investigation of specific phenomena of great relevance in interdisciplinary fields such as biotechnology, medicine, and advanced materials. Here, we discuss the crucial role and the advantages of thin film deposition strategies based on cluster-assembling from supersonic cluster beams. We select cluster-assembled nanostructured titania (ns-TiO{sub 2}) as a case study to demonstrate that accurate control over morphological parameters can be routinely achieved, and consequently, over several relevantmore » interfacial properties and phenomena, like surface charging in a liquid electrolyte, and proteins and nanoparticles adsorption. In particular, we show that the very good control of nanoscale morphology is obtained by taking advantage of simple scaling laws governing the ballistic deposition regime of low-energy, mass-dispersed clusters with reduced surface mobility.« less

Computational models for the berry phase in semiconductor quantum dots

DOE Office of Scientific and Technical Information (OSTI.GOV)

Prabhakar, S., E-mail: rmelnik@wlu.ca; Melnik, R. V. N., E-mail: rmelnik@wlu.ca; Sebetci, A.

2014-10-06

By developing a new model and its finite element implementation, we analyze the Berry phase low-dimensional semiconductor nanostructures, focusing on quantum dots (QDs). In particular, we solve the Schrödinger equation and investigate the evolution of the spin dynamics during the adiabatic transport of the QDs in the 2D plane along circular trajectory. Based on this study, we reveal that the Berry phase is highly sensitive to the Rashba and Dresselhaus spin-orbit lengths.

Morphological and Electrochemical Characterization of Nanostructured Li 4Ti 5O 12 Electrodes Using Multiple Imaging Mode Synchrotron X-ray Computed Tomography

DOE PAGES

Kashkooli, Ali Ghorbani; Foreman, Evan; Farhad, Siamak; ...

2017-09-21

In this study, synchrotron X-ray computed tomography has been utilized using two different imaging modes, absorption and Zernike phase contrast, to reconstruct the real three-dimensional (3D) morphology of nanostructured Li 4Ti 5O 12 (LTO) electrodes. The morphology of the high atomic number active material has been obtained using the absorption contrast mode, whereas the percolated solid network composed of active material and carbon-doped polymer binder domain (CBD) has been obtained using the Zernike phase contrast mode. The 3D absorption contrast image revealed that some LTO nano-particles tend to agglomerate and form secondary micro-sized particles with varying degrees of sphericity. Themore » tortuosity of electrode’s pore and solid phases were found to have directional dependence, different from Bruggeman’s tortuosity commonly used in macro-homogeneous models. The electrode’s heterogeneous structure was investigated by developing a numerical model to simulate galvanostatic discharge process using the Zernike phase contrast mode. The inclusion of CBD in the Zernike phase contrast results in an integrated percolated network of active material and CBD that is highly suited for continuum modeling. As a result, the simulation results highlight the importance of using the real 3D geometry since the spatial distribution of physical and electrochemical properties have a strong non-uniformity due to microstructural heterogeneities.« less

Interpretation of diffusion coefficients in nanostructured materials from random walk numerical simulation.

PubMed

Anta, Juan A; Mora-Seró, Iván; Dittrich, Thomas; Bisquert, Juan

2008-08-14

We make use of the numerical simulation random walk (RWNS) method to compute the "jump" diffusion coefficient of electrons in nanostructured materials via mean-square displacement. First, a summary of analytical results is given that relates the diffusion coefficient obtained from RWNS to those in the multiple-trapping (MT) and hopping models. Simulations are performed in a three-dimensional lattice of trap sites with energies distributed according to an exponential distribution and with a step-function distribution centered at the Fermi level. It is observed that once the stationary state is reached, the ensemble of particles follow Fermi-Dirac statistics with a well-defined Fermi level. In this stationary situation the diffusion coefficient obeys the theoretical predictions so that RWNS effectively reproduces the MT model. Mobilities can be also computed when an electrical bias is applied and they are observed to comply with the Einstein relation when compared with steady-state diffusion coefficients. The evolution of the system towards the stationary situation is also studied. When the diffusion coefficients are monitored along simulation time a transition from anomalous to trap-limited transport is observed. The nature of this transition is discussed in terms of the evolution of electron distribution and the Fermi level. All these results will facilitate the use of RW simulation and related methods to interpret steady-state as well as transient experimental techniques.

Evaluation of size, morphology, concentration, and surface effect of gold nanoparticles on X-ray attenuation in computed tomography.

PubMed

Khademi, Sara; Sarkar, Saeed; Kharrazi, Sharmin; Amini, Seyed Mohammad; Shakeri-Zadeh, Ali; Ay, Mohammad Reza; Ghadiri, Hossein

2018-01-01

Increasing attention has been focused on the use of nanostructures as contrast enhancement agents in medical imaging, especially in computed tomography (CT). To date, gold nanoparticles (GNPs) have been demonstrated to have great potential as contrast agents for CT imaging. This study was designed to evaluate any effect on X-ray attenuation that might result from employing GNPs with a variety of shapes, sizes, surface chemistries, and concentrations. Gold nanorods (GNRs) and spherical GNPs were synthesized for this application. X-ray attenuation was quantified by Hounsfield unit (HU) in CT. Our findings indicated that smaller spherical GNPs (13 nm) had higher X-ray attenuation than larger ones (60 nm) and GNRs with larger aspect ratio exhibited great effect on X-ray attenuation. Moreover, poly ethylene glycol (PEG) coating on GNRs declined X-ray attenuation as a result of limiting the aggregation of GNRs. We observed X-ray attenuation increased when mass concentration of GNPs was elevated. Overall, smaller spherical GNPs can be suggested as a better alternative to Omnipaque, a good contrast agent for CT imaging. This data can be also considered for the application of gold nanostructures in radiation dose enhancement where nanoparticles with high X-ray attenuation are applied. Copyright © 2017 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

Dispersion and separation of nanostructured carbon in organic solvents

NASA Technical Reports Server (NTRS)

Evans, Christopher M. (Inventor); Ruf, Herbert J. (Inventor); Landi, Brian J. (Inventor); Raffaelle, Ryne P. (Inventor)

2011-01-01

The present invention relates to dispersions of nanostructured carbon in organic solvents containing alkyl amide compounds and/or diamide compounds. The invention also relates to methods of dispersing nanostructured carbon in organic solvents and methods of mobilizing nanostructured carbon. Also disclosed are methods of determining the purity of nanostructured carbon.

Inorganic nanostructure-organic polymer heterostructures useful for thermoelectric devices

DOE Office of Scientific and Technical Information (OSTI.GOV)

See, Kevin C.; Urban, Jeffrey J.; Segalman, Rachel A.

The present invention provides for an inorganic nanostructure-organic polymer heterostructure, useful as a thermoelectric composite material, comprising (a) an inorganic nanostructure, and (b) an electrically conductive organic polymer disposed on the inorganic nanostructure. Both the inorganic nanostructure and the electrically conductive organic polymer are solution-processable.

Dendritic Core-Frame and Frame Multimetallic Rhombic Dodecahedra: A Comparison Study of Composition and Structure Effects on Electrocatalysis of Methanol Oxidation

DOE PAGES

Mathurin, Leanne E.; Tao, Jing; Xin, Huolin; ...

2017-11-03

The composition and structure of multimetallic nanostructures can be tailored to enhance electrocatalytic properties. This work reports a seed-mediated synthesis of novel multimetallic dendritic core-frame and frame nanostructures with a rhombic dodecahedral shape for enhanced methanol oxidation reaction (MOR). The synthesis involves in situ formation of Cu seeds and the subsequent selective deposition of Pt and Ru on the edges and vertices of the Cu seeds to generate CuPt and CuPtRu dendritic core-frame nanostructures. The core-frame nanostructures undergo a post acetic acid etching process to form the frame nanostructures. While transmission electron microscopy reveals the morphology and elemental distribution ofmore » the nanostructures, X-ray diffraction patterns confirm the alloy compositions of dendritic frames for both the core-frame and frame nanostructures. Compared to the bimetallic CuPt nanostructures, the trimetallic CuPtRu nanostructures lower the onset potential and completely suppress the peak current in the reverse scan for MOR. The CuPtRu alloyed frame nanostructures are the best to prevent Ru leaching compared to the CuPtRu core-frame nanostructures and PtRu catalysts. X-ray photoelectron spectroscopy reveals that all three elements become more electron rich in the frame nanostructures. Thus, further refining the composition ratio of the CuPtRu alloyed dendritic frame nanostructures can lead to more efficient catalysts at a lower cost for MOR.« less

Dendritic Core-Frame and Frame Multimetallic Rhombic Dodecahedra: A Comparison Study of Composition and Structure Effects on Electrocatalysis of Methanol Oxidation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mathurin, Leanne E.; Tao, Jing; Xin, Huolin

The composition and structure of multimetallic nanostructures can be tailored to enhance electrocatalytic properties. This work reports a seed-mediated synthesis of novel multimetallic dendritic core-frame and frame nanostructures with a rhombic dodecahedral shape for enhanced methanol oxidation reaction (MOR). The synthesis involves in situ formation of Cu seeds and the subsequent selective deposition of Pt and Ru on the edges and vertices of the Cu seeds to generate CuPt and CuPtRu dendritic core-frame nanostructures. The core-frame nanostructures undergo a post acetic acid etching process to form the frame nanostructures. While transmission electron microscopy reveals the morphology and elemental distribution ofmore » the nanostructures, X-ray diffraction patterns confirm the alloy compositions of dendritic frames for both the core-frame and frame nanostructures. Compared to the bimetallic CuPt nanostructures, the trimetallic CuPtRu nanostructures lower the onset potential and completely suppress the peak current in the reverse scan for MOR. The CuPtRu alloyed frame nanostructures are the best to prevent Ru leaching compared to the CuPtRu core-frame nanostructures and PtRu catalysts. X-ray photoelectron spectroscopy reveals that all three elements become more electron rich in the frame nanostructures. Thus, further refining the composition ratio of the CuPtRu alloyed dendritic frame nanostructures can lead to more efficient catalysts at a lower cost for MOR.« less

From Spintronics to CFD/ContractForDifferences

NASA Astrophysics Data System (ADS)

Maksoed, W. H.

2015-11-01

Involve the CFD/Computational Fluid Dynamics & HCCI/Homogeneous Charge Compression Ignition - Marcine Frackowiak, dissertation, 2009, for CFD/Contract For Differences accompanied by ``One Man's Crusade to Exonerate Hydrogen for Hindenburg Disaster'' of Addison BAIN, APS News, v. 9, n.7 (July 2000) concludes ``ignition of the blaze'' are responsible to those May, 1937 Accidents. Spintronics their selves include active control & manipulation of spin degree of freedom ever denotes: the nano-obelisk of scanning electron microscopy of galliumnitride/GaN nanostructures-Yong-Hon Cho et al.:``Novel Photonic Device using core-shell nanostructures'', SPIE-newsroom,10.1117/2.1201503.005864. Herewith commercial activated carbon/C can be imaged directly using abberation-corrected transmission electron microscopy[PJF Harris et al.: ``Imaging the Atomic Structures of activated C'', J. Phys. Condens. Matt, 20 (2008) in fig b & c- images networks of hexagonal rings can be clearly be seen depicts equal etchings of 340 px Akhenaten, Nefertiti & their childrens. Incredible acknowledgments to Minister of Education & Culture RI 1998-1999 HE. Mr. Prof. Ir. WIRANTO ARISMUNANDAR, MSME.

A methodology for modeling surface effects on stiff and soft solids

NASA Astrophysics Data System (ADS)

He, Jin; Park, Harold S.

