Self-Assembly Strategies for Integrating Light Harvesting and Charge Separation in Artificial Photosynthetic Systems

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

Wasielewski, Michael R.

In natural photosynthesis, organisms optimize solar energy conversion through organized assemblies of photofunctional chromophores and catalysts within proteins that provide specifically tailored environments for chemical reactions. As with their natural counterparts, artificial photosynthetic systems for practical solar fuels production must collect light energy, separate charge, and transport charge to catalytic sites where multielectron redox processes will occur. While encouraging progress has been made on each aspect of this complex problem, researchers have not yet developed self-ordering and self-assembling components and the tailored environments necessary to realize a fully-functional artificial system. Previously researchers have used complex, covalent molecular systems comprised ofmore » chromophores, electron donors, and electron acceptors to mimic both the light-harvesting and the charge separation functions of photosynthetic proteins. These systems allow for study of the dependencies of electron transfer rate constants on donor?acceptor distance and orientation, electronic interaction, and the free energy of the reaction. The most useful and informative systems are those in which structural constraints control both the distance and the orientation between the electron donors and acceptors. Self-assembly provides a facile means for organizing large numbers of molecules into supramolecular structures that can bridge length scales from nanometers to macroscopic dimensions. The resulting structures must provide pathways for migration of light excitation energy among antenna chromophores, and from antennas to reaction centers. They also must incorporate charge conduits, that is, molecular 'wires' that can efficiently move electrons and holes between reaction centers and catalytic sites. The central scientific challenge is to develop small, functional building blocks with a minimum number of covalent linkages, which also have the appropriate molecular recognition properties to facilitate self-assembly of complete, functional artificial photosynthetic systems. In this Account, we explore how self-assembly strategies involving ?-stacking can be used to integrate light harvesting with charge separation and transport.« less

Recombinant spider silk from aqueous solutions via a bio-inspired microfluidic chip

NASA Astrophysics Data System (ADS)

Peng, Qingfa; Zhang, Yaopeng; Lu, Li; Shao, Huili; Qin, Kankan; Hu, Xuechao; Xia, Xiaoxia

2016-11-01

Spiders achieve superior silk fibres by controlling the molecular assembly of silk proteins and the hierarchical structure of fibres. However, current wet-spinning process for recombinant spidroins oversimplifies the natural spinning process. Here, water-soluble recombinant spider dragline silk protein (with a low molecular weight of 47 kDa) was adopted to prepare aqueous spinning dope. Artificial spider silks were spun via microfluidic wet-spinning, using a continuous post-spin drawing process (WS-PSD). By mimicking the natural spinning apparatus, shearing and elongational sections were integrated in the microfluidic spinning chip to induce assembly, orientation of spidroins, and fibril structure formation. The additional post-spin drawing process following the wet-spinning section partially mimics the spinning process of natural spider silk and substantially contributes to the compact aggregation of microfibrils. Subsequent post-stretching further improves the hierarchical structure of the fibres, including the crystalline structure, orientation, and fibril melting. The tensile strength and elongation of post-treated fibres reached up to 510 MPa and 15%, respectively.

Evolution of an ancient protein function involved in organized multicellularity in animals

PubMed Central

Anderson, Douglas P; Whitney, Dustin S; Hanson-Smith, Victor; Woznica, Arielle; Campodonico-Burnett, William; Volkman, Brian F; King, Nicole; Thornton, Joseph W; Prehoda, Kenneth E

2016-01-01

To form and maintain organized tissues, multicellular organisms orient their mitotic spindles relative to neighboring cells. A molecular complex scaffolded by the GK protein-interaction domain (GKPID) mediates spindle orientation in diverse animal taxa by linking microtubule motor proteins to a marker protein on the cell cortex localized by external cues. Here we illuminate how this complex evolved and commandeered control of spindle orientation from a more ancient mechanism. The complex was assembled through a series of molecular exploitation events, one of which – the evolution of GKPID’s capacity to bind the cortical marker protein – can be recapitulated by reintroducing a single historical substitution into the reconstructed ancestral GKPID. This change revealed and repurposed an ancient molecular surface that previously had a radically different function. We show how the physical simplicity of this binding interface enabled the evolution of a new protein function now essential to the biological complexity of many animals. DOI: http://dx.doi.org/10.7554/eLife.10147.001 PMID:26740169

Self-assembled monolayers from biphenyldithiol derivatives: optimization of the deprotection procedure and effect of the molecular conformation.

PubMed

Shaporenko, Andrey; Elbing, Mark; Błaszczyk, Alfred; von Hänisch, Carsten; Mayor, Marcel; Zharnikov, Michael

2006-03-09

A series of biphenyl-derived dithiol (BDDT) compounds with terminal acetyl-protected sulfur groups and different structural arrangements of both phenyl rings have been synthesized and fully characterized. The different arrangements were achieved by introducing hydrocarbon substituents in the 2 and 2' positions of the biphenyl backbone. The presented model compounds enable the investigation of the correlation between the intramolecular conformation and other physical properties of interest, like, e.g., molecular assembly or electronic transport properties. Here, the ability of these model compounds to form self-assembled monolayers (SAMs) on Au(111) and Ag(111) is investigated in details. The deprotection of the target molecules was performed in situ using either NH4OH or triethylamine (TEA) deprotection agent. The fabricated films were characterized by synchrotron-based high-resolution photoelectron spectroscopy and near-edge absorption fine structure spectroscopy. Whereas the deprotection by NH4OH was found to result in the formation of multilayer films, the deprotection by TEA allowed the preparation of densely packed BDDT SAMs with a noticeably higher orientational order and smaller molecular inclination on Ag than on Au. Introduction of the alkyl bridge between the individual rings of the biphenyl backbone did not lead to a noticeable change in the structure and packing density of the BDDT SAMs as long as the molecule had a planar conformation in the respective SAM. The deviation from this conformation resulted in the deterioration of the film quality and a decrease of the orientational order.

One-dimensional Confinement Effect on the Self-assembly of Symmetric H-shaped Copolymers in a Thin Film.

PubMed

Mu, Dan; Li, Jian-Quan; Feng, Sheng-Yu

2017-10-19

The self-assembly of a reformed symmetric H-shaped copolymer with four hydrophilic branches and one hydrophobic stem was systematically investigated. The existence of vacancies is vital to regulate the sizes of self-assembled cylinders to be able to form a hexagonal arrangement. With the introduction of horizontal-orientated confinement, a micellar structure is formed through a coalescence mechanism. The short acting distance and large influencing area of the confinement produces numerous small-sized micelles. Additionally, the cycled "contraction-expansion" change helps achieve hexagonal arrangement. In contrast, the introduction of lateral-oriented confinement with long acting distance and small influencing area cannot change the cylindrical structure. Under the fission mechanism, in which the larger cylinder splits into smaller ones, it is quite efficient to generate hierarchical-sized cylinders from larger-sized cylinders in the middle region and smaller-sized cylinders near both walls. The results indicate the possibility of regulating the characteristics of a nanomaterial by tuning the molecular structure of the copolymer and the parameters of the introduced confinement, which are closely related to the self-assembly structure.

Nanopatched Graphene with Molecular Self-Assembly Toward Graphene-Organic Hybrid Soft Electronics.

PubMed

Kang, Boseok; Lee, Seong Kyu; Jung, Jaehyuck; Joe, Minwoong; Lee, Seon Baek; Kim, Jinsung; Lee, Changgu; Cho, Kilwon

2018-06-01

Increasing the mechanical durability of large-area polycrystalline single-atom-thick materials is a necessary step toward the development of practical and reliable soft electronics based on these materials. Here, it is shown that the surface assembly of organosilane by weak epitaxy forms nanometer-thick organic patches on a monolayer graphene surface and dramatically increases the material's resistance to harsh postprocessing environments, thereby increasing the number of ways in which graphene can be processed. The nanopatched graphene with the improved mechanical durability enables stable operation when used as transparent electrodes of wearable strain sensors. Also, the nanopatched graphene applied as an electrode modulates the molecular orientation of deposited organic semiconductor layers, and yields favorable nominal charge injection for organic transistors. These results demonstrate the potential for use of self-assembled organic nanopatches in graphene-based soft electronics. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Competing Thermodynamic and Dynamic Factors Select Molecular Assemblies on a Gold Surface

NASA Astrophysics Data System (ADS)

Haxton, Thomas K.; Zhou, Hui; Tamblyn, Isaac; Eom, Daejin; Hu, Zonghai; Neaton, Jeffrey B.; Heinz, Tony F.; Whitelam, Stephen

2013-12-01

Controlling the self-assembly of surface-adsorbed molecules into nanostructures requires understanding physical mechanisms that act across multiple length and time scales. By combining scanning tunneling microscopy with hierarchical ab initio and statistical mechanical modeling of 1,4-substituted benzenediamine (BDA) molecules adsorbed on a gold (111) surface, we demonstrate that apparently simple nanostructures are selected by a subtle competition of thermodynamics and dynamics. Of the collection of possible BDA nanostructures mechanically stabilized by hydrogen bonding, the interplay of intermolecular forces, surface modulation, and assembly dynamics select at low temperature a particular subset: low free energy oriented linear chains of monomers and high free energy branched chains.

Molecular orientation of organic thin films on dielectric solid substrates: a phase-sensitive vibrational SFG study.

PubMed

Ge, Aimin; Peng, Qiling; Qiao, Lin; Yepuri, Nageshwar R; Darwish, Tamim A; Matsusaki, Michiya; Akashi, Mitsuru; Ye, Shen

2015-07-21

Broadband phase-sensitive vibrational sum frequency generation (SFG) spectroscopy was utilized to study the molecular orientation of molecules adsorbed on dielectric solid substrates. A gold thin film was employed to generate a SFG signal as a local oscillator (LO). To simplify the phase measurement, a self-assembled monolayer (SAM) of octadecyltrichlorosilane (OTS) was used as a standard sample for phase correction of the phase-sensitive SFG measurements on the solid/air interface. It was demonstrated that the absolute orientation of molecules in the LB films on a fused quartz surface can be clearly distinguished by phase-sensitive SFG measurement. In addition, the observation on the SAM of d35-OTS reveals that the two C-H stretching modes for α-CH2 group are in opposite phase. Furthermore, by using the present phase-sensitive SFG setup, the orientation flipping of water molecules on positively and negatively charged solid/liquid interface can be distinguished.

Chiral symmetry breaking during the self-assembly of monolayers from achiral purine molecules.

PubMed

Sowerby, S J; Heckl, W M; Petersen, G B

1996-11-01

Scanning tunneling microscopy was used to investigate the structure of the two-dimensional adsorbate formed by molecular self-assembly of the purine base, adenine, on the surfaces of the naturally occurring mineral molybdenite and the synthetic crystal highly oriented pyrolytic graphite. Although formed from adenine, which is achiral, the observed adsorbate surface structures were enantiomorphic on molybdenite. This phenomenon suggests a mechanism for the introduction of a localized chiral symmetry break by the spontaneous crystallization of these prebiotically available molecules on inorganic surfaces and may have some role in the origin of biomolecular optical asymmetry. The possibility that purine-pyrimidine arrays assembled on naturally occurring mineral surfaces might act as possible templates for biomolecular assembly is discussed.

Amphiphile-Induced Reorganization of Nematic Liquid Crystals at Aqueous Interfaces

NASA Astrophysics Data System (ADS)

Rahimi, Amin; Ramezani-Dakhel, Hadi; Pendery, Joel; Abbott, Nicholas; de Pablo, Juan; Juan de Pablo Team, Prof; Nicholas Abbott Collaboration, Prof

Recent studies have shown that ordering transitions in 4-cyano-4'-pentylbiphenyl (5CB) molecules can be triggered by the self-assembly of specific amphiphiles near a flat aqueous-LC interface. In the absence of adsorbed amphiphiles, LC molecules adopt a parallel orientation at the aqueous interface. Self-assembly of amphiphile molecules at the LC-aqueous interface triggers a spontaneous reorientation of the LC at the aqueous interface. A number of observations indicate that the hydrophilic headgroup of the surfactant has marginal effect on the orientation of 5CB whereas the aliphatic tail structure, length, and conformation greatly affect the ordering of the LC. The structural reorganization of liquid crystals at aqueous interfaces has been primarily ascribed to a weakening of the surface anchoring strength induced by amphiphile molecules. Such explanations, however, have only been supported by a posteriorimicroscopic observations. The underlying mechanism of such an ordering transition and the effect of amphiphile structure remain poorly understood. Here, we study the nature of molecular interactions between amphiphiles, 5CB, and water to understand the mechanism of ordering transitions using atomistic molecular dynamics simulations.

Effect of head group orientation on phospholipid assembly

NASA Astrophysics Data System (ADS)

Paul, Tanay; Saha, Jayashree

2017-06-01

The relationship between bilayer stability and lipid head group orientation is reported. In this work, molecular-dynamics simulations are performed to analyze the structure-property relationship of lipid biomembranes, taking into account coarse-grained model lipid interactions. The work explains the molecular scale mechanism of the phase behavior of lipid systems due to ion-lipid or anesthetic-lipid interactions, where reorientations of dipoles play a key role in modifying lipid phases and thereby alter biomembrane function. Our study demonstrates that simple dipolar reorientation is indeed sufficient in tuning a bilayer to a randomly flipped nonbilayer lamellar phase. This study may be used to assess the impact of changes in lipid phase characteristics on biomembrane structure due to the presence of anesthetics and ions.

Molecular architecture of the human Mediator-RNA polymerase II-TFIIF assembly.

PubMed

Bernecky, Carrie; Grob, Patricia; Ebmeier, Christopher C; Nogales, Eva; Taatjes, Dylan J

2011-03-01

The macromolecular assembly required to initiate transcription of protein-coding genes, known as the Pre-Initiation Complex (PIC), consists of multiple protein complexes and is approximately 3.5 MDa in size. At the heart of this assembly is the Mediator complex, which helps regulate PIC activity and interacts with the RNA polymerase II (pol II) enzyme. The structure of the human Mediator-pol II interface is not well-characterized, whereas attempts to structurally define the Mediator-pol II interaction in yeast have relied on incomplete assemblies of Mediator and/or pol II and have yielded inconsistent interpretations. We have assembled the complete, 1.9 MDa human Mediator-pol II-TFIIF complex from purified components and have characterized its structural organization using cryo-electron microscopy and single-particle reconstruction techniques. The orientation of pol II within this assembly was determined by crystal structure docking and further validated with projection matching experiments, allowing the structural organization of the entire human PIC to be envisioned. Significantly, pol II orientation within the Mediator-pol II-TFIIF assembly can be reconciled with past studies that determined the location of other PIC components relative to pol II itself. Pol II surfaces required for interacting with TFIIB, TFIIE, and promoter DNA (i.e., the pol II cleft) are exposed within the Mediator-pol II-TFIIF structure; RNA exit is unhindered along the RPB4/7 subunits; upstream and downstream DNA is accessible for binding additional factors; and no major structural re-organization is necessary to accommodate the large, multi-subunit TFIIH or TFIID complexes. The data also reveal how pol II binding excludes Mediator-CDK8 subcomplex interactions and provide a structural basis for Mediator-dependent control of PIC assembly and function. Finally, parallel structural analysis of Mediator-pol II complexes lacking TFIIF reveal that TFIIF plays a key role in stabilizing pol II orientation within the assembly.

Molecular Architecture of the Human Mediator–RNA Polymerase II–TFIIF Assembly

PubMed Central

Bernecky, Carrie; Grob, Patricia; Ebmeier, Christopher C.; Nogales, Eva; Taatjes, Dylan J.

2011-01-01

The macromolecular assembly required to initiate transcription of protein-coding genes, known as the Pre-Initiation Complex (PIC), consists of multiple protein complexes and is approximately 3.5 MDa in size. At the heart of this assembly is the Mediator complex, which helps regulate PIC activity and interacts with the RNA polymerase II (pol II) enzyme. The structure of the human Mediator–pol II interface is not well-characterized, whereas attempts to structurally define the Mediator–pol II interaction in yeast have relied on incomplete assemblies of Mediator and/or pol II and have yielded inconsistent interpretations. We have assembled the complete, 1.9 MDa human Mediator–pol II–TFIIF complex from purified components and have characterized its structural organization using cryo-electron microscopy and single-particle reconstruction techniques. The orientation of pol II within this assembly was determined by crystal structure docking and further validated with projection matching experiments, allowing the structural organization of the entire human PIC to be envisioned. Significantly, pol II orientation within the Mediator–pol II–TFIIF assembly can be reconciled with past studies that determined the location of other PIC components relative to pol II itself. Pol II surfaces required for interacting with TFIIB, TFIIE, and promoter DNA (i.e., the pol II cleft) are exposed within the Mediator–pol II–TFIIF structure; RNA exit is unhindered along the RPB4/7 subunits; upstream and downstream DNA is accessible for binding additional factors; and no major structural re-organization is necessary to accommodate the large, multi-subunit TFIIH or TFIID complexes. The data also reveal how pol II binding excludes Mediator–CDK8 subcomplex interactions and provide a structural basis for Mediator-dependent control of PIC assembly and function. Finally, parallel structural analysis of Mediator–pol II complexes lacking TFIIF reveal that TFIIF plays a key role in stabilizing pol II orientation within the assembly. PMID:21468301

Strategic placement of stereogenic centers in molecular materials for second harmonic generation.

PubMed

Gangopadhyay, P; Rao, D Narayana; Agranat, Israel; Radhakrishnan, T P

2002-01-01

Basic aspects of the nonlinear optical phenomenon of second harmonic generation (SHG) and the assembly of molecular materials for SHG are reviewed. Extensive use of chirality as a convenient tool to generate noncentrosymmetricity in molecular lattices, an essential requirement for the development of quadratic nonlinear optical materials, is noted. An overview of our investigations of chiral diaminodicyanoquinodimethanes is presented, which provides insight into a systematic approach to the effective deployment of chirality to achieve optimal molecular orientations for enhanced solid state SHG. Extension of these ideas to the realization of strong SHG in materials based on helical superstructures is outlined.

Chiral Asymmetric Structures in Aspartic Acid and Valine Crystals Assessed by Atomic Force Microscopy.

PubMed

Teschke, Omar; Soares, David Mendez

2016-03-29

Structures of crystallized deposits formed by the molecular self-assembly of aspartic acid and valine on silicon substrates were imaged by atomic force microscopy. Images of d- and l-aspartic acid crystal surfaces showing extended molecularly flat sheets or regions separated by single molecule thick steps are presented. Distinct orientation surfaces were imaged, which, combined with the single molecule step size, defines the geometry of the crystal. However, single molecule step growth also reveals the crystal chirality, i.e., growth orientations. The imaged ordered lattice of aspartic acid (asp) and valine (val) mostly revealed periodicities corresponding to bulk terminations, but a previously unreported molecular hexagonal lattice configuration was observed for both l-asp and l-val but not for d-asp or d-val. Atomic force microscopy can then be used to identify the different chiral forms of aspartic acid and valine crystals.

Chiral symmetry breaking by spatial confinement in tactoidal droplets of lyotropic chromonic liquid crystals

PubMed Central

Tortora, Luana; Lavrentovich, Oleg D.

2011-01-01

In many colloidal systems, an orientationally ordered nematic (N) phase emerges from the isotropic (I) melt in the form of spindle-like birefringent tactoids. In cases studied so far, the tactoids always reveal a mirror-symmetric nonchiral structure, sometimes even when the building units are chiral. We report on chiral symmetry breaking in the nematic tactoids formed in molecularly nonchiral polymer-crowded aqueous solutions of low-molecular weight disodium cromoglycate. The parity is broken by twisted packing of self-assembled molecular aggregates within the tactoids as manifested by the observed optical activity. Fluorescent confocal microscopy reveals that the chiral N tactoids are located at the boundaries of cells. We explain the chirality induction as a replacement of energetically costly splay packing of the aggregates within the curved bipolar tactoidal shape with twisted packing. The effect represents a simple pathway of macroscopic chirality induction in an organic system with no molecular chirality, as the only requirements are orientational order and curved shape of confinement. PMID:21402929

Molecular resolution friction microscopy of Cu phthalocyanine thin films on dolomite (104) in water

NASA Astrophysics Data System (ADS)

Nita, Paweł; Pimentel, Carlos; Luo, Feng; Milián-Medina, Begoña; Gierschner, Johannes; Pina, Carlos M.; Gnecco, Enrico

2014-06-01

The reliability of ultrathin organic layers as active components for molecular electronic devices depends ultimately on an accurate characterization of the layer morphology and ability to withstand mechanical stresses on the nanoscale. To this end, since the molecular layers need to be electrically decoupled using thick insulating substrates, the use of AFM becomes mandatory. Here, we show how friction force microscopy (FFM) in water allows us to identify the orientation of copper(ii)phthalocyanine (CuPc) molecules previously self-assembled on a dolomite (104) mineral surface in ultra-high vacuum. The molecular features observed in the friction images show that the CuPc molecules are stacked in parallel rows with no preferential orientation with respect to the dolomite lattice, while the stacking features resemble well the single CuPc crystal structure. This proves that the substrate induction is low and makes friction force microscopy in water a suitable alternative to more demanding dynamic AFM techniques in ultra-high vacuum.

Molecular resolution friction microscopy of Cu phthalocyanine thin films on dolomite (104) in water.

PubMed

Nita, Paweł; Pimentel, Carlos; Luo, Feng; Milián-Medina, Begoña; Gierschner, Johannes; Pina, Carlos M; Gnecco, Enrico

2014-07-21

The reliability of ultrathin organic layers as active components for molecular electronic devices depends ultimately on an accurate characterization of the layer morphology and ability to withstand mechanical stresses on the nanoscale. To this end, since the molecular layers need to be electrically decoupled using thick insulating substrates, the use of AFM becomes mandatory. Here, we show how friction force microscopy (FFM) in water allows us to identify the orientation of copper(ii)phthalocyanine (CuPc) molecules previously self-assembled on a dolomite (104) mineral surface in ultra-high vacuum. The molecular features observed in the friction images show that the CuPc molecules are stacked in parallel rows with no preferential orientation with respect to the dolomite lattice, while the stacking features resemble well the single CuPc crystal structure. This proves that the substrate induction is low and makes friction force microscopy in water a suitable alternative to more demanding dynamic AFM techniques in ultra-high vacuum.

Quantitative nanoscale imaging of orientational order in biological filaments by polarized superresolution microscopy

PubMed Central

Valades Cruz, Cesar Augusto; Shaban, Haitham Ahmed; Kress, Alla; Bertaux, Nicolas; Monneret, Serge; Mavrakis, Manos; Savatier, Julien; Brasselet, Sophie

2016-01-01

Essential cellular functions as diverse as genome maintenance and tissue morphogenesis rely on the dynamic organization of filamentous assemblies. For example, the precise structural organization of DNA filaments has profound consequences on all DNA-mediated processes including gene expression, whereas control over the precise spatial arrangement of cytoskeletal protein filaments is key for mechanical force generation driving animal tissue morphogenesis. Polarized fluorescence is currently used to extract structural organization of fluorescently labeled biological filaments by determining the orientation of fluorescent labels, however with a strong drawback: polarized fluorescence imaging is indeed spatially limited by optical diffraction, and is thus unable to discriminate between the intrinsic orientational mobility of the fluorophore labels and the real structural disorder of the labeled biomolecules. Here, we demonstrate that quantitative single-molecule polarized detection in biological filament assemblies allows not only to correct for the rotational flexibility of the label but also to image orientational order of filaments at the nanoscale using superresolution capabilities. The method is based on polarized direct stochastic optical reconstruction microscopy, using dedicated optical scheme and image analysis to determine both molecular localization and orientation with high precision. We apply this method to double-stranded DNA in vitro and microtubules and actin stress fibers in whole cells. PMID:26831082

Green fluorescent protein nanopolygons as monodisperse supramolecular assemblies of functional proteins with defined valency

PubMed Central

Kim, Young Eun; Kim, Yu-na; Kim, Jung A.; Kim, Ho Min; Jung, Yongwon

2015-01-01

Supramolecular protein assemblies offer novel nanoscale architectures with molecular precision and unparalleled functional diversity. A key challenge, however, is to create precise nano-assemblies of functional proteins with both defined structures and a controlled number of protein-building blocks. Here we report a series of supramolecular green fluorescent protein oligomers that are assembled in precise polygonal geometries and prepared in a monodisperse population. Green fluorescent protein is engineered to be self-assembled in cells into oligomeric assemblies that are natively separated in a single-protein resolution by surface charge manipulation, affording monodisperse protein (nano)polygons from dimer to decamer. Several functional proteins are multivalently displayed on the oligomers with controlled orientations. Spatial arrangements of protein oligomers and displayed functional proteins are directly visualized by a transmission electron microscope. By employing our functional protein assemblies, we provide experimental insight into multivalent protein–protein interactions and tools to manipulate receptor clustering on live cell surfaces. PMID:25972078

Visualization of Bacterial Microcompartment Facet Assembly Using High-Speed Atomic Force Microscopy

DOE PAGES

Sutter, Markus; Faulkner, Matthew; Aussignargues, Clément; ...

2015-11-30

Bacterial microcompartments (BMCs) are proteinaceous organelles widespread among bacterial phyla. They compartmentalize enzymes within a selectively permeable shell and play important roles in CO 2 fixation, pathogenesis, and microbial ecology. Here, we combine X-ray crystallography and high-speed atomic force microscopy to characterize, at molecular resolution, the structure and dynamics of BMC shell facet assembly. Our results show that preformed hexamers assemble into uniformly oriented shell layers, a single hexamer thick. We also observe the dynamic process of shell facet assembly. Shell hexamers can dissociate from and incorporate into assembled sheets, indicating a flexible intermolecular interaction. Furthermore, we demonstrate that themore » self-assembly and dynamics of shell proteins are governed by specific contacts at the interfaces of shell proteins. Our study provides novel insights into the formation, interactions, and dynamics of BMC shell facets, which are essential for the design and engineering of self-assembled biological nanoreactors and scaffolds based on BMC architectures.« less

Scanning tunneling microscopy investigation of copper phthalocyanine and truxenone derivative binary superstructures on graphite.

PubMed

Liu, Jia; Wang, Dong; Wang, Jie-Yu; Pei, Jian; Wan, Li-Jun

2011-02-01

The binary self-assembly of copper phthalocyanine (CuPc) and 2,3,7,8,12,13-hexahexyloxy-truxenone (TrO23) at the solid/liquid interface of highly oriented pyrolytic graphite (HOPG) was investigated by using scanning tunneling microscopy (STM) and scanning tunneling spectroscopy (STS). Pseduohexagonal and linear patterned superstructures of CuPc are obtained by co-adsorbing with TrO23. High-resolution STM images reveal the structural details of the arrangement of TrO23 and CuPc in the binary assembly structures. The molecular ratio between CuPc and TrO23 in the adlayer can be modulated by the CuPc concentration in liquid phase. The electronic properties of CuPc and TrO23 in the co-adsorbed self-assembly are investigated by STS. The results presented here are helpful to the design and fabrication of multi-component functional molecular nanostructures. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Clustering and negative feedback by endocytosis in planar cell polarity signaling is modulated by ubiquitinylation of prickle.

PubMed

Cho, Bomsoo; Pierre-Louis, Gandhy; Sagner, Andreas; Eaton, Suzanne; Axelrod, Jeffrey D

2015-05-01

The core components of the planar cell polarity (PCP) signaling system, including both transmembrane and peripheral membrane associated proteins, form asymmetric complexes that bridge apical intercellular junctions. While these can assemble in either orientation, coordinated cell polarization requires the enrichment of complexes of a given orientation at specific junctions. This might occur by both positive and negative feedback between oppositely oriented complexes, and requires the peripheral membrane associated PCP components. However, the molecular mechanisms underlying feedback are not understood. We find that the E3 ubiquitin ligase complex Cullin1(Cul1)/SkpA/Supernumerary limbs(Slimb) regulates the stability of one of the peripheral membrane components, Prickle (Pk). Excess Pk disrupts PCP feedback and prevents asymmetry. We show that Pk participates in negative feedback by mediating internalization of PCP complexes containing the transmembrane components Van Gogh (Vang) and Flamingo (Fmi), and that internalization is activated by oppositely oriented complexes within clusters. Pk also participates in positive feedback through an unknown mechanism promoting clustering. Our results therefore identify a molecular mechanism underlying generation of asymmetry in PCP signaling.

Examining the Self-Assembly of Rod-Coil Block Copolymers via Physics Based Polymer Models and Polarized X-Ray Scattering

NASA Astrophysics Data System (ADS)

Hannon, Adam; Sunday, Daniel; Windover, Donald; Liman, Christopher; Bowen, Alec; Khaira, Gurdaman; de Pablo, Juan; Delongchamp, Dean; Kline, R. Joseph

Photovoltaics, flexible electronics, and stimuli-responsive materials all require enhanced methodology to examine their nanoscale molecular orientation. The mechanical, electronic, optical, and transport properties of devices made from these materials are all a function of this orientation. The polymer chains in these materials are best modeled as semi-flexible to rigid rods. Characterizing the rigidity and molecular orientation of these polymers non-invasively is currently being pursued by using polarized resonant soft X-ray scattering (P-RSoXS). In this presentation, we show recent work on implementing such a characterization process using a rod-coil block copolymer system in the rigid-rod limit. We first demonstrate how we have used physics based models such as self-consistent field theory (SCFT) in non-polarized RSoXS work to fit scattering profiles for thin film coil-coil PS- b-PMMA block copolymer systems. We then show by using a wormlike chain partition function in the SCFT formulism to model the rigid-rod block, the methodology can be used there as well to extract the molecular orientation of the rod block from a simulated P-RSoXS experiment. The results from the work show the potential of the technique to extract thermodynamic and morphological sample information.

Influence of Chirality in Ordered Block Copolymer Phases

NASA Astrophysics Data System (ADS)

Prasad, Ishan; Grason, Gregory

2015-03-01

Block copolymers are known to assemble into rich spectrum of ordered phases, with many complex phases driven by asymmetry in copolymer architecture. Despite decades of study, the influence of intrinsic chirality on equilibrium mesophase assembly of block copolymers is not well understood and largely unexplored. Self-consistent field theory has played a major role in prediction of physical properties of polymeric systems. Only recently, a polar orientational self-consistent field (oSCF) approach was adopted to model chiral BCP having a thermodynamic preference for cholesteric ordering in chiral segments. We implement oSCF theory for chiral nematic copolymers, where segment orientations are characterized by quadrupolar chiral interactions, and focus our study on the thermodynamic stability of bi-continuous network morphologies, and the transfer of molecular chirality to mesoscale chirality of networks. Unique photonic properties observed in butterfly wings have been attributed to presence of chiral single-gyroid networks, this has made it an attractive target for chiral metamaterial design.

Surface-directed molecular assembly of pentacene on monolayer graphene for high-performance organic transistors.

PubMed

Lee, Wi Hyoung; Park, Jaesung; Sim, Sung Hyun; Lim, Soojin; Kim, Kwang S; Hong, Byung Hee; Cho, Kilwon

2011-03-30

Organic electronic devices that use graphene electrodes have received considerable attention because graphene is regarded as an ideal candidate electrode material. Transfer and lithographic processes during fabrication of patterned graphene electrodes typically leave polymer residues on the graphene surfaces. However, the impact of these residues on the organic semiconductor growth mechanism on graphene surface has not been reported yet. Here, we demonstrate that polymer residues remaining on graphene surfaces induce a stand-up orientation of pentacene, thereby controlling pentacene growth such that the molecular assembly is optimal for charge transport. Thus, pentacene field-effect transistors (FETs) using source/drain monolayer graphene electrodes with polymer residues show a high field-effect mobility of 1.2 cm(2)/V s. In contrast, epitaxial growth of pentacene having molecular assembly of lying-down structure is facilitated by π-π interaction between pentacene and the clean graphene electrode without polymer residues, which adversely affects lateral charge transport at the interface between electrode and channel. Our studies provide that the obtained high field-effect mobility in pentacene FETs using monolayer graphene electrodes arises from the extrinsic effects of polymer residues as well as the intrinsic characteristics of the highly conductive, ultrathin two-dimensional monolayer graphene electrodes.

Epitaxially grown strained pentacene thin film on graphene membrane.

PubMed

Kim, Kwanpyo; Santos, Elton J G; Lee, Tae Hoon; Nishi, Yoshio; Bao, Zhenan

2015-05-06

Organic-graphene system has emerged as a new platform for various applications such as flexible organic photovoltaics and organic light emitting diodes. Due to its important implication in charge transport, the study and reliable control of molecular packing structures at the graphene-molecule interface are of great importance for successful incorporation of graphene in related organic devices. Here, an ideal membrane of suspended graphene as a molecular assembly template is utilized to investigate thin-film epitaxial behaviors. Using transmission electron microscopy, two distinct molecular packing structures of pentacene on graphene are found. One observed packing structure is similar to the well-known bulk-phase, which adapts a face-on molecular orientation on graphene substrate. On the other hand, a rare polymorph of pentacene crystal, which shows significant strain along the c-axis, is identified. In particular, the strained film exhibits a specific molecular orientation and a strong azimuthal correlation with underlying graphene. Through ab initio electronic structure calculations, including van der Waals interactions, the unusual polymorph is attributed to the strong graphene-pentacene interaction. The observed strained organic film growth on graphene demonstrates the possibility to tune molecular packing via graphene-molecule interactions. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Mono- and multilayers of molecular spoked carbazole wheels on graphite

PubMed Central

Aggarwal, A Vikas; Kalle, Daniel; Höger, Sigurd

2014-01-01

Summary Self-assembled monolayers of a molecular spoked wheel (a shape-persistent macrocycle with an intraannular spoke/hub system) and its synthetic precursor are investigated by scanning tunneling microscopy (STM) at the liquid/solid interface of 1-octanoic acid and highly oriented pyrolytic graphite. The submolecularly resolved STM images reveal that the molecules indeed behave as more or less rigid objects of certain sizes and shapes – depending on their chemical structures. In addition, the images provide insight into the multilayer growth of the molecular spoked wheels (MSWs), where the first adlayer acts as a template for the commensurate adsorption of molecules in the second layer. PMID:25550744

Mono- and multilayers of molecular spoked carbazole wheels on graphite.

PubMed

Jester, Stefan-S; Aggarwal, A Vikas; Kalle, Daniel; Höger, Sigurd

2014-01-01

Self-assembled monolayers of a molecular spoked wheel (a shape-persistent macrocycle with an intraannular spoke/hub system) and its synthetic precursor are investigated by scanning tunneling microscopy (STM) at the liquid/solid interface of 1-octanoic acid and highly oriented pyrolytic graphite. The submolecularly resolved STM images reveal that the molecules indeed behave as more or less rigid objects of certain sizes and shapes - depending on their chemical structures. In addition, the images provide insight into the multilayer growth of the molecular spoked wheels (MSWs), where the first adlayer acts as a template for the commensurate adsorption of molecules in the second layer.

Stable mirror mount

DOEpatents

Cutburth, R.W.

1983-11-04

An improved mirror mount assembly is disclosed. The mirror mount assembly provides a post assembly slidable in a Y-axis orientation and a nut plate assembly slidable in an X-axis orientation and means for simultaneously locking said post assembly and said key assembly in a fixed position.

Stable mirror mount

DOEpatents

Cutburth, Ronald W.

1990-01-01

An improved mirror mount assembly is disclosed. The mirror mount assembly provides a post assembly slidable in a Y-axis orientation and a nut plate assembly slidable in an X-axis orientation and a device for simultaneously locking the post assembly and the key assembly in a fixed position.

Investigation of Radiation Resistant Polymer Photodetectors for Space Applications

DTIC Science & Technology

2002-09-11

54 A. XPD Data 54 B. Bibliography 56 iv FIGURES Figure Page 1. Electron transfer in a self-assembled dye-sensitized heterojunction device...electrooptic technology for space applications. By employing molecular engineering to achieve selective orientation of π- electrons within the polymer...temperature, vacuum and radiation induced degradation. Many of these adverse effects are well known for a wide variety of inorganic electronic materials

Conformational adaptation and manipulation of manganese tetra(4-pyridyl)porphyrin molecules on Cu(111)

NASA Astrophysics Data System (ADS)

Chen, Xianwen; Lei, Shulai; Lotze, Christian; Czekelius, Constantin; Paulus, Beate; Franke, Katharina J.

2017-03-01

Porphyrins are highly flexible molecules and well known to adapt to their local environment via conformational changes. We studied the self-assembly of manganese meso-tetra(4-pyridyl)porphyrin (Mn-TPyP) molecules on a Cu(111) surface by low temperature scanning tunneling microscopy (STM) and atomic force microscopy (ATM). We observe molecular chains along the ⟨1 1 ¯ 0 ⟩ direction of the substrate. Within these chains, we identify two molecular conformations, which differ by the orientation of the upward bending of the macrocycle. Using density functional theory, we show that this saddle shape is a consequence of the rotation and inclination of the pyridyl groups towards Cu adatoms, which stabilize the metal-organic chains. The molecular conformations obey a strict alternation, reflecting the mutual enforcement of conformational adaptation in densely packed structures. Tunneling electrons from the STM tip can induce changes in the orientation of the pyridyl endgroups. The switching behaviour varies with the different adsorption configurations.

Structure and dynamics of optically directed self-assembly of nanoparticles

PubMed Central

Roy, Debjit; Mondal, Dipankar; Goswami, Debabrata

2016-01-01

Self-assembly of nanoparticles leading to the formation of colloidal clusters often serves as the representative analogue for understanding molecular assembly. Unravelling the in situ structure and dynamics of such clusters in liquid suspensions is highly challenging. Presently colloidal clusters are first isolated from their generating environment and then their structures are probed by light scattering methods. In order to measure the in situ structure and dynamics of colloidal clusters, we have generated them using the high-repetition-rate femtosecond laser pulse optical tweezer. Since the constituent of our dimer, trimer or tetramer clusters are 250 nm radius two-photon resonant fluorophore coated nanospheres under the optical trap, they inherently produce Two-Photon Fluorescence, which undergo intra-nanosphere Fluorescence Energy Transfer. This unique energy transfer signature, in turn, enables us to visualize structures and orientations of these colloidal clusters during the process of their formation and subsequent dynamics in a liquid suspension. We also show that due to shape-birefringence, orientation and structural control of these colloidal clusters are possible as the polarization of the trapping laser is changed from linear to circular. We thus report important progress in sampling the smallest possible aggregates of nanoparticles, dimers, trimers or tetramers, formed early in the self-assembly process. PMID:27006305

Molecular origin of photovoltaic performance in donor- block-acceptor all-conjugated block copolymers

DOE PAGES

Smith, Kendall A.; Lin, Yen -Hao; Mok, Jorge W.; ...

2015-11-03

All-conjugated block copolymers may be an effective route to self-assembled photovoltaic devices, but we lack basic information on the relationship between molecular characteristics and photovoltaic performance. Here, we synthesize a library of poly(3-hexylthiophene) (P3HT) block poly((9,9-dialkylfluorene)-2,7-diyl-alt-[4,7-bis(alkylthiophen-5-yl)-2,1,3-benzothiadiazole]-2',2''-diyl) (PFTBT) donor- block-acceptor all-conjugated block copolymers and carry out a comprehensive study of processing conditions, crystallinity, domain sizes, and side-chain structure on photovoltaic device performance. We find that all block copolymers studied exhibit an out-of-plane crystal orientation after deposition, and on thermal annealing at high temperatures the crystal orientation flips to an in-plane orientation. By varying processing conditions on polymer photovoltaic devices, we showmore » that the crystal orientation has only a modest effect (15-20%) on photovoltaic performance. The addition of side-chains to the PFTBT block is found to decrease photovoltaic power conversion efficiencies by at least an order of magnitude. Through grazing-incidence X-ray measurements we find that the addition of side-chains to the PFTBT acceptor block results in weak segregation and small (< 10 nm) block copolymer self-assembled donor and acceptor domains. This work is the most comprehensive to date on all-conjugated block copolymer systems and suggests that photovoltaic performance of block copolymers depends strongly on the miscibility of donor and acceptor blocks, which impacts donor and acceptor domain sizes and purity. Lastly, strategies for improving the device performance of block copolymer photovoltaics should seek to increase segregation between donor and acceptor polymer domains.« less

Molecular origin of photovoltaic performance in donor- block-acceptor all-conjugated block copolymers

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

Smith, Kendall A.; Lin, Yen -Hao; Mok, Jorge W.

All-conjugated block copolymers may be an effective route to self-assembled photovoltaic devices, but we lack basic information on the relationship between molecular characteristics and photovoltaic performance. Here, we synthesize a library of poly(3-hexylthiophene) (P3HT) block poly((9,9-dialkylfluorene)-2,7-diyl-alt-[4,7-bis(alkylthiophen-5-yl)-2,1,3-benzothiadiazole]-2',2''-diyl) (PFTBT) donor- block-acceptor all-conjugated block copolymers and carry out a comprehensive study of processing conditions, crystallinity, domain sizes, and side-chain structure on photovoltaic device performance. We find that all block copolymers studied exhibit an out-of-plane crystal orientation after deposition, and on thermal annealing at high temperatures the crystal orientation flips to an in-plane orientation. By varying processing conditions on polymer photovoltaic devices, we showmore » that the crystal orientation has only a modest effect (15-20%) on photovoltaic performance. The addition of side-chains to the PFTBT block is found to decrease photovoltaic power conversion efficiencies by at least an order of magnitude. Through grazing-incidence X-ray measurements we find that the addition of side-chains to the PFTBT acceptor block results in weak segregation and small (< 10 nm) block copolymer self-assembled donor and acceptor domains. This work is the most comprehensive to date on all-conjugated block copolymer systems and suggests that photovoltaic performance of block copolymers depends strongly on the miscibility of donor and acceptor blocks, which impacts donor and acceptor domain sizes and purity. Lastly, strategies for improving the device performance of block copolymer photovoltaics should seek to increase segregation between donor and acceptor polymer domains.« less

Role of topographical defects in organic film growth of 4,4' -biphenyldicarboxylic acid on graphene: A low-energy electron microscopy study

NASA Astrophysics Data System (ADS)

Khokhar, Fawad S.; van Gastel, Raoul; Poelsema, Bene

2010-11-01

We have used low-energy electron microscopy (LEEM) to study the formation of self-assembled molecular networks on graphene sheets. 4,4' -biphenyldicarboxylic acid (BDA) molecular networks were grown using organic molecular beam epitaxy. LEEM images provide direct insight in the growth dynamics and show that defects in the graphene play a crucial role in the final morphology of the molecular film that forms. BDA is demonstrated to form hydrogen bond-stabilized chains on graphene. Dark-field LEEM images reveal that the same defects that determine the morphology of the film, also direct the orientation of the domains, highlighting the importance of understanding the role of defects in epitaxial processes on graphene.

Molecular structure of self-assembled chiral nanoribbons and nanotubules revealed in the hydrated state.

PubMed

Oda, Reiko; Artzner, Franck; Laguerre, Michel; Huc, Ivan

2008-11-05

A detailed molecular organization of racemic 16-2-16 tartrate self-assembled multi-bilayer ribbons in the hydrated state is proposed where 16-2-16 amphiphiles, tartrate ions, and water molecules are all accurately positioned by comparing experimental X-ray powder diffraction and diffraction patterns derived from modeling studies. X-ray diffuse scattering studies show that molecular organization is not fundamentally altered when comparing the flat ribbons of the racemate to chirally twisted or helical ribbons of the pure tartrate enantiomer. Essential features of the three-dimensional molecular organizations of these structures include interdigitation of alkyl chains within each bilayer and well-defined networks of ionic and hydrogen bonds between cations, anions, and water molecules between bilayers. The detailed study of diffraction patterns also indicated that the gemini headgroups are oriented parallel to the long edge of the ribbons. The structure thus possesses a high cohesion and good crystallinity, and for the first time, we could relate the packing of the chiral molecules to the expression of the chirality at a mesoscopic scale. The organization of the ribbons at the molecular level sheds light on a number of their macroscopic features. Among these are the reason why enantiomerically pure 16-2-16 tartrate forms ribbons that consist of exactly two bilayers, and a plausible mechanism by which a chirally twisted or helical shape may emerge from the packing of chiral tartrate ions. Importantly, the distinction between commonly observed helical and twisted morphologies could be related to a subtle symmetry breaking. These results demonstrate that accurately solving the molecular structure of self-assembled soft materials--a process rarely achieved--is within reach, that it is a valid approach to correlate molecular parameters to macroscopic properties, and thus that it offers opportunities to modulate properties through molecular design.

Self assembled monolayers on silicon for molecular electronics.

PubMed

Aswal, D K; Lenfant, S; Guerin, D; Yakhmi, J V; Vuillaume, D

2006-05-24

We present an overview of various aspects of the self-assembly of organic monolayers on silicon substrates for molecular electronics applications. Different chemical strategies employed for grafting the self-assembled monolayers (SAMs) of alkanes having different chain lengths on native oxide of Si or on bare Si have been reviewed. The utility of different characterization techniques in determination of the thickness, molecular ordering and orientation, surface coverage, growth kinetics and chemical composition of the SAMs has been discussed by choosing appropriate examples. The metal counterelectrodes are an integral part of SAMs for measuring their electrical properties as well as using them for molecular electronic devices. A brief discussion on the variety of options available for the deposition of metal counterelectrodes, that is, soft metal contacts, vapor deposition and soft lithography, has been presented. Various theoretical models, namely, tunneling (direct and Fowler-Nordheim), thermionic emission, Poole-Frenkel emission and hopping conduction, used for explaining the electronic transport in dielectric SAMs have been outlined and, some experimental data on alkane SAMs have been analyzed using these models. It has been found that short alkyl chains show excellent agreement with tunneling models; while more experimental data on long alkyl chains are required to understand their transport mechanism(s). Finally, the concepts and realization of various molecular electronic components, that is, diodes, resonant tunnel diodes, memories and transistors, based on appropriate architecture of SAMs comprising of alkyl chains (sigma- molecule) and conjugated molecules (pi-molecule) have been presented.

Self-assembled liposomal nanoparticles in photodynamic therapy

PubMed Central

Sadasivam, Magesh; Avci, Pinar; Gupta, Gaurav K.; Lakshmanan, Shanmugamurthy; Chandran, Rakkiyappan; Huang, Ying-Ying; Kumar, Raj; Hamblin, Michael R.

2013-01-01

Photodynamic therapy (PDT) employs the combination of non-toxic photosensitizers (PS) together with harmless visible light of the appropriate wavelength to produce reactive oxygen species that kill unwanted cells. Because many PS are hydrophobic molecules prone to aggregation, numerous drug delivery vehicles have been tested to solubilize these molecules, render them biocompatible and enhance the ease of administration after intravenous injection. The recent rise in nanotechnology has markedly expanded the range of these nanoparticulate delivery vehicles beyond the well-established liposomes and micelles. Self-assembled nanoparticles are formed by judicious choice of monomer building blocks that spontaneously form a well-oriented 3-dimensional structure that incorporates the PS when subjected to the appropriate conditions. This self-assembly process is governed by a subtle interplay of forces on the molecular level. This review will cover the state of the art in the preparation and use of self-assembled liposomal nanoparticles within the context of PDT. PMID:24348377

Self-assembly modes of glycyrrhetinic acid esters in view of the crystal packing of related triterpene molecules.

PubMed

Langer, Dominik; Wicher, Barbara; Szczołko, Wojciech; Gdaniec, Maria; Tykarska, Ewa

2016-08-01

The crystal structures of three ester derivatives of glycyrrhetinic acid (GE) are reported. X-ray crystallography revealed that despite differences in the size of the ester substituents (ethyl, isopropyl and 2-morpholinoethyl) the scheme of molecular self-assembly is similar in all three cases but differs significantly from that observed in other known GE esters. According to our analysis, the two basic patterns of self-assembly of GE esters observed in their unsolvated crystals correspond to two distinct orientations of the ester groups relative to the triterpene backbone. Moreover, comparison of the self-assembly modes of GE esters in their unsolvated forms with the supramolecular organization of GE and carbenoxolone in their solvated crystals revealed that ester substituents replace solvent molecules hydrogen bonded to the COOH group at the triterpene skeleton, resulting in similar packing arrangements of these compounds.

V-Shaped Molecular Configuration of Wax Esters of Jojoba Oil in a Langmuir Film Model.

PubMed

Caruso, Benjamín; Martini, M Florencia; Pickholz, Mónica; Perillo, María A

2018-06-19

The aim of the present work was to understand the interfacial properties of a complex mixture of wax esters (WEs) obtained from Jojoba oil (JO). Previously, on the basis of molecular area measurements, a hairpin structure was proposed as the hypothetical configuration of WEs, allowing their organization as compressible monolayers at the air-water interface. In the present work, we contributed with further experimental evidence by combining surface pressure (π), surface potential (Δ V), and PM-IRRAS measurements of JO monolayers and molecular dynamic simulations (MD) on a modified JO model. WEs were self-assembled in Langmuir films. Compression isotherms exhibited π lift-off at 100 Å 2 /molecule mean molecular area ( A lift-off ) and a collapse point at π c ≈ 2.2 mN/m and A c ≈ 77 Å 2 /molecule. The Δ V profile reflected two dipolar reorganizations, with one of them at A > A lift-off due to the release of loosely bound water molecules and another one at A c < A < A lift-off possibly due to reorientations of a more tightly bound water population. This was consistent with the maximal SP value that was calculated according to a model that considered two populations of oriented water and was very close to the experimental value. The orientation of the ester group that was assumed in that calculation was coherent with the PM-IRRAS behavior of the carbonyl group with the C═O oriented toward the water and the C-O oriented parallel to the surface and was in accordance with their orientational angles (∼45 and ∼90°, respectively) determined by MD simulations. Taken together, the present results confirm a V shape rather than a hairpin configuration of WEs at the air-water interface.

Micropatterning stretched and aligned DNA using microfluidics and surface patterning for applications in hybridization-mediated templated assembly of nanostructures

NASA Astrophysics Data System (ADS)

Carbeck, Jeffrey; Petit, Cecilia

2004-03-01

Current efforts in nanotechnology use one of two basic approaches: top-down fabrication and bottom-up assembly. Top-down strategies use lithography and contact printing to create patterned surfaces and microfluidic channels that, in turn, can corral and organize nanoscale structures. Bottom-up approaches use templates to direct the assembly of atoms, molecules, and nanoparticles through molecular recognition. The goal of this work is to integrate these strategies by first patterning and orienting DNA molecules through top-down tools so that single DNA chains can then serve as templates for the bottom-up construction of hetero-structures composed of proteins and nanoparticles, both metallic and semi-conducting. The first part of this talk focuses on the top-down strategies used to create microscopic patterns of stretched and aligned molecules of DNA. Specifically, it presents a new method in which molecular combing -- a process by which molecules are deposited and stretched onto a surface by the passage of an air-water interface -- is performed in microchannels. This approach demonstrates that the shape and motion of this interface serve as an effective local field directing the chains dynamically as they are stretched onto the surface. The geometry of the microchannel directs the placement of the DNA molecules, while the geometry of the air-water interface directs the local orientation and curvature of the molecules. This ability to control both the placement and orientation of chains has implication for the use of this technique in genetic analysis and in the bottom up approach to nanofabrication.The second half of this talk presents our bottom-up strategy, which allows placement of nanoparticles along individual DNA chains with a theoretical resolution of less than 1 nm. Specifically, we demonstrate the sequence-specific patterning of nanoparticles via the hybridization of functionalized complementary probes to surface-bound chains of double-stranded DNA. Using this technique, we demonstrate the ability to assemble metals, semiconductors, and a composite of both on a single molecule.

Layer-by-Layer Molecular Assemblies for Dye-Sensitized Photoelectrosynthesis Cells Prepared by Atomic Layer Deposition

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

Wang, Degao; Sheridan, Matthew V.; Shan, Bing

2017-08-30

In a Dye Sensitized Photoelectrosynthesis Cell (DSPEC) the relative orientation of catalyst and chromophore play important roles. Here we introduce a new, robust, Atomic Layer Deposition (ALD) procedure for the preparation of assemblies on wide bandgap semiconductors. In the procedure, phosphonated metal complex precursors react with metal ion bridging to an external chromophore or catalyst to give assemblies bridged by Al(III), Sn(IV), Ti(IV), or Zr(IV) metal oxide units as bridges. The procedure has been extended to chromophore-catalyst assemblies for water oxidation catalysis. A SnO2 bridged assembly on SnO2/TiO2 core/shell electrodes undergoes water splitting with an incident photon conversion efficiency (IPCE)more » of 17.1% at 440 nm. Reduction of water at a Ni(II)-based catalyst on NiO films has been shown to give H2. Compared to conventional solution-based procedures, the ALD approach offers significant advantages in scope and flexibility for the preparation of stable surface structures.« less

Multilayer block copolymer meshes by orthogonal self-assembly

PubMed Central

Tavakkoli K. G., Amir; Nicaise, Samuel M.; Gadelrab, Karim R.; Alexander-Katz, Alfredo; Ross, Caroline A.; Berggren, Karl K.

2016-01-01

Continued scaling-down of lithographic-pattern feature sizes has brought templated self-assembly of block copolymers (BCPs) into the forefront of nanofabrication research. Technologies now exist that facilitate significant control over otherwise unorganized assembly of BCP microdomains to form both long-range and locally complex monolayer patterns. In contrast, the extension of this control into multilayers or 3D structures of BCP microdomains remains limited, despite the possible technological applications in next-generation devices. Here, we develop and analyse an orthogonal self-assembly method in which multiple layers of distinct-molecular-weight BCPs naturally produce nanomesh structures of cylindrical microdomains without requiring layer-by-layer alignment or high-resolution lithographic templating. The mechanisms for orthogonal self-assembly are investigated with both experiment and simulation, and we determine that the control over height and chemical preference of templates are critical process parameters. The method is employed to produce nanomeshes with the shapes of circles and Y-intersections, and is extended to produce three layers of orthogonally oriented cylinders. PMID:26796218

Surface confined metallosupramolecular architectures: formation and scanning tunneling microscopy characterization.

PubMed

Li, Shan-Shan; Northrop, Brian H; Yuan, Qun-Hui; Wan, Li-Jun; Stang, Peter J

2009-02-17

Metallosupramolecular compounds have attracted a great deal of attention over the past two decades largely because of their unique, highly complex structural characteristics and their potential electronic, magnetic, optical, and catalytic properties. These molecules can be prepared with relative ease using coordination-driven self-assembly techniques. In particular, the use of electron-poor square-planar Pt(II) transition metals in conjunction with rigid, electron-rich pyridyl donors has enabled the spontaneous self-assembly of a rich library of 2D metallacyclic and 3D metallacage assemblies via the directional-bonding approach. With this progress in the preparation and characterization of metallosupramolecules, researchers have now turned their attention toward fully exploring and developing their materials properties. Assembling metallosupramolecular compounds on solid supports represents a vitally important step toward developing their materials properties. Surfaces provide a means of uniformly aligning and orienting these highly symmetric metallacycles and metallacages. This uniformity increases the level of coherence between molecules above that which can be achieved in the solution phase and provides a way to integrate adsorbed layers, or adlayers, into a solid-state materials setting. The dynamic nature of kinetically labile Pt(II)-N coordination bonds requires us to adjust deposition and imaging conditions to retain the assemblies' stability. Toward these aims, we have used scanning tunneling microscopy (STM) to image these adlayers and to understand the factors that govern surface self-assembly and the interactions that influence their structure and stability. This Account describes our efforts to deposit 2D rectangular and square metallacycles and 3D trigonal bipyramidal and chiral trigonal prism metallacages on highly oriented pyrolytic graphite (HOPG) and Au(111) substrates to give intact assemblies and ordered adlayers. We have investigated the effects of varying the size, symmetry, and dimensionality of supramolecular adsorbates, the choice of substrate, the use of a molecular template, and the effects of chirality. Our systematic investigations provide insights into the various adsorbate-adsorbate and substrate-adsorbate interactions that largely determine the architecture of each assembly and affect their performance in a materials setting. Rational control over adlayer formation and structure will greatly enhance the potential of these supramolecules to be used in a variety of applications such as host-guest sensing/diagnostic systems, molecular electronic devices, and heterogeneous stereoselective synthesis and catalysis.