2017-09-01

We present a computational method that can be applied to capture surface stress and surface tension-driven effects in both stiff, crystalline nanostructures, like size-dependent mechanical properties, and soft solids, like elastocapillary effects. We show that the method is equivalent to the classical Young-Laplace model. The method is based on converting surface tension and surface elasticity on a zero-thickness surface to an initial stress and corresponding elastic properties on a finite thickness shell, where the consideration of geometric nonlinearity enables capturing the out-of-plane component of the surface tension that results for curved surfaces through evaluation of the surface stress in the deformed configuration. In doing so, we are able to use commercially available finite element technology, and thus do not require consideration and implementation of the classical Young-Laplace equation. Several examples are presented to demonstrate the capability of the methodology for modeling surface stress in both soft solids and crystalline nanostructures.

A methodology for modeling surface effects on stiff and soft solids

NASA Astrophysics Data System (ADS)

He, Jin; Park, Harold S.

2018-06-01

We present a computational method that can be applied to capture surface stress and surface tension-driven effects in both stiff, crystalline nanostructures, like size-dependent mechanical properties, and soft solids, like elastocapillary effects. We show that the method is equivalent to the classical Young-Laplace model. The method is based on converting surface tension and surface elasticity on a zero-thickness surface to an initial stress and corresponding elastic properties on a finite thickness shell, where the consideration of geometric nonlinearity enables capturing the out-of-plane component of the surface tension that results for curved surfaces through evaluation of the surface stress in the deformed configuration. In doing so, we are able to use commercially available finite element technology, and thus do not require consideration and implementation of the classical Young-Laplace equation. Several examples are presented to demonstrate the capability of the methodology for modeling surface stress in both soft solids and crystalline nanostructures.

Impact of distributions on the archetypes and prototypes in heterogeneous nanoparticle ensembles.

PubMed

Fernandez, Michael; Wilson, Hugh F; Barnard, Amanda S

2017-01-05

The magnitude and complexity of the structural and functional data available on nanomaterials requires data analytics, statistical analysis and information technology to drive discovery. We demonstrate that multivariate statistical analysis can recognise the sets of truly significant nanostructures and their most relevant properties in heterogeneous ensembles with different probability distributions. The prototypical and archetypal nanostructures of five virtual ensembles of Si quantum dots (SiQDs) with Boltzmann, frequency, normal, Poisson and random distributions are identified using clustering and archetypal analysis, where we find that their diversity is defined by size and shape, regardless of the type of distribution. At the complex hull of the SiQD ensembles, simple configuration archetypes can efficiently describe a large number of SiQDs, whereas more complex shapes are needed to represent the average ordering of the ensembles. This approach provides a route towards the characterisation of computationally intractable virtual nanomaterial spaces, which can convert big data into smart data, and significantly reduce the workload to simulate experimentally relevant virtual samples.

Selective far-field addressing of coupled quantum dots in a plasmonic nanocavity.

PubMed

Tang, Jianwei; Xia, Juan; Fang, Maodong; Bao, Fanglin; Cao, Guanjun; Shen, Jianqi; Evans, Julian; He, Sailing

2018-04-27

Plasmon-emitter hybrid nanocavity systems exhibit strong plasmon-exciton interactions at the single-emitter level, showing great potential as testbeds and building blocks for quantum optics and informatics. However, reported experiments involve only one addressable emitting site, which limits their relevance for many fundamental questions and devices involving interactions among emitters. Here we open up this critical degree of freedom by demonstrating selective far-field excitation and detection of two coupled quantum dot emitters in a U-shaped gold nanostructure. The gold nanostructure functions as a nanocavity to enhance emitter interactions and a nanoantenna to make the emitters selectively excitable and detectable. When we selectively excite or detect either emitter, we observe photon emission predominantly from the target emitter with up to 132-fold Purcell-enhanced emission rate, indicating individual addressability and strong plasmon-exciton interactions. Our work represents a step towards a broad class of plasmonic devices that will enable faster, more compact optics, communication and computation.

Actively addressed single pixel full-colour plasmonic display

PubMed Central

Franklin, Daniel; Frank, Russell; Wu, Shin-Tson; Chanda, Debashis

2017-01-01

Dynamic, colour-changing surfaces have many applications including displays, wearables and active camouflage. Plasmonic nanostructures can fill this role by having the advantages of ultra-small pixels, high reflectivity and post-fabrication tuning through control of the surrounding media. However, previous reports of post-fabrication tuning have yet to cover a full red-green-blue (RGB) colour basis set with a single nanostructure of singular dimensions. Here, we report a method which greatly advances this tuning and demonstrates a liquid crystal-plasmonic system that covers the full RGB colour basis set, only as a function of voltage. This is accomplished through a surface morphology-induced, polarization-dependent plasmonic resonance and a combination of bulk and surface liquid crystal effects that manifest at different voltages. We further demonstrate the system's compatibility with existing LCD technology by integrating it with a commercially available thin-film-transistor array. The imprinted surface interfaces readily with computers to display images as well as video. PMID:28488671

Approaching the resolution limit of W-C nano-gaps using focused ion beam chemical vapour deposition

NASA Astrophysics Data System (ADS)

Dai, Jun; Chang, Hui; Maeda, Etsuo; Warisawa, Shin'ichi; Kometani, Reo

2018-01-01

Nano-gaps are fundamental building blocks for nanochannels, plasmonic nanostructures and superconducting Josephson junctions. We present a systematic study on the formation mechanism and resolution limit of W-C nano-gaps fabricated using focused-ion-beam chemical vapour deposition (FIB-CVD). First, the deposition size of the nanostructures is evaluated. The size averaged over 100 dots is 32 nm at FWHM. Line and space are also fabricated with the smallest size, having a spacing of only 5 nm at FWHM. Then, a model is developed to study the formation mechanism and provides the design basis for W-C nano-gaps. Both experimental and simulation results reveal that the shrinkage of W-C nano-gaps is accelerated as the Gaussian parts of the nano-wire profiles overlap. A Nano-gap with a length of 5 nm and height difference as high as 42 nm is synthesized. We believe that FIB-CVD opens avenues for novel functional nanodevices that can be potentially used for biosensing, photodetecting, or quantum computing.

Using a double-doping strategy to improve physical properties of nanostructured CdO films

NASA Astrophysics Data System (ADS)

Aydin, R.; Sahin, B.

2018-06-01

In this present study nanostructured dually doped samples of Cd1‑x‑yMgxMyO (M: Sn, Pb, Bi) are synthesized by SILAR method. The effects of the mono and dual doping on the structural, morphological and optoelectronic characteristics of CdO nanoparticles are examined. The SEM images verify that deposited CdO films are nano-sized. Also the SEM computations demonstrated that the morphological surface structures of the films were influenced from the Mg mono doping and (Mg, Sn), (Mg, Pb) and (Mg, Bi) dual doping. The XRD designs specified that all the CdO samples have polycrystalline structure exhibiting cubic crystal form with dominant peaks of (111) and (220). The results display that Mg and (Mg, Sn), (Mg, Pb) and (Mg, Bi) ions were successfully doped into CdO film matrix. The UV spectroscopy results show that the optical energy band gap of the CdO films, ranging from 2.21 to 2.66 eV, altered with the dopant materials.

Assessment of Automated Analyses of Cell Migration on Flat and Nanostructured Surfaces

PubMed Central

Grădinaru, Cristian; Łopacińska, Joanna M.; Huth, Johannes; Kestler, Hans A.; Flyvbjerg, Henrik; Mølhave, Kristian

2012-01-01

Motility studies of cells often rely on computer software that analyzes time-lapse recorded movies and establishes cell trajectories fully automatically. This raises the question of reproducibility of results, since different programs could yield significantly different results of such automated analysis. The fact that the segmentation routines of such programs are often challenged by nanostructured surfaces makes the question more pertinent. Here we illustrate how it is possible to track cells on bright field microscopy images with image analysis routines implemented in an open-source cell tracking program, PACT (Program for Automated Cell Tracking). We compare the automated motility analysis of three cell tracking programs, PACT, Autozell, and TLA, using the same movies as input for all three programs. We find that different programs track overlapping, but different subsets of cells due to different segmentation methods. Unfortunately, population averages based on such different cell populations, differ significantly in some cases. Thus, results obtained with one software package are not necessarily reproducible by other software. PMID:24688640

Effects of hierarchical structures and insulating liquid media on adhesion

NASA Astrophysics Data System (ADS)

Yang, Weixu; Wang, Xiaoli; Li, Hanqing; Song, Xintao

2017-11-01

Effects of hierarchical structures and insulating liquid media on adhesion are investigated through a numerical adhesive contact model established in this paper, in which hierarchical structures are considered by introducing the height distribution into the surface gap equation, and media are taken into account through the Hamaker constant in Lifshitz-Hamaker approach. Computational methods such as inexact Newton method, bi-conjugate stabilized (Bi-CGSTAB) method and fast Fourier transform (FFT) technique are employed to obtain the adhesive force. It is shown that hierarchical structured surface exhibits excellent anti-adhesive properties compared with flat, micro or nano structured surfaces. Adhesion force is more dependent on the sizes of nanostructures than those of microstructures, and the optimal ranges of nanostructure pitch and maximum height for small adhesion force are presented. Insulating liquid media effectively decrease the adhesive interaction and 1-bromonaphthalene exhibits the smallest adhesion force among the five selected media. In addition, effects of hierarchical structures with optimal sizes on reducing adhesion are more obvious than those of the selected insulating liquid media.

Light absorption and plasmon – exciton interaction in three-layer nanorods with a gold core and outer shell composed of molecular J- and H-aggregates of dyes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shapiro, B I; Tyshkunova, E S; Kondorskiy, A D

2015-12-31

Optical properties of hybrid rod-like nanoparticles, consisting of a gold core, an intermediate passive organic layer (spacer) and outer layer of ordered molecular cyanine dye aggregates, are experimentally and theoretically investigated. It is shown that these dyes can form not only ordered J-aggregates but also H-aggregates (differing by the packing angle of dye molecules in an aggregate and having other spectral characteristics) in the outer shell of the hybrid nanostructure. Absorption spectra of synthesised three-layer nanorods are recorded, and their sizes are determined. The optical properties of the composite nanostructures under study are found to differ significantly, depending on themore » type of the molecular aggregate formed in the outer shell. The experimental data are quantitatively explained based on computer simulation using the finite-difference time-domain (FDTD) method, and characteristic features of the plasmon – exciton interaction in the systems under study are revealed. (nanophotonics)« less

Polymer adsorption-driven self-assembly of nanostructures.

PubMed

Chakraborty, A K; Golumbfskie, A J

2001-01-01

Driven by prospective applications, there is much interest in developing materials that can perform specific functions in response to external conditions. One way to design such materials is to create systems which, in response to external inputs, can self-assemble to form structures that are functionally useful. This review focuses on the principles that can be employed to design macromolecules that when presented with an appropriate two-dimensional surface, will self-assemble to form nanostructures that may be functionally useful. We discuss three specific examples: (a) biomimetic recognition between polymers and patterned surfaces. (b) control and manipulation of nanomechanical motion generated by biopolymer adsorption and binding, and (c) creation of patterned nanostructuctures by exposing molten diblock copolymers to patterned surfaces. The discussion serves to illustrate how polymer sequence can be manipulated to affect self-assembly characteristics near adsorbing surfaces. The focus of this review is on theoretical and computational work aimed toward elucidating the principles underlying the phenomena pertinent to the three topics noted above. However, synergistic experiments are also described in the appropriate context.