Structural basis of human PCNA sliding on DNA

NASA Astrophysics Data System (ADS)

de March, Matteo; Merino, Nekane; Barrera-Vilarmau, Susana; Crehuet, Ramon; Onesti, Silvia; Blanco, Francisco J.; de Biasio, Alfredo

2017-01-01

Sliding clamps encircle DNA and tether polymerases and other factors to the genomic template. However, the molecular mechanism of clamp sliding on DNA is unknown. Using crystallography, NMR and molecular dynamics simulations, here we show that the human clamp PCNA recognizes DNA through a double patch of basic residues within the ring channel, arranged in a right-hand spiral that matches the pitch of B-DNA. We propose that PCNA slides by tracking the DNA backbone via a `cogwheel' mechanism based on short-lived polar interactions, which keep the orientation of the clamp invariant relative to DNA. Mutation of residues at the PCNA-DNA interface has been shown to impair the initiation of DNA synthesis by polymerase δ (pol δ). Therefore, our findings suggest that a clamp correctly oriented on DNA is necessary for the assembly of a replication-competent PCNA-pol δ holoenzyme.

Functionality in Electrospun Nanofibrous Membranes Based on Fiber's Size, Surface Area, and Molecular Orientation

PubMed Central

Matsumoto, Hidetoshi; Tanioka, Akihiko

2011-01-01

Electrospinning is a versatile method for forming continuous thin fibers based on an electrohydrodynamic process. This method has the following advantages: (i) the ability to produce thin fibers with diameters in the micrometer and nanometer ranges; (ii) one-step forming of the two- or three-dimensional nanofiber network assemblies (nanofibrous membranes); and (iii) applicability for a broad spectrum of molecules, such as synthetic and biological polymers and polymerless sol-gel systems. Electrospun nanofibrous membranes have received significant attention in terms of their practical applications. The major advantages of nanofibers or nanofibrous membranes are the functionalities based on their nanoscaled-size, highly specific surface area, and highly molecular orientation. These functionalities of the nanofibrous membranes can be controlled by their fiber diameter, surface chemistry and topology, and internal structure of the nanofibers. This report focuses on our studies and describes fundamental aspects and applications of electrospun nanofibrous membranes. PMID:24957735

Adlayer structure of octa-alkoxy-substituted copper(II) phthalocyanine on Au(111) by electrochemical scanning tunneling microscopy.

PubMed

Wang, Li; Ou-Yang, Liangyue; Yau, Shueh-Lin

2008-01-01

Electrochemical scanning tunneling microscopy (ECSTM) has been used to examine the adlayer of octa-alkoxy-substituted copper(II) phthalocyanines (CuPc(OC(8)H(17))(8)) on Au(111) in 0.1 M HClO(4), where the molecular adlayer was prepared by spontaneous adsorption from a benzene solution containing this molecule. Topography STM scans revealed long-range ordered, interweaved arrays of CuPc(OC(8)H(17))(8) with coexistent rectangular and hexagonal symmetries. High-quality STM molecular resolution yielded the internal molecular structure and the orientation of CuPc(OC(8)H(17))(8) admolecules. These STM results could shed insight into the method of generating ordered molecular assemblies of phthalocyanine molecules with long-chained substitutes on metal surface. 2007 Wiley-Liss, Inc

Molecular Packing of Amphiphilic Nanosheets Resolved by X-ray Scattering

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

Harutyunyan, Boris; Dannenhoffer, Adam; Kewalramani, Sumit

2016-12-29

Molecular packing in light harvesting 2D assemblies of photocatalytic materials is a critical factor for solar-to-fuel conversion efficiency. However, structure–function correlations have yet to be fully established. This is partly due to the difficulties in extracting the molecular arrangements from the complex 3D powder averaged diffraction patterns of 2D lattices, obtained via in situ wide-angle X-ray scattering. Here, we develop a scattering theory formalism and couple it with a simple geometrical model for the molecular shape of chromophore 9-methoxy-N-(sodium hexanoate)perylene-3,4-dicarboximide (MeO-PMI) used in our study. This generally applicable method fully reproduces the measured diffraction pattern including the asymmetric line shapesmore » for the Bragg reflections and yields the molecular packing arrangement within a 2D crystal structure with a remarkable degree of detail. We find an approximate edge-centered herringbone structure for the PMI fused aromatic rings and ordering of the carboxypentyl chains above and below the nanosheets. Such a packing arrangement differs from the more symmetric face-to-face orientation of the unsubstituted PMI rings. This structural difference is correlated to our measurement of the reduced catalytic performance of MeO-PMI nanosheets as compared to the mesoscopically similar unsubstituted PMI assemblies.« less

Shuttlecock-Shaped Molecular Rectifier: Asymmetric Electron Transport Coupled with Controlled Molecular Motion.

PubMed

Ryu, Taekhee; Lansac, Yves; Jang, Yun Hee

2017-07-12

A fullerene derivative with five hydroxyphenyl groups attached around a pentagon, (4-HOC 6 H 4 ) 5 HC 60 (1), has shown an asymmetric current-voltage (I-V) curve in a conducting atomic force microscopy experiment on gold. Such molecular rectification has been ascribed to the asymmetric distribution of frontier molecular orbitals over its shuttlecock-shaped structure. Our nonequilibrium Green's function (NEGF) calculations based on density functional theory (DFT) indeed exhibit an asymmetric I-V curve for 1 standing up between two Au(111) electrodes, but the resulting rectification ratio (RR ∼ 3) is insufficient to explain the wide range of RR observed in experiments performed under a high bias voltage. Therefore, we formulate a hypothesis that high RR (>10) may come from molecular orientation switching induced by a strong electric field applied between two electrodes. Indeed, molecular dynamics simulations of a self-assembled monolayer of 1 on Au(111) show that the orientation of 1 can be switched between standing-up and lying-on-the-side configurations in a manner to align its molecular dipole moment with the direction of the applied electric field. The DFT-NEGF calculations taking into account such field-induced reorientation between up and side configurations indeed yield RR of ∼13, which agrees well with the experimental value obtained under a high bias voltage.

Scanning tunneling microscopy of the formation, transformation, and property of oligothiophene self-organizations on graphite and gold surfaces.

PubMed

Yang, Zhi-Yong; Zhang, Hui-Min; Yan, Cun-Ji; Li, Shan-Shan; Yan, Hui-Juan; Song, Wei-Guo; Wan, Li-Jun

2007-03-06

Two alkyl-substituted dual oligothiophenes, quarterthiophene (4T)-trimethylene (tm)-octithiophene (8T) and 4T-tm-4T, were used to fabricate molecular structures on highly oriented pyrolytic graphite and Au(111) surfaces. The resulted structures were investigated by scanning tunneling microscopy. The 4T-tm-8T and 4T-tm-4T molecules self-organize into long-range ordered structures with linear and/or quasi-hexagonal patterns on highly oriented pyrolytic graphite at ambient temperature. Thermal annealing induced a phase transformation from quasi-hexagonal to linear in 4T-tm-8T adlayer. The molecules adsorbed on Au(111) surface in randomly folded and linear conformation. Based on scanning tunneling microscopy results, the structural models for different self-organizations were proposed. Scanning tunneling spectroscopy measurement showed the electronic property of individual molecules in the patterns. These results are significant in understanding the chemistry of molecular structure, including its formation, transformation, and electronic properties. They also help to fabricate oligothiophene assemblies with desired structures for future molecular devices.

Surface Confined Metallosupramolecular Architectures: Formation and STM Characterization

PubMed Central

Li, Shan-Shan; Northrop, Brian H.; Yuan, Qun-Hui; Wan, Li-Jun; Stang, Peter J.

2009-01-01

CONSPECTUS Metallosupramolecular compounds have attracted a great deal of attention over the past two decades largely because of their unique, highly-complex structural characteristics, the fact that they can be prepared with relative ease using coordination-driven self-assembly techniques, and their potential electronic, magnetic, optical, and catalytic properties. In particular, the use of electron-poor square planar Pt(II) transition metals in conjunction with rigid, electron-rich pyridyl donors had enabled the spontaneous self-assembly of a rich library of 2D metallacyclic and 3D metallacage assemblies via the directional-bonding approach. With the tremendous progress that has been made in the preparation and characterization of metallosupramolecules, much attention is now being turned toward fully exploring and developing their materials properties. Assembling metallosupramolecular compounds on solid supports represents a vitally important step toward developing their materials properties. Surfaces provide a means of uniformly aligning and orienting these highly symmetric metallacycles and metallacages, which increases the level of coherence between molecules above that which can be achieved in the solution phase and affords a means of integrating adlayers into a solid-state materials setting. The dynamic nature of kinetically labile Pt(II)-N coordination bonds, however, requires that deposition and imaging conditions be appropriate to retain the assemblies' stability. Toward these aims it is imperative to understand the factors that govern surface self-assembly and the interactions that influence the structure and stability of the resulting adlayer. Such insight can be obtained from Scanning Tunneling Microscopy (STM), which has emerged as a powerful technique for the imaging and characterization of self-assembled adlayers. This account describes the means by which 2D rectangular and square metallacycles and 3D trigonal bipyrimidal and chiral trigonal prism metallacages can be deposited on Highly Oriented Pyrolytic Graphite (HOPG) and Au(111) substrates such that the assemblies remain intact and result in ordered adlayers. The effects of varying the size, symmetry, and dimensionality of supramolecular adsorbates, the choice of substrate, the use of a molecular template, and the effects of chirality have been investigated. These systematic investigations provide much insight into the various adsorbate-adsorbate and substrate-adsorbate interactions that largely determine the architecture of each assembly and affect their performance in a materials setting. Exhibiting the ability to rationally control adlayer formation and structure will greatly enhance the potential of these supramolecules to be used in a variety of applications such as in host-guest sensing/diagnostic systems, molecular electronic devices, and in heterogeneous stereoselective synthesis and catalysis. PMID:19072706

Freely oriented portable superconducting magnet

DOEpatents

Schmierer, Eric N [Los Alamos, NM; Prenger, F Coyne [Los Alamos, NM; Hill, Dallas D [Los Alamos, NM

2010-01-12

A freely oriented portable superconducting magnet is disclosed. Coolant is supplied to the superconducting magnet from a repository separate from the magnet, enabling portability of the magnet. A plurality of support assemblies structurally anchor and thermally isolate the magnet within a thermal shield. A plurality of support assemblies structurally anchor and thermally isolate the thermal shield within a vacuum vessel. The support assemblies restrain movement of the magnet resulting from energizing and cooldown, as well as from changes in orientation, enabling the magnet to be freely orientable.

Theoretical Foundation for Electric-Dipole-Allowed Chiral-Specific Fluorescence Optical Rotary Dispersion (F-ORD) from Interfacial Assemblies.

PubMed

Deng, Fengyuan; Ulcickas, James R W; Simpson, Garth J

2016-11-03

Fluorescence optical rotary dispersion (F-ORD) is proposed as a novel chiral-specific and interface-specific spectroscopic method. F-ORD measurements of uniaxial assemblies are predicted to be fully electric-dipole-allowed, with corresponding increases in sensitivity to chirality relative to chiral-specific measurements in isotropic assemblies that are commonly interpreted through coupling between electric and magnetic dynamic dipoles. Observations of strong chiral sensitivity in prior single-molecule fluorescence measurements of chiral interfacial molecules are in excellent qualitative agreement with the predictions of the F-ORD mechanism and challenging to otherwise explain. F-ORD may provide methods to suppress background fluorescence in studies of biological interfaces, as the detected signal requires both polar local order and interfacial chirality. In addition, the molecular-level descriptions of the mechanisms underpinning F-ORD may also potentially apply to aid in interpreting chiral-specific Raman and surface-enhanced Raman spectroscopy measurements of uniaxially oriented assemblies, opening up opportunities for chiral-specific and interface-specific vibrational spectroscopy.

Self-assembly of (perfluoroalkyl)alkanes on a substrate surface from solutions in supercritical carbon dioxide.

PubMed

Gallyamov, Marat O; Mourran, Ahmed; Tartsch, Bernd; Vinokur, Rostislav A; Nikitin, Lev N; Khokhlov, Alexei R; Schaumburg, Kjeld; Möller, Martin

2006-06-14

Toroidal self-assembled structures of perfluorododecylnonadecane and perfluorotetradecyloctadecane have been deposited on mica and highly oriented pyrolytic graphite surfaces by exposure of the substrates to solutions of the (pefluoroalkyl)alkanes in supercritical carbon dioxide. Scanning force microscopy (SFM) images have displayed a high degree of regularity of these self-assembled nanoobjects regarding size, shape, and packing in a monolayer. Analysis of SFM images allowed us to estimate that each toroidal domain has an outer diameter of about 50 nm and consists of several thousands of molecules. We propose a simple model explaining the clustering of the molecules to objects with a finite size. The model based on the close-packing principles predicts formation of toroids, whose size is determined by the molecular geometry. Here, we consider the amphiphilic nature of the (perfluoroalkyl)alkane molecules in combination with incommensurable packing parameters of the alkyl- and the perfluoralkyl-segments to be a key factor for such a self-assembly.

An assembly process model based on object-oriented hierarchical time Petri Nets

NASA Astrophysics Data System (ADS)

Wang, Jiapeng; Liu, Shaoli; Liu, Jianhua; Du, Zenghui

2017-04-01

In order to improve the versatility, accuracy and integrity of the assembly process model of complex products, an assembly process model based on object-oriented hierarchical time Petri Nets is presented. A complete assembly process information model including assembly resources, assembly inspection, time, structure and flexible parts is established, and this model describes the static and dynamic data involved in the assembly process. Through the analysis of three-dimensional assembly process information, the assembly information is hierarchically divided from the whole, the local to the details and the subnet model of different levels of object-oriented Petri Nets is established. The communication problem between Petri subnets is solved by using message database, and it reduces the complexity of system modeling effectively. Finally, the modeling process is presented, and a five layer Petri Nets model is established based on the hoisting process of the engine compartment of a wheeled armored vehicle.

Coordination polymer gels with important environmental and biological applications.

PubMed

Jung, Jong Hwa; Lee, Ji Ha; Silverman, Julian R; John, George

2013-02-07

Coordination Polymer Gels (CPGs) constitute a subset of solid-like metal ion and bridging organic ligand structures (similar to metal-organic frameworks) that form multi-dimensional networks through a trapped solvent as a result of non-covalent interactions. While physical properties of these gels are similar to conventional high molecular weight organic polymer gels, coordination polymer gel systems are often fully reversible and can be assembled and disassembled in the presence of additional energy (heat, sonication, shaking) to give a solution of solvated gelators. Compared to gels resulting from purely organic self-assembled low molecular weight gelators, metal ions incorporated into the fibrilar networks spanning the bulk solvent can impart CPGs with added functionalities. The solid/liquid nature of the gels allows for species to migrate through the gel system and interact with metals, ligands, and the solvent. Chemosensing, catalysis, fluorescence, and drug-delivery applications are some of the many potential uses for these dynamic systems, taking advantage of the metal ion's coordination, the organic polydentate ligand's orientation and functionality, or a combination of these properties. By fine tuning these systems through metal ion and ligand selection and by directing self-assembly with external stimuli the rational synthesis of practical systems can be envisaged.

Substrate effect on nanoporous structure of silica wires by channel-confined self-assembly of block-copolymer and sol-gel precursors

DOE PAGES

Hu, Michael Z.; Lai, Peng

2015-09-22

Nanoporous silica wires of various wire diameters were developed by space-confined molecular self-assembly of triblock copolymer ethylene/propylene/ethylene (P123) and silica alkoxide precursor (tetraethylorthosilicate, TEOS). Two distinctive hard-templating substrates, anodized aluminum oxide (AAO) and track-etched polycarbonate (EPC), with channel diameters in the range between 10 nm and 200 nm were employed for space-confinement of soft molecular self-assembly driven by the block-copolymer microphase separation. It was observed in the scanning and transmission electron microscope (STEM) studies that the substrate geometry and material characteristics had pronounced effects on the structure and morphology of the silica nanowires. A substrate wall effect was proposed tomore » explain the ordering and orientation of the intra-wire mesostructure. Circular and spiral nanostructures were found only in wires formed in AAO substrate, not in EPC. Pore-size differences and distinctive wall morphologies of the nanowires relating to the substrates were discussed. It was shown that the material and channel wall characteristics of different substrates play key roles in the ordering and morphology of the intra-wire nanostructures.« less

Molecular Self-Assembly and Interfacial Engineering for Highly Efficient Organic Field Effect Transistors and Solar Cells

DTIC Science & Technology

2012-09-23

balance between disordered SAMs to promote large pentacene grains and thick SAMs to aid in physically buffering the charge carriers in pentacene from...to 0.76 µF/cm2), and enhanced pentacene OFET device performance such as higher charge carrier mobility, current on/off ratio, and lower threshold...surface charge trap • Tuning of surface energy • Control of surface group orientation SAM/MO ultrathin dielectric: • Low-voltage operation

A component-based software environment for visualizing large macromolecular assemblies.

PubMed

Sanner, Michel F

2005-03-01

The interactive visualization of large biological assemblies poses a number of challenging problems, including the development of multiresolution representations and new interaction methods for navigating and analyzing these complex systems. An additional challenge is the development of flexible software environments that will facilitate the integration and interoperation of computational models and techniques from a wide variety of scientific disciplines. In this paper, we present a component-based software development strategy centered on the high-level, object-oriented, interpretive programming language: Python. We present several software components, discuss their integration, and describe some of their features that are relevant to the visualization of large molecular assemblies. Several examples are given to illustrate the interoperation of these software components and the integration of structural data from a variety of experimental sources. These examples illustrate how combining visual programming with component-based software development facilitates the rapid prototyping of novel visualization tools.

Active Transport of Nanomaterials Using Motor Proteins -Final Report

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

Hess, Henry

During the six months of funding we have focused first on the completion of the research begun at the University of Washington in the previous funding cycle. Specifically, we developed a method to polymerize oriented networks of microtubules on lithographically patterned surfaces (M.S. thesis Robert Doot). The properties of active transport have been studied detail, yielding insights into the dispersion mechanisms (Nitta et al.). The assembly of multifunctional structures with a microtubule core has been investigated (Ramachandran et al.). Isaac Luria (B.S. in physics, U. of Florida 2005) worked on the directed assembly of nanoscale, non-equilibrium structures as a summermore » intern. He is now a graduate student in my group at the University of Florida. T. Nitta and H. Hess: Dispersion in Active Transport by Kinesin-Powered Molecular Shuttles, Nano Letters, 5, 1337-1342 (2005) S. Ramachandran, K.-H. Ernst, G. D. Bachand, V. Vogel, H. Hess*: Selective Loading of Kinesin-Powered Molecular Shuttles with Protein Cargo and its Application to Biosensing, submitted to Small (2005)« less

Compression-Induced Conformation and Orientation Changes in an n-Alkane Monolayer on a Au(111) Surface.

PubMed

Endo, Osamu; Nakamura, Masashi; Amemiya, Kenta; Ozaki, Hiroyuki

2017-04-25

The influence of the preparation method and adsorbed amount of n-tetratetracontane (n-C 44 H 90 ) on its orientation in a monolayer on the Au(111) surface is studied by near carbon K-edge X-ray absorption fine structure spectroscopy (C K-NEXAFS), scanning tunneling microscopy (STM) under ultrahigh vacuum, and infrared reflection-absorption spectroscopy (IRAS) at the electrochemical interface in sulfuric acid solution. The n-C 44 H 90 molecules form self-assembled lamellar structures with the chain axis parallel to the surface, as observed by STM. For small amounts adsorbed, the carbon plane is parallel to the surface (flat-on orientation). An increase in the adsorbed amount by ∼10-20% induces compression of the lamellar structure either along the lamellar axis or alkyl chain axis. The compressed molecular arrangement is observed by STM, and induced conformation and orientation changes are confirmed by in situ IRAS and C K-NEXAFS.

Microtubule dynamics in cell division: exploring living cells with polarized light microscopy.

PubMed

Inoué, Shinya

2008-01-01

This Perspective is an account of my early experience while I studied the dynamic organization and behavior of the mitotic spindle and its submicroscopic filaments using polarized light microscopy. The birefringence of spindle filaments in normally dividing plant and animal cells, and those treated by various agents, revealed (a) the reality of spindle fibers and fibrils in healthy living cells; (b) the labile, dynamic nature of the molecular filaments making up the spindle fibers; (c) the mode of fibrogenesis and action of orienting centers; and (d) force-generating properties based on the disassembly and assembly of the fibrils. These studies, which were carried out directly on living cells using improved polarizing microscopes, in fact predicted the reversible assembly properties of microtubules.

Modeling pressure-driven assembly of polymer coated nanoparticles

NASA Astrophysics Data System (ADS)

Lane, J. Matthew D.; Salerno, K. Michael; Grest, Gary S.; Fan, Hongyou

2017-06-01

High-pressure experiments have successfully produced a variety of gold nanostructures by compressing polymer coated spherical nanoparticles. We apply atomistic simulation to understand the role of the soft polymer response in determining the pressure-driven assembly of gold nanostructures. Quasi-isentropic experiments have shown that 1D, 2D and 3D nanostructures can be formed and recovered from dynamic compression of fcc superlattices of alkanethiol-coated gold nanocrystals on Sandia's Veloce pulsed power accelerator. Molecular modeling has shown that the dimensionality of the final structures depends on the orientation of the superlattice and the uniaxial loading. We describe the role of coating ligand length and grafting density, on ligand migration and deformation processes during pressure-driven coalescence of the cores into permanent nanowires, nanosheets and 3D structures. The role of uniaxial vs isotropic pressure and the effects of compression along various superlattice orientations will be discussed. Sandia National Laboratories is a multi-mission laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

Molecularly Defined Nanostructures Based on a Novel AAA-DDD Triple Hydrogen-Bonding Motif.

PubMed

Papmeyer, Marcus; Vuilleumier, Clément A; Pavan, Giovanni M; Zhurov, Konstantin O; Severin, Kay

2016-01-26

A facile and flexible method for the synthesis of a new AAA-DDD triple hydrogen-bonding motif is described. Polytopic supramolecular building blocks with precisely oriented AAA and DDD groups are thus accessible in few steps. These building blocks were used for the assembly of large macrocycles featuring four AAA-DDD interactions and a macrobicyclic complex with a total of six AAA-DDD interactions. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Functional group selective STM Imaging in self-assembled monolayers: Benzeneselenol on Au(111)

NASA Astrophysics Data System (ADS)

Azzam, Waleed; Zharnikov, Michael; Rohwerde, Michael; Bashir, Asif

2018-01-01

Benzeneselenol (PSe) self-assembled monolayers (SAMs) formed on Au(111) substrate by the immersion procedure with an immersion time of 24 h and 4 weeks were studied by high-resolution scanning tunneling microscopy (STM). The short molecular rows, which have been previously attributed to irregular translational domains, were found to be regularly repeated within a single domain in the SAMs fabricated upon the immersion for 4 weeks, forming adlayer structure with a very large unit cell. This structure could be assigned as a (27 × 5) superlattice (α phase) containing 36 molecules in the oblique unit cell. This phase coexisted with a different phase having a commensurate (8√{ 3 } × 4) superstructure (β phase) containing 28 protrusions per rectangular unit cell. Analysis of the STM images suggested that each PSe molecule in the β phase was imaged not as one but as a pair of protrusions, which were attributed to the benzene ring and the selenium headgroup of the PSe molecule. At the given molecular length, the spacing between the protrusions defined the molecular tilt, allowing us to derive the orientation of the SAM constituents directly from the STM image.

Orientational analysis of dodecanethiol and p-nitrothiophenol SAMs on metals with polarisation-dependent SFG spectroscopy.

PubMed

Cecchet, Francesca; Lis, Dan; Guthmuller, Julien; Champagne, Benoît; Caudano, Yves; Silien, Christophe; Mani, Alaa Addin; Thiry, Paul A; Peremans, André

2010-02-22

Polarisation-dependent sum frequency generation (SFG) spectroscopy is used to investigate the orientation of molecules on metallic surfaces. In particular, self-assembled monolayers (SAMs) of dodecanethiol (DDT) and of p-nitrothiophenol (p-NTP), grown on Pt and on Au, have been chosen as models to highlight the ability of combining ppp and ssp polarisations sets (representing the polarisation of the involved beams in the conventional order of SFG, Vis and IR beam) to infer orientational information at metallic interfaces. Indeed, using only the ppp set of data, as it is usually done for metallic surfaces, is not sufficient to determine the full molecular orientation. We show here that simply combining ppp and ssp polarisations enables both the tilt and rotation angles of methyl groups in DDT SAMs to be determined. Moreover, for p-NTP, while the SFG active vibrations detected with the ppp polarisation alone provide no orientational information, however, the combination with ssp spectra enables to retrieve the tilt angle of the p-NTP 1,4 axis. Though orientational information obtained by polarisation-dependent measurements has been extensively used at insulating interfaces, we report here their first application to metallic surfaces.

Integration of the Gene Ontology into an object-oriented architecture.

PubMed

Shegogue, Daniel; Zheng, W Jim

2005-05-10

To standardize gene product descriptions, a formal vocabulary defined as the Gene Ontology (GO) has been developed. GO terms have been categorized into biological processes, molecular functions, and cellular components. However, there is no single representation that integrates all the terms into one cohesive model. Furthermore, GO definitions have little information explaining the underlying architecture that forms these terms, such as the dynamic and static events occurring in a process. In contrast, object-oriented models have been developed to show dynamic and static events. A portion of the TGF-beta signaling pathway, which is involved in numerous cellular events including cancer, differentiation and development, was used to demonstrate the feasibility of integrating the Gene Ontology into an object-oriented model. Using object-oriented models we have captured the static and dynamic events that occur during a representative GO process, "transforming growth factor-beta (TGF-beta) receptor complex assembly" (GO:0007181). We demonstrate that the utility of GO terms can be enhanced by object-oriented technology, and that the GO terms can be integrated into an object-oriented model by serving as a basis for the generation of object functions and attributes.

Integration of the Gene Ontology into an object-oriented architecture

PubMed Central

Shegogue, Daniel; Zheng, W Jim

2005-01-01

Background To standardize gene product descriptions, a formal vocabulary defined as the Gene Ontology (GO) has been developed. GO terms have been categorized into biological processes, molecular functions, and cellular components. However, there is no single representation that integrates all the terms into one cohesive model. Furthermore, GO definitions have little information explaining the underlying architecture that forms these terms, such as the dynamic and static events occurring in a process. In contrast, object-oriented models have been developed to show dynamic and static events. A portion of the TGF-beta signaling pathway, which is involved in numerous cellular events including cancer, differentiation and development, was used to demonstrate the feasibility of integrating the Gene Ontology into an object-oriented model. Results Using object-oriented models we have captured the static and dynamic events that occur during a representative GO process, "transforming growth factor-beta (TGF-beta) receptor complex assembly" (GO:0007181). Conclusion We demonstrate that the utility of GO terms can be enhanced by object-oriented technology, and that the GO terms can be integrated into an object-oriented model by serving as a basis for the generation of object functions and attributes. PMID:15885145

Preferred Molecular Orientation of Coumarin 343 on TiO 2 Surfaces: Application to Dye-Sensitized Solar Cells

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

McCree-Grey, Jonathan; Cole, Jacqueline M.; Evans, Peter J.

2015-07-21

The dye…TiO2 interfacial structure in working electrodes of dye-sensitized solar cells (DSCs) is known to influence its photovoltaic device performance. Despite this, direct and quantitative reports of such structure remain sparse. This case study presents the application of X-ray reflectometry to determine the preferred structural orientation and molecular packing of the organic dye, coumarin 343, adsorbed onto amorphous TiO2. Results show that the dye molecules are, on average, tilted by 61.1° relative to the TiO2 surface, and are separated from each other by 8.2 Å. These findings emulate the molecular packing arrangement of a monolayer of coumarin 343 within itsmore » crystal structure. This suggests that the dye adsorbs onto TiO2 in one of its lowest energy configurations, i.e. dye…TiO2 self assembly is driven more by thermodynamic rather than kinetic means. Complementary DSC device tests illustrate that this interfacial structure compromises photovoltaic performance, unless a suitably sized co-adsorbant is interdispersed between the coumarin 343 chromophores on the TiO2 surface.« less

The Peach v2.0 release: high-resolution linkage mapping and deep resequencing improve chromosome-scale assembly and contiguity.

PubMed

Verde, Ignazio; Jenkins, Jerry; Dondini, Luca; Micali, Sabrina; Pagliarani, Giulia; Vendramin, Elisa; Paris, Roberta; Aramini, Valeria; Gazza, Laura; Rossini, Laura; Bassi, Daniele; Troggio, Michela; Shu, Shengqiang; Grimwood, Jane; Tartarini, Stefano; Dettori, Maria Teresa; Schmutz, Jeremy

2017-03-11

The availability of the peach genome sequence has fostered relevant research in peach and related Prunus species enabling the identification of genes underlying important horticultural traits as well as the development of advanced tools for genetic and genomic analyses. The first release of the peach genome (Peach v1.0) represented a high-quality WGS (Whole Genome Shotgun) chromosome-scale assembly with high contiguity (contig L50 214.2 kb), large portions of mapped sequences (96%) and high base accuracy (99.96%). The aim of this work was to improve the quality of the first assembly by increasing the portion of mapped and oriented sequences, correcting misassemblies and improving the contiguity and base accuracy using high-throughput linkage mapping and deep resequencing approaches. Four linkage maps with 3,576 molecular markers were used to improve the portion of mapped and oriented sequences (from 96.0% and 85.6% of Peach v1.0 to 99.2% and 98.2% of v2.0, respectively) and enabled a more detailed identification of discernible misassemblies (10.4 Mb in total). The deep resequencing approach fixed 859 homozygous SNPs (Single Nucleotide Polymorphisms) and 1347 homozygous indels. Moreover, the assembled NGS contigs enabled the closing of 212 gaps with an improvement in the contig L50 of 19.2%. The improved high quality peach genome assembly (Peach v2.0) represents a valuable tool for the analysis of the genetic diversity, domestication, and as a vehicle for genetic improvement of peach and related Prunus species. Moreover, the important phylogenetic position of peach and the absence of recent whole genome duplication (WGD) events make peach a pivotal species for comparative genomics studies aiming at elucidating plant speciation and diversification processes.

Photon Upconversion and Molecular Solar Energy Storage by Maximizing the Potential of Molecular Self-Assembly.

PubMed

Kimizuka, Nobuo; Yanai, Nobuhiro; Morikawa, Masa-Aki

2016-11-29

The self-assembly of functional molecules into ordered molecular assemblies and the fulfillment of potentials unique to their nanotomesoscopic structures have been one of the central challenges in chemistry. This Feature Article provides an overview of recent progress in the field of molecular self-assembly with the focus on the triplet-triplet annihilation-based photon upconversion (TTA-UC) and supramolecular storage of photon energy. On the basis of the integration of molecular self-assembly and photon energy harvesting, triplet energy migration-based TTA-UC has been achieved in varied molecular systems. Interestingly, some molecular self-assemblies dispersed in solution or organogels revealed oxygen barrier properties, which allowed TTA-UC even under aerated conditions. The elements of molecular self-assembly were also introduced to the field of molecular solar thermal fuel, where reversible photoliquefaction of ionic crystals to ionic liquids was found to double the molecular storage capacity with the simultaneous pursuit of switching ionic conductivity. A future prospect in terms of innovating molecular self-assembly toward molecular systems chemistry is also discussed.

Directing folding pathways for multi-component DNA origami nanostructures with complex topology

NASA Astrophysics Data System (ADS)

Marras, A. E.; Zhou, L.; Kolliopoulos, V.; Su, H.-J.; Castro, C. E.

2016-05-01

Molecular self-assembly has become a well-established technique to design complex nanostructures and hierarchical mesoscale assemblies. The typical approach is to design binding complementarity into nucleotide or amino acid sequences to achieve the desired final geometry. However, with an increasing interest in dynamic nanodevices, the need to design structures with motion has necessitated the development of multi-component structures. While this has been achieved through hierarchical assembly of similar structural units, here we focus on the assembly of topologically complex structures, specifically with concentric components, where post-folding assembly is not feasible. We exploit the ability to direct folding pathways to program the sequence of assembly and present a novel approach of designing the strand topology of intermediate folding states to program the topology of the final structure, in this case a DNA origami slider structure that functions much like a piston-cylinder assembly in an engine. The ability to program the sequence and control orientation and topology of multi-component DNA origami nanostructures provides a foundation for a new class of structures with internal and external moving parts and complex scaffold topology. Furthermore, this work provides critical insight to guide the design of intermediate states along a DNA origami folding pathway and to further understand the details of DNA origami self-assembly to more broadly control folding states and landscapes.

Kinetics of DNA Tile Dimerization

PubMed Central

2015-01-01

Investigating how individual molecular components interact with one another within DNA nanoarchitectures, both in terms of their spatial and temporal interactions, is fundamentally important for a better understanding of their physical behaviors. This will provide researchers with valuable insight for designing more complex higher-order structures that can be assembled more efficiently. In this report, we examined several spatial factors that affect the kinetics of bivalent, double-helical (DH) tile dimerization, including the orientation and number of sticky ends (SEs), the flexibility of the double helical domains, and the size of the tiles. The rate constants we obtained confirm our hypothesis that increased nucleation opportunities and well-aligned SEs accelerate tile–tile dimerization. Increased flexibility in the tiles causes slower dimerization rates, an effect that can be reversed by introducing restrictions to the tile flexibility. The higher dimerization rates of more rigid tiles results from the opposing effects of higher activation energies and higher pre-exponential factors from the Arrhenius equation, where the pre-exponential factor dominates. We believe that the results presented here will assist in improved implementation of DNA tile based algorithmic self-assembly, DNA based molecular robotics, and other specific nucleic acid systems, and will provide guidance to design and assembly processes to improve overall yield and efficiency. PMID:24794259

Kinetics of DNA tile dimerization.

PubMed

Jiang, Shuoxing; Yan, Hao; Liu, Yan

2014-06-24

Investigating how individual molecular components interact with one another within DNA nanoarchitectures, both in terms of their spatial and temporal interactions, is fundamentally important for a better understanding of their physical behaviors. This will provide researchers with valuable insight for designing more complex higher-order structures that can be assembled more efficiently. In this report, we examined several spatial factors that affect the kinetics of bivalent, double-helical (DH) tile dimerization, including the orientation and number of sticky ends (SEs), the flexibility of the double helical domains, and the size of the tiles. The rate constants we obtained confirm our hypothesis that increased nucleation opportunities and well-aligned SEs accelerate tile-tile dimerization. Increased flexibility in the tiles causes slower dimerization rates, an effect that can be reversed by introducing restrictions to the tile flexibility. The higher dimerization rates of more rigid tiles results from the opposing effects of higher activation energies and higher pre-exponential factors from the Arrhenius equation, where the pre-exponential factor dominates. We believe that the results presented here will assist in improved implementation of DNA tile based algorithmic self-assembly, DNA based molecular robotics, and other specific nucleic acid systems, and will provide guidance to design and assembly processes to improve overall yield and efficiency.

Interplay between spherical confinement and particle shape on the self-assembly of rounded cubes.

PubMed

Wang, Da; Hermes, Michiel; Kotni, Ramakrishna; Wu, Yaoting; Tasios, Nikos; Liu, Yang; de Nijs, Bart; van der Wee, Ernest B; Murray, Christopher B; Dijkstra, Marjolein; van Blaaderen, Alfons

2018-06-08

Self-assembly of nanoparticles (NPs) inside drying emulsion droplets provides a general strategy for hierarchical structuring of matter at different length scales. The local orientation of neighboring crystalline NPs can be crucial to optimize for instance the optical and electronic properties of the self-assembled superstructures. By integrating experiments and computer simulations, we demonstrate that the orientational correlations of cubic NPs inside drying emulsion droplets are significantly determined by their flat faces. We analyze the rich interplay of positional and orientational order as the particle shape changes from a sharp cube to a rounded cube. Sharp cubes strongly align to form simple-cubic superstructures whereas rounded cubes assemble into icosahedral clusters with additionally strong local orientational correlations. This demonstrates that the interplay between packing, confinement and shape can be utilized to develop new materials with novel properties.

Electrostatic interactions and binding orientation of HIV-1 matrix studied by neutron reflectivity.

PubMed

Nanda, Hirsh; Datta, Siddhartha A K; Heinrich, Frank; Lösche, Mathias; Rein, Alan; Krueger, Susan; Curtis, Joseph E

2010-10-20

The N-terminal matrix (MA) domain of the HIV-1 Gag protein is responsible for binding to the plasma membrane of host cells during viral assembly. The putative membrane-binding interface of MA was previously mapped by means of mutagenesis and analysis of its trimeric crystal structure. However, the orientation of MA on membranes has not been directly determined by experimental measurements. We present neutron reflectivity measurements that resolve the one-dimensional scattering length density profile of MA bound to a biomimetic of the native viral membrane. A molecular refinement procedure was developed using atomic structures of MA to determine the orientation of the protein on the membrane. The orientation defines a lipid-binding interface consistent with previous mutagenesis results. The MA protein maintains this orientation without the presence of a myristate group, driven only by electrostatic interactions. Furthermore, MA is found to penetrate the membrane headgroup region peripherally such that only the side chains of specific Lys and Arg residues interact with the surface. The results suggest that electrostatic interactions are sufficient to favorably orient MA on viral membrane mimics. The spatial determination of the membrane-bound protein demonstrates the ability of neutron reflectivity to discern orientation and penetration under physiologically relevant conditions. Copyright © 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

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.

Collaborated measurement of three-dimensional position and orientation errors of assembled miniature devices with two vision systems

NASA Astrophysics Data System (ADS)

Wang, Xiaodong; Zhang, Wei; Luo, Yi; Yang, Weimin; Chen, Liang

2013-01-01

In assembly of miniature devices, the position and orientation of the parts to be assembled should be guaranteed during or after assembly. In some cases, the relative position or orientation errors among the parts can not be measured from only one direction using visual method, because of visual occlusion or for the features of parts located in a three-dimensional way. An automatic assembly system for precise miniature devices is introduced. In the modular assembly system, two machine vision systems were employed for measurement of the three-dimensionally distributed assembly errors. High resolution CCD cameras and high position repeatability precision stages were integrated to realize high precision measurement in large work space. The two cameras worked in collaboration in measurement procedure to eliminate the influence of movement errors of the rotational or translational stages. A set of templates were designed for calibration of the vision systems and evaluation of the system's measurement accuracy.

Controlling carbon-nanotube-phospholipid solubility by curvature-dependent self-assembly.

PubMed

Määttä, Jukka; Vierros, Sampsa; Sammalkorpi, Maria

2015-03-12

Control of aqueous dispersion is central in the processing and usage of nanoscale hydrophobic objects. However, selecting dispersive agents based on the size and form of the hydrophobic object and the role of coating morphology in dispersion efficiency remain important open questions. Here, the effect of the substrate and the dispersing molecule curvature, as well as, the influence of dispersant concentration on the adsorption morphology are examined by molecular simulations of graphene and carbon nanotube (CNT) substrates with phospholipids of varying curvature as the dispersing agents. Lipid spontaneous curvature is increased from close to zero (effectively cylindrical lipid) to highly positive (effectively conical lipid) by studying double tailed dipalmitoylphosphadidylcholine (DPPC) and single tailed lysophosphadidylcholine (LPC) which differ in the number of acyl chains but have identical headgroup. We find that lipids are good dispersion agents for both planar and curved nanoparticles and induce a dispersive barrier nonsize selectively. Differences in dispersion efficiency arise from lipid headgroup density and their extension from the hydrophobic substrate in the adsorption morphology. We map the packing morphology contributing factors and report that the aggregate morphologies depend on the competition of interactions rising from (1) hydrophobicity driven maximization of lipid-substrate contacts and lipid self-adhesion, (2) tail bending energy cost, (3) preferential alignment along the graphitic substrate principal axes, and (4) lipid headgroup preferential packing. Curved substrates adjust the morphology by changing the balance between the interaction strengths. Jointly, the findings show substrate curvature and dimensions are a way to tune lipid adsorption to desired, self-assembling patterns. Besides engineering dispersion efficiency, the findings could bear significance in designing materials with defined molecular scale, molecular coatings for orientation specific CNT assembly or lipid-based molecular masks and patterning on graphene.

Soft 2D nanoarchitectonics

NASA Astrophysics Data System (ADS)

Ariga, Katsuhiko; Watanabe, Shun; Mori, Taizo; Takeya, Jun

2018-04-01

Nanoarchitectonics is a new paradigm to combine and unify nanotechnology with other sciences and technologies, such as supramolecular chemistry, self-assembly, self-organization, materials technology for manipulation of the size of material objects, and even biotechnology for hybridization with bio-components. The nanoarchitectonic concept leads to the synergistic combination of various methodologies in materials production, including atomic/molecular-level control, self-organization, and field-controlled organization. The focus of this review is on soft 2D nanoarchitectonics. Scientific views on soft 2D nanomaterials are not fully established compared with those on rigid 2D materials. Here, we collect recent examples of 2D nanoarchitectonic constructions of functional materials and systems with soft components. These examples are selected according to the following three categories on the basis of 2D spatial density and motional freedom: (i) well-packed and oriented organic 2D materials with rational design of component molecules and device applications, (ii) well-defined assemblies with 2D porous structures as 2D network materials, and (iii) 2D control of molecular machines and receptors on the basis of certain motional freedom confined in two dimensions.

Room-temperature isolation of V(benzene)2 sandwich clusters via soft-landing into n-alkanethiol self-assembled monolayers.

PubMed

Nagaoka, Shuhei; Matsumoto, Takeshi; Okada, Eiji; Mitsui, Masaaki; Nakajima, Atsushi

2006-08-17

The adsorption state and thermal stability of V(benzene)2 sandwich clusters soft-landed onto a self-assembled monolayer of different chain-length n-alkanethiols (Cn-SAM, n = 8, 12, 16, 18, and 22) were studied by means of infrared reflection absorption spectroscopy (IRAS) and temperature-programmed desorption (TPD). The IRAS measurement confirmed that V(benzene)2 clusters are molecularly adsorbed and maintain a sandwich structure on all of the SAM substrates. In addition, the clusters supported on the SAM substrates are oriented with their molecular axes tilted 70-80 degrees off the surface normal. An Arrhenius analysis of the TPD spectra reveals that the activation energy for the desorption of the supported clusters increases linearly with the chain length of the SAMs. For the longest chain C22-SAM, the activation energy reaches approximately 150 kJ/mol, and the thermal desorption of the supported clusters can be considerably suppressed near room temperature. The clear chain-length-dependent thermal stability of the supported clusters observed here can be explained well in terms of the cluster penetration into the SAM matrixes.

Real-space identification of intermolecular bonding with atomic force microscopy.

PubMed

Zhang, Jun; Chen, Pengcheng; Yuan, Bingkai; Ji, Wei; Cheng, Zhihai; Qiu, Xiaohui

2013-11-01

We report a real-space visualization of the formation of hydrogen bonding in 8-hydroxyquinoline (8-hq) molecular assemblies on a Cu(111) substrate, using noncontact atomic force microscopy (NC-AFM). The atomically resolved molecular structures enable a precise determination of the characteristics of hydrogen bonding networks, including the bonding sites, orientations, and lengths. The observation of bond contrast was interpreted by ab initio density functional calculations, which indicated the electron density contribution from the hybridized electronic state of the hydrogen bond. Intermolecular coordination between the dehydrogenated 8-hq and Cu adatoms was also revealed by the submolecular resolution AFM characterization. The direct identification of local bonding configurations by NC-AFM would facilitate detailed investigations of intermolecular interactions in complex molecules with multiple active sites.

Controlled self-assembly of conjugated rod-coil block copolymers for applications in organic optoelectronics

NASA Astrophysics Data System (ADS)

Tao, Yuefei

Organic electronics are of great interest in manufacturing light weight, mechanical flexible, and inexpensive large area devices. While significant improvements have been made over the last several years and it is now clear that morphology on the lengthscale of exciton diffusion (10nm) is of crucial importance, a clear relationship between structure and device properties has not emerged. This lack of understanding largely emerges from an inability to control morphology on this lengthscale. This thesis will center around an approach, based on block copolymer self-assembly, to generate equilibrium nanostructures on the 10 nm lengthscale of exciton diffusion and study their effects on device performance. Self-assembly of semiconducting block copolymers is complicated by the non-classical chain shape of conjugated polymers. Unlike classical polymers, the chains do not assume a Gaussian coil shape which is stretched near block copolymer interfaces, instead the chains are elongated and liquid crystalline. Previous work has demonstrated how these new molecular interactions and shapes control the phase diagram of so-called rod-coil block copolymers. Here, we will focus on controlling domain size, orientation, and chemical structure. While domain size can be controlled directly through molecular weight, this requires significant additional synthesis of domain size is to be varied. Here, the domain size is controlled by blending homopolymers into a self-assembling rod-coil block copolymer. When coil-like blocks are incorporated, the domains swell, as expected. When rod-like blocks are incorporated, they interdigitate with the rods of the block copolymers. This results in an increase in interfacial area which forces the coils to rearrange and an overall decrease in domain size with increasing rod content. Control over lamellar orientation is crucial in order to design and control charge transport pathways and exciton recombination or separation interfaces. While numerous techniques have been demonstrated for classical block copolymers, the pi conjugation in the rod blocks allow for additional control mechanisms. Liquid crystals are traditionally aligned in magnetic fields. Here, it is demonstrated that if the rod-like blocks are aligned unidirectionally, the block copolymer interfaces follow to create macroscopic alignment of the nanostructures. Organic Light Emitting Diodes (OLEDs) are generally composed of electron transporting and hole transporting moieties to balance charge recombination. Here, a new multifunctional bipolar rod-coil block copolymer containing the hole transporting and electron transporting materials is synthesized. Self-assembly of this new block copolymer results in 15nm lamellae oriented in grains both parallel and perpendicula to the anode. The self-assembled block copolymer shows superior device performance to controls consisting of a luminescent, analogous homopolymer, and a blend of the two component homopolymers. The effects of the morphologies and chemical structure on photovoltaics is explored with a rod-coil block copolymer, (poly(3-hexylthiophene-b-acrylic perylene)). By varying the kinetics of self-assembly through processing, the block copolymer can be disordered, ordered with only short range registry between the nanodomains, or with long-range order. The short range ordered samples showed the best device performance suggesting that the connectivity that is a biproduct of poor order is beneficial for device performance.

The Assembling of Poly (3-Octyl-Thiophene) on CVD Grown Single Layer Graphene

NASA Astrophysics Data System (ADS)

Jiang, Yanqiu; Yang, Ling; Guo, Zongxia; Lei, Shengbin

2015-12-01

The interface between organic semiconductor and graphene electrode, especially the structure of the first few molecular layers at the interface, is crucial for the device properties such as the charge transport in organic field effect transistors. In this work, we have used scanning tunneling microscopy to investigate the poly (3-octyl-thiophene) (P3OT)-graphene interface. Our results reveal the dynamic assembling of P3OT on single layer graphene. As on other substrates the epitaxial effect plays a role in determining the orientation of the P3OT assembling, however, the inter-thiophene distance along the backbone is consistent with that optimized in vaccum, no compression was observed. Adsorption of P3OT on ripples is weaker due to local curvature, which has been verified both by scanning tunneling microscopy and density functional theory simulation. Scanning tunneling microscopy also reveals that P3OT tends to form hairpin folds when meets a ripple.

Binding Modes of Thioflavin T Molecules to Prion Peptide Assemblies Identified by Using Scanning Tunneling Microscopy

PubMed Central

2011-01-01

The widely used method to monitor the aggregation process of amyloid peptide is thioflavin T (ThT) assay, while the detailed molecular mechanism is still not clear. In this work, we report here the direct identification of the binding modes of ThT molecules with the prion peptide GNNQQNY by using scanning tunneling microscopy (STM). The assembly structures of GNNQQNY were first observed by STM on a graphite surface, and the introduction of ThT molecules to the surface facilitated the STM observations of the adsorption conformations of ThT with peptide strands. ThT molecules are apt to adsorb on the peptide assembly with β-sheet structure and oriented parallel with the peptide strands adopting four different binding modes. This effort could benefit the understanding of the mechanisms of the interactions between labeling species or inhibitory ligands and amyloid peptides, which is keenly needed for developing diagnostic and therapeutic approaches. PMID:22778872

Horizontal high speed stacking for batteries with prismatic cans

DOEpatents

Bartos, Andrew L.; Lin, Yhu-Tin; Turner, III, Raymond D.

2016-06-14

A system and method for stacking battery cells or related assembled components. Generally planar, rectangular (prismatic-shaped) battery cells are moved from an as-received generally vertical stacking orientation to a generally horizontal stacking orientation without the need for robotic pick-and-place equipment. The system includes numerous conveyor belts that work in cooperation with one another to deliver, rotate and stack the cells or their affiliated assemblies. The belts are outfitted with components to facilitate the cell transport and rotation. The coordinated movement between the belts and the components promote the orderly transport and rotation of the cells from a substantially vertical stacking orientation into a substantially horizontal stacking orientation. The approach of the present invention helps keep the stacked assemblies stable so that subsequent assembly steps--such as compressing the cells or attaching electrical leads or thermal management components--may proceed with a reduced chance of error.

Beneath the Surface: Understanding Patterns of Intra-Domain Orientational Order

NASA Astrophysics Data System (ADS)

Prasad, Ishan; Seo, Youngmi; Hall, Lisa; Grason, Gregory

Block copolymers (BCP) self assemble into a rich spectrum of ordered phases due to asymmetry in copolymer architecture. Despite extensive study of spatially-ordered composition patterns of BCP, knowledge of orientational order of chain segments that underlie these spatial patterns is evidently missing. We show using self consistent field (SCF) theory and coarse-grained molecular dynamics (MD) simulations that, even without explicit orientational interactions between segments, BCP exhibit generic patterns of intra-domain segment orientation, which vary both within a given morphology and from morphology to morphology. We find that segment alignment is usually both normal and parallel to the interface within different local regions of a BCP sub-domain. We describe principles that control relative strength and directionality of alignment in different morphologies and report a surprising yet generic emergence of biaxial segment order in morphologies with anisotropic curved interfaces, such as cylinders and gyroid phases. Finally, we focus our study on cholesteric textures that pervade mesochiral BCP morphologies, specifically alternating double gyroid (aDG) and helical cylinder (H*) phases, and analyze patterns of twisted (nematic and polar) segment order within these domains.

Influence of Geometries on the Assembly of Snowman-Shaped Janus Nanoparticles.

PubMed

Kang, Chengjun; Honciuc, Andrei

2018-04-24

The self-assembly of micro/nanoparticles into suprastructures is a promising way to develop reconfigurable materials and to gain insights into the fundamental question of how matter organizes itself. The geometry of particles, especially those deviating from perfectly spherical shapes, is of significant importance in colloidal assembly because it influences the particle "recognition", determines the particle packing, and ultimately dictates the formation of assembled suprastructures. In order to organize particles into desired structures, it is of vital importance to understand the relationship between the shape of the colloidal building blocks and the assembled suprastructures. This fundamental issue is an enduring topic in the assembly of molecular surfactants, but it remained elusive in colloidal assembly. To address this issue, we use snowman-shaped Janus nanoparticles (JNPs) as a model to systematically study the effect of colloidal geometries on their assembled suprastructures. Ten types of JNPs with identical chemical compositions but with different geometries were synthesized. Specifically, the synthesized JNPs differ in their lobe size ratios, phase separation degrees, and overall sizes. We show that by altering these parameters, both finite suprastructures, such as capsules with different curvatures, and nonfinite suprastructures, including free-standing single-layered or double-layered JNPs sheets, can be obtained via self-assembly. All these different types of suprastructures are constituted by highly oriented and hexagonally packed JNPs. These findings demonstrate the significance of geometries in colloidal assembly, such that slightly changing the building block geometries could result in a large variety of very different assembled structures, without altering the chemistry of the particles.

Functionalization of quantum rods with oligonucleotides for programmable assembly with DNA origami

NASA Astrophysics Data System (ADS)

Doane, Tennyson L.; Alam, Rabeka; Maye, Mathew M.

2015-02-01

The DNA-mediated self-assembly of CdSe/CdS quantum rods (QRs) onto DNA origami is described. Two QR types with unique optical emission and high polarization were synthesized, and then functionalized with oligonucleotides (ssDNA) using a novel protection-deprotection approach, which harnessed ssDNA's tailorable rigidity and denaturation temperature to increase DNA coverage by reducing non-specific coordination and wrapping. The QR assembly was programmable, and occurred at two different assembly zones that had capture strands in parallel alignment. QRs with different optical properties were assembled, opening up future studies on orientation dependent QR FRET. The QR-origami conjugates could be purified via gel electrophoresis and sucrose gradient ultracentrifugation. Assembly yields, QR stoichiometry and orientation, as well as energy transfer implications were studied in light of QR distances, origami flexibility, and conditions.The DNA-mediated self-assembly of CdSe/CdS quantum rods (QRs) onto DNA origami is described. Two QR types with unique optical emission and high polarization were synthesized, and then functionalized with oligonucleotides (ssDNA) using a novel protection-deprotection approach, which harnessed ssDNA's tailorable rigidity and denaturation temperature to increase DNA coverage by reducing non-specific coordination and wrapping. The QR assembly was programmable, and occurred at two different assembly zones that had capture strands in parallel alignment. QRs with different optical properties were assembled, opening up future studies on orientation dependent QR FRET. The QR-origami conjugates could be purified via gel electrophoresis and sucrose gradient ultracentrifugation. Assembly yields, QR stoichiometry and orientation, as well as energy transfer implications were studied in light of QR distances, origami flexibility, and conditions. Electronic supplementary information (ESI) available: Experimental conditions, DNA origami blueprint and sequences, FRET calculations. Additional Fig. S1-S13. See DOI: 10.1039/c4nr07662a

Electrochemically Triggered Co-Conformational Switching in a [2]catenane Comprising a Non-Symmetric Calix[6]arene Wheel and a Two-Station Oriented Macrocycle.

PubMed

Zanichelli, Valeria; Dallacasagrande, Luca; Arduini, Arturo; Secchi, Andrea; Ragazzon, Giulio; Silvi, Serena; Credi, Alberto

2018-05-11

Catenanes with desymmetrized ring components can undergo co-conformational rearrangements upon external stimulation and can form the basis for the development of molecular rotary motors. We describe the design, synthesis and properties of a [2]catenane consisting of a macrocycle-the 'track' ring-endowed with two distinct recognition sites (a bipyridinium and an ammonium) for a calix[6]arene-the 'shuttle' ring. By exploiting the ability of the calixarene to thread appropriate non-symmetric axles with directional selectivity, we assembled an oriented pseudorotaxane and converted it into the corresponding oriented catenane by intramolecular ring closing metathesis. Cyclic voltammetric experiments indicate that the calixarene wheel initially surrounds the bipyridinium site, moves away from it when it is reduced, and returns in the original position upon reoxidation. A comparison with appropriate model compounds shows that the presence of the ammonium station is necessary for the calixarene to leave the reduced bipyridinium site.

Self-assembled growth of MnSi~1.7 nanowires with a single orientation and a large aspect ratio on Si(110) surfaces

PubMed Central

2013-01-01

MnSi~1.7 nanowires (NWs) with a single orientation and a large aspect ratio have been formed on a Si(110) surface with the molecular beam epitaxy method by a delicate control of growth parameters, such as temperature, deposition rate, and deposition time. Scanning tunneling microscopy (STM) was employed to study the influence of these parameters on the growth of NWs. The supply of free Si atoms per unit time during the silicide reaction plays a critical role in the growth kinetics of the NWs. High growth temperature and low deposition rate are favorable for the formation of NWs with a large aspect ratio. The orientation relationship between the NWs and the reconstruction rows of the Si(110) surface suggests that the NWs grow along the 11¯0 direction of the silicon substrate. High-resolution STM and backscattered electron scanning electron microscopy images indicate that the NWs are composed of MnSi~1.7. PMID:23339353

Effect of contact angle on the orientation, stability, and assembly of dense floating cubes.