Interaction of plasmas with lithium and tungsten fusion plasma facing components

NASA Astrophysics Data System (ADS)

Fiflis, Peter Robert

One of the largest outstanding issues in magnetic confinement fusion is the interaction of the fusion plasma with the first wall of the device; an interaction which is strongest in the divertor region. Erosion, melting, sputtering, and deformation are all concerns which inform choices of divertor material. Of the many materials proposed for use in the divertor, only a few remain as promising choices. Tungsten has been chosen as the material for the ITER divertor, and liquid lithium stands poised as its replacement in higher heat flux devices. As a refractory metal, tungsten's large melting point and thermal conductivity as well as its low sputtering yield have led to its selection as the material of choice of the ITER divertor. Experiments have reinforced this choice demonstrating tungsten's ability to withstand large heat fluxes when adequately cooled. However, tungsten has shown a propensity to nanostructure under exposure within a certain temperature range to large fluxes of helium ions. These nanostructures if disrupted into the plasma as dust by an off-normal event would cause quenching of the plasma from the generated dust. Liquid lithium, meanwhile, has gathered growing interest within the fusion community in recent years as a divertor, limiter, and alternative first wall material. Liquid lithium is attractive as a low-Z material replacement for refractory metals due to its ability to getter impurities, while also being self-healing in nature. However, concerns exist about the stability of a liquid metal surface at the edge of a fusion device. Liquid metal pools, such as the Li-DiMes probe, have shown evidence of macroscopic lithium displacement as well as droplet formation and ejection into the plasma. These issues must be mitigated in future implementations of liquid lithium divertor concepts. Rayleigh-Taylor-like (RT) and Kelvin-Helmholtz-like (KH) instabilities have been claimed as the initiators of droplet ejection, yet not enough data exists to delineate a stability boundary. The influences of plasma pressure and current driven instabilities on lithium surfaces that lead to droplet ejection are investigated to determine which of the two effects is dominant for a given set of plasma conditions. This work studies the influence of large plasma fluxes on these two materials to better inform the selection and design of plasma facing components (PFCs). The nanostructuring of tungsten was investigated to determine the mechanisms by which tungsten nanostructures so that its formation may be mitigated. Experiments investigated the dependence of nanostructuring on temperature, looked at the morphological evolution, and grew nanostructures on a variety of metals to examine their similarity to tungsten. Additionally, a computational model is presented for the initial stages of fuzz formation showing good quantitative and qualitative agreement with experimental observations. The influences of RT and KH instabilities on the surface of liquid lithium were experimentally observed and quantified on the ThermoElectric-driven Liquid-metal plasma-facing Structures (TELS) chamber at the University of Illinois at Urbana-Champaign and the stabilizing effect of surface tension, an effect employed by the LiMIT concept as well as other liquid lithium concepts, was studied, and the stability boundary afforded by surface tension was compared between experiment, computational simulation, and theory.

Synthesis of polymer nanostructures via the use of surfactant surface aggregates as templates

NASA Astrophysics Data System (ADS)

Marquez, Maricel

The subject of this work is the synthesis of polymer nanostructures via the use of surfactant surface aggregates as templates, also termed Template Assisted Admicellar Polymerization (TAAP). The first chapter reviews some of the most current nanopatterning techniques (including both top-down and bottom-up approaches), with particular emphasis on the fabrication of organic and inorganic patterned nanostructures via particle lithography. In chapter 2, highly ordered hexagonal arrays of latex spheres were prepared on highly ordered pyrolytic graphite (HOPG) from a variation of the Langmuir Blodgett technique, using an anionic surfactant (SDS), and a low molecular weight (ca. 10000) polyacrylamide as spreading agents. When a nonionic polyethoxylated (EO = 9) surfactant was used as the spreading agent, no ordered arrays were observed. Based on the correlation found between the surface tension in the presence of the latex particles and the critical concentration at which hexagonal arrangements of latex spheres occurs; a model was proposed to explain the role of the spreading agent in forming stable monolayers at the air/liquid interface, which in turn are necessary for the formation of well-ordered monolayers on a solid substrate from the LB technique. According to this model, solid-like regions of small numbers of latex spheres form at the liquid-air interface, which are then transferred to the substrate. These ordered regions then act as nuclei for the formation of 2D arrays of latex spheres on the surface upon water evaporation. The role of other factors such as relative humidity, substrate and solvent choice, and pulling vs. compression speed were also found to affect the quality of the monolayers formed. Finally, a simple, easy to automate, yet effective surface tension method was proposed to predict the optimal conditions for the formation of ordered monolayers using a variation of the LB deposition method from any monodisperse set of spheres. In chapter 3, a novel method for the formation of nanometer-scale polymer structures on solid surfaces via template assisted admicellar polymerization (TAAP) is described. Admicellar polymerization uses a surfactant layer adsorbed on a surface to localize monomer to the surface prior to polymerization of the monomer. TAAP refers to nanostructures that form by restricting adsorption to the uncovered sites of an already-templated surface. In this case, the interstitial sites between adsorbed latex spheres were used as the template. Unlike most other process that form polymer nanostructures, polymer dimensions can be significantly smaller than the interstitial size because of sphere-surfactant-monomer interactions. As a proof of concept, nanostructures formed via TAAP were compared to structures prepared by others via adsorption of three different proteins (Bovine serum albumin, fibrinogen, and anti-mouse IgG) in the interstitial sites of colloidal monolayers. The size and shape of the nanostructures formed (honeycomb vs. pillars) was dependent upon the size of the spheres utilized and the method of polymer deposition (i.e. admicellar polymerization vs. polymer adsorption). Thinner honeycomb walls, and larger separation distances between the template and the nanostructures were consistently found for TAAP. In chapter 4, an in-depth study of the factors affecting TAAP is presented for three different monomers: aniline, pyrrole and methyl methacrylate; and three different surfaces: highly ordered pyrolytic graphite (HOPG), gold, and SiO2. Among the parameters discussed are the effect of monomer and surfactant concentration, surfactant chain length, polymerization time and temperature, solution ionic strength, substrate choice and surface treatment. Control over these parameters allowed the synthesis of polymer nanopillars, nanorings, honeycombs, and "honeytubes." Experimental results showed that the nanostructures' morphology can be effectively modified by changing the length of the hydrophobic chain of the surfactant. Nanostructures with fewer defects were found for surfactants with the longest hydrophobic tails (i.e. 12 carbon atoms). The hydrophobic nature of the monomer also seemed to affect the morphology of the nanostructure; poly(methyl methacrylate) (PMMA) honeycombs showed thicker walls compared to polyaniline (PANI) and polypyrrole (Ppy). In general, HOPG seems to be a better choice of substrate for TAAP compared to gold-coated glass and SiO2 wafers. Preliminary results on the formation of layered polymer nanostructures via multiple TAAP sequences were also presented.

Computational Prediction of Protein-Protein Interactions

PubMed Central

Ehrenberger, Tobias; Cantley, Lewis C.; Yaffe, Michael B.

2015-01-01

The prediction of protein-protein interactions and kinase-specific phosphorylation sites on individual proteins is critical for correctly placing proteins within signaling pathways and networks. The importance of this type of annotation continues to increase with the continued explosion of genomic and proteomic data, particularly with emerging data categorizing posttranslational modifications on a large scale. A variety of computational tools are available for this purpose. In this chapter, we review the general methodologies for these types of computational predictions and present a detailed user-focused tutorial of one such method and computational tool, Scansite, which is freely available to the entire scientific community over the Internet. PMID:25859943

NASA Tech Briefs, October 2006

NASA Technical Reports Server (NTRS)

2006-01-01

Topics covered include: Protein Sensors Based on Optical Ring Resonators; Phase Sensor for Aligning a Segmented Telescope Mirror; Control Software for Advanced Video Guidance Sensor; Generating Control Commands From Gestures Sensed by EMG; Multiple-Flat-Panel System Displays Multidimensional Data; 3D X-Ray Luggage-Screening System; Probe Station and Near-Field Scanner for Testing Antennas; Photodetector Arrays for Multicolor Visible/Infrared Imaging; Semiconductor Bolometers Give Background-Limited Performance; Multichannel X-Band Dielectric-Resonator Oscillator; Automatic Alignment of Displacement-Measuring Interferometer; Earth Observing System Data Gateway; Power User Interface; Mercury Shopping Cart Interface; Cassini Archive Tracking System; Architecture Adaptive Computing Environment; Computing Fault Displacements from Surface Deformations; Oxygen-Permeable, Hydrophobic Membranes of Silanized alpha-Al2O3; SiC Composite Turbine Vanes; Retaining Device for the Interior Structure of a Spacecraft Payload; Tool for Torquing Circular Electrical-Connector Collars; System for Continuous Deaeration of Hydraulic Oil; Solar-Powered Cooler and Heater for an Automobile Interior; Improved Oxygen-Beam Texturing of Glucose-Monitoring Optics; Tool for Two Types of Friction Stir Welding; Stationary Apparatus Would Apply Forces of Walking to Feet; Instrument Would Detect and Collect Biological Aerosols; Boundary Condition for Modeling Semiconductor Nanostructures; Miniature Distillation Column for Producing LOX From Air; Even Illumination from Fiber-Optic-Coupled Laser Diodes; Optically Driven Deformable Mirrors; Algorithm for Automated Detection of Edges of Clouds; Exploiting Quantum Resonance to Solve Combinatorial Problems; Hybrid Terrain Database; On Release of Microbe-Laden Particles from Mars Landers; A Concept for Run-Time Support of the Chapel Language; Thermoelectric Inhomogeneities in (Ag(sub 1-y)SbTe2)(sub x)(PbTe)(sub 1-x); and Spacecraft Escape Capsule.

Multiscale Simulation of Microbe Structure and Dynamics

PubMed Central

Joshi, Harshad; Singharoy, Abhishek; Sereda, Yuriy V.; Cheluvaraja, Srinath C.; Ortoleva, Peter J.

2012-01-01

A multiscale mathematical and computational approach is developed that captures the hierarchical organization of a microbe. It is found that a natural perspective for understanding a microbe is in terms of a hierarchy of variables at various levels of resolution. This hierarchy starts with the N -atom description and terminates with order parameters characterizing a whole microbe. This conceptual framework is used to guide the analysis of the Liouville equation for the probability density of the positions and momenta of the N atoms constituting the microbe and its environment. Using multiscale mathematical techniques, we derive equations for the co-evolution of the order parameters and the probability density of the N-atom state. This approach yields a rigorous way to transfer information between variables on different space-time scales. It elucidates the interplay between equilibrium and far-from-equilibrium processes underlying microbial behavior. It also provides framework for using coarse-grained nanocharacterization data to guide microbial simulation. It enables a methodical search for free-energy minimizing structures, many of which are typically supported by the set of macromolecules and membranes constituting a given microbe. This suite of capabilities provides a natural framework for arriving at a fundamental understanding of microbial behavior, the analysis of nanocharacterization data, and the computer-aided design of nanostructures for biotechnical and medical purposes. Selected features of the methodology are demonstrated using our multiscale bionanosystem simulator DeductiveMultiscaleSimulator. Systems used to demonstrate the approach are structural transitions in the cowpea chlorotic mosaic virus, RNA of satellite tobacco mosaic virus, virus-like particles related to human papillomavirus, and iron-binding protein lactoferrin. PMID:21802438

Fabrication of Nanostructures on Implantable Biomaterials for Biocompatibility Enhancement and Infection Resistance

NASA Astrophysics Data System (ADS)