PubMed

Daniello, Robert; Khan, Kashan; Donnell, Michael; Rothstein, Jonathan P

2014-02-01

In this paper, the effect of contact angle, density, and size on the orientation, stability, and assembly of floating cubes was investigated. All the cubes tested were more dense than water. Floatation occurred as a result of capillary stresses induced by deformation of the air-water interface. The advancing contact angle of the bare acrylic cubes was measured to be 85°. The contact angle of the cubes was increased by painting the cubes with a commercially available superhydrophobic paint to reach an advancing contact angle of 150°. Depending on their size, density, and contact angle, the cubes were observed to float in one of three primary orientations: edge up, vertex up, and face up. An experimental apparatus was built such that the sum of the gravitational force, buoyancy force, and capillary forces could be measured using a force transducer as a function of cube position as it was lowered through the air-water interface. Measurements showed that the maximum capillary forces were always experienced for the face up orientation. However, when floatation was possible in the vertex up orientation, it was found to be the most stable cube orientation because it had the lowest center of gravity. A series of theoretical predictions were performed for the cubes floating in each of the three primary orientations to calculate the net force on the cube. The theoretical predictions were found to match the experimental measurements well. A cube stability diagram of cube orientation as a function of cube contact angle and size was prepared from the predictions of theory and found to match the experimental observations quite well. The assembly of cubes floating face up and vertex up were also studied for assemblies of two, three, and many cubes. Cubes floating face up were found to assemble face-to-face and form regular square lattice patterns with no free interface between cubes. Cubes floating vertex up were found to assemble in a variety of different arrangements including edge-to-edge, vertex-to-vertex, face-to-face, and vertex-to-face with the most probably assembly being edge-to-edge. Large numbers of vertex up cubes were found to pack with a distribution of orientations and alignments.

Stereodynamics in state-resolved scattering at the gas–liquid interface

PubMed Central

Perkins, Bradford G.; Nesbitt, David J.

2008-01-01

Stereodynamics at the gas–liquid interface provides insight into the important physical interactions that directly influence heterogeneous chemistry at the surface and within the bulk liquid. We investigate molecular beam scattering of CO2 from a liquid perfluoropolyether (PFPE) surface in vacuum [incident energy Einc = 10.6(8) kcal/mol, incident angle θinc = 60°] to specifically reveal rotational angular-momentum directions for scattered molecules. Experimentally, internal quantum state populations and MJ distributions are probed by high-resolution polarization-modulated infrared laser spectroscopy. Analysis of J-state populations reveals dual-channel scattering dynamics characterized by a two-temperature Boltzmann distribution for trapping–desorption and impulsive scattering. In addition, molecular dynamics simulations of CO2 + fluorinated self-assembled monolayers have been used to model CO2 + PFPE dynamics. Experimental results and molecular dynamics simulations reveal highly oriented CO2 distributions that preferentially scatter with “top spin” as a strongly increasing function of J state. PMID:18678907

Fibre Optic Connections And Method For Using Same

DOEpatents

Chan, Benson; Cohen, Mitchell S.; Fortier, Paul F.; Freitag, Ladd W.; Hall, Richard R.; Johnson, Glen W.; Lin, How Tzu; Sherman, John H.

2004-03-30

A package is described that couples a twelve channel wide fiber optic cable to a twelve channel Vertical Cavity Surface Emitting Laser (VCSEL) transmitter and a multiple channel Perpendicularly Aligned Integrated Die (PAID) receiver. The package allows for reduction in the height of the assembly package by vertically orienting certain dies parallel to the fiber optic cable and horizontally orienting certain other dies. The assembly allows the vertically oriented optoelectronic dies to be perpendicularly attached to the horizontally oriented laminate via a flexible circuit.

Likelihood-based molecular-replacement solution for a highly pathological crystal with tetartohedral twinning and sevenfold translational noncrystallographic symmetry

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

Sliwiak, Joanna; Jaskolski, Mariusz, E-mail: mariuszj@amu.edu.pl; A. Mickiewicz University, Grunwaldzka 6, 60-780 Poznan

With the implementation of a molecular-replacement likelihood target that accounts for translational noncrystallographic symmetry, it became possible to solve the crystal structure of a protein with seven tetrameric assemblies arrayed translationally along the c axis. The new algorithm found 56 protein molecules in reduced symmetry (P1), which was used to resolve space-group ambiguity caused by severe twinning. Translational noncrystallographic symmetry (tNCS) is a pathology of protein crystals in which multiple copies of a molecule or assembly are found in similar orientations. Structure solution is problematic because this breaks the assumptions used in current likelihood-based methods. To cope with such cases,more » new likelihood approaches have been developed and implemented in Phaser to account for the statistical effects of tNCS in molecular replacement. Using these new approaches, it was possible to solve the crystal structure of a protein exhibiting an extreme form of this pathology with seven tetrameric assemblies arrayed along the c axis. To resolve space-group ambiguities caused by tetartohedral twinning, the structure was initially solved by placing 56 copies of the monomer in space group P1 and using the symmetry of the solution to define the true space group, C2. The resulting structure of Hyp-1, a pathogenesis-related class 10 (PR-10) protein from the medicinal herb St John’s wort, reveals the binding modes of the fluorescent probe 8-anilino-1-naphthalene sulfonate (ANS), providing insight into the function of the protein in binding or storing hydrophobic ligands.« less

Facile "modular assembly" for fast construction of a highly oriented crystalline MOF nanofilm.

PubMed

Xu, Gang; Yamada, Teppei; Otsubo, Kazuya; Sakaida, Shun; Kitagawa, Hiroshi

2012-10-10

The preparation of crystalline, ordered thin films of metal-organic frameworks (MOFs) will be a critical process for MOF-based nanodevices in the future. MOF thin films with perfect orientation and excellent crystallinity were formed with novel nanosheet-structured components, Cu-TCPP [TCPP = 5,10,15,20-tetrakis(4-carboxyphenyl)porphyrin], by a new "modular assembly" strategy. The modular assembly process involves two steps: a "modularization" step is used to synthesize highly crystalline "modules" with a nanosized structure that can be conveniently assembled into a thin film in the following "assembly" step. With this method, MOF thin films can easily be set up on different substrates at very high speed with controllable thickness. This new approach also enabled us to prepare highly oriented crystalline thin films of MOFs that cannot be prepared in thin-film form by traditional techniques.

Directed Block Copolymer Assembly versus Electron Beam Lithography for Bit-Patterned Media with Areal Density of 1 Terabit/inch(2) and Beyond.

PubMed

Yang, Xiaomin; Wan, Lei; Xiao, Shuaigang; Xu, Yuan; Weller, Dieter K

2009-07-28

The directed self-assembly of block copolymer (BCP) offers a new route to perfect nanolithographic patterning at sub-50 nm length scale with molecular scale precision. We have explored the feasibility of using the BCP approach versus the conventional electron beam (e-beam) lithography to create highly dense dot patterns for bit-patterned media (BPM) applications. Cylinder-forming poly(styrene-b-methyl methacrylate) (PS-b-PMMA) directly self-assembled on a chemically prepatterned substrate. The nearly perfect hexagonal arrays of perpendicularly oriented cylindrical pores at a density of approximately 1 Terabit per square inch (Tb/in.(2)) are achieved over an arbitrarily large area. Considerable gains in the BCP process are observed relative to the conventional e-beam lithography in terms of the dot size variation, the placement accuracy, the pattern uniformity, and the exposure latitude. The maximum dimensional latitude in the cylinder-forming BCP patterns and the maximum skew angle that the BCP can tolerate have been investigated for the first time. The dimensional latitude restricts the formation of more than one lattice configuration in certain ranges. More defects in BCP patterns are observed when using low molecular weight BCP materials or on non-hexagonal prepatterns due to the dimensional latitude restriction. Finally, the limitations and challenges in the BCP approach that are associated with BPM applications will be briefly discussed.

Spin interactions in InAs quantum dots

NASA Astrophysics Data System (ADS)

Doty, M. F.; Ware, M. E.; Stinaff, E. A.; Scheibner, M.; Bracker, A. S.; Gammon, D.; Ponomarev, I. V.; Reinecke, T. L.; Korenev, V. L.

2006-03-01

Fine structure splittings in optical spectra of self-assembled InAs quantum dots (QDs) generally arise from spin interactions between particles confined in the dots. We present experimental studies of the fine structure that arises from multiple charges confined in a single dot [1] or in molecular orbitals of coupled pairs of dots. To probe the underlying spin interactions we inject particles with a known spin orientation (by using polarized light to perform photoluminescence excitation spectroscopy experiments) or use a magnetic field to orient and/or mix the spin states. We develop a model of the spin interactions that aids in the development of quantum information processing applications based on controllable interactions between spins confined to QDs. [1] Polarized Fine Structure in the Photoluminescence Excitation Spectrum of a Negatively Charged Quantum Dot, Phys. Rev. Lett. 95, 177403 (2005)

Magnetic Alignment of Block Copolymer Microdomains by Intrinsic Chain Anisotropy.

PubMed

Rokhlenko, Yekaterina; Gopinadhan, Manesh; Osuji, Chinedum O; Zhang, Kai; O'Hern, Corey S; Larson, Steven R; Gopalan, Padma; Majewski, Paweł W; Yager, Kevin G

2015-12-18

We examine the role of intrinsic chain susceptibility anisotropy in magnetic field directed self-assembly of a block copolymer using in situ x-ray scattering. Alignment of a lamellar mesophase is observed on cooling across the disorder-order transition with the resulting orientational order inversely proportional to the cooling rate. We discuss the origin of the susceptibility anisotropy, Δχ, that drives alignment and calculate its magnitude using coarse-grained molecular dynamics to sample conformations of surface-tethered chains, finding Δχ≈2×10^{-8}. From field-dependent scattering data, we estimate that grains of ≈1.2  μm are present during alignment. These results demonstrate that intrinsic anisotropy is sufficient to support strong field-induced mesophase alignment and suggest a versatile strategy for field control of orientational order in block copolymers.

Direct observation of subunit exchange along mature vimentin intermediate filaments.

PubMed

Nöding, Bernd; Herrmann, Harald; Köster, Sarah

2014-12-16

Actin filaments, microtubules, and intermediate filaments (IFs) are central elements of the metazoan cytoskeleton. At the molecular level, the assembly mechanism for actin filaments and microtubules is fundamentally different from that of IFs. The former two types of filaments assemble from globular proteins. By contrast, IFs assemble from tetrameric complexes of extended, half-staggered, and antiparallel oriented coiled-coils. These tetramers laterally associate into unit-length filaments; subsequent longitudinal annealing of unit-length filaments yields mature IFs. In vitro, IFs form open structures without a fixed number of tetramers per cross-section along the filament. Therefore, a central question for the structural biology of IFs is whether individual subunits can dissociate from assembled filaments and rebind at other sites. Using the fluorescently labeled IF-protein vimentin for assembly, we directly observe and quantitatively determine subunit exchange events between filaments as well as with soluble vimentin pools. Thereby we demonstrate that the cross-sectional polymorphism of donor and acceptor filaments plays an important role. We propose that in segments of donor filaments with more than the standard 32 molecules per cross-section, subunits are not as tightly bound and are predisposed to be released from the filament. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

Active Glutaminase C Self-assembles into a Supratetrameric Oligomer That Can Be Disrupted by an Allosteric Inhibitor*

PubMed Central

Ferreira, Amanda Petrina Scotá; Cassago, Alexandre; Gonçalves, Kaliandra de Almeida; Dias, Marília Meira; Adamoski, Douglas; Ascenção, Carolline Fernanda Rodrigues; Honorato, Rodrigo Vargas; de Oliveira, Juliana Ferreira; Ferreira, Igor Monteze; Fornezari, Camila; Bettini, Jefferson; Oliveira, Paulo Sérgio Lopes; Paes Leme, Adriana Franco; Portugal, Rodrigo Villares; Ambrosio, Andre Luis Berteli; Dias, Sandra Martha Gomes

2013-01-01

The phosphate-dependent transition between enzymatically inert dimers into catalytically capable tetramers has long been the accepted mechanism for the glutaminase activation. Here, we demonstrate that activated glutaminase C (GAC) self-assembles into a helical, fiber-like double-stranded oligomer and propose a molecular model consisting of seven tetramer copies per turn per strand interacting via the N-terminal domains. The loop 321LRFNKL326 is projected as the major regulating element for self-assembly and enzyme activation. Furthermore, the previously identified in vivo lysine acetylation (Lys311 in humans, Lys316 in mouse) is here proposed as an important down-regulator of superoligomer assembly and protein activation. Bis-2-(5-phenylacetamido-1,3,4-thiadiazol-2-yl)ethyl sulfide, a known glutaminase inhibitor, completely disrupted the higher order oligomer, explaining its allosteric mechanism of inhibition via tetramer stabilization. A direct correlation between the tendency to self-assemble and the activity levels of the three mammalian glutaminase isozymes was established, with GAC being the most active enzyme while forming the longest structures. Lastly, the ectopic expression of a fiber-prone superactive GAC mutant in MDA-MB 231 cancer cells provided considerable proliferative advantages to transformed cells. These findings yield unique implications for the development of GAC-oriented therapeutics targeting tumor metabolism. PMID:23935106

Asymmetric van der Waals Forces Drive Orientation of Compositionally Anisotropic Nanocylinders within Smectic Arrays: Experiment and Simulation

PubMed Central

Smith, Benjamin D.; Fichthorn, Kristen A.; Kirby, David J.; Quimby, Lisa M.; Triplett, Derek A.; González, Pedro; Hernández, Darimar; Keating, Christine D.

2014-01-01

Understanding how micro- and nanoparticles interact is important for achieving bottom-up assembly of desired structures. Here, we examine the self-assembly of two-component, compositionally asymmetric nanocylinders that sediment from solution onto a solid surface. These particles spontaneously formed smectic arrays. Within the rows of an array, nanocylinders tended to assemble such that neighboring particles had the same orientation of their segments. As a probe of interparticle interactions, we classified nanocylinder alignments by measuring the segment orientations of many sets of neighboring particles. Monte Carlo simulations incorporating an exact expression for the van der Waals (vdW) energy indicate that differences in the vdW interactions, even when small, are the key factor in producing observed segment alignment. These results point to asymmetrical vdW interactions as a potentially powerful means of controlling orientation in multicomponent cylinder arrays, and suggest that designing for these interactions could yield new ways to control self-assembly. PMID:24308771

Synthesis, Self-Assembly, and Drug-Release Properties of New Amphipathic Liquid Crystal Polycarbonates

PubMed Central

Xie, Yujiao; Liu, Xiaofeng; Hu, Zhuang; Hou, Zhipeng; Chen, Zhangpei; Hu, Jianshe; Yang, Liqun

2018-01-01

New amphiphilic liquid crystal (LC) polycarbonate block copolymers containing side-chain cholesteryl units were synthesized. Their structure, thermal stability, and LC phase behavior were characterized with Fourier transform infrared (FT-IR) spectrum, 1H NMR, gel permeation chromatographic (GPC), thermogravimetric analysis (TGA), differential scanning calorimetry (DSC), polarizing optical microscope (POM), and XRD methods. The results demonstrated that the LC copolymers showed a double molecular arrangement of a smectic A phase at room temperature. With the elevating of LC unit content in such LC copolymers, the corresponding properties including decomposition temperature (Td), glass temperature (Tg), and isotropic temperature (Ti) increased. The LC copolymers showed pH-responsive self-assembly behavior under the weakly acidic condition, and with more side-chain LC units, the self-assembly process was faster, and the formed particle size was smaller. It indicated that the self-assembly driving force was derived from the orientational ability of LC. The particle size and morphologies of self-assembled microspheres loaded with doxorubicin (DOX), together with drug release tracking, were evaluated by dynamic light scattering (DLS), SEM, and UV–vis spectroscopy. The results showed that DOX could be quickly released in a weakly acidic environment due to the pH response of the self-assembled microspheres. This would offer a new strategy for drug delivery in clinic applications. PMID:29584691

Charge transport in vertically aligned, self-assembled peptide nanotube junctions.

PubMed

Mizrahi, Mordechay; Zakrassov, Alexander; Lerner-Yardeni, Jenny; Ashkenasy, Nurit

2012-01-21

The self-assembly propensity of peptides has been extensively utilized in recent years for the formation of supramolecular nanostructures. In particular, the self-assembly of peptides into fibrils and nanotubes makes them promising building blocks for electronic and electro-optic applications. However, the mechanisms of charge transfer in these wire-like structures, especially in ambient conditions, are not yet fully understood. We describe here a layer-by-layer deposition methodology of short self-assembled cyclic peptide nanotubes, which results in vertically oriented nanotubes on gold substrates. Using this novel deposition methodology, we have fabricated molecular junctions with a conductive atomic force microscopy tip as a second electrode. Studies of the junctions' current-voltage characteristics as a function of the nanotube length revealed an efficient charge transfer in these supramolecular structures, with a low current attenuation constant of 0.1 Å(-1), which indicate that electron transfer is dominated by hopping. Moreover, the threshold voltage to field-emission dominated transport was found to increase with peptide length in a manner that depends on the nature of the contact with the electrodes. The flexibility in the design of the peptide monomers and the ability to control their sequential order over the nanotube by means of the layer-by-layer assembly process, which is demonstrated in this work, can be used to engineer the electronic properties of self-assembled peptide nanotubes toward device applications.

Two-dimensional protein crystals (S-layers): fundamentals and applications.

PubMed

Sleytr, U B; Sára, M; Messner, P; Pum, D

1994-10-01

Two-dimensional crystalline surface layers (S-layers) composed of protein or glycoprotein subunits are one of the most commonly observed prokaryotic cell envelope structures. Isolated S-layer subunits are endowed with the ability to assemble into monomolecular arrays in suspension, on surfaces or interfaces by an entropy-driven process. S-layer lattices are isoporous structures with functional groups located on the surface in an identical position and orientation. These characteristic features have already led to applications of S-layers as (1) ultrafiltration membranes with well-defined molecular weight cut-offs and excellent antifouling characteristics, (2) immobilization matrices for functional molecules as required for affinity and enzyme membranes, affinity microcarriers and biosensors, (3) conjugate vaccines, (4) carriers for Langmuir-Blodgett films and reconstituted biological membranes, and (5) patterning elements in molecular nanotechnology.

Identification of Putative Olfactory Genes from the Oriental Fruit Moth Grapholita molesta via an Antennal Transcriptome Analysis

PubMed Central

Li, Yiping; Wu, Junxiang

2015-01-01

Background The oriental fruit moth, Grapholita molesta, is an extremely important oligophagous pest species of stone and pome fruits throughout the world. As a host-switching species, adult moths, especially females, depend on olfactory cues to a large extent in locating host plants, finding mates, and selecting oviposition sites. The identification of olfactory genes can facilitate investigation on mechanisms for chemical communications. Methodology/Principal Finding We generated transcriptome of female antennae of G.molesta using the next-generation sequencing technique, and assembled transcripts from RNA-seq reads using Trinity, SOAPdenovo-trans and Abyss-trans assemblers. We identified 124 putative olfactory genes. Among the identified olfactory genes, 118 were novel to this species, including 28 transcripts encoding for odorant binding proteins, 17 chemosensory proteins, 48 odorant receptors, four gustatory receptors, 24 ionotropic receptors, two sensory neuron membrane proteins, and one odor degrading enzyme. The identified genes were further confirmed through semi-quantitative reverse transcription PCR for transcripts coding for 26 OBPs and 17 CSPs. OBP transcripts showed an obvious antenna bias, whereas CSP transcripts were detected in different tissues. Conclusion Antennal transcriptome data derived from the oriental fruit moth constituted an abundant molecular resource for the identification of genes potentially involved in the olfaction process of the species. This study provides a foundation for future research on the molecules involved in olfactory recognition of this insect pest, and in particular, the feasibility of using semiochemicals to control this pest. PMID:26540284

Two-stages of chiral selectivity in the molecular self-assembly of tryptophan

NASA Astrophysics Data System (ADS)

Guisinger, Nathan

Both chirality and molecular assembly are essential and key components to life. In this study we explore the molecular assembly of the amino acid tryptophan (both L- and D- chiralities) on Cu(111). Our investigation utilizes low temperature scanning tunneling microscopy to observe resulting assemblies at the molecular scale. We find that depositing a racemic mixture of both L- and D- tryptophan results in the assembly of basic 6 molecule ``Lego'' structures that are enantiopure. These enantiopure ``Legos'' further assemble into 1-dimensional chains one block at a time. These resulting chains are also enantiopure with chiral selectivity occurring at two stages of assembly. Utilizing scanning tunneling spectroscopy we are able to probe the electronic structure of the chiral Legos that give insight into the root of the observed selectivity. Two-stages of chiral selectivity in the molecular self-assembly of tryptophan.

Direction-dependent force-induced dissociation dynamics of an entropic-driven lock-and-key assembly.

PubMed

Chen, Yen-Fu; Chen, Hsuan-Yi; Sheng, Yu-Jane; Tsao, Heng-Kwong

2017-09-01

The unbinding dynamics of a nanosized sphere-and-cavity assembly under the pulling of constant force and constant loading rate is explored by dissipative particle dynamics simulations. The formation of this matched lock-and-key pair in a polymer solution is driven by the depletion attraction. The two-dimensional free energy landscape U(x,z) associated with this assembly is constructed. Our results indicate that the unbinding pathway along the orientation of the assembly is unfavorable due to the relatively high energy barrier compared to that along the tortuous minimum path whose energy barrier is not high. It is also found that the dissociation rate depends on the direction of the external force (θ) with respect to the assembly orientation. The presence of the force component perpendicular to the assembly orientation can reduce the bond lifetime significantly by driving the key particle to approach the minimum path. Moreover, the dissociation dynamics can be facilitated even by a pushing force compared to the spontaneous dissociation (without forces). To elucidate the effective pathway under pulling, the escaping position is analyzed and its mean direction with respect to the assembly orientation rises generally with increasing θ, revealing that the presence of the force component along the minimum pathway is helpful. The importance of the direction of the external pulling has been demonstrated in our simple system. Therefore, this effect should be considered in more complicated unbinding experiments.

Direction-dependent force-induced dissociation dynamics of an entropic-driven lock-and-key assembly

NASA Astrophysics Data System (ADS)

Chen, Yen-Fu; Chen, Hsuan-Yi; Sheng, Yu-Jane; Tsao, Heng-Kwong

2017-09-01

The unbinding dynamics of a nanosized sphere-and-cavity assembly under the pulling of constant force and constant loading rate is explored by dissipative particle dynamics simulations. The formation of this matched lock-and-key pair in a polymer solution is driven by the depletion attraction. The two-dimensional free energy landscape U (x ,z ) associated with this assembly is constructed. Our results indicate that the unbinding pathway along the orientation of the assembly is unfavorable due to the relatively high energy barrier compared to that along the tortuous minimum path whose energy barrier is not high. It is also found that the dissociation rate depends on the direction of the external force (θ ) with respect to the assembly orientation. The presence of the force component perpendicular to the assembly orientation can reduce the bond lifetime significantly by driving the key particle to approach the minimum path. Moreover, the dissociation dynamics can be facilitated even by a pushing force compared to the spontaneous dissociation (without forces). To elucidate the effective pathway under pulling, the escaping position is analyzed and its mean direction with respect to the assembly orientation rises generally with increasing θ , revealing that the presence of the force component along the minimum pathway is helpful. The importance of the direction of the external pulling has been demonstrated in our simple system. Therefore, this effect should be considered in more complicated unbinding experiments.

The Electrochemical Assembly of Semiconducting Organic-Inorganic Lamellar Domains for Photovoltaics

NASA Astrophysics Data System (ADS)

Herman, David John

This dissertation investigates the one-step electrodeposition of alternating nanoscale domains of n-type ZnO and p-type organic molecules for photovoltaics. In such hybrid photovoltaic systems, a nanoscale lamellar periodicity of 5-10 nm between electron donor and electron acceptor materials is ideal for efficient exciton separation. In addition, achieving uniform density and substrate-wide alignment of the hybrid lamellar structures with orientation perpendicular to substrate surfaces is important in providing direct pathways for charge carriers to the electrodes. To this end, it is first reported how to control the assembly of the pyrene-based surfactant 1-pyrenebutyric acid (PyBA) with zinc hydroxide (a precursor to the semiconductor ZnO), resulting in a nanoscale lamellar structure with a periodicity of 3.2 nm. By exploring solution chemistry parameters, the surfactant concentration and solvent composition are shown to have the greatest effect on the morphology of lamellar growth. By studying the early nucleation and growth on indium tin oxide (ITO) substrates with 2D grazing incidence small angle X-ray scattering, it is revealed that the lamellae preferentially nucleate parallel to the hydrophilic ITO surface. It is hypothesized that the conductive and more hydrophobic poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS) surface increases the affinity for the pyrene functions to the surface, and therefore the oriented growth of the lamellae changes from parallel to perpendicular with respect to the substrate surface. The second part of this thesis investigates the effects of conjugated surfactant design in directing the growth of hybrid lamellar structures by incorporating either a pyrene or terthiophene moiety and varying overall molecular design. It is found that high aspect ratio and amphiphilic surfactants possessing a flexible alkyl spacer between the carboxylic acid and conjugated moiety consistently allow for the controlled and directed assembly of lamellae with orientations either parallel (on ITO) or perpendicular (on PEDOT:PSS) to the substrate. For surfactants without the spacer or with bolaamphiphilic design, the decrease in entropic freedom either during surface assembly or during lamellae growth is believed to result in uncontrolled orientations and heterogeneous morphologies. In all cases, the lack or low-density of solution micelles at the deposition conditions implied that the growth and orientation of lamellar structures is mediated by surfactant-substrate interactions and assemblies. Finally, the controlled deposition of quinquethiophene surfactant and ZnO lamellae with a periodicity of 2.5 nm was achieved. By optimizing the device architecture with an inverted design, the photovoltaic efficiency improved from 0.0008% to 0.01%. Converting the Zn(OH)2 to ZnO by annealing at 150 °C and pulsing the electrodeposition potential led to a three-fold improvement in efficiency to 0.035%. External quantum efficiency measurements indicate that pulsed depositions lead to better π-π stacking of the thiophenes inside the lamellar galleries. Although the seemingly ideal assembly between n- and p-type materials is approached and photovoltaic devices are demonstrated, the efficiencies remain limited due to high charge carrier resistances from the excess active layer thickness, which was required to prevent electrode shorting during device fabrication.

A pyrene-based fluorescent sensor for Zn2+ ions: a molecular 'butterfly'.

PubMed

Manandhar, Erendra; Broome, J Hugh; Myrick, Jalin; Lagrone, Whitney; Cragg, Peter J; Wallace, Karl J

2011-08-21

A simple pyrene-based triazole receptor has been synthesised and shown to self-assemble in the presence of ZnCl(2) in an exclusively 2:1 ratio, whereas a mixture of 2:1 and 1:1 ratios are observed for other Zn(2+) salts. The pyrene units are syn in orientation; this is supported by a strong excimer signal observed at 410 nm in the presence of ZnCl(2) in acetonitrile. DFT calculations and 2D NMR support the proposed structure. This journal is © The Royal Society of Chemistry 2011

Cluster analysis in systems of magnetic spheres and cubes

NASA Astrophysics Data System (ADS)

Pyanzina, E. S.; Gudkova, A. V.; Donaldson, J. G.; Kantorovich, S. S.

2017-06-01

In the present work we use molecular dynamics simulations and graph-theory based cluster analysis to compare self-assembly in systems of magnetic spheres, and cubes where the dipole moment is oriented along the side of the cube in the [001] crystallographic direction. We show that under the same conditions cubes aggregate far less than their spherical counterparts. This difference can be explained in terms of the volume of phase space in which the formation of the bond is thermodynamically advantageous. It follows that this volume is much larger for a dipolar sphere than for a dipolar cube.

Gigadalton-scale shape-programmable DNA assemblies

NASA Astrophysics Data System (ADS)

Wagenbauer, Klaus F.; Sigl, Christian; Dietz, Hendrik

2017-12-01

Natural biomolecular assemblies such as molecular motors, enzymes, viruses and subcellular structures often form by self-limiting hierarchical oligomerization of multiple subunits. Large structures can also assemble efficiently from a few components by combining hierarchical assembly and symmetry, a strategy exemplified by viral capsids. De novo protein design and RNA and DNA nanotechnology aim to mimic these capabilities, but the bottom-up construction of artificial structures with the dimensions and complexity of viruses and other subcellular components remains challenging. Here we show that natural assembly principles can be combined with the methods of DNA origami to produce gigadalton-scale structures with controlled sizes. DNA sequence information is used to encode the shapes of individual DNA origami building blocks, and the geometry and details of the interactions between these building blocks then control their copy numbers, positions and orientations within higher-order assemblies. We illustrate this strategy by creating planar rings of up to 350 nanometres in diameter and with atomic masses of up to 330 megadaltons, micrometre-long, thick tubes commensurate in size to some bacilli, and three-dimensional polyhedral assemblies with sizes of up to 1.2 gigadaltons and 450 nanometres in diameter. We achieve efficient assembly, with yields of up to 90 per cent, by using building blocks with validated structure and sufficient rigidity, and an accurate design with interaction motifs that ensure that hierarchical assembly is self-limiting and able to proceed in equilibrium to allow for error correction. We expect that our method, which enables the self-assembly of structures with sizes approaching that of viruses and cellular organelles, can readily be used to create a range of other complex structures with well defined sizes, by exploiting the modularity and high degree of addressability of the DNA origami building blocks used.

Gigadalton-scale shape-programmable DNA assemblies.

PubMed

Wagenbauer, Klaus F; Sigl, Christian; Dietz, Hendrik

2017-12-06

Natural biomolecular assemblies such as molecular motors, enzymes, viruses and subcellular structures often form by self-limiting hierarchical oligomerization of multiple subunits. Large structures can also assemble efficiently from a few components by combining hierarchical assembly and symmetry, a strategy exemplified by viral capsids. De novo protein design and RNA and DNA nanotechnology aim to mimic these capabilities, but the bottom-up construction of artificial structures with the dimensions and complexity of viruses and other subcellular components remains challenging. Here we show that natural assembly principles can be combined with the methods of DNA origami to produce gigadalton-scale structures with controlled sizes. DNA sequence information is used to encode the shapes of individual DNA origami building blocks, and the geometry and details of the interactions between these building blocks then control their copy numbers, positions and orientations within higher-order assemblies. We illustrate this strategy by creating planar rings of up to 350 nanometres in diameter and with atomic masses of up to 330 megadaltons, micrometre-long, thick tubes commensurate in size to some bacilli, and three-dimensional polyhedral assemblies with sizes of up to 1.2 gigadaltons and 450 nanometres in diameter. We achieve efficient assembly, with yields of up to 90 per cent, by using building blocks with validated structure and sufficient rigidity, and an accurate design with interaction motifs that ensure that hierarchical assembly is self-limiting and able to proceed in equilibrium to allow for error correction. We expect that our method, which enables the self-assembly of structures with sizes approaching that of viruses and cellular organelles, can readily be used to create a range of other complex structures with well defined sizes, by exploiting the modularity and high degree of addressability of the DNA origami building blocks used.

FAST TRACK COMMUNICATION Temperature-driven phase transformation in self-assembled diphenylalanine peptide nanotubes

NASA Astrophysics Data System (ADS)

Heredia, A.; Bdikin, I.; Kopyl, S.; Mishina, E.; Semin, S.; Sigov, A.; German, K.; Bystrov, V.; Gracio, J.; Kholkin, A. L.

2010-11-01

Diphenylalanine (FF) peptide nanotubes (PNTs) represent a unique class of self-assembled functional biomaterials owing to a wide range of useful properties including nanostructural variability, mechanical rigidity and chemical stability. In addition, strong piezoelectric activity has recently been observed paving the way to their use as nanoscale sensors and actuators. In this work, we fabricated both horizontal and vertical FF PNTs and examined their optical second harmonic generation and local piezoresponse as a function of temperature. The measurements show a gradual decrease in polarization with increasing temperature accompanied by an irreversible phase transition into another crystalline phase at about 140-150 °C. The results are corroborated by the molecular dynamic simulations predicting an order-disorder phase transition into a centrosymmetric (possibly, orthorhombic) phase with antiparallel polarization orientation in neighbouring FF rings. Partial piezoresponse hysteresis indicates incomplete polarization switching due to the high coercive field in FF PNTs.

Metallization of ultra-thin, non-thiol SAMs with flat-lying molecular units: Pd on 1, 4-dicyanobenzene.

PubMed

Eberle, Felix; Metzler, Martin; Kolb, Dieter M; Saitner, Marc; Wagner, Patrick; Boyen, Hans-Gerd

2010-09-10

Self-assembled monolayers of 1,4-dicyanobenzene on Au(111) electrodes are studied by cyclic voltammetry, in-situ STM and ex-situ XPS. High-resolution STM images reveal a long-range order of propeller-like assemblies each of which consists of three molecules, all lying flat on the gold substrate with the cyano groups oriented parallel to the metal surface. It is demonstrated that both functional groups can act as complexation sites for metal ions from solution. Surprisingly, such arrangements still allow the metal to be deposited on top of the molecules by electrochemical reduction despite the close vicinity to the Au surface. The latter is demonstrated by angle-resolved XPS which unequivocally shows that the metal indeed resides on top of the organic layer rather than underneath, despite the flat arrangement of the molecules.

Interaction of DNA bases with silver nanoparticles: assembly quantified through SPRS and SERS.

PubMed

Basu, Soumen; Jana, Subhra; Pande, Surojit; Pal, Tarasankar

2008-05-15

Colloidal silver nanoparticles were prepared by reducing silver nitrate with sodium borohydride. The synthesized silver particles show an intense surface plasmon band in the visible region. The work reported here describes the interaction between nanoscale silver particles and various DNA bases (adenine, guanine, cytosine, and thymine), which are used as molecular linkers because of their biological significance. In colloidal solutions, the color of silver nanoparticles may range from red to purple to orange to blue, depending on the degree of aggregation as well as the orientation of the individual particles within the aggregates. Transmission electron microscopy (TEM), X-ray diffraction (XRD), and absorption spectroscopy were used to characterize the assemblies. DNA base-induced differential silver nanoparticle aggregation was quantified from the peak separation (relates to color) of surface plasmon resonance spectroscopy (SPRS) and the signal intensity of surface-enhanced Raman scattering (SERS), which rationalize the extent of silver-nucleobase interactions.

Supramolecular Porphyrin Cages Assembled at Molecular–Materials Interfaces for Electrocatalytic CO Reduction

DOE PAGES

Gong, Ming; Cao, Zhi; Liu, Wei; ...

2017-09-13

Conversion of carbon monoxide (CO), a major one-carbon product of carbon dioxide (CO 2) reduction, into value-added multicarbon species is a challenge to addressing global energy demands and climate change. Here in this paper, we report a modular synthetic approach for aqueous electrochemical CO reduction to carbon-carbon coupled products via self-assembly of supramolecular cages at molecular-materials interfaces. Heterobimetallic cavities formed by face-to-face coordination of thiol-terminated metalloporphyrins to copper electrodes through varying organic struts convert CO to C2 products with high faradaic efficiency (FE = 83% total with 57% to ethanol) and current density (1.34 mA/cm 2) at a potential ofmore » -0.40 V vs RHE. The cage-functionalized electrodes offer an order of magnitude improvement in both selectivity and activity for electrocatalytic carbon fixation compared to parent copper surfaces or copper functionalized with porphyrins in an edge-on orientation.« less

Reconstruction from limited single-particle diffraction data via simultaneous determination of state, orientation, intensity, and phase

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

Donatelli, Jeffrey J.; Sethian, James A.; Zwart, Peter H.

Free-electron lasers now have the ability to collect X-ray diffraction patterns from individual molecules; however, each sample is delivered at unknown orientation and may be in one of several conformational states, each with a different molecular structure. Hit rates are often low, typically around 0.1%, limiting the number of useful images that can be collected. Determining accurate structural information requires classifying and orienting each image, accurately assembling them into a 3D diffraction intensity function, and determining missing phase information. Additionally, single particles typically scatter very few photons, leading to high image noise levels. We develop a multitiered iterative phasing algorithmmore » to reconstruct structural information from singleparticle diffraction data by simultaneously determining the states, orientations, intensities, phases, and underlying structure in a single iterative procedure. We leverage real-space constraints on the structure to help guide optimization and reconstruct underlying structure from very few images with excellent global convergence properties. We show that this approach can determine structural resolution beyond what is suggested by standard Shannon sampling arguments for ideal images and is also robust to noise.« less

Reconstruction from limited single-particle diffraction data via simultaneous determination of state, orientation, intensity, and phase

DOE PAGES

Donatelli, Jeffrey J.; Sethian, James A.; Zwart, Peter H.

2017-06-26

Free-electron lasers now have the ability to collect X-ray diffraction patterns from individual molecules; however, each sample is delivered at unknown orientation and may be in one of several conformational states, each with a different molecular structure. Hit rates are often low, typically around 0.1%, limiting the number of useful images that can be collected. Determining accurate structural information requires classifying and orienting each image, accurately assembling them into a 3D diffraction intensity function, and determining missing phase information. Additionally, single particles typically scatter very few photons, leading to high image noise levels. We develop a multitiered iterative phasing algorithmmore » to reconstruct structural information from singleparticle diffraction data by simultaneously determining the states, orientations, intensities, phases, and underlying structure in a single iterative procedure. We leverage real-space constraints on the structure to help guide optimization and reconstruct underlying structure from very few images with excellent global convergence properties. We show that this approach can determine structural resolution beyond what is suggested by standard Shannon sampling arguments for ideal images and is also robust to noise.« less

Orientational ordering of lamellar structures on closed surfaces

NASA Astrophysics Data System (ADS)

PÈ©kalski, J.; Ciach, A.

2018-05-01

Self-assembly of particles with short-range attraction and long-range repulsion interactions on a flat and on a spherical surface is compared. Molecular dynamics simulations are performed for the two systems having the same area and the density optimal for formation of stripes of particles. Structural characteristics, e.g., a cluster size distribution, a number of defects, and an orientational order parameter (OP), as well as the specific heat, are obtained for a range of temperatures. In both cases, the cluster size distribution becomes bimodal and elongated clusters appear at the temperature corresponding to the maximum of the specific heat. When the temperature decreases, orientational ordering of the stripes takes place and the number of particles per cluster or stripe increases in both cases. However, only on the flat surface, the specific heat has another maximum at the temperature corresponding to a rapid change of the OP. On the sphere, the crossover between the isotropic and anisotropic structures occur in a much broader temperature interval; the orientational order is weaker and occurs at significantly lower temperature. At low temperature, the stripes on the sphere form spirals and the defects resemble defects in the nematic phase of rods adsorbed at a sphere.

Functional Nanopores: A Solid-state Concept for Artificial Reaction Compartments and Molecular Factories.

PubMed

Puebla-Hellmann, Gabriel; Mayor, Marcel; Lörtscher, Emanuel

2016-01-01

On the road towards the long-term goal of the NCCR Molecular Systems Engineering to create artificial molecular factories, we aim at introducing a compartmentalization strategy based on solid-state silicon technology targeting zeptoliter reaction volumes and simultaneous electrical contact to ensembles of well-oriented molecules. This approach allows the probing of molecular building blocks under a controlled environment prior to their use in a complex molecular factory. Furthermore, these ultra-sensitive electrical conductance measurements allow molecular responses to a variety of external triggers to be used as sensing and feedback mechanisms. So far, we demonstrate the proof-of-concept by electrically contacting self-assembled mono-layers of alkane-dithiols as an established test system. Here, the molecular films are laterally constrained by a circular dielectric confinement, forming a so-called 'nanopore'. Device yields above 85% are consistently achieved down to sub-50 nm nanopore diameters. This generic platform will be extended to create distributed, cascaded reactors with individually addressable reaction sites, including interconnecting micro-fluidic channels for electrochemical communication among nanopores and sensing sites for reaction control and feedback. In this scientific outlook, we will sketch how such a solid-state nanopore concept can be used to study various aspects of molecular compounds tailored for operation in a molecular factory.

Dewetting dynamics of a gold film on graphene: implications for nanoparticle formation.

PubMed

Namsani, Sadanandam; Singh, Jayant K

2016-01-01

The dynamics of dewetting of gold films on graphene surfaces is investigated using molecular dynamics simulation. The effect of temperature (973-1533 K), film diameter (30-40 nm) and film thickness (0.5-3 nm) on the dewetting mechanism, leading to the formation of nanoparticles, is reported. The dewetting behavior for films ≤5 Å is in contrast to the behavior seen for thicker films. The retraction velocity, in the order of ∼300 m s(-1) for a 1 nm film, decreases with an increase in film thickness, whereas it increases with temperature. However at no point do nanoparticles detach from the surface within the temperature range considered in this work. We further investigated the self-assembly behavior of nanoparticles on graphene at different temperatures (673-1073 K). The process of self-assembly of gold nanoparticles is favorable at lower temperatures than at higher temperatures, based on the free-energy landscape analysis. Furthermore, the shape of an assembled structure is found to change from spherical to hexagonal, with a marked propensity towards an icosahedral structure based on the bond-orientational order parameters.

Periodic Grating-like Patterns Induced by Self-Assembly of Gelator Fibres in Nematic Gels.

PubMed

Topnani, Neha B; Prutha, N; Pratibha, R

2018-03-15

Periodic orientation patterns occurring in nematic gels, revealed by optical and scanning electron microscopy, are found to be formed by spontaneous self-assembly of fibrous aggregates of a low-molecular-weight organogelator in an aligned thermotropic liquid crystal (LC). Self-organization into periodic structures is also reflected in a calorimetric study, which shows the occurrence of three thermoreversible states, namely, isotropic liquid, nematic and nematic gel. The segregation and self-assembly of the fibrous aggregates leading to pattern formation are attributed to the highly polar LC and to hydrogen bonding between gelator molecules, as shown by X-ray diffraction and vibrational spectroscopy. This study aims to investigate in detail the effect of the chemical nature and alignment of an anisotropic solvent on the morphology of the gelator fibres and the resulting gelation process. The periodic organization of LC-rich and fibre-rich regions can also provide a way to obtain templates for positioning nanoparticle arrays in an LC matrix, which can lead to novel devices. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Effect of intermolecular dipole-dipole interactions on interfacial supramolecular structures of C3-symmetric hexa-peri-hexabenzocoronene derivatives.

PubMed

Mu, Zhongcheng; Shao, Qi; Ye, Jun; Zeng, Zebing; Zhao, Yang; Hng, Huey Hoon; Boey, Freddy Yin Chiang; Wu, Jishan; Chen, Xiaodong

2011-02-15

Two-dimensional (2D) supramolecular assemblies of a series of novel C(3)-symmetric hexa-peri-hexabenzocoronene (HBC) derivatives bearing different substituents adsorbed on highly oriented pyrolytic graphite were studied by using scanning tunneling microscopy at a solid-liquid interface. It was found that the intermolecular dipole-dipole interactions play a critical role in controlling the interfacial supramolecular assembly of these C(3)-symmetric HBC derivatives at the solid-liquid interface. The HBC molecule bearing three -CF(3) groups could form 2D honeycomb structures because of antiparallel dipole-dipole interactions, whereas HBC molecules bearing three -CN or -NO(2) groups could form hexagonal superstructures because of a special trimeric arrangement induced by dipole-dipole interactions and weak hydrogen bonding interactions ([C-H···NC-] or [C-H···O(2)N-]). Molecular mechanics and dynamics simulations were performed to reveal the physics behind the 2D structures as well as detailed functional group interactions. This work provides an example of how intermolecular dipole-dipole interactions could enable fine control over the self-assembly of disklike π-conjugated molecules.

Facile and controllable one-step fabrication of molecularly imprinted polymer membrane by magnetic field directed self-assembly for electrochemical sensing of glutathione.

PubMed

Zhu, Wanying; Jiang, Guoyi; Xu, Lei; Li, Bingzhi; Cai, Qizhi; Jiang, Huijun; Zhou, Xuemin

2015-07-30

Based on magnetic field directed self-assembly (MDSA) of the ternary Fe3O4@PANI/rGO nanocomposites, a facile and controllable molecularly imprinted electrochemical sensor (MIES) was fabricated through a one-step approach for detection of glutathione (GSH). The ternary Fe3O4@PANI/rGO nanocomposites were obtained by chemical oxidative polymerization and intercalation of Fe3O4@PANI into the graphene oxide layers via π-π stacking interaction, followed by reduction of graphene oxide in the presence of hydrazine hydrate. In molecular imprinting process, the pre-polymers, including GSH as template molecule, Fe3O4@PANI/rGO nanocomposites as functional monomers and pyrrole as both cross-linker and co-monomer, was assembled through N-H hydrogen bonds and the electrostatic interaction, and then was rapidly oriented onto the surface of MGCE under the magnetic field induction. Subsequently, the electrochemical GSH sensor was formed by electropolymerization. In this work, the ternary Fe3O4@PANI/rGO nanocomposites could not only provide available functionalized sites in the matrix to form hydrogen bond and electrostatic interaction with GSH, but also afford a promoting network for electron transfer. Moreover, the biomimetic sensing membrane could be controlled more conveniently and effectively by adjusting the magnetic field strength. The as-prepared controllable sensor showed good stability and reproducibility for the determination of GSH with the detection limit reaching 3 nmol L(-1) (S/N = 3). In addition, the highly sensitive and selective biomimetic sensor has been successfully used for the clinical determination of GSH in biological samples. Copyright © 2015 Elsevier B.V. All rights reserved.

Immune activation with peptide assemblies carrying Lewis y tumor-associated carbohydrate antigen.

PubMed

Yamazaki, Yuji; Watabe, Naoki; Obata, Hiroaki; Hara, Eri; Ohmae, Masashi; Kimura, Shunsaku

2017-02-01

Molecular assemblies varying morphologies in a wide range from spherical micelle, nanosheet, curved sheet, nanotube and vesicle were prepared and loaded with Lewis y (Le y ) tumor-associated carbohydrate antigen on the assembly surface. The molecular assemblies were composed of poly(sarcosine) m -block-poly(L-lactic acid) 30 (m = 15 or 50, Lactosome), poly(sarcosine) m -block-(D/L-Leu-Aib) n (m = 22 or 30, n = 6 or 8) and their combinations. The molecular assemblies carrying Le y on the surface were administered in BALB/c nu/nu mice. The major epitopes of the molecular assemblies are commonly Le y and poly(sarcosine). IgM productions upon administrations of the molecular assemblies were assayed by ELISA, showing that anti-poly(sarcosine) IgM was highly produced by Lactosome of spherical micelle but with a negligible amount of anti-Le y IgM. On the other hand, the nanosheet of the interdigitated monolayer triggered the production of anti-Le y IgM but with less anti-poly(sarcosine) IgM production. Taken together, IgM specificity differs according to the molecular environment of the epitopes in the molecular assemblies. The antigenicity of poly(sarcosine) was augmented in polymeric micelle providing loose environment for B cells to penetrate in, whereas a high density of Le y on the molecular assembly was required for anti-Le y IgM production. The antigenicity of Le y is therefore dependent on the molecular assemblies on which Le y is displayed on the surface. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd.

Magnetic alignment of block copolymer microdomains by intrinsic chain anisotropy

DOE PAGES

Rokhlenko, Yekaterina; Yager, Kevin G.; Gopinadhan, Manesh; ...

2015-12-18

We examine the role of intrinsic chain susceptibility anisotropy in magnetic field directed self-assembly of a block copolymer using in situ x-ray scattering. Alignment of a lamellar mesophase is observed on cooling across the disorder-order transition with the resulting orientational order inversely proportional to the cooling rate. We discuss the origin of the susceptibility anisotropy, Δ χ, that drives alignment and calculate its magnitude using coarse-grained molecular dynamics to sample conformations of surface-tethered chains, finding Δ χ ≈ 2×10 –8. From field-dependent scattering data, we estimate that grains of ≈ 1.2 μm are present during alignment. Furthermore, these results demonstratemore » that intrinsic anisotropy is sufficient to support strong field-induced mesophase alignment and suggest a versatile strategy for field control of orientational order in block copolymers.« less

Magnetic alignment of block copolymer microdomains by intrinsic chain anisotropy

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

Rokhlenko, Yekaterina; Yager, Kevin G.; Gopinadhan, Manesh

We examine the role of intrinsic chain susceptibility anisotropy in magnetic field directed self-assembly of a block copolymer using in situ x-ray scattering. Alignment of a lamellar mesophase is observed on cooling across the disorder-order transition with the resulting orientational order inversely proportional to the cooling rate. We discuss the origin of the susceptibility anisotropy, Δ χ, that drives alignment and calculate its magnitude using coarse-grained molecular dynamics to sample conformations of surface-tethered chains, finding Δ χ ≈ 2×10 –8. From field-dependent scattering data, we estimate that grains of ≈ 1.2 μm are present during alignment. Furthermore, these results demonstratemore » that intrinsic anisotropy is sufficient to support strong field-induced mesophase alignment and suggest a versatile strategy for field control of orientational order in block copolymers.« less

Ionic self-assembly for functional hierarchical nanostructured materials.

PubMed

Faul, Charl F J

2014-12-16

CONSPECTUS: The challenge of constructing soft functional materials over multiple length scales can be addressed by a number of different routes based on the principles of self-assembly, with the judicious use of various noncovalent interactions providing the tools to control such self-assembly processes. It is within the context of this challenge that we have extensively explored the use of an important approach for materials construction over the past decade: exploiting electrostatic interactions in our ionic self-assembly (ISA) method. In this approach, cooperative assembly of carefully chosen charged surfactants and oppositely charged building blocks (or tectons) provides a facile noncovalent route for the rational design and production of functional nanostructured materials. Generally, our research efforts have developed with an initial focus on establishing rules for the construction of novel noncovalent liquid-crystalline (LC) materials. We found that the use of double-tailed surfactant species (especially branched double-tailed surfactants) led to the facile formation of thermotropic (and, in certain cases, lyotropic) phases, as demonstrated by extensive temperature-dependent X-ray and light microscopy investigations. From this core area of activity, research expanded to cover issues beyond simple construction of anisotropic materials, turning to the challenge of inclusion and exploitation of switchable functionality. The use of photoactive azobenzene-containing ISA materials afforded opportunities to exploit both photo-orientation and surface relief grating formation. The preparation of these anisotropic LC materials was of interest, as the aim was the facile production of disposable and low-cost optical components for display applications and data storage. However, the prohibitive cost of the photo-orientation processes hampered further exploitation of these materials. We also expanded our activities to explore ISA of biologically relevant tectons, specifically deoxyguanosine monophosphate. This approach proved, in combination with block copolymer (BCP) self-assembly, very fruitful for the construction of complex and hierarchical functional materials across multiple length scales. Molecular frustration and incommensurability, which played a major role in structure formation in combination with nucleotide assembly, have now become important tools to tune supramolecular structure formation. These concepts, that is, the use of BCP assembly and incommensurability, in combination with metal-containing polymeric materials, have provided access to novel supramolecular morphologies and, more importantly, design rules to prepare such constructs. These design rules are now also being applied to the assembly of electroactive oligo(aniline)-based materials for the preparation of highly ordered functional soft materials, and present an opportunity for materials development for applications in energy storage. In this Account, we therefore discuss investigations into (i) the inclusion and preparation of supramolecular photoactive and electroactive materials; (ii) the exploitation and control over multiple noncovalent interactions to fine-tune function, internal structure, and long-range order and (iii) exploration of construction over multiple length scales by combination of ISA with well-known BCP self-assembly. Combination of ISA with tuning of volume fractions, mutual compatibility, and molecular frustration now provides a versatile tool kit to construct complex and hierarchical functional materials in a facile noncovalent way. A direct challenge for future ISA activities would certainly be the construction of functional mesoscale objects. However, within a broader scientific context, the challenge would be to exploit this powerful assembly tool for application in areas of research with societal impact, for example, energy storage and generation. The hope is that this Account will provide a platform for such future research activities and opportunities.

Oriented attachment by enantioselective facet recognition in millimeter-sized gypsum crystals.

PubMed

Viedma, Cristóbal; Cuccia, Louis A; McTaggart, Alicia; Kahr, Bart; Martin, Alexander T; McBride, J Michael; Cintas, Pedro

2016-09-22

Crystal growth by oriented attachment involves the spontaneous self-assembly of adjoining crystals with common crystallographic orientations. Herein, we report the oriented attachment of gypsum crystals on agitation to form stereoselective mesoscale aggregates.

Exhaustively sampling peptide adsorption with metadynamics.

PubMed

Deighan, Michael; Pfaendtner, Jim

2013-06-25

Simulating the adsorption of a peptide or protein and obtaining quantitative estimates of thermodynamic observables remains challenging for many reasons. One reason is the dearth of molecular scale experimental data available for validating such computational models. We also lack simulation methodologies that effectively address the dual challenges of simulating protein adsorption: overcoming strong surface binding and sampling conformational changes. Unbiased classical simulations do not address either of these challenges. Previous attempts that apply enhanced sampling generally focus on only one of the two issues, leaving the other to chance or brute force computing. To improve our ability to accurately resolve adsorbed protein orientation and conformational states, we have applied the Parallel Tempering Metadynamics in the Well-Tempered Ensemble (PTMetaD-WTE) method to several explicitly solvated protein/surface systems. We simulated the adsorption behavior of two peptides, LKα14 and LKβ15, onto two self-assembled monolayer (SAM) surfaces with carboxyl and methyl terminal functionalities. PTMetaD-WTE proved effective at achieving rapid convergence of the simulations, whose results elucidated different aspects of peptide adsorption including: binding free energies, side chain orientations, and preferred conformations. We investigated how specific molecular features of the surface/protein interface change the shape of the multidimensional peptide binding free energy landscape. Additionally, we compared our enhanced sampling technique with umbrella sampling and also evaluated three commonly used molecular dynamics force fields.

Influence of topographically patterned angled guidelines on directed self-assembly of block copolymers

NASA Astrophysics Data System (ADS)

Rebello, Nathan; Sethuraman, Vaidyanathan; Blachut, Gregory; Ellison, Christopher J.; Willson, C. Grant; Ganesan, Venkat

2017-11-01

Single chain in mean-field Monte Carlo simulations were employed to study the self-assembly of block copolymers (BCP) in thin films that use trapezoidal guidelines to direct the orientation and alignment of lamellar patterns. The present study explored the influence of sidewall interactions and geometry of the trapezoidal guidelines on the self-assembly of perpendicularly oriented lamellar morphologies. When both the sidewall and the top surface exhibit preferential interactions to the same block of the BCP, trapezoidal guidelines with intermediate taper angles were found to result in less defective perpendicularly orientated morphologies. Similarly, when the sidewall and top surface are preferential to distinct blocks of the BCP, intermediate tapering angles were found to be optimal in promoting defect free structures. Such results are rationalized based on the energetics arising in the formation of perpendicularly oriented lamella on patterned substrates.

Molecular Orientation in Two Component Vapor-Deposited Glasses: Effect of Substrate Temperature and Molecular Shape

NASA Astrophysics Data System (ADS)

Powell, Charles; Jiang, Jing; Walters, Diane; Ediger, Mark

Vapor-deposited glasses are widely investigated for use in organic electronics including the emitting layers of OLED devices. These materials, while macroscopically homogenous, have anisotropic packing and molecular orientation. By controlling this orientation, outcoupling efficiency can be increased by aligning the transition dipole moment of the light-emitting molecules parallel to the substrate. Light-emitting molecules are typically dispersed in a host matrix, as such, it is imperative to understand molecular orientation in two-component systems. In this study we examine two-component vapor-deposited films and the orientations of the constituent molecules using spectroscopic ellipsometry, UV-vis and IR spectroscopy. The role of temperature, composition and molecular shape as it effects molecular orientation is examined for mixtures of DSA-Ph in Alq3 and in TPD. Deposition temperature relative to the glass transition temperature of the two-component mixture is the primary controlling factor for molecular orientation. In mixtures of DSA-Ph in Alq3, the linear DSA-Ph has a horizontal orientation at low temperatures and slight vertical orientation maximized at 0.96Tg,mixture, analogous to one-component films.

Architectonics: Design of Molecular Architecture for Functional Applications.