Liu, Luting

An implant or implantable medical device, which is used to replace or restore the function of traumatized or degenerated tissues or organs, or acts as a fraction of or the whole biological structure, has been used in many different parts of the body for various applications (such as orthopedics, cardiovascular stents, or drug delivery systems for medical treatment). The best performance of the vast majority of implants is achieved when the biomaterial used promotes some biological activity (such as bone regeneration) while minimizing undesirable activity (such as infection, one of the most common reasons for the failure of many implants). The surface of the implant, through its interactions with proteins, bacteria and tissue forming cells, plays a critical role in the success or failure of the implant. Therefore, in this study, we sought to employ various nanofabrication techniques for tailoring implant surfaces to minimize bacteria and promote mammalian cell functions without using drugs. Titanium (Ti) and polyetheretherketone (PEEK) are commonly used biomaterials in orthopedic implants. Further surface modification is needed to support osseointegration while inhibiting bacteria attachment. Herein, temperature controlled atomic layer deposition (ALD) was utilized to provide unique nanostructured TiO2 coatings on commercial Ti. In vitro bacteria experiments revealed that the nano-TiO2 coatings showed promising antimicrobial efficacy towards Gram-positive bacteria (S. aureus), Gram-negative bacteria (E. coli) and antibiotic-resistant bacteria ( MRSA). Impressively, cell results indicated that this nano-TiO 2 coating stimulated osteoblast (or bone forming cell) adhesion and proliferation while suppressing undesirable fibroblast functions. The same procedure was performed on PEEK and also resulted in enhanced osteoblast functions and produced antimicrobial properties. In another study, to isolate the effect of surface chemistry on cell and bacteria activities, a simple template-molding method (in which a material with a special structure is used as a template to imprint its structure onto another material) with nanotubular anodized Ti was used to formulate a physical nanostructured pattern on a PDMS (a commonly used polymeric catheter material) surface without changing its surface chemistry. Results showed that increased PDMS surface nanoscale roughness alone inhibited both Gram-negative ( E. coli) and Gram-positive (S. aureus) bacteria adhesion and growth without using antibiotics while remaining non-toxic to fibroblasts and endothelial cells. A model was developed for the first time to correlate bacteria responses to nanoscale roughness with initial protein adsorption (specifically, casein protein, which is well known for preventing bacteria attachment). Data also revealed that an increase in nanoscale roughness and greater surface hydrophilicity together contributed to increased protein adsorption, which may decrease the interactions at the bacteria-nanorough surface interface and achieve effective antimicrobial properties. Mechanistically, this thesis also investigated the influence of specific surface properties (i.e., nanoscale surface roughness, surface wettability and associated surface energy) on cell and bacteria functions. Results showed a direct proportional linear correlation of surface energy with surface roughness. It was found that surface energy plays a major role in determining cell and bacteria functions, and specifically all proposed nanofabricated samples with an initial surface energy at 40 mJ/m2 showed relatively promising antibacterial properties and desirable cellular functions. Overall, the results of this study provided alternative, inexpensive, methods for fabricating various implant surfaces with nanostructures to enhance biocompatibility and prevent bacterial attachment simultaneously, which will be beneficial for numerous biomedical applications.

Molecular mechanics of silk nanostructures under varied mechanical loading.

PubMed

Bratzel, Graham; Buehler, Markus J

2012-06-01

Spider dragline silk is a self-assembling tunable protein composite fiber that rivals many engineering fibers in tensile strength, extensibility, and toughness, making it one of the most versatile biocompatible materials and most inviting for synthetic mimicry. While experimental studies have shown that the peptide sequence and molecular structure of silk have a direct influence on the stiffness, toughness, and failure strength of silk, few molecular-level analyses of the nanostructure of silk assemblies, in particular, under variations of genetic sequences have been reported. In this study, atomistic-level structures of wildtype as well as modified MaSp1 protein from the Nephila clavipes spider dragline silk sequences, obtained using an in silico approach based on replica exchange molecular dynamics and explicit water molecular dynamics, are subjected to simulated nanomechanical testing using different force-control loading conditions including stretch, pull-out, and peel. The authors have explored the effects of the poly-alanine length of the N. clavipes MaSp1 peptide sequence and identify differences in nanomechanical loading conditions on the behavior of a unit cell of 15 strands with 840-990 total residues used to represent a cross-linking β-sheet crystal node in the network within a fibril of the dragline silk thread. The specific loading condition used, representing concepts derived from the protein network connectivity at larger scales, have a significant effect on the mechanical behavior. Our analysis incorporates stretching, pull-out, and peel testing to connect biochemical features to mechanical behavior. The method used in this study could find broad applications in de novo design of silk-like tunable materials for an array of applications. Copyright © 2011 Wiley Periodicals, Inc.

Decreased bacteria activity on Si3N4 surfaces compared with PEEK or titanium

PubMed Central

Gorth, Deborah J; Puckett, Sabrina; Ercan, Batur; Webster, Thomas J; Rahaman, Mohamed; Bal, B Sonny

2012-01-01

A significant need exists for orthopedic implants that can intrinsically resist bacterial colonization. In this study, three biomaterials that are used in spinal implants – titanium (Ti), polyether-ether-ketone (PEEK), and silicon nitride (Si3N4) – were tested to understand their respective susceptibility to bacterial infection with Staphylococcus epidermidis, Staphlococcus aureus, Pseudomonas aeruginosa, Escherichia coli and Enterococcus. Specifically, the surface chemistry, wettability, and nanostructured topography of respective biomaterials, and the effects on bacterial biofilm formation, colonization, and growth were investigated. Ti and PEEK were received with as-machined surfaces; both materials are hydrophobic, with net negative surface charges. Two surface finishes of Si3N4 were examined: as-fired and polished. In contrast to Ti and PEEK, the surface of Si3N4 is hydrophilic, with a net positive charge. A decreased biofilm formation was found, as well as fewer live bacteria on both the as-fired and polished Si3N4. These differences may reflect differential surface chemistry and surface nanostructure properties between the biomaterials tested. Because protein adsorption on material surfaces affects bacterial adhesion, the adsorption of fibronectin, vitronectin, and laminin on Ti, PEEK, and Si3N4 were also examined. Significantly greater amounts of these proteins adhered to Si3N4 than to Ti or PEEK. The findings of this study suggest that surface properties of biomaterials lead to differential adsorption of physiologic proteins, and that this phenomenon could explain the observed in-vitro differences in bacterial affinity for the respective biomaterials. Intrinsic biomaterial properties as they relate to resistance to bacterial colonization may reflect a novel strategy toward designing future orthopedic implants. PMID:22973102

Confined-space synthesis of nanostructured anatase, directed by genetically engineered living organisms for lithium-ion batteries.

PubMed

Ping, Hang; Xie, Hao; Xiang, Mingyu; Su, Bao-Lian; Wang, Yucheng; Zhang, Jinyong; Zhang, Fan; Fu, Zhengyi

2016-10-01

Biomineral formation processes in nature are temporally and spatially regulated under the functions of biomolecules in a confined space. It is potentially very productive to rationally design a mineralized system by taking into account confined space as well as biomolecules. The laboratory technique of "bacterial cell surface display" is an ideal platform to host catalytically active proteins in a three-dimensionally confined space. In the present study, aiming to regulate the synthesis of nanostructured TiO 2 anatase, repeating segments of silaffin were displayed on Escherichia coli surfaces through genetic manipulation. The displayed protein electrostatically interacted with a titanium source and catalyzed the hydrolysis of titanium dioxide precursors through hydrogen bonding interactions on the cell surface. In the subsequent calcination process, the genetically modified cells not only served as a framework for producing rod-shaped TiO 2 assembled by nanoparticles, but also provided a carbon source in situ . The size of nanoparticles was controlled by changing the number of tandem repeats of the protein segment. The as prepared TiO 2 anatase exhibited unique characteristics including nanosized anatase crystals, mesoporous structure and carbon coating. When tested as the anode electrode of a lithium-ion battery, it showed excellent lithium storage performance. The carbon coated anatase anode shows a higher specific capacity of 207 mA h g -1 after 200 cycles at a current rate of 1C and an ultra-long cycling lifetime of 5000 cycles with an outstanding retention capacity of 149 mA h g -1 at a higher rate of 10C. This bioprocess-inspired approach may help broaden the scope and impact of nanosized biominerals.

Toward high-resolution computational design of helical membrane protein structure and function

PubMed Central

Barth, Patrick; Senes, Alessandro

2016-01-01

The computational design of α-helical membrane proteins is still in its infancy but has made important progress. De novo design has produced stable, specific and active minimalistic oligomeric systems. Computational re-engineering can improve stability and modulate the function of natural membrane proteins. Currently, the major hurdle for the field is not computational, but the experimental characterization of the designs. The emergence of new structural methods for membrane proteins will accelerate progress PMID:27273630

Growth of and defect reduction in nanoscale materials

DOEpatents

Jensen, Kenneth J [Berkeley, CA; Mickelson, William E [San Francisco, CA; Zettl, Alex K [Kensington, CA

2011-01-04

Methods by which the growth of a nanostructure may be precisely controlled by an electrical current are described here. In one embodiment, an interior nanostructure is grown to a predetermined geometry inside another nanostructure, which serves as a reaction chamber. The growth is effected by a catalytic agent loaded with feedstock for the interior nanostructure. Another embodiment allows a preexisting marginal quality nanostructure to be zone refined into a higher-quality nanostructure by driving a catalytic agent down a controlled length of the nanostructure with an electric current. In both embodiments, the speed of nanostructure formation is adjustable, and the growth may be stopped and restarted at will. The catalytic agent may be doped or undoped to produce semiconductor effects, and the bead may be removed via acid etching.

Enhanced photoluminescence of Alq3 via patterned array silver dendritic nanostructures

NASA Astrophysics Data System (ADS)

Hsu, Wei-Hsiu; Hsieh, Ming-Hao; Lo, Shih-Shou

2012-04-01

Various silver nanostructures, semi-ball, jungle, and dendritic, are demonstrated by an electrical deposition process. The formation of silver nanostructures with various morphologies is studied by the mechanism of the diffusion limited aggregation (DLA) model. A array pattern of silver nanostructures can be obtained when the conductive substrate was used in a uniform electrical filed. A thickness 500 nm of Alq3 thin-film was covered on the silver nanostructure by thermal evaporation method. The strongest intensity of Alq3 green emission was observed when the pattern-array dendritic silver nanostructure was covered by Alq3. It can be explained with the plasmonic coupling due to the Alq3 and dendritic nanostructure. The result can help us to further application the patterned-array silver dendritic nanostructure for advanced opto-electronic device.

DOE Office of Scientific and Technical Information (OSTI.GOV)

An, Bo; Jenkins, Janelle E; Sampath, Sujatha

Dragline silk from orb-weaving spiders is a copolymer of two large proteins, major ampullate spidroin 1 (MaSp1) and 2 (MaSp2). The ratio of these proteins is known to have a large variation across different species of orb-weaving spiders. NMR results from gland material of two different species of spiders, N. clavipes and A. aurantia, indicates that MaSp1 proteins are more easily formed into β-sheet nanostructures, while MaSp2 proteins form random coil and helical structures. To test if this behavior of natural silk proteins could be reproduced by recombinantly produced spider silk mimic protein, recombinant MaSp1/MaSp2 mixed fibers as well asmore » chimeric silk fibers from MaSp1 and MaSp2 sequences in a single protein were produced based on the variable ratio and conserved motifs of MaSp1 and MaSp2 in native silk fiber. Mechanical properties, solid-state NMR, and XRD results of tested synthetic fibers indicate the differing roles of MaSp1 and MaSp2 in the fiber and verify the importance of postspin stretching treatment in helping the fiber to form the proper spatial structure.« less

A Review on Potential of Proteins as an Excipient for Developing a Nano-Carrier Delivery System.