PubMed

Avinash, M B; Govindaraju, Thimmaiah

2018-02-20

The term architectonics has its roots in the architectural and philosophical (as early as 1600s) literature that refers to "the theory of structure" and "the structure of theory", respectively. The concept of architectonics has been adapted to advance the field of molecular self-assembly and termed as molecular architectonics. In essence, the methodology of organizing molecular units in the required and controlled configurations to develop advanced functional systems for materials and biological applications comprises the field of molecular architectonics. This concept of designing noncovalent systems enables to focus on different functional aspects of designer molecules for biological and nonbiological applications and also strengthens our efforts toward the mastery over the art of controlled molecular self-assemblies. Programming complex molecular interactions and assemblies for specific functions has been one of the most challenging tasks in the modern era. Meticulously ordered molecular assemblies can impart remarkable developments in several areas spanning energy, health, and environment. For example, the well-defined nano-, micro-, and macroarchitectures of functional molecules with specific molecular ordering possess potential applications in flexible electronics, photovoltaics, photonic crystals, microreactors, sensors, drug delivery, biomedicine, and superhydrophobic coatings, among others. The functional molecular architectures having unparalleled properties are widely evident in various designs of Nature. By drawing inspirations from Nature, intended molecular architectures can be designed and developed to harvest various functions, as there is an inexhaustible resource and scope. In this Account, we present exquisite designer molecules developed by our group and others with an objective to master the art of molecular recognition and self-assembly for functional applications. We demonstrate the tailor-ability of molecular self-assemblies by employing biomolecules like amino acids and nucleobases as auxiliaries. Naphthalenediimide (NDI), perylenediimide (PDI), and few other molecular systems serve as functional modules. The effects of stereochemistry and minute structural modifications in the molecular designs on the supramolecular interactions, and construction of self-assembled zero-dimensional (OD), one-dimensional (1D), and two-dimensional (2D) nano- and microarchitectures like particles, spheres, cups, bowls, fibers, belts, helical belts, supercoiled helices, sheets, fractals, and honeycomb-like arrays are discussed in extensive detail. Additionally, we present molecular systems that showcase the elegant designs of coassembly, templated assembly, hierarchical assembly, transient self-assembly, chiral denaturation, retentive helical memory, self-replication, supramolecular regulation, supramolecular speciation, supernon linearity, dynamic pathway complexity, supramolecular heterojunction, living supramolecular polymerization, and molecular machines. Finally, we describe the molecular engineering principles learnt over the years that have led to several applications, namely, organic electronics, self-cleaning, high-mechanical strength, and tissue engineering.

Topological defects in liquid crystals and molecular self-assembly (Conference Presentation)

NASA Astrophysics Data System (ADS)

Abbott, Nicholas L.

2017-02-01

Topological defects in liquid crystals (LCs) have been widely used to organize colloidal dispersions and template polymerizations, leading to a range of elastomers and gels with complex mechanical and optical properties. However, little is understood about molecular-level assembly processes within defects. This presentation will describe an experimental study that reveals that nanoscopic environments defined by LC topological defects can selectively trigger processes of molecular self-assembly. By using fluorescence microscopy, cryogenic transmission electron microscopy and super-resolution optical microscopy, key signatures of molecular self-assembly of amphiphilic molecules in topological defects are observed - including cooperativity, reversibility, and controlled growth of the molecular assemblies. By using polymerizable amphiphiles, we also demonstrate preservation of molecular assemblies templated by defects, including nanoscopic "o-rings" synthesized from "Saturn-ring" disclinations. Our results reveal that topological defects in LCs are a versatile class of three-dimensional, dynamic and reconfigurable templates that can direct processes of molecular self-assembly in a manner that is strongly analogous to other classes of macromolecular templates (e.g., polymer—surfactant complexes). Opportunities for the design of exquisitely responsive soft materials will be discussed using bacterial endotoxin as an example.

Depletion forces drive polymer-like self-assembly in vibrofluidized granular materials†

PubMed Central

Nossal, Ralph

2011-01-01

Ranging from nano- to granular-scales, control of particle assembly can be achieved by limiting the available free space, for example by increasing the concentration of particles (“crowding”) or through their restriction to 2D environments. It is unclear, however, if self-assembly principles governing thermally-equilibrated molecules can also apply to mechanically-excited macroscopic particles in non-equilibrium steady-state. Here we show that low densities of vibrofluidized steel rods, when crowded by high densities of spheres and confined to quasi-2D planes, can self-assemble into linear polymer-like structures. Our 2D Monte Carlo simulations show similar finite sized aggregates in thermally equilibrated binary mixtures. Using theory and simulations, we demonstrate how depletion interactions create oriented “binding” forces between rigid rods to form these “living polymers.” Unlike rod-sphere mixtures in 3D that can demonstrate well-defined equilibrium phases, our mixtures confined to 2D lack these transitions because lower dimensionality favors the formation of linear aggregates, thus suppressing a true phase transition. The qualitative and quantitative agreement between equilibrium and granular patterning for these mixtures suggests that entropy maximization is the determining driving force for bundling. Furthermore, this study uncovers a previously unknown patterning behavior at both the granular and nanoscales, and may provide insights into the role of crowding at interfaces in molecular assembly. PMID:22039392

Functional nanocomposites prepared by self-assembly and polymerization of diacetylene surfactants and silicic acid

NASA Technical Reports Server (NTRS)

Yang, Yi; Lu, Yunfeng; Lu, Mengcheng; Huang, Jinman; Haddad, Raid; Xomeritakis, George; Liu, Nanguo; Malanoski, Anthony P.; Sturmayr, Dietmar; Fan, Hongyou;

A new strategy to engineer polymer bulk heterojunction solar cells with thick active layers via self-assembly of the tertiary columnar phase

DOE PAGES

Li, Hongfei; Yang, Zhenhua; Pan, Cheng; ...

2017-07-14

Here, we report that the addition of a non-photoactive tertiary polymer phase in the binary bulk heterojunction (BHJ) polymer solar cell leads to a self-assembled columnar nanostructure, enhancing the charge mobilities and photovoltaic efficiency with surprisingly increased optimal active blend thicknesses over 300 nm, 3–4 times larger than that of the binary counterpart. Using the prototypical poly(3-hexylthiophene) (P3HT):fullerene blend as a model BHJ system, we discover that the inert poly(methyl methacrylate) (PMMA) added in the binary BHJ blend self-assembles into vertical columns, which not only template the phase segregation of electron acceptor fullerenes but also induce the out-of-plane rotation ofmore » the edge-on-orientated crystalline P3HT phase. Using complementary interrogation methods including neutron reflectivity, X-ray scattering, atomic force microscopy, transmission electron microscopy, and molecular dynamics simulations, we show that the enhanced charge transport originates from the more randomized molecular stacking of the P3HT phase and the spontaneous segregation of fullerenes at the P3HT/PMMA interface, driven by the high surface tension between the two polymeric components. The results demonstrate a potential method for increasing the thicknesses of high-performance polymer BHJ solar cells with improved photovoltaic efficiency, alleviating the burden of stringently controlling the ultrathin blend thickness during the roll-to-roll-type large-area manufacturing environment.« less

Assembly of Nanowire Arrays: Exploring Interparticle Interactions, Particle Orientation, and Mixed Particle Arrays

NASA Astrophysics Data System (ADS)

Kirby, David J.

This dissertation explores the fundamental interparticle and particle-substrate forces that contribute to nanowire assembly. Nanowires have a large aspect ratio which has made them favorable materials for applications in energy and sensing technologies. However, this anisotropy means that nanowires must be positioned and oriented during an assembly process. Within this work, the roles of gravity, van der Waals (VDW) attractions, and electrostatic repulsions are explored when different nanowire assemblies are created. Particles were synthesized by the template electrodeposition process so that stripes of different materials and therefore different VDW interactions could be patterned along the particle length. Electrostatic repulsions were provided by a small molecule coating or a porous silica shell to prevent aggregation during the assembly process. Chapters 2, 3, 5, 6, and 8 all used particles whose asymmetry was further adjusted by removal of a sacrificial segment to leave a partially etched nanowire (PEN), a rigid silica shell partially filled with a metal core. For these particles, the role of gravity was amplified due to the drastic density differences between the two segments. Topographic and high VDW surface interactions were patterned onto assembly substrates using photolithographic processing. These forces served as a passive template to direct nanowire assembly. The segment anisotropy of PENs allowed gravity to drive their sedimentation with the long axis perpendicular to the surface. The density difference between the two ends allowed them to convert between the horizontal and vertical orientation as they diffused on the substrate. Vertical arrays formed as particle concentrations increased while VDW attractions from neighboring PENs or the physical barrier of a microwell wall supported this structure. While vertical arrays were typically PENs, microwell walls were also able to enforce a vertical orientation on solid Au nanowires. These particles typically formed horizontal arrays on planar surfaces, but careful design of the microwell and nanowire dimensions enabled these particles to take on the vertical orientation. Solid nanowires and PENs with greater segment symmetry aligned parallel to the surface as gravity did not allow a conversion to the vertical orientation. When concentrated, these particles formed smectic row arrangements which were previously shown to originate from a balance of VDW attractions and electrostatic repulsions. Within rows of segmented particles, a preference was observed for like orientation of nearest neighbor particles (Chapter 6). With the aid of Monte Carlo simulations, it was determined that this observation was the result of small differences in VDW attractions between the two nanowire ends. Differences in VDW attraction were also applied to patterned surfaces (Chapter 7). Stripes of high VDW material (Au) were placed on a silica surface (a low VDW material). When relatively low surface concentrations were used, the high VDW regions collected Au nanowires and organized them into rows that were reminiscent of those observed on un-patterned surfaces at high particle concentrations. VDW and the gravitational force were explored as they combined to influence array orientation in binary PEN mixtures. Depending on the geometries of the particles combined, the contributions of gravity and interparticle interactions exhibited different balance in creating the final array. VDW and gravitational forces could also act as a force for reconfigurable nanowire assembly. In chapter 8, fluid flow was used to concentrate PENs and force them into horizontal arrangements. When fluid flow was stopped, van der Waals forces and gravity were responsible for a reorientation of the assembled particles into a standing array. These studies represent early steps into the future of nanowire assembly methods. I conclude this dissertation by discussing the implications of my work and providing perspective on their importance to the scientific community. I also offer suggestions for future work in nanowire assembly. These areas focus on the development of assembled nanowire devices, mixed nanowire assembly techniques, and potential stimuli responsive reconfigurable assemblies.

Modulating the forces between self-assembling molecules to control the shape of vesicles and the mechanics and alignment of nanofiber networks

NASA Astrophysics Data System (ADS)

Greenfield, Megan Ann

One of the great challenges in supramolecular chemistry is the design of molecules that can self-assemble into functional aggregates with well-defined three-dimensional structures and bulk material properties. Since the self-assembly of nanostructures is greatly influenced by both the nature of the self-assembling components and the environmental conditions in which the components assemble, this work explores how changes in the molecular design and the environment affect the properties of self-assembled structures. We first explore how to control the mechanical properties of self-assembled fibrillar networks by changing environmental conditions. We report here on how changing pH, screening ions, and solution temperature affect the gelation, stiffness, and response to deformation of peptide amphiphile gels. Although the morphology of PA gels formed by charge neutralization and salt-mediated charge screening are similar by electron microscopy, rheological measurements indicate that the calcium-mediated ionic bridges in CaCl2-PA gels form stronger intra- and inter-fiber crosslinks than the hydrogen bonds formed by the protonated carboxylic acid residues in HCl-PA gels. In contrast, the structure of PA gels changes drastically when the PA solution is annealed prior to gel formation. Annealed PA solutions are birefringent and can form viscoelastic strings of aligned nanofibers when manually dragged across a thin film of CaCl2. These aligned arrays of PA nanofibers hold great promise in controlling the orientation of cells in three-dimensions. Separately, we applied the principles of molecular design to create buckled membrane nanostructures that mimic the shape of viruses. When oppositely charged amphiphilic molecules are mixed they can form vesicles with a periodic two-dimensional ionic lattice that opposes the membrane's natural curvature and can result in vesicle buckling. Our results demonstrate that a large +3 to -1 charge imbalance between the cationic and anionic head groups of amphiphiles enables their co-assembly into small buckled vesicles. In contrast to previous reports, the structures described here form without the rigorous exclusion of salt and are tolerant to physiological salt concentrations. Our work opens a new path for exploring how ionic laterally correlated domains can influence the morphology of self-assembled nanostructures.

Organic Photovoltaic Devices Based on Oriented n-Type Molecular Films Deposited on Oriented Polythiophene Films.

PubMed

Mizokuro, Toshiko; Tanigaki, Nobutaka; Miyadera, Tetsuhiko; Shibata, Yousei; Koganezawa, Tomoyuki

2018-04-01

The molecular orientation of π-conjugated molecules has been reported to significantly affect the performance of organic photovoltaic devices (OPVs) based on molecular films. Hence, the control of molecular orientation is a key issue toward the improvement of OPV performance. In this research, oriented thin films of an n-type molecule, 3,4,9,10-Perylenetetracarboxylic Bisbenzimida-zole (PTCBI), were formed by deposition on in-plane oriented polythiophene (PT) films. Orientation of the PTCBI films was evaluated by polarized UV-vis spectroscopy and 2D-Grazing incidence X-ray diffraction. Results indicated that PTCBI molecules on PT film exhibit nearly edge-on and in-plane orientation (with molecular long axis along the substrate), whereas PTCBI molecules without PT film exhibit neither. OPVs composed of PTCBI molecular film with and without PT were fabricated and evaluated for correlation of orientation with performance. The OPVs composed of PTCBI film with PT showed higher power conversion efficiency (PCE) than that of film without PT. The experiment indicated that in-plane orientation of PTCBI molecules absorbs incident light more efficiently, leading to increase in PCE.

Supra-molecular networks for CO2 capture

NASA Astrophysics Data System (ADS)

Sadowski, Jerzy; Kestell, John

Utilizing capabilities of low-energy electron microscopy (LEEM) for non-destructive interrogation of the real-time molecular self-assembly, we have investigated supramolecular systems based on carboxylic acid-metal complexes, such as trimesic and mellitic acid, doped with transition metals. Such 2D networks can act as host systems for transition-metal phthalocyanines (MPc; M = Fe, Ti, Sc). The electrostatic interactions of CO2 molecules with transition metal ions can be tuned by controlling the type of TM ion and the size of the pore in the host network. We further applied infrared reflection-absorption spectroscopy (IRRAS) to determine of the molecular orientation of the functional groups and the whole molecule in the 2D monolayers of carboxylic acid. The kinetics and mechanism of the CO2 adsorption/desorption on the 2D molecular network, with and without the TM ion doping, have been also investigated. This research used resources of the Center for Functional Nanomaterials, which is the U.S. DOE Office of Science User Facility, at Brookhaven National Laboratory under Contract No. DE-SC0012704.

Interfacial self-organization of bolaamphiphiles bearing mesogenic groups: relationships between the molecular structures and their self-organized morphologies.

PubMed

Song, Bo; Liu, Guanqing; Xu, Rui; Yin, Shouchun; Wang, Zhiqiang; Zhang, Xi

2008-04-15

This article discusses the relationship between the molecular structure of bolaamphiphiles bearing mesogenic groups and their interfacial self-organized morphology. On the basis of the molecular structures of bolaamphiphiles, we designed and synthesized a series of molecules with different hydrophobic alkyl chain lengths, hydrophilic headgroups, mesogenic groups, and connectors between the alkyl chains and the mesogenic group. Through investigating their interfacial self-organization behavior, some experiential rules are summarized: (1) An appropriate alkyl chain length is necessary to form stable surface micelles; (2) different categories of headgroups have a great effect on the interfacial self-organized morphology; (3) different types of mesogenic groups have little effect on the structure of the interfacial assembly when it is changed from biphenyl to azobenzene or stilbene; (4) the orientation of the ester linker between the mesogenic group and alkyl chain can greatly influence the interfacial self-organization behavior. It is anticipated that this line of research may be helpful for the molecular engineering of bolaamphiphiles to form tailor-made morphologies.

Molecular Level Understanding of Interfaces and Excited State Electronic Structure in Organic Solar Cells Using Soft X-ray Techniques

NASA Astrophysics Data System (ADS)

Gliboff, Matthew

Transparent conductive oxides like indium tin oxide (ITO) are common substrates for optoelectronic devices, including organic light emitting diodes and organic solar cells. Tailoring the interface between the oxide and the active layer by adjusting the work function or wettability of the oxide can improve the performance of these devices in both emissive and photovoltaic applications. Molecular design of self-assembled monolayers (SAMs) allows for a range of surface properties using the same oxide material. The molecular ordering and conformation adopted by the SAMs determine properties such as work function and wettability at these critical interfaces. I use angle-dependent near edge x-ray absorption fine structure (NEXAFS) spectroscopy, to determine the molecular orientations of a variety of dipolar phosphonic acid surface modifiers. For a model system, phenylphosphonic acid on indium zinc oxide, the SAMs prove to be surprisingly well-oriented, with the phenyl ring adopting a well-defined tilt angle of 12-16° from the surface normal. The NEXAFS results agree with polarization modulation infrared reflection absorption spectroscopy (PM-IRRAS) results and orientations calculated from density functional theory (DFT). These results not only provide a detailed picture of the molecular structure of a technologically important class of SAMs, but they also resolve a long-standing ambiguity regarding the vibrational-mode assignments for phosphonic acids on oxide surfaces, thus improving the utility of PM-IRRAS for future studies. The effect of fluorination on the orientation of these phosponic-acid SAMs is non-trivial, due to the combined effects of the fluorination on binding mode and steric packing. The latter effects are found to be more dominant in aliphatic SAMs, leading to a more upright orientation in the fluorinated SAM. In the aromatic case, the fluorinated SAM adopted a less upright orientation which I attribute to changes in binding mode. The relationship between structure and performance in active layer polymers for organic electronics is not yet well understood. To gain insight into the effect of the excited state electronic structure on device performance, we examine two similar donor-acceptor polymers: PCPDTBT and PCDTBT, which produce devices with internal quantum efficiency (IQE) of 70% and 100% respectively. We use time-dependent density functional theory (TD-DFT) in combination with near edge x-ray absorption fine structure (NEXAFS) and resonant Auger spectroscopy to predict the electronic structure of the lowest unoccupied molecular orbital (LUMO). The resonant Auger results are found to be independent of film morphology and likely dominated by monomer structure. We show that the degree of LUMO localization onto the benzothiadiazole acceptor group in each polymer is similar, indicating that that the differences in IQE between these two polymers are driven by larger-scale morphology and not explained by the electronic structure of the excited state.

The Self- and Directed Assembly of Nanowires

NASA Astrophysics Data System (ADS)

Smith, Benjamin David

This thesis explores the self- and directed assembly of nanowires. Specifically, we examine the driving forces behind nanowire self-assembly and the macro-structures that are formed. Particle-dense, oriented nanowire structures show promise in the fields of photonics, energy, sensing, catalysis, and electronics. Arrays of spherical particles have already found uses in electronic inks, sensing arrays, and many other commercial applications; but, it is a challenge to create specific arrays of morphologically and/or compositionally anisotropic particles. The following chapters illuminate the interactions that drive the assembly of anisotropic particles in high density solutions in the absence of applied fields or solution drying. Special emphasis is placed on the structures that are formed. The properties of micro- and nanoparticles and their assembly are introduced in Chapter 1. In particular, the properties of shape and material anisotropic particles are highlighted, while challenges in producing desired arrays are discussed. In this thesis, metallic nanowires of increasing complexity were used to examine the self-assembly behavior of both shape and material anisotropic particles. Nanowires were synthesized through templated electrodeposition. In this process, porous alumina membranes served as a template in which metal salts were reduced to form particles. Upon template dissolution, billions of nominally identical particles were released. We specifically focused on segmented, metallic nanowires 2-13 mum in length and 180 to 350 nm in diameter. Since these particles have strong van der Waals (VDWs) attractions, an electrostatically repulsive coating was necessary to prevent aggregation; we used small molecule, DNA, or amorphous silica coatings. Nanowires and their coatings were characterized by electron microscopy. In order to study self-assembly behavior, particle-dense aqueous suspensions were placed within an assembly chamber defined by a silicone spacer. The nanowires rapidly sedimented due to gravity onto a glass cover slip to concentrate and form a dense film. Particles and assemblies were imaged using inverted optical microscopy. We quantitatively analyzed the images and movies captured in order to track and classify particles and classify the overall arrays formed. We then correlated how particle characteristics, e.g., materials, size, segmentation, etc. changed the ordering and alignment observed. With that knowledge, we hope to be able to form new and interesting structures. We began our studies by examining the assembly of single component nanowires. Chapter 2 describes this work, in which solid Au nanowires measuring 2-7 mum in length and 290 nm in diameter self-assembled into smectic rows. By both experiment and theory, we determined that these rows formed due to a balance of electrostatic repulsions and van der Waals attractions. Final assemblies were stable for at least several days. Monte Carlo methods were used to simulate assemblies and showed structures that mirrored those experimentally observed. Simulations indicated that the smectic phase was preferred over others, i.e., nematic, when an additional small charge was added to the ends of the nanowires. Our particles have rough tips, which might create these additional electrostatic repulsions. To increase the particle and array complexity, two-component, metallic nanowire assembly was explored in Chapter 3. We examined numerous types of nanowires by changing the segment length, ratio, and material, the nanowire length, the surface coating, and the presence of small third segments. These segmented nanowires were generally Au-Ag and also ordered into smectic rows. Segmented wires arranged in rows, however, can be aligned in two possible ways with respect to a neighboring particle. The Au segments on neighboring particles can be oriented in the same direction or opposed to each other. Orientation was quantified in terms of an order parameter that took into account alignment with respect to nearest neighbor particles. All experiments showed order parameters indicating a slight preference for orientational ordering that was relatively insensitive to segment size, nanowire size, and nanowire coating. Monte Carlo simulations pointed towards this alignment as a consequence of small differences in the van der Waals attractions between the segments. Experimentally, ordering might to be limited by the large size of the nanowires, which results in kinetically trapped structures. In an attempt to obtain better ordering within rows, silica coated nanowires with partial Au cores were made. The synthesis involved silica-coating the nanowires and selectively etching a Ag segment. These particles have extremely different VDWs attractions between their segments, as the Au cores are much more attractive than the solvent-filled etched ends. The assembly of these partially etched nanowires (PENs) is detailed in Chapters 4, 5, and 6. When allowed to self-assemble, we observed the formation of either vertically or horizontally oriented arrays depending on PEN composition. The formation of vertically oriented arrays of anisotropic particles is important, since not many methods to produce these structures are currently available for particles of this size. We examined the effects of PEN length, PEN diameter, and the size, number, and location of the core segments. Our findings showed a large etched segment at one end (which resulted in a large offset in the center of mass and concentrated the VDWs attractions to one end of the particle) resulted in the best columnar assemblies. These vertically orientated arrays formed in a two part process. First, after PENs sedimented, they fell flat and oriented parallel to the surface. These PENs then sampled many orientations, including rotating out of the surface plane. When higher surface concentrations of particles built as more PENs fell to the surface of the cover slip, neighboring particles stabilized vertical orientations. Second, particles fell oriented vertically and when the surface concentrations were high, they retained this orientation upon reaching the substrate. Since vertically aligned PENs supported each other, assembly into vertical arrays was highly dependent on the surface concentration. But, oriented arrays could be easily formed on larger or smaller substrates, provided a particle concentration scaled to the substrate were used. The mixing of these particles to form heterogeneous arrays was examined. The overall array structure favored that of particles which sedimented more quickly and/or were present in higher amounts. The semi-automated counting of PENs in images by software is used heavily in Chapters 4 and 5. Appendix A describes the use, development, and validation of macros within Image-Pro. The structure, syntax, and use are specifically examined for three nanowire counting macros. The counting results; including: number of particles in an image, number of horizontally vs. vertically oriented PENs, and PENs in microwells; are compared with manual hand counts. Chapter 7 examines the overall conclusions and future directions for this research. By combining our assembly techniques with known directing forces (e.g., electric or magnetic fields) more specific alignment and/or positioning could be achieved. We have also begun to explore directing assembly through lithographic microwells. Further work needs to explore the integration of arrays into devices and the use of functional materials. Then, high density, oriented arrays could be created for photonic, energy, sensing, catalytic, and electronic applications.

Computational characterization of DNA/peptide/nanotube self assembly for bioenergy applications

NASA Astrophysics Data System (ADS)

Ortiz, Vanessa; Araki, Ruriko; Collier, Galen

2012-02-01

Multi-enzyme pathways have become a subject of increasing interest for their role in the engineering of biomimetic systems for applications including biosensors, bioelectronics, and bioenergy. The efficiencies found in natural metabolic pathways partially arise from biomolecular self-assembly of the component enzymes in an effort to avoid transport limitations. The ultimate goal of this effort is to design and build biofuel cells with efficiencies similar to those of native systems by introducing biomimetic structures that immobilize multiple enzymes in specific orientations on a bioelectrode. To achieve site-specific immobilization, the specificity of DNA-binding domains is exploited with an approach that allows any redox enzyme to be modified to site-specifically bind to double stranded (ds) DNA while retaining activity. Because of its many desirable properties, the bioelectrode of choice is single-wall carbon nanotubes (SWNTs), but little is known about dsDNA/SWNT assembly and how this might affect the activity of the DNA-binding domains. Here we evaluate the feasibility of the proposed assembly by performing atomistic molecular dynamics simulations to look at the stability and conformations adopted by dsDNA when bound to a SWNT. We also evaluate the effects of the presence of a SWNT on the stability of the complex formed by a DNA-binding domain and DNA.

Physical vapor deposition as a route to glasses with liquid crystalline order

NASA Astrophysics Data System (ADS)

Gomez, Jaritza

Physical vapor deposition (PVD) is an effective route to prepare glasses with a unique combination of properties. Substrate temperatures near the glass transition (Tg) and slow deposition rates can access enhanced mobility at the surface of the glass allowing molecules at the surface additional time to sample different molecular configurations. The temperature of the substrate can be used to control molecular mobility during deposition and properties in the resulting glasses such as higher density, kinetic stability and preferential molecular orientation. PVD was used to prepare glasses of itraconazole, a smectic A liquid crystal. We characterized molecular orientation using infrared and ellipsometry. Molecular orientation can be controlled by choice of Tsubstrate in a range of temperatures near Tg. Glasses deposited at Tsubstrate = Tg show nearly vertical molecular orientation relative to the substrate; at lower Tsubstrate, molecules are nearly parallel to the substrate. The molecular orientation depends on the temperature of the substrate during preparation and not on the molecular orientation of the underlying layer. This allows preparing samples of layers with differing orientations. We find these glasses are homogeneous solids without evidence of domain boundaries and are molecularly flat. We interpret the combination of properties obtained for vapor-deposited glasses of itraconazole to result from a process where molecular orientation is determined by the structure and dynamics at the free surface of the glass during deposition. We report the thermal and structural properties of glasses prepared using PVD of a rod-like molecule, posaconazole, which does not show equilibrium liquid crystal phases. These glasses show substantial molecular orientation that can be controlled by choice of Tsubstrate during deposition. Ellipsometry and IR indicate that glasses prepared at Tg - 3 K are highly ordered. At these Tsubstrate, molecules show preferential vertical orientation and orientation is similar to that measured in aligned nematic liquid crystal. Our results are consistent with a recently proposed mechanism where molecular orientation in equilibrium liquids can be trapped in PVD glasses and suggest that the orientation at the free surface of posaconazole is nematic-like. In addition, we show posaconazole glasses show high kinetic stability controlled by Tsubstrate.

Coarse Grained Modeling of Block Copolymer Lithography: The Effects of Pattern Design on the Thermodynamics and Kinetics of the Directed Self Assembly of Block Copolymers

NASA Astrophysics Data System (ADS)

Garner, Grant Parker

The directed self assembly of block copolymers is an exciting complimentary technique for the fabrication of nanoscale structures for lithographic applications. Typically a directed self assembly process is driven through substrates with chemical (chemoepitaxy) or topographical (graphoepitaxy) guiding features. These patterning strategies have led to the ability to assemble structures with a high degree of perfection over large areas. However, a guiding pattern has not been created which assembles the desired features with a defect density that is commensurate with industrial standards of 1 defect/100cm 2. This work focuses on using molecular simulations on the Theoretically Informed Coarse Grained model to provide design rules for substrate patterns which drive the assembly of desired, device-oriented morphologies. Prior to the work presented in Chapter 2, the TICG model has been used in conjunction with a chemical pattern that is approximated as a hard-impenetrable surface. As many experimental systems use polymer brushes to help guide the polymer melt deposited on the substrate, this work analyzes the consequences of such an assumption by comparing a model where the polymer brush is explicitly implemented to the hard-wall substrate used in the past. Then, a methodology which utilizes a evolutionary optimization method is used to map the parameters of the more detailed model to the hard-surface model. This provides a qualitative understanding of how to interpret the model parameters used in previous works in the context of real experimental pattern designs. Chapter 3 discuss the concept of competitive assemblies in regards to defining a thermodynamic processing window in design space for assembling lines-and-spaces. The most competitive assembly to the desired orientation of the lamella is defined as a rotation of assembled lamella to the underlying pattern. Thermodynamic integration is used to calculate the free-energy difference between these assemblies over chemical patterns with varied design parameters. Local maximums in the free-energy difference are observed over pattern designs that are in qualitatively agreement with the pattern designs which produce the most perfect assemblies in experiments. The analysis is extended to study how choice of chemistry impacts this thermodynamic selection for the desired morphology. Finally, Chapter 4 provides insight into the kinetics of patterned directed self-assembly by investigating cylinder forming block copolymers within cylindrical confinements. Through the use of the string method, the minimum free-energy path between a defective state and the desired assembled morphology is calculated and clear transition states are highlighted. The effects of key parameters of the confinement design on the calculated minimum free energy path are calculated to identify design rules which should lead to a better understanding of optimal connement design for eliminating defects. In addition, a specific modification to existing cylindrical confinements is discussed as a possibility for tackling the problem of placement accuracy for a cylinder that is assembled within the confinement.