PubMed

Chakraborty, Amrita; Dhar, Pubali

2017-01-01

In neo-age research, nano-materials have emerged as potential tools for the revolution of diagnostic and therapeutic field because of their nano-scale effects, increased surface area-volume ratio, and other beneficial properties. For the last few decades, protein has been regarded as the most attractive and versatile natural bio-macromolecule among all of the available biopolymers. Protein is largely exploited as a nano-carrier system in the pharmaceutical industry due to its low cytotoxocity, biocompatibility, biodegradability, abundant renewable sources, significant attaching ability, clinically useful targeting, and site-specific efficient uptake. This review mainly emphasizes on the latest development and progress achieved in the utilization of protein as a nano-vehicle for a large number of therapeutics such as drugs, genes, hormones, enzymse, nutraceuticals, antibodies, peptides, etc. We also discuss the sources of protein materials, fabrication aspects, advantages, constraints, in vivo and in vitro studies and provide a comparative analysis between the different types of proteins as nano-carriers. The variation of the release pattern and molecular mechanism of the encapsulated molecule with respect to different protein types and various nano-structures are also highlighted here to explore the enormous promises of this novel approach.

Physical Aspects of Photodynamic Corneal Collagen Crosslinking

NASA Astrophysics Data System (ADS)

Kornfield, Julia

2012-02-01

Healthy vision depends on the stability of the shape of the cornea, which provides most of the lens power of the optical system of the eye. Diseases in which the cornea progressively undergoes irregular deformation over time (e.g., keratoconus) can be treated clinically by inducing additional protein-protein crosslinks using a photosensitizing drug and a tailored dose of light. Unfortunately, the treatment moving through clinical trials is toxic to cells in and on the cornea. A path to a safer treatment is offered by the nanostructure of the corneal stroma---reminiscent of a HEX phase in block copolymers with 30nm diameter collagen cylinders spaced 60nm center-to-center in a hydrogel matrix of proteoglycans and water. We show that using a photosensitizing drug that sequesters itself in the collagen fibrils can minimize the toxicity of therapeutic protein-protein cross-linking. Photorheology and transport measurements are used to quantify the parameters of a simple physical model that is useful for optimizing clinical protocols.

Controllable synthesis of protein-conjugated lead sulfide nanocubes by using bovine hemoglobin as a capping agent

NASA Astrophysics Data System (ADS)

Yang, Guangrui; Qin, Dezhi; Zhang, Li

2014-06-01

A simple, convenient, and controllable strategy was reported in this contribution for protein-assisted synthesis BHb-conjugated PbS nanocubes. Powder X-ray diffraction, energy disperse X-ray spectroscopy, transmission electron microscopy, high-resolution transmission electron microscopy, and selected-area electron diffraction characterizations were used to determine the structure and morphology of BHb-conjugated PbS nanocubes. The prepared PbS nanocrystals with cubic rock salt structure were uniform and monodispersed with homogeneous size around 12 nm. The results of Fourier transform infrared and circular dichroism assay proved that Pb2+/PbS had coordination interaction with functional groups of BHb besides physical-binding effect, and the secondary structure of protein significantly changed with this interaction. Thermogravimetric analysis results confirmed the existence of BHb in PbS nanocrystals and indicated that the conjugate bonds existed between PbS and BHb. A clear perspective was shown here that special nanostructure could be created by using proteins as a mediating template at the inorganic-organic interface.

Preparation and characterization of photocatalytic carbon dots-sensitized electrospun titania nanostructured fibers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Haopeng; Zhu, Yihua, E-mail: yhzhu@ecust.edu.cn; Cao, Huimin

2013-02-15

Graphical abstract: Display Omitted Highlights: ► The TiO{sub 2}-CDs nanostructured fibers are fabricated by using APS combining the electrospinning TiO{sub 2} nanostructured fibers and CDs. ► The CD can work as a photosensitizer in the degradation of rhodamine B under visible light irradiation. ► The TiO{sub 2}-CDs nanostructured fibers exhibit enhanced photocatalytic efficiency and can be easily handled and recycled. -- Abstract: The carbon dots (CDs) are new functional carbon-aceous materials. Compared to conventional dye molecules and semiconductor quantum dots, CDs are superior in chemical inertness and low toxicity. The TiO{sub 2}-CDs nanostructured fibers were fabricated by combining the electrospinningmore » technique and reflux method. Compared with the pure TiO{sub 2} nanostructured fibers and P25, the TiO{sub 2}-CDs nanostructured fibers exhibited enhanced photocatalytic efficiency of photodegradation of rhodamine B (RhB) under visible light irradiation. The enhanced photocatalytic activity of TiO{sub 2}-CDs nanostructured fibers could be attributed to the presence of CDs embedded in TiO{sub 2} nanostructured fibers. The CD can work as a photosensitizer in the degradation. Furthermore, the TiO{sub 2}-CDs nanostructured fibers could be easily handled and recycled due to their one-dimensional nanostructural property.« less

Hierarchical concave layered triangular PtCu alloy nanostructures: rational integration of dendritic nanostructures for efficient formic acid electrooxidation.

PubMed

Wu, Fengxia; Lai, Jianping; Zhang, Ling; Niu, Wenxin; Lou, Baohua; Luque, Rafael; Xu, Guobao

2018-05-08

The rational construction of multi-dimensional layered noble metal nanostructures is a great challenge since noble metals are not layer-structured materials. Herein, we report a one-pot hydrothermal synthetic method for PtCu hierarchical concave layered triangular (HCLT) nanostructures using dl-carnitine, KI, poly(vinylpyrrolidone), CuCl2, and H2PtCl6. The PtCu HCLT nanostructure is comprised of multilayered triangular dendrites. Its layer number is tunable by changing dl-carnitine concentrations, and the concavity/convexity of the PtCu triangle nanostructures is tunable by changing the H2PtCl6/CuCl2 ratio or KI concentrations. Hierarchical trigonal bipyramid nanoframes are also obtained under certain conditions. Because of its advantageous nanostructure and bimetallic synergetic effect, the obtained PtCu HCLT nanostructure exhibits enhanced electrocatalytic activity and prolonged stability to formic acid oxidation compared to commercial Pt black, Pd/C and some other nanostructures.

PREFACE: 3rd Workshop on Theory, Modelling and Computational Methods for Semiconductors (TMCSIII)

NASA Astrophysics Data System (ADS)

Califano, Marco; Migliorato, Max; Probert, Matt

2012-05-01

These conference proceedings contain the written papers of the contributions presented at the 3rd International Conference on Theory, Modelling and Computational Methods for Semiconductor materials and nanostructures. The conference was held at the School of Electronic and Electrical Engineering, University of Leeds, Leeds, UK on 18-20 January 2012. The previous conferences in this series took place in 2010 at St William's College, York and in 2008 at the University of Manchester, UK. The development of high-speed computer architectures is finally allowing the routine use of accurate methods for calculating the structural, thermodynamic, vibrational, optical and electronic properties of semiconductors and their hetero- and nano-structures. The scope of this conference embraces modelling, theory and the use of sophisticated computational tools in semiconductor science and technology, where there is substantial potential for time-saving in R&D. Theoretical approaches represented in this meeting included: Density Functional Theory, Tight Binding, Semiempirical Pseudopotential Methods, Effective Mass Models, Empirical Potential Methods and Multiscale Approaches. Topics included, but were not limited to: Optical and Transport Properties of Quantum Nanostructures including Colloids and Nanotubes, Plasmonics, Magnetic Semiconductors, Graphene, Lasers, Photonic Structures, Photovoltaic and Electronic Devices. This workshop ran for three days, with the objective of bringing together UK and international leading experts in the theoretical modelling of Group IV, III-V and II-VI semiconductors, as well as students, postdocs and early-career researchers. The first day focused on providing an introduction and overview of this vast field, aimed particularly at students, with several lectures given by recognised experts in various theoretical approaches. The following two days showcased some of the best theoretical research carried out in the UK in this field, with several contributions also from representatives of renowned theoretical groups from many European countries (Spain, France, Ireland, Germany, Italy, Poland, Denmark, Sweden, Serbia, Greece, etc.), as well as Asia (India) and Africa (Algeria, Tunisia and South Africa). We would like to thank all participants for making this a very successful meeting and for their contribution to the conference programme and these proceedings. We would also like to acknowledge the financial support from the Institute of Physics (Computational Physics group and Semiconductor Physics group), and QuantumWise (distributors of Atomistix). The Editors Acknowledgments Conference Organising Committee: Marco Califano (University of Leeds) Max Migliorato (University of Manchester) Matt Probert (University of York) Programme Committee: Stewart Clark (University of Durham) Aldo Di Carlo (University of Rome 'Tor Vergata', Italy) Ben Hourahine (University of Strathclyde) Lev Kantorovich (King's College London) Risto Nieminen (Helsinki University of Technology, Finland) Eoin O'Reilly (Tyndall Institute Cork, Republic of Ireland) Mauro Pereira (Sheffield Hallam University) John Robertson (University of Cambridge) Mervin Roy (University of Leicester) Stanko Tomic (University of Salford) David Whittaker (University of Sheffield) The proceedings were edited and compiled by Marco Califano, Max Migliorato and Matt Probert.

Research Results

NASA Astrophysics Data System (ADS)

2011-12-01

Research on Global Carbon Emission and Sequestration NSFC Funded Project Made Significant Progress in Quantum Dynamics Functional Human Blood Protein Obtained from Rice How Giant Pandas Thrive on a Bamboo Diet New Evidence of Interpersonal Violence from 129,000 Years Ago Found in China Aptamer-Mediated Efficient Capture and Release of T Lymphocytes on Nanostructured Surfaces BGI Study Results on Resequencing 50 Accessions of Rice Cast New Light on Molecular Breeding BGI Reports Study Results on Frequent Mutation of Genes Encoding UMPP Components in Kidney Cancer Research on Habitat Shift Promoting Species Diversification

Controlled placement and orientation of nanostructures

DOEpatents

Zettl, Alex K; Yuzvinsky, Thomas D; Fennimore, Adam M

2014-04-08

A method for controlled deposition and orientation of molecular sized nanoelectromechanical systems (NEMS) on substrates is disclosed. The method comprised: forming a thin layer of polymer coating on a substrate; exposing a selected portion of the thin layer of polymer to alter a selected portion of the thin layer of polymer; forming a suspension of nanostructures in a solvent, wherein the solvent suspends the nanostructures and activates the nanostructures in the solvent for deposition; and flowing a suspension of nanostructures across the layer of polymer in a flow direction; thereby: depositing a nanostructure in the suspension of nanostructures only to the selected portion of the thin layer of polymer coating on the substrate to form a deposited nanostructure oriented in the flow direction. By selectively employing portions of the method above, complex NEMS may be built of simpler NEMSs components.

Parallel Computational Protein Design.

PubMed

Zhou, Yichao; Donald, Bruce R; Zeng, Jianyang

2017-01-01

Computational structure-based protein design (CSPD) is an important problem in computational biology, which aims to design or improve a prescribed protein function based on a protein structure template. It provides a practical tool for real-world protein engineering applications. A popular CSPD method that guarantees to find the global minimum energy solution (GMEC) is to combine both dead-end elimination (DEE) and A* tree search algorithms. However, in this framework, the A* search algorithm can run in exponential time in the worst case, which may become the computation bottleneck of large-scale computational protein design process. To address this issue, we extend and add a new module to the OSPREY program that was previously developed in the Donald lab (Gainza et al., Methods Enzymol 523:87, 2013) to implement a GPU-based massively parallel A* algorithm for improving protein design pipeline. By exploiting the modern GPU computational framework and optimizing the computation of the heuristic function for A* search, our new program, called gOSPREY, can provide up to four orders of magnitude speedups in large protein design cases with a small memory overhead comparing to the traditional A* search algorithm implementation, while still guaranteeing the optimality. In addition, gOSPREY can be configured to run in a bounded-memory mode to tackle the problems in which the conformation space is too large and the global optimal solution cannot be computed previously. Furthermore, the GPU-based A* algorithm implemented in the gOSPREY program can be combined with the state-of-the-art rotamer pruning algorithms such as iMinDEE (Gainza et al., PLoS Comput Biol 8:e1002335, 2012) and DEEPer (Hallen et al., Proteins 81:18-39, 2013) to also consider continuous backbone and side-chain flexibility.

Phage Wrapping with Cationic Polymers Eliminates Non-specific Binding between M13 Phage and High pI Target Proteins

PubMed Central

Lamboy, Jorge A.; Arter, Jessica A.; Knopp, Kristeene A.; Der, Denise; Overstreet, Cathie M.; Palermo, Edmund; Urakami, Hiromitsu; Yu, Ting-Bin; Tezgel, Ozgul; Tew, Gregory; Guan, Zhibin; Kuroda, Kenichi; Weiss, Gregory A.

2011-01-01

M13 phage have provided scaffolds for nanostructure synthesis based upon self-assembled inorganic and hard materials interacting with phage-displayed peptides. Additionally, phage display has been used to identify binders to plastic, TiO2, and other surfaces. However, synthesis of phage-based materials through the hybridization of soft materials with the phage surface remains unexplored. Here, we present an efficient “phage wrapping” strategy for the facile synthesis of phage coated with soluble, cationic polymers. Polymers bearing high positive charge densities demonstrated the most effective phage wrapping, as shown by assays for blocking non-specific binding of the anionic phage coat to a high pI target protein. The results establish the functional group requirements for hybridizing phage with soft materials, and solve a major problem in phage display – non-specific binding by the phage to high pI target proteins. PMID:19856910

Phage wrapping with cationic polymers eliminates nonspecific binding between M13 phage and high pI target proteins.

PubMed

Lamboy, Jorge A; Arter, Jessica A; Knopp, Kristeene A; Der, Denise; Overstreet, Cathie M; Palermo, Edmund F; Urakami, Hiromitsu; Yu, Ting-Bin; Tezgel, Ozgul; Tew, Gregory N; Guan, Zhibin; Kuroda, Kenichi; Weiss, Gregory A

2009-11-18

M13 phage have provided scaffolds for nanostructure synthesis based upon self-assembled inorganic and hard materials interacting with phage-displayed peptides. Additionally, phage display has been used to identify binders to plastic, TiO(2), and other surfaces. However, synthesis of phage-based materials through the hybridization of soft materials with the phage surface remains unexplored. Here, we present an efficient "phage wrapping" strategy for the facile synthesis of phage coated with soluble, cationic polymers. Polymers bearing high positive charge densities demonstrated the most effective phage wrapping, as shown by assays for blocking nonspecific binding of the anionic phage coat to a high pI target protein. The results establish the functional group requirements for hybridizing phage with soft materials and solve a major problem in phage display-nonspecific binding by the phage to high pI target proteins.

Unravelling the biodiversity of nanoscale signatures of spider silk fibres

NASA Astrophysics Data System (ADS)

Silva, Luciano P.; Rech, Elibio L.

2013-12-01

Living organisms are masters at designing outstanding self-assembled nanostructures through a hierarchical organization of modular proteins. Protein-based biopolymers improved and selected by the driving forces of molecular evolution are among the most impressive archetypes of nanomaterials. One of these biomacromolecules is the myriad of compound fibroins of spider silks, which combine surprisingly high tensile strength with great elasticity. However, no consensus on the nano-organization of spider silk fibres has been reached. Here we explore the biodiversity of spider silk fibres, focusing on nanoscale characterization with high-resolution atomic force microscopy. Our results reveal an evolution of the nanoroughness, nanostiffness, nanoviscoelastic, nanotribological and nanoelectric organization of microfibres, even when they share similar sizes and shapes. These features are related to unique aspects of their molecular structures. The results show that combined nanoscale analyses of spider silks may enable the screening of appropriate motifs for bioengineering synthetic fibres from recombinant proteins.

Highly selective luminescent nanostructures for mitochondrial imaging and targeting

NASA Astrophysics Data System (ADS)

Fanizza, E.; Iacobazzi, R. M.; Laquintana, V.; Valente, G.; Caliandro, G.; Striccoli, M.; Agostiano, A.; Cutrignelli, A.; Lopedota, A.; Curri, M. L.; Franco, M.; Depalo, N.; Denora, N.

2016-02-01

Here a luminescent hybrid nanostructure based on functionalized quantum dots (QDs) is used as a fluorescent imaging agent able to target selectively mitochondria thanks to the molecular recognition of the translocator protein (TSPO). The selective targeting of such an 18 kDa protein mainly located in the outer mitochondrial membrane and overexpressed in several pathological states including neurodegenerative diseases and cancers may provide valuable information for the early diagnosis and therapy of human disorders. In particular, the rational design of amino functionalized luminescent silica coated QD nanoparticles (QD@SiO2 NPs) provides a versatile nanoplatform to anchor a potent and selective TSPO ligand, characterized by a 2-phenyl-imidazo[1,2-a]pyridine acetamide structure along with a derivatizable carboxylic end group, useful to conjugate the TSPO ligand and achieve TSPO-QD@SiO2 NPs by means of a covalent amide bond. The colloidal stability and optical properties of the proposed nanomaterials are comprehensively investigated and their potential as mitochondrial imaging agents is fully assessed. Sub-cellular fractionation, together with confocal laser scanning fluorescence microscopy and co-localization analysis of targeted TSPO-QD@SiO2 NPs in C6 glioma cells overexpressing the TSPO, proves the great potential of these multifunctional nanosystems as in vitro selective mitochondrial imaging agents.Here a luminescent hybrid nanostructure based on functionalized quantum dots (QDs) is used as a fluorescent imaging agent able to target selectively mitochondria thanks to the molecular recognition of the translocator protein (TSPO). The selective targeting of such an 18 kDa protein mainly located in the outer mitochondrial membrane and overexpressed in several pathological states including neurodegenerative diseases and cancers may provide valuable information for the early diagnosis and therapy of human disorders. In particular, the rational design of amino functionalized luminescent silica coated QD nanoparticles (QD@SiO2 NPs) provides a versatile nanoplatform to anchor a potent and selective TSPO ligand, characterized by a 2-phenyl-imidazo[1,2-a]pyridine acetamide structure along with a derivatizable carboxylic end group, useful to conjugate the TSPO ligand and achieve TSPO-QD@SiO2 NPs by means of a covalent amide bond. The colloidal stability and optical properties of the proposed nanomaterials are comprehensively investigated and their potential as mitochondrial imaging agents is fully assessed. Sub-cellular fractionation, together with confocal laser scanning fluorescence microscopy and co-localization analysis of targeted TSPO-QD@SiO2 NPs in C6 glioma cells overexpressing the TSPO, proves the great potential of these multifunctional nanosystems as in vitro selective mitochondrial imaging agents. Electronic supplementary information (ESI) available: Additional TEM micrographs, fluorescence and UV-Vis absorbance spectra of silica coated QD nanoparticles and TSPO ligand. See DOI: 10.1039/c5nr08139d

From Interfaces to Bulk: Experimental-Computational Studies Across Time and Length Scales of Multi-Functional Ionic Polymers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Perahia, Dvora; Grest, Gary S.

Neutron experiments coupled with computational components have resulted in unprecedented understanding of the factors that impact the behavior of ionic structured polymers. Additionally, new computational tools to study macromolecules, were developed. In parallel, this DOE funding have enabled the education of the next generation of material researchers who are able to take the advantage neutron tools offer to the understanding and design of advanced materials. Our research has provided unprecedented insight into one of the major factors that limits the use of ionizable polymers, combining the macroscopic view obtained from the experimental techniques with molecular insight extracted from computational studiesmore » leading to transformative knowledge that will impact the design of nano-structured, materials. With the focus on model systems, of broad interest to the scientific community and to industry, the research addressed challenges that cut across a large number of polymers, independent of the specific chemical structure or the transported species.« less

Super sensitive UV detector using polymer functionalized nanobelts

DOEpatents

Wang, Zhong L; Lao, Changshi; Zhou, Jun

2012-10-23

An ultraviolet light sensor includes an elongated metal oxide nanostructure, a layer of an ultraviolet light-absorbing polymer, a current source and a current detector. The elongated metal oxide nanostructure has a first end and an opposite second end. The layer of an ultraviolet light-absorbing polymer is disposed about at least a portion of the metal oxide nanostructure. The current source is configured to provide electrons to the first end of the metal oxide nanostructure. The current detector is configured to detect an amount of current flowing through the metal oxide nanostructure. The amount of current flowing through the metal oxide nanostructure corresponds to an amount of ultraviolet light impinging on the metal oxide nanostructure.

Metal-like transport in proteins: A new paradigm for biological electron transfer

NASA Astrophysics Data System (ADS)

Malvankar, Nikhil; Vargas, Madeline; Tuominen, Mark; Lovley, Derek

2012-02-01

Electron flow in biologically proteins generally occurs via tunneling or hopping and the possibility of electron delocalization has long been discounted. Here we report metal-like transport in protein nanofilaments, pili, of bacteria Geobacter sulfurreducens that challenges this long-standing belief [1]. Pili exhibit conductivities comparable to synthetic organic metallic nanostructures. The temperature, magnetic field and gate-voltage dependence of pili conductivity is akin to that of quasi-1D disordered metals, suggesting a metal-insulator transition. Magnetoresistance (MR) data provide evidence for quantum interference and weak localization at room temperature, as well as a temperature and field-induced crossover from negative to positive MR. Furthermore, pili can be doped with protons. Structural studies suggest the possibility of molecular pi stacking in pili, causing electron delocalization. Reducing the disorder increases the metallic nature of pili. These electronically functional proteins are a new class of electrically conductive biological proteins that can be used to generate future generation of inexpensive and environmentally-sustainable nanomaterials and nanolectronic devices such as transistors and supercapacitors. [1] Malvankar et al. Nature Nanotechnology, 6, 573-579 (2011)

Carbon nanotubes as templates for polymerized lipid assemblies

NASA Astrophysics Data System (ADS)

Thauvin, Cédric; Rickling, Stéphane; Schultz, Patrick; Célia, Hervé; Meunier, Stéphane; Mioskowski, Charles

2008-12-01

Amphiphilic molecules-molecules that have both hydrophobic and hydrophilic properties-can self-assemble in water to form diverse structures such as micelles, vesicles and tubes, and these nanostructures can be used for delivering drugs, stabilizing membrane proteins or as nanoreactors. We have previously shown that lipids can self-organize on the surface of single-walled carbon nanotubes into regular ring-shaped assemblies. Here we show that these lipid assemblies can be polymerized and isolated from the nanotube template by application of an electric field. We also demonstrate that these assemblies are monodispersed, water-soluble, and can dissolve various hydrophobic rylene dyes, fullerenes and membrane proteins. The stability of these constructs and their diverse applications will be useful in the fields of cosmetics, medicine and material sciences.

Bridging Zirconia Nodes within a Metal–Organic Framework via Catalytic Ni-Hydroxo Clusters to Form Heterobimetallic Nanowires

DOE Office of Scientific and Technical Information (OSTI.GOV)

Platero-Prats, Ana E.; League, Aaron B.; Bernales, Varinia

2017-07-24

Metal-organic frameworks (MOFs), with their well-ordered pore networks and tunable surface chemistries, offer a versatile platform for preparing well-defined nanostructures wherein functionality such as catalysis can be incorporated. We resolved the atomic structure of Ni-oxo species deposited in the MOF NU-1000 through atomic layer deposition using local and long-range structure probes, including X-ray absorption spectroscopy, pair distribution function analysis and difference envelope density analysis, with electron microscopy imaging and computational modeling.

Fabrication of Porous Carbon-based Nanostructure for Energy Storage and Transfer Applications

DTIC Science & Technology

2014-06-09

in the voltage range of 3.0 to 0.005 V (versus Li/Li+). Cyclic voltammetry (CV) was performed on a computer controlled MacPile II unit (Biological...performed at current density of 37mAg–1, voltage: 3.0-0.005V vs. Li/Li+. Cyclic voltammetry was performed at a scan rate of 58 µs/V. Red plots...pseudocapacitve storage behaviour of the electrode.19 The Li storage mechanism of both electrodes can also be studied carefully by slow scanning cyclic

One-dimensional ZnO nanostructures.

PubMed

Jayadevan, K P; Tseng, T Y

2012-06-01

The wide-gap semiconductor ZnO with nanostructures such as nanoparticle, nanorod, nanowire, nanobelt, nanotube has high potential for a variety of applications. This article reviews the fundamentals of one-dimensional ZnO nanostructures, including processing, structure, property, application and their processing-microstructure-property correlation. Various fabrication methods of the ZnO nanostructures including vapor-liquid-solid process, vapor-solid growth, solution growth, solvothermal growth, template-assisted growth and self-assembly are introduced. The characterization and properties of the ZnO nanostructures are described. The possible applications of these nanostructures are also discussed.

Prediction of Surface and pH-Specific Binding of Peptides to Metal and Oxide Nanoparticles

NASA Astrophysics Data System (ADS)

Heinz, Hendrik; Lin, Tzu-Jen; Emami, Fateme Sadat; Ramezani-Dakhel, Hadi; Naik, Rajesh; Knecht, Marc; Perry, Carole C.; Huang, Yu

2015-03-01

The mechanism of specific peptide adsorption onto metallic and oxidic nanostructures has been elucidated in atomic resolution using novel force fields and surface models in comparison to measurements. As an example, variations in peptide adsorption on Pd and Pt nanoparticles depending on shape, size, and location of peptides on specific bounding facets are explained. Accurate computational predictions of reaction rates in C-C coupling reactions using particle models derived from HE-XRD and PDF data illustrate the utility of computational methods for the rational design of new catalysts. On oxidic nanoparticles such as silica and apatites, it is revealed how changes in pH lead to similarity scores of attracted peptides lower than 20%, supported by appropriate model surfaces and data from adsorption isotherms. The results demonstrate how new computational methods can support the design of nanoparticle carriers for drug release and the understanding of calcification mechanisms in the human body.

Evolution-Inspired Computational Design of Symmetric Proteins.

PubMed

Voet, Arnout R D; Simoncini, David; Tame, Jeremy R H; Zhang, Kam Y J

2017-01-01

Monomeric proteins with a number of identical repeats creating symmetrical structures are potentially very valuable building blocks with a variety of bionanotechnological applications. As such proteins do not occur naturally, the emerging field of computational protein design serves as an excellent tool to create them from nonsymmetrical templates. Existing pseudo-symmetrical proteins are believed to have evolved from oligomeric precursors by duplication and fusion of identical repeats. Here we describe a computational workflow to reverse-engineer this evolutionary process in order to create stable proteins consisting of identical sequence repeats.

Nanostructure Diffraction Gratings for Integrated Spectroscopy and Sensing

NASA Technical Reports Server (NTRS)

Guo, Junpeng (Inventor)

2015-01-01

The present disclosure pertains to metal or dielectric nanostructures of the subwavelength scale within the grating lines of optical diffraction gratings. The nanostructures have surface plasmon resonances or non-plasmon optical resonances. A linear photodetector array is used to capture the resonance spectra from one of the diffraction orders. The combined nanostructure super-grating and photodetector array eliminates the use of external optical spectrometers for measuring surface plasmon or optical resonance frequency shift caused by the presence of chemical and biological agents. The nanostructure super-gratings can be used for building integrated surface enhanced Raman scattering (SERS) spectrometers. The nanostructures within the diffraction grating lines enhance Raman scattering signal light while the diffraction grating pattern of the nanostructures diffracts Raman scattering light to different directions of propagation according to their wavelengths. Therefore, the nanostructure super-gratings allows for the use of a photodetector array to capture the surface enhanced Raman scattering spectra.

Nanostructure Diffraction Gratings for Integrated Spectroscopy and Sensing

NASA Technical Reports Server (NTRS)

Guo, Junpeng (Inventor)

2016-01-01

The present disclosure pertains to metal or dielectric nanostructures of the subwavelength scale within the grating lines of optical diffraction gratings. The nanostructures have surface plasmon resonances or non-plasmon optical resonances. A linear photodetector array is used to capture the resonance spectra from one of the diffraction orders. The combined nanostructure super-grating and photodetector array eliminates the use of external optical spectrometers for measuring surface plasmon or optical resonance frequency shift caused by the presence of chemical and biological agents. The nanostructure super-gratings can be used for building integrated surface enhanced Raman scattering (SERS) spectrometers. The nanostructures within the diffraction grating lines enhance Raman scattering signal light while the diffraction grating pattern of the nanostructures diffracts Raman scattering light to different directions of propagation according to their wavelengths. Therefore, the nanostructure super-gratings allows for the use of a photodetector array to capture the surface enhanced Raman scattering spectra.

The Development of Metal Oxide Chemical Sensing Nanostructures

NASA Technical Reports Server (NTRS)

Hunter, G. W.; VanderWal,R. L.; Xu, J. C.; Evans, L. J.; Berger, G. M.; Kulis, M. J.

2008-01-01

This paper discusses sensor development based on metal oxide nanostructures and microsystems technology. While nanostructures such as nanowires show significant potential as enabling materials for chemical sensors, a number of significant technical challenges remain. This paper discusses development to address each of these technical barriers: 1) Improved contact and integration of the nanostructured materials with microsystems in a sensor structure; 2) Control of nanostructure crystallinity to allow control of the detection mechanism; and 3) Widening the range of gases that can be detected by fabricating multiple nanostructured materials. A sensor structure composed of three nanostructured oxides aligned on a single microsensor has been fabricated and tested. Results of this testing are discussed and future development approaches are suggested. It is concluded that while this work lays the foundation for further development, these are the beginning steps towards realization of repeatable, controlled sensor systems using oxide based nanostructures.

Bioinspired peony-like beta-Ni(OH)2 nanostructures with enhanced electrochemical activity and superhydrophobicity.

PubMed

Cao, Huaqiang; Zheng, He; Liu, Kaiyu; Warner, Jamie H

2010-02-01

Constructing complex nanostructures has become increasingly important in the development of hydrogen storage, self-cleaning materials, and the formation of chiral branched nanowires. Several approaches have been developed to generate complex nanostructures, which have led to novel applications. Combining biology and nanotechnology through the utilization of biomolecules to chemically template the growth of complex nanostructures during synthesis has aroused great interest. Herein, we use a biomolecule-assisted hydrothermal method to synthesize beta-phase Ni(OH)(2) peony-like complex nanostructures with second-order structure nanoplate structure. The novel beta-Ni(OH)(2) nanostructures exhibit high-power Ni/MH battery performance, close to the theoretical capacity of Ni(OH)(2), as well as controlled wetting behavior. We demonstrate that this bioinspired route to generate a complex nanostructure has applications in environmental protection and green secondary cells. This approach opens up opportunities for the synthesis and potential applications of new kinds of nanostructures.

Nanostructured cerium oxide: preparation, characterization, and application in energy and environmental catalysis

DOE PAGES

Tang, Wen-Xiang; Gao, Pu-Xian

2016-11-10

Nanostructured cerium oxide (CeO 2) with outstanding physical and chemical properties has attracted extensive interests over the past few decades in environment and energy-related applications. With controllable synthesis of nanostructured CeO 2, much more features were technologically brought out from defect chemistry to structure-derived effects. This paper highlights recent progress on the synthesis and characterization of nanostructured ceria-based materials as well as the traditional and new applications. Specifically, several typical applications based on the desired ceria nanostructures are focused to showcase the importance of nanostructure-derived effects. Moreover, some challenges and perspectives on the nanostructured ceria are presented, such as defectsmore » controlling and retainment, scale-up fabrication, and monolithic devices. Hopefully, this paper can provide an improved understanding of nanostructured CeO 2 and offer new opportunities to promote the further research and applications in the future.« less

Epitaxial growth of hybrid nanostructures

NASA Astrophysics Data System (ADS)

Tan, Chaoliang; Chen, Junze; Wu, Xue-Jun; Zhang, Hua

2018-02-01

Hybrid nanostructures are a class of materials that are typically composed of two or more different components, in which each component has at least one dimension on the nanoscale. The rational design and controlled synthesis of hybrid nanostructures are of great importance in enabling the fine tuning of their properties and functions. Epitaxial growth is a promising approach to the controlled synthesis of hybrid nanostructures with desired structures, crystal phases, exposed facets and/or interfaces. This Review provides a critical summary of the state of the art in the field of epitaxial growth of hybrid nanostructures. We discuss the historical development, architectures and compositions, epitaxy methods, characterization techniques and advantages of epitaxial hybrid nanostructures. Finally, we provide insight into future research directions in this area, which include the epitaxial growth of hybrid nanostructures from a wider range of materials, the study of the underlying mechanism and determining the role of epitaxial growth in influencing the properties and application performance of hybrid nanostructures.

An analytical computation of magnetic field generated from a cylinder ferromagnet

NASA Astrophysics Data System (ADS)

Taniguchi, Tomohiro

2018-04-01

An analytical formulation to compute a magnetic field generated from an uniformly magnetized cylinder ferromagnet is developed. Exact solutions of the magnetic field generated from the magnetization pointing in an arbitrary direction are derived, which are applicable both inside and outside the ferromagnet. The validities of the present formulas are confirmed by comparing them with demagnetization coefficients estimated in earlier works. The results will be useful for designing practical applications, such as high-density magnetic recording and microwave generators, where nanostructured ferromagnets are coupled to each other through the dipole interactions and show cooperative phenomena such as synchronization. As an example, the magnetic field generated from a spin torque oscillator for magnetic recording based on microwave assisted magnetization reversal is studied.

Electronic and Optical properties of Graphene Nanoribbons

NASA Astrophysics Data System (ADS)

Molinari, Elisa; Ferretti, Andrea; Cardoso, Claudia; Prezzi, Deborah; Ruini, Alice

Narrow graphene nanoribbons (GNRs) exhibit substantial electronic band gaps, and optical properties expected to be fundamentally different from the ones of their parent material graphene. Unlike graphene the optical response of GNRs may be tuned by the ribbon width and the directly related electronic band gap. We have addressed the optical properties of chevron-like and finite-size armchair nanoribbons by computing the fundamental and optical gap from ab initio methods. Our results are in very good agreement with the experimental values obtained by STS, ARPES, and differential reflectance spectroscopy, indicating that this computational scheme can be quantitatively predictive for electronic and optical spectroscopies of nanostructures. These study has been partly supported by the EU Centre of Excellence ''MaX - MAterials design at the eXascale''.

Sequence-structure correlations in silk: Poly-Ala repeat of N. clavipes MaSp1 is naturally optimized at a critical length scale.

PubMed

Bratzel, Graham; Buehler, Markus J

2012-03-01

Spider silk is a self-assembling biopolymer that outperforms many known materials in terms of its mechanical performance despite being constructed from simple and inferior building blocks. While experimental studies have shown that the molecular structure of silk has a direct influence on the stiffness, toughness, and failure strength of silk, few molecular-level analyses of the nanostructure of silk assemblies in particular under variations of genetic sequences have been reported. Here we report atomistic-level structures of the MaSp1 protein from the Nephila Clavipes spider dragline silk sequence, obtained using an in silico approach based on replica exchange molecular dynamics (REMD) and explicit water molecular dynamics. We apply this method to study the effects of a systematic variation of the poly-alanine repeat lengths, a parameter controlled by the genetic makeup of silk, on the resulting molecular structure of silk at the nanoscale. Confirming earlier experimental and computational work, a structural analysis reveals that poly-alanine regions in silk predominantly form distinct and orderly β-sheet crystal domains while disorderly regions are formed by glycine-rich repeats that consist of 3(10)-helix type structures and β-turns. Our predictions are directly validated against experimental data based on dihedral angle pair calculations presented in Ramachandran plots combined with an analysis of the secondary structure content. The key result of our study is our finding of a strong dependence of the resulting silk nanostructure depending on the poly-alanine length. We observe that the wildtype poly-alanine repeat length of six residues defines a critical minimum length that consistently results in clearly defined β-sheet nanocrystals. For poly-alanine lengths below six, the β-sheet nanocrystals are not well-defined or not visible at all, while for poly-alanine lengths at and above six, the characteristic nanocomposite structure of silk emerges with no significant improvement of the quality of the β-sheet nanocrystal geometry. We present a simple biophysical model that explains these computational observations based on the mechanistic insight gained from the molecular simulations. Our findings set the stage for understanding how variations in the spidroin sequence can be used to engineer the structure and thereby functional properties of this biological superfiber, and present a design strategy for the genetic optimization of spidroins for enhanced mechanical properties. The approach used here may also find application in the design of other self-assembled molecular structures and fibers and in particular biologically inspired or completely synthetic systems. Copyright © 2011 Elsevier Ltd. All rights reserved.

Soft Computing Techniques for the Protein Folding Problem on High Performance Computing Architectures.

PubMed

Llanes, Antonio; Muñoz, Andrés; Bueno-Crespo, Andrés; García-Valverde, Teresa; Sánchez, Antonia; Arcas-Túnez, Francisco; Pérez-Sánchez, Horacio; Cecilia, José M

2016-01-01

The protein-folding problem has been extensively studied during the last fifty years. The understanding of the dynamics of global shape of a protein and the influence on its biological function can help us to discover new and more effective drugs to deal with diseases of pharmacological relevance. Different computational approaches have been developed by different researchers in order to foresee the threedimensional arrangement of atoms of proteins from their sequences. However, the computational complexity of this problem makes mandatory the search for new models, novel algorithmic strategies and hardware platforms that provide solutions in a reasonable time frame. We present in this revision work the past and last tendencies regarding protein folding simulations from both perspectives; hardware and software. Of particular interest to us are both the use of inexact solutions to this computationally hard problem as well as which hardware platforms have been used for running this kind of Soft Computing techniques.

Electrolyte-free Amperometric Immunosensor using a Dendritic Nanotip†

PubMed Central

Kim, Jong-Hoon; Hiraiwa, Morgan; Lee, Hyun-Boo; Lee, Kyong-Hoon; Cangelosi, Gerard A.; Chung, Jae-Hyun

2013-01-01

Electric detection using a nanocomponent may lead to platforms for rapid and simple biosensing. Sensors composed of nanotips or nanodots have been described for highly sensitive amperometry enabled by confined geometry. However, both fabrication and use of nanostructured sensors remain challenging. This paper describes a dendritic nanotip used as an amperometric biosensor for highly sensitive detection of target bacteria. A dendritic nanotip is structured by Si nanowires coated with single-walled carbon nanotubes (SWCNTs) for generation of a high electric field. For reliable measurement using the dendritic structure, Si nanowires were uniformly fabricated by ultraviolet (UV) lithography and etching. The dendritic structure effectively increased the electric current density near the terminal end of the nanotip according to numerical computation. The electrical characteristics of a dendritic nanotip with additional protein layers was studied by cyclic voltammetry and I–V measurement in deionized (DI) water. When the target bacteria dielectrophoretically captured onto a nanotip were bound with fluorescence antibodies, the electric current through DI water decreased. Measurement results were consistent with fluorescence- and electron microscopy. The sensitivity of the amperometry was 10 cfu/sample volume (103 cfu/mL), which was equivalent to the more laborious fluorescence measurement method. The simple configuration of a dendritic nanotip can potentially offer an electrolyte-free detection platform for sensitive and rapid biosensors. PMID:23585927

Electrolyte-free Amperometric Immunosensor using a Dendritic Nanotip.

PubMed

Kim, Jong-Hoon; Hiraiwa, Morgan; Lee, Hyun-Boo; Lee, Kyong-Hoon; Cangelosi, Gerard A; Chung, Jae-Hyun

2013-01-01

Electric detection using a nanocomponent may lead to platforms for rapid and simple biosensing. Sensors composed of nanotips or nanodots have been described for highly sensitive amperometry enabled by confined geometry. However, both fabrication and use of nanostructured sensors remain challenging. This paper describes a dendritic nanotip used as an amperometric biosensor for highly sensitive detection of target bacteria. A dendritic nanotip is structured by Si nanowires coated with single-walled carbon nanotubes (SWCNTs) for generation of a high electric field. For reliable measurement using the dendritic structure, Si nanowires were uniformly fabricated by ultraviolet (UV) lithography and etching. The dendritic structure effectively increased the electric current density near the terminal end of the nanotip according to numerical computation. The electrical characteristics of a dendritic nanotip with additional protein layers was studied by cyclic voltammetry and I-V measurement in deionized (DI) water. When the target bacteria dielectrophoretically captured onto a nanotip were bound with fluorescence antibodies, the electric current through DI water decreased. Measurement results were consistent with fluorescence- and electron microscopy. The sensitivity of the amperometry was 10 cfu/sample volume (10 3 cfu/mL), which was equivalent to the more laborious fluorescence measurement method. The simple configuration of a dendritic nanotip can potentially offer an electrolyte-free detection platform for sensitive and rapid biosensors.

Nanostructural and mechanical property changes to spider silk as a consequence of insecticide exposure.

PubMed

Benamú, Marco; Lacava, Mariángeles; García, Luis F; Santana, Martín; Fang, Jian; Wang, Xungai; Blamires, Sean J

2017-08-01

Neonicotinoids are one of the world's most extensively used insecticides, but their sub-lethal influences on non-target and beneficial organisms are not well known. Here we exposed the orb web spider Parawixia audax, which is found on arable lands in Uruguay, to a sub-lethal concentration of the broad spectrum insecticide Geonex (thiamethoxam + lambda-cyhalothrin) and monitored their web building. We collected their major ampullate silk and subjected it to tensile tests, wide-angle X-ray diffraction (WAXS) analysis, and amino acid composition analysis. Around half of the exposed spiders failed to build webs. Those that built webs produced irregular webs lacking spiral threads. The mechanical properties, nanostructures, and amino acid compositions of the silk were all significantly affected when the spiders were exposed to insecticides. We found that silk proline, glutamine, alanine and glycine compositions differed between treatments, indicating that insecticide exposure induced downregulation of the silk protein MaSp2. The spiders in the control group had stronger, tougher and more extensible silks than those in the insecticide exposed group. Our WAXS analyses showed the amorphous region nanostructures became misaligned in insecticide exposed silks, explaining their greater stiffness. While the insecticide dose we subjected P. audax to was evidently sub-lethal, the changes in silk physicochemical properties and the impairment to web building will indelibly affect their ability to catch prey. Copyright © 2017 Elsevier Ltd. All rights reserved.

Nanostructured composite reinforced material

DOEpatents

Seals, Roland D [Oak Ridge, TN; Ripley, Edward B [Knoxville, TN; Ludtka, Gerard M [Oak Ridge, TN

2012-07-31

A family of materials wherein nanostructures and/or nanotubes are incorporated into a multi-component material arrangement, such as a metallic or ceramic alloy or composite/aggregate, producing a new material or metallic/ceramic alloy. The new material has significantly increased strength, up to several thousands of times normal and perhaps substantially more, as well as significantly decreased weight. The new materials may be manufactured into a component where the nanostructure or nanostructure reinforcement is incorporated into the bulk and/or matrix material, or as a coating where the nanostructure or nanostructure reinforcement is incorporated into the coating or surface of a "normal" substrate material. The nanostructures are incorporated into the material structure either randomly or aligned, within grains, or along or across grain boundaries.

Theoretical investigation on the magnetostatic interaction between two wire-tube nanostructures

NASA Astrophysics Data System (ADS)

Riveros, A.; Salazar-Aravena, D.; Escrig, J.

2017-04-01

In this paper we have calculated analytically the magnetostatic interaction between two wire-tube nanostructures as a function of their magnetic and geometric parameters. As expected, the interaction energy increases as the nanostructures approach, but interestingly when the nanostructures are close enough, a non-monotonic behavior with the wire-tube portions is reported. Besides, we investigate the hysteresis loop for two interacting Ni81Fe19 wire-tube nanostructures by micromagnetic simulations in order to study how the interaction affects the magnetic properties of these nanostructures. This work allows for the study of magnetostatic interactions between wire-tube nanostructures that have been proposed as an interesting alternative to store information or even perform logic functions, because to their ability to pin a domain wall.

Computational protein design with backbone plasticity

PubMed Central

MacDonald, James T.; Freemont, Paul S.

2016-01-01

The computational algorithms used in the design of artificial proteins have become increasingly sophisticated in recent years, producing a series of remarkable successes. The most dramatic of these is the de novo design of artificial enzymes. The majority of these designs have reused naturally occurring protein structures as ‘scaffolds’ onto which novel functionality can be grafted without having to redesign the backbone structure. The incorporation of backbone flexibility into protein design is a much more computationally challenging problem due to the greatly increased search space, but promises to remove the limitations of reusing natural protein scaffolds. In this review, we outline the principles of computational protein design methods and discuss recent efforts to consider backbone plasticity in the design process. PMID:27911735

Nanostructured materials for hydrogen storage

DOEpatents

Williamson, Andrew J.; Reboredo, Fernando A.

2007-12-04

A system for hydrogen storage comprising a porous nano-structured material with hydrogen absorbed on the surfaces of the porous nano-structured material. The system of hydrogen storage comprises absorbing hydrogen on the surfaces of a porous nano-structured semiconductor material.

Do C-reactive protein level, white blood cell count, and pain location guide the selection of patients for computed tomography imaging in non-traumatic acute abdomen?

PubMed

Ozan, E; Atac, G K; Evrin, T; Alisar, K; Sonmez, L O; Alhan, A

2017-02-01

The value of abdominal computed tomography in non-traumatic abdominal pain has been well established. On the other hand, to manage computed tomography, appropriateness has become more of an issue as a result of the concomitant increase in patient radiation exposure with increased computed tomography use. The purpose of this study was to investigate whether C-reactive protein, white blood cell count, and pain location may guide the selection of patients for computed tomography in non-traumatic acute abdomen. Patients presenting with acute abdomen to the emergency department over a 12-month period and who subsequently underwent computed tomography were retrospectively reviewed. Those with serum C-reactive protein and white blood cell count measured on admission or within 24 h of the computed tomography were selected. Computed tomography examinations were retrospectively reviewed, and final diagnoses were designated either positive or negative for pathology relating to presentation with acute abdomen. White blood cell counts, C-reactive protein levels, and pain locations were analyzed to determine whether they increased or decreased the likelihood of producing a diagnostic computed tomography. The likelihood ratio for computed tomography positivity with a C-reactive protein level above 5 mg/L was 1.71, while this increased to 7.71 in patients with combined elevated C-reactive protein level and white blood cell count and right lower quadrant pain. Combined elevated C-reactive protein level and white blood cell count in patients with right lower quadrant pain may represent a potential factor that could guide the decision to perform computed tomography in non-traumatic acute abdomen.