Heating equipment installation system

DOEpatents

Meuschke, Robert E.; Pomaibo, Paul P.

1991-01-01

A method for installing a heater unit assembly (52, 54) in a reactor pressure vessel (2) for performance of an annealing treatment on the vessel (2), the vessel (2) having a vertical axis, being open at the top, being provided at the top with a flange (6) having a horizontal surface, and being provided internally, at a location below the flange (6), with orientation elements (8) which are asymmetrical with respect to the vertical axis, by the steps of: providing an orientation fixture (10) having an upwardly extending guide member (18) and orientation elements (14, 16) and installing the orientation fixture (10) in the vessel (2) so that the orientation elements (14,16) of the orientation fixture (10) mate with the orientation elements (8) of the pressure vessel (2) in order to establish a defined position of the orientation fixture (10) in the pressure vessel (2), and so that the guide member (18) projects above the pressure vessel (2) flange (6); placing a seal ring (30) in a defined position on the pressure vessel (2) flange (6) with the aid of the guide member (18); mounting at least one vertical, upwardly extending guide stud (40) upon the seal ring (30); withdrawing the orientation fixture (10) from the pressure vessel (2); and moving the heater unit assembly (52,54) vertically downwardly into the pressure vessel (2) while guiding the heater unit assembly (52,54) along a path with the aid of the guide stud (40).

Cytoskeletal motor-driven active self-assembly in in vitro systems

DOE PAGES

Lam, A. T.; VanDelinder, V.; Kabir, A. M. R.; ...

2015-11-11

Molecular motor-driven self-assembly has been an active area of soft matter research for the past decade. Because molecular motors transform chemical energy into mechanical work, systems which employ molecular motors to drive self-assembly processes are able to overcome kinetic and thermodynamic limits on assembly time, size, complexity, and structure. Here, we review the progress in elucidating and demonstrating the rules and capabilities of motor-driven active self-assembly. Lastly, we focus on the types of structures created and the degree of control realized over these structures, and discuss the next steps necessary to achieve the full potential of this assembly mode whichmore » complements robotic manipulation and passive self-assembly.« less

In Situ Self Assembly of Nanocomposites: Competition of Chaotic Advection and Interfacial Effects as Observed by X-Ray Diffreaction

PubMed Central

Ratnaweera, Dilru R.; Mahesha, Chaitra; Zumbrunnen, David A.; Perahia, Dvora

2015-01-01

The effects of chaotic advection on the in situ assembly of a hierarchal nanocomposite of Poly Amide 6, (nylon 6 or PA6) and platelet shape nanoparticles (NPs) were studied. The assemblies were formed by chaotic advection, where melts of pristine PA6 and a mixture of PA6 with NPs were segregated into discrete layers and extruded into film in a continuous process. The process assembles the nanocomposite into alternating pristine-polymer and oriented NP/polymer layers. The structure of these hierarchal assemblies was probed by X-rays as a processing parameter, N, was varied. This parameter provides a measure of the extent of in situ structuring by chaotic advection. We found that all assemblies are semi-crystalline at room temperature. Increasing N impacts the ratio of α to γ crystalline forms. The effects of the chaotic advection vary with the concentration of the NPs. For nanocomposites with lower NP concentrations the amount of the γ crystalline form increased with N. However, at higher NP concentrations, interfacial effects of the NP play a significant role in determining the structure, where the NPs oriented along the melt flow direction and the polymer chains oriented perpendicular to the NP surfaces. PMID:28347015

Diels-Alder active-template synthesis of rotaxanes and metal-ion-switchable molecular shuttles.

PubMed

Crowley, James D; Hänni, Kevin D; Leigh, David A; Slawin, Alexandra M Z

2010-04-14

A synthesis of [2]rotaxanes in which Zn(II) or Cu(II) Lewis acids catalyze a Diels-Alder cycloaddition to form the axle while simultaneously acting as the template for the assembly of the interlocked molecules is described. Coordination of the Lewis acid to a multidentate endotopic 2,6-di(methyleneoxymethyl)pyridyl- or bipyridine-containing macrocycle orients a chelated dienophile through the macrocycle cavity. Lewis acid activation of the double bond causes it to react with an incoming "stoppered" diene, affording the [2]rotaxane in up to 91% yield. Unusually for an active-template synthesis, the metal binding site "lives on" in these rotaxanes. This was exploited in the synthesis of a molecular shuttle containing two different ligating sites in which the position of the macrocycle could be switched by complexation with metal ions [Zn(II) and Pd(II)] with different preferred coordination geometries.

Interfacial activity of acid functionalized single-walled carbon nanotubes (SWCNTs) at the fluid-fluid interface

NASA Astrophysics Data System (ADS)

Feng, Tao; Russell, Thomas; Hoagland, David

2013-03-01

Interfacial assembly of acid-functionalized single-walled carbon nanotubes at the oil/water interface is achieved by the addition of low molecular weight (MW) amino-terminated polystyrene in the oil phase. The surface activity of carboxylated SWCNTs is strongly influenced by the end-group chemistry and molecular weight of the polystyrene component, the concentrations of this component and the SWCNTs, along with the degree of functionalization of the SWCNTs. The prerequisites for interfacial trapping are amino termini on chains with MW less than 5K and 6 hours or longer incubation of pristine SWCNTs to achieve their carboxylation. Plummets in interfacial tension resembling those for surfactants were observed at critical bulk concentrations of both SWCNTs and PS-NH2. In dried droplets, SWCNTs densely packed with associated PS-NH2 form a bird nest-like interfacial structure, with the SWCNTs preferentially oriented perpendicular to the original interface. Advisor

Multiscale simulations of anisotropic particles combining molecular dynamics and Green's function reaction dynamics

NASA Astrophysics Data System (ADS)

Vijaykumar, Adithya; Ouldridge, Thomas E.; ten Wolde, Pieter Rein; Bolhuis, Peter G.

2017-03-01

The modeling of complex reaction-diffusion processes in, for instance, cellular biochemical networks or self-assembling soft matter can be tremendously sped up by employing a multiscale algorithm which combines the mesoscopic Green's Function Reaction Dynamics (GFRD) method with explicit stochastic Brownian, Langevin, or deterministic molecular dynamics to treat reactants at the microscopic scale [A. Vijaykumar, P. G. Bolhuis, and P. R. ten Wolde, J. Chem. Phys. 143, 214102 (2015)]. Here we extend this multiscale MD-GFRD approach to include the orientational dynamics that is crucial to describe the anisotropic interactions often prevalent in biomolecular systems. We present the novel algorithm focusing on Brownian dynamics only, although the methodology is generic. We illustrate the novel algorithm using a simple patchy particle model. After validation of the algorithm, we discuss its performance. The rotational Brownian dynamics MD-GFRD multiscale method will open up the possibility for large scale simulations of protein signalling networks.

High molecular weight DNA assembly in vivo for synthetic biology applications.

PubMed

Juhas, Mario; Ajioka, James W

2017-05-01

DNA assembly is the key technology of the emerging interdisciplinary field of synthetic biology. While the assembly of smaller DNA fragments is usually performed in vitro, high molecular weight DNA molecules are assembled in vivo via homologous recombination in the host cell. Escherichia coli, Bacillus subtilis and Saccharomyces cerevisiae are the main hosts used for DNA assembly in vivo. Progress in DNA assembly over the last few years has paved the way for the construction of whole genomes. This review provides an update on recent synthetic biology advances with particular emphasis on high molecular weight DNA assembly in vivo in E. coli, B. subtilis and S. cerevisiae. Special attention is paid to the assembly of whole genomes, such as those of the first synthetic cell, synthetic yeast and minimal genomes.

Two-dimensional hexagonally oriented CdCl2.H2O nanorod assembly: formation and replication.

PubMed

Deng, Zhaoxiang; Mao, Chengde

2004-09-14

This paper reports a simple bottom-up method that can controllably fabricate 2D hexagonally oriented and randomly distributed CdCl(2).H(2)O nanorods on mica surfaces. The as-formed nanorod assemblies have been successfully replicated into various matrixes, including gold, poly(dimethylsiloxane), and polyurethane. Thus, this method is compatible with soft-lithography towards further applications.

Tuning polymorphism and orientation in organic semiconductor thin films via post-deposition processing.

PubMed

Hiszpanski, Anna M; Baur, Robin M; Kim, Bumjung; Tremblay, Noah J; Nuckolls, Colin; Woll, Arthur R; Loo, Yueh-Lin

2014-11-05

Though both the crystal structure and molecular orientation of organic semiconductors are known to impact charge transport in thin-film devices, separately accessing different polymorphs and varying the out-of-plane molecular orientation is challenging, typically requiring stringent control over film deposition conditions, film thickness, and substrate chemistry. Here we demonstrate independent tuning of the crystalline polymorph and molecular orientation in thin films of contorted hexabenzocoronene, c-HBC, during post-deposition processing without the need to adjust deposition conditions. Three polymorphs are observed, two of which have not been previously reported. Using our ability to independently tune the crystal structure and out-of-plane molecular orientation in thin films of c-HBC, we have decoupled and evaluated the effects that molecular packing and orientation have on device performance in thin-film transistors (TFTs). In the case of TFTs comprising c-HBC, polymorphism and molecular orientation are equally important; independently changing either one affects the field-effect mobility by an order of magnitude.

Molecular Processes Underlying the Structure and Assembly of Thin Films and Nanoparticles at Complex interfaces

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

Richmond, Geraldine

Since 1995 we have pursued a number of different studies that are quite diverse in nature but with the common theme of using novel laser based methods to study important processes at buried interfaces. Studies of Corrosion, Passivation on n-GaAs(100)Methanol Photoelectrochemical Cell In these studies we have used picosecond photoluminescence and electrochemical studies to understand the GaAs/methanol interface. In our most extensive set of studies we conducted photo-illumination and XPS experiments to understand the chemistry occurring in the GaAs/methanol photoelectrochemical during photoexcitation. An important distinction between photocorrosion and photoetching of GaAs is elucidated by these studies. The dependence of GaAsmore » photocorrosion on light intensity has been explored to better understand intrinsic differences between the lamplight studies and the picosecond photoluminescence studies. The effect of coating the GaAs with a sulfide layer prior to immersion in the cell has also been explored. This last result has led us to examine n-GaAs as a function of crystallographic orientation after exposure to aqueous Na 2S containing solutions has been studied as a function of crystallographic orientation of the GaAs surface. The (100) and (110) surfaces are relatively similar, with significant amounts of As-S species present at the interface. The (111)B surface lacks this constituent, but shows significant amounts of metallic As. The XPS results have been correlated with the results of previous photocorrosion and passivation studies conducted in a photoelectrochemical cell. The studies indicate that the metallic As present at (111)B surface contributes strongly to the large surface recombination velocity found there, and to the inability of Na 2S to passivate the (111)B surface. SAMS Under Water: Water Molecular Structure and Bonding at Hydrophobic Surfaces In these DOE sponsored studies we have been interested in learning the similarities and differences in how water behaves at hydrophobic self-assembled monolayer (SAMS)/water interfaces relative to the organic liquid/water interfaces. Several monolayer films have been examined in these studies using a combination of vibrational sum frequency spectroscopy (VSFS), contact angle measurements and AFM. At the hydrocarbon monolayer/water interface we find that water has a weak bonding interaction with the monolayer film that results in an orientation of water at the terminus of these hydrocarbon chains. The water-film interaction is still present for fluorinated films but it is found to be considerably weaker. Hydration and Surfactant Adsorption at Salt/Water Interfaces This set of studies has examined the molecular characteristics of the CaF 2/water interface using VSFS. Our first studies detailed the structure and orientation of water molecules adsorbed at this mineral surfaces including studies of the surface in the presence of aqueous solutions of salts. These studies have been followed by a series of static and time-resolved studies of the adsorption of carboxylic acid containing organics at this surface, specifically carboxylic acid surfactants and acetic acid. In the latter we have developed a new method for time resolved studies that involve sequential wavelength tuning and automated control of spatial beam overlap at the target can probe amplitude changes of sum-frequency resonances in widely spaced infrared regions. This offers great advantages for the study of the synchronism of molecular processes at interfaces. This approach is particularly suitable to investigate the synchronization of interfacial processes such as surfactant adsorption at charged mineral surfaces. Macromolecular Assembly at Liquid/Liquid Interfaces Macromolecular assembly at the interface between water and a hydrophobic surface underlies some of the most important biological and environmental processes on the planet. Our work has examined polymer adsorption and assembly of carboxylic acid-containing polyelectrolytes at the carbon tetrachloride–water interface, a model system for an oil–water interface. Using VSFS and interfacial tension techniques, these unique set of studies identify the factors that dictate whether or not polyelectrolytes will adsorb to the oil–water interface and also describe the specifics of the adsorption process that depend upon factors such as polymer size, charge density, hydrophobicity, conformation, and the effect of metal ion electrostatics and bonding. The systems studied include polyelectrolytes polyacrylic acid (PAA) and polymethylacrylic acid (PMA) of different polymer sizes and under different aqueous solution conditions. The studies are the first to show the highly ordered nature of the adsorption of the first monolayer with subsequent monolayers disordered. The second set of studies have examined how peptoid nanosheets assemble at the oil/water interface. Peptoid nanosheets are a recently discovered class of two-dimensional (2D) nanomaterial, which form from the self-assembly of a sequence-specific peptoid polymer at an air-water interface. Nanosheet formation occurs first through the assembly of a peptoid monolayer and subsequent compression into a bilayer structure. In these highly successful studies we have shown that the oil-water interface provides another opportunity for growth of these unique and highly ordered peptoid sheets. The monolayer formed at this interface are found through surface spectroscopic measurements to be highly ordered and electrostatic interactions between the charged moieties, namely carboxylate and ammonium residues, of the peptoid are essential in the ability of these peptoids to form ordered nanosheets at the oil-water interface.« less

The structure and intermolecular forces of DNA condensates.

PubMed

Yoo, Jejoong; Aksimentiev, Aleksei

2016-03-18

Spontaneous assembly of DNA molecules into compact structures is ubiquitous in biological systems. Experiment has shown that polycations can turn electrostatic self-repulsion of DNA into attraction, yet the physical mechanism of DNA condensation has remained elusive. Here, we report the results of atomistic molecular dynamics simulations that elucidated the microscopic structure of dense DNA assemblies and the physics of interactions that makes such assemblies possible. Reproducing the setup of the DNA condensation experiments, we measured the internal pressure of DNA arrays as a function of the DNA-DNA distance, showing a quantitative agreement between the results of our simulations and the experimental data. Analysis of the MD trajectories determined the DNA-DNA force in a DNA condensate to be pairwise, the DNA condensation to be driven by electrostatics of polycations and not hydration, and the concentration of bridging cations, not adsorbed cations, to determine the magnitude and the sign of the DNA-DNA force. Finally, our simulations quantitatively characterized the orientational correlations of DNA in DNA arrays as well as diffusive motion of DNA and cations. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Biocompatible Materials Based on Self-Assembling Peptides on Ti25Nb10Zr Alloy: Molecular Structure and Organization Investigated by Synchrotron Radiation Induced Techniques.

PubMed

Secchi, Valeria; Franchi, Stefano; Santi, Marta; Vladescu, Alina; Braic, Mariana; Skála, Tomáš; Nováková, Jaroslava; Dettin, Monica; Zamuner, Annj; Iucci, Giovanna; Battocchio, Chiara

2018-03-07

In this work, we applied advanced Synchrotron Radiation (SR) induced techniques to the study of the chemisorption of the Self Assembling Peptide EAbuK16, i.e., H-Abu-Glu-Abu-Glu-Abu-Lys-Abu-Lys-Abu-Glu-Abu-Glu-Abu-Lys-Abu-Lys-NH₂ that is able to spontaneously aggregate in anti-parallel β-sheet conformation, onto annealed Ti25Nb10Zr alloy surfaces. This synthetic amphiphilic oligopeptide is a good candidate to mimic extracellular matrix for bone prosthesis, since its β-sheets stack onto each other in a multilayer oriented nanostructure with internal pores of 5-200 nm size. To prepare the biomimetic material, Ti25Nb10Zr discs were treated with aqueous solutions of EAbuK16 at different pH values. Here we present the results achieved by performing SR-induced X-ray Photoelectron Spectroscopy (SR-XPS), angle-dependent Near Edge X-ray Absorption Fine Structure (NEXAFS) spectroscopy, FESEM and AFM imaging on Ti25Nb10Zr discs after incubation with self-assembling peptide solution at five different pH values, selected deliberately to investigate the best conditions for peptide immobilization.

Coarse-Grained Molecular Simulation of the Hierarchical Self-Assembly of π-Conjugated Optoelectronic Peptides

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

Mansbach, Rachael A.; Ferguson, Andrew L.

Self-assembled aggregates of peptides containing aromatic groups possess optoelectronic properties that make them attractive targets for the fabrication of biocompatible electronics. Molecular-level understanding of how the microscopic peptide chemistry influences the properties of the aggregates is vital for rational peptide design. We construct a coarse-grained model of Asp-Phe-Ala-Gly-OPV3-Gly-Ala-Phe-Asp (DFAG-OPV3-GAFD) peptides containing OPV3 (distyrylbenzene) π-conjugated cores explicitly parameterized against all-atom calculations and perform molecular dynamics simulations of the self-assembly of hundreds of molecules over hundreds of nanoseconds. We observe a hierarchical assembly mechanism wherein ~2-8 peptides assemble into stacks with aligned aromatic cores that subsequently form elliptical aggregates and ultimately amore » branched network with a fractal dimensionality of ~1.5. The assembly dynamics are well described by a Smoluchowski coagulation process for which we extract rate constants from the molecular simulations to both furnish insight into the microscopic assembly kinetics and extrapolate our aggregation predictions to time and length scales beyond the reach of molecular simulation. Lastly, this study presents new molecular-level understanding of the morphology and dynamics of the spontaneous self-assembly of DFAG-OPV3-GAFD peptides and establishes a systematic protocol to develop coarse-grained models of optoelectronic peptides for the exploration and design of π-conjugated peptides with tunable optoelectronic properties.« less

Coarse-Grained Molecular Simulation of the Hierarchical Self-Assembly of π-Conjugated Optoelectronic Peptides

DOE PAGES

Mansbach, Rachael A.; Ferguson, Andrew L.

2017-02-10

Self-assembled aggregates of peptides containing aromatic groups possess optoelectronic properties that make them attractive targets for the fabrication of biocompatible electronics. Molecular-level understanding of how the microscopic peptide chemistry influences the properties of the aggregates is vital for rational peptide design. We construct a coarse-grained model of Asp-Phe-Ala-Gly-OPV3-Gly-Ala-Phe-Asp (DFAG-OPV3-GAFD) peptides containing OPV3 (distyrylbenzene) π-conjugated cores explicitly parameterized against all-atom calculations and perform molecular dynamics simulations of the self-assembly of hundreds of molecules over hundreds of nanoseconds. We observe a hierarchical assembly mechanism wherein ~2-8 peptides assemble into stacks with aligned aromatic cores that subsequently form elliptical aggregates and ultimately amore » branched network with a fractal dimensionality of ~1.5. The assembly dynamics are well described by a Smoluchowski coagulation process for which we extract rate constants from the molecular simulations to both furnish insight into the microscopic assembly kinetics and extrapolate our aggregation predictions to time and length scales beyond the reach of molecular simulation. Lastly, this study presents new molecular-level understanding of the morphology and dynamics of the spontaneous self-assembly of DFAG-OPV3-GAFD peptides and establishes a systematic protocol to develop coarse-grained models of optoelectronic peptides for the exploration and design of π-conjugated peptides with tunable optoelectronic properties.« less

A nine-scaffold genome assembly of the nine chromosome sugar beet

USDA-ARS?s Scientific Manuscript database

Over the course of 20 months, we assembled a sugar beet genome (700 - 800 Mb) into a close representation of the nine haploid chromosomes of beet. This result was obtained by sequentially assembling sequences >40 kb in length, orienting these assemblies via optical mapping, and scaffolding with in v...

Assembly of Triblock Amphiphilic Peptides into One-Dimensional Aggregates and Network Formation.

PubMed

Ozgur, Beytullah; Sayar, Mehmet

2016-10-06

Peptide assembly plays a key role in both neurological diseases and development of novel biomaterials with well-defined nanostructures. Synthetic model peptides provide a unique platform to explore the role of intermolecular interactions in the assembly process. A triblock peptide architecture designed by the Hartgerink group is a versatile system which relies on Coulomb interactions, hydrogen bonding, and hydrophobicity to guide these peptides' assembly at three different length scales: β-sheets, double-wall ribbon-like aggregates, and finally a highly porous network structure which can support gels with ≤1% by weight peptide concentration. In this study, by using molecular dynamics simulations of a structure based implicit solvent coarse grained model, we analyzed this hierarchical assembly process. Parametrization of our CG model is based on multiple-state points from atomistic simulations, which enables this model to represent the conformational adaptability of the triblock peptide molecule based on the surrounding medium. Our results indicate that emergence of the double-wall β-sheet packing mechanism, proposed in light of the experimental evidence, strongly depends on the subtle balance of the intermolecular forces. We demonstrate that, even though backbone hydrogen bonding dominates the early nucleation stages, depending on the strength of the hydrophobic and Coulomb forces, alternative structures such as zero-dimensional aggregates with two β-sheets oriented orthogonally (which we refer to as a cross-packed structure) and β-sheets with misoriented hydrophobic side chains are also feasible. We discuss the implications of these competing structures for the three different length scales of assembly by systematically investigating the influence of density, counterion valency, and hydrophobicity.

Artificial muscle-like function from hierarchical supramolecular assembly of photoresponsive molecular motors

NASA Astrophysics Data System (ADS)

Chen, Jiawen; Leung, Franco King-Chi; Stuart, Marc C. A.; Kajitani, Takashi; Fukushima, Takanori; van der Giessen, Erik; Feringa, Ben L.

2018-02-01

A striking feature of living systems is their ability to produce motility by amplification of collective molecular motion from the nanoscale up to macroscopic dimensions. Some of nature's protein motors, such as myosin in muscle tissue, consist of a hierarchical supramolecular assembly of very large proteins, in which mechanical stress induces a coordinated movement. However, artificial molecular muscles have often relied on covalent polymer-based actuators. Here, we describe the macroscopic contractile muscle-like motion of a supramolecular system (comprising 95% water) formed by the hierarchical self-assembly of a photoresponsive amphiphilic molecular motor. The molecular motor first assembles into nanofibres, which further assemble into aligned bundles that make up centimetre-long strings. Irradiation induces rotary motion of the molecular motors, and propagation and accumulation of this motion lead to contraction of the fibres towards the light source. This system supports large-amplitude motion, fast response, precise control over shape, as well as weight-lifting experiments in water and air.

Assembly of Huntingtin headpiece into α-helical bundles.

PubMed

Ozgur, Beytullah; Sayar, Mehmet

2017-05-24

Protein aggregation is a hallmark of neurodegenerative disorders. In this group of brain-related disorders, a disease-specific "host" protein or fragment misfolds and adopts a metastatic, aggregate-prone conformation. Often, this misfolded conformation is structurally and thermodynamically different from its native state. Intermolecular contacts, which arise in this non-native state, promote aggregation. In this regard, understanding the molecular principles and mechanisms that lead to the formation of such a non-native state and further promote the formation of the critical nucleus for fiber growth is essential. In this study, the authors analyze the aggregation propensity of Huntingtin headpiece (htt NT ), which is known to facilitate the polyQ aggregation, in relation to the helix mediated aggregation mechanism proposed by the Wetzel group. The authors demonstrate that even though htt NT displays a degenerate conformational spectrum on its own, interfaces of macroscopic or molecular origin can promote the α-helix conformation, eliminating all other alternatives in the conformational phase space. Our findings indicate that htt NT molecules do not have a strong orientational preference for parallel or antiparallel orientation of the helices within the aggregate. However, a parallel packed bundle of helices would support the idea of increased polyglutamine concentration, to pave the way for cross-β structures.

Female Meiosis: Synapsis, Recombination, and Segregation in Drosophila melanogaster

PubMed Central

Hughes, Stacie E.; Miller, Danny E.; Miller, Angela L.; Hawley, R. Scott

2018-01-01

A century of genetic studies of the meiotic process in Drosophila melanogaster females has been greatly augmented by both modern molecular biology and major advances in cytology. These approaches, and the findings they have allowed, are the subject of this review. Specifically, these efforts have revealed that meiotic pairing in Drosophila females is not an extension of somatic pairing, but rather occurs by a poorly understood process during premeiotic mitoses. This process of meiotic pairing requires the function of several components of the synaptonemal complex (SC). When fully assembled, the SC also plays a critical role in maintaining homolog synapsis and in facilitating the maturation of double-strand breaks (DSBs) into mature crossover (CO) events. Considerable progress has been made in elucidating not only the structure, function, and assembly of the SC, but also the proteins that facilitate the formation and repair of DSBs into both COs and noncrossovers (NCOs). The events that control the decision to mature a DSB as either a CO or an NCO, as well as determining which of the two CO pathways (class I or class II) might be employed, are also being characterized by genetic and genomic approaches. These advances allow a reconsideration of meiotic phenomena such as interference and the centromere effect, which were previously described only by genetic studies. In delineating the mechanisms by which the oocyte controls the number and position of COs, it becomes possible to understand the role of CO position in ensuring the proper orientation of homologs on the first meiotic spindle. Studies of bivalent orientation have occurred in the context of numerous investigations into the assembly, structure, and function of the first meiotic spindle. Additionally, studies have examined the mechanisms ensuring the segregation of chromosomes that have failed to undergo crossing over. PMID:29487146

The Release 6 reference sequence of the Drosophila melanogaster genome

DOE PAGES

Hoskins, Roger A.; Carlson, Joseph W.; Wan, Kenneth H.; ...

2015-01-14

Drosophila melanogaster plays an important role in molecular, genetic, and genomic studies of heredity, development, metabolism, behavior, and human disease. The initial reference genome sequence reported more than a decade ago had a profound impact on progress in Drosophila research, and improving the accuracy and completeness of this sequence continues to be important to further progress. We previously described improvement of the 117-Mb sequence in the euchromatic portion of the genome and 21 Mb in the heterochromatic portion, using a whole-genome shotgun assembly, BAC physical mapping, and clone-based finishing. Here, we report an improved reference sequence of the single-copy andmore » middle-repetitive regions of the genome, produced using cytogenetic mapping to mitotic and polytene chromosomes, clone-based finishing and BAC fingerprint verification, ordering of scaffolds by alignment to cDNA sequences, incorporation of other map and sequence data, and validation by whole-genome optical restriction mapping. These data substantially improve the accuracy and completeness of the reference sequence and the order and orientation of sequence scaffolds into chromosome arm assemblies. Representation of the Y chromosome and other heterochromatic regions is particularly improved. The new 143.9-Mb reference sequence, designated Release 6, effectively exhausts clone-based technologies for mapping and sequencing. Highly repeat-rich regions, including large satellite blocks and functional elements such as the ribosomal RNA genes and the centromeres, are largely inaccessible to current sequencing and assembly methods and remain poorly represented. In conclusion, further significant improvements will require sequencing technologies that do not depend on molecular cloning and that produce very long reads.« less

The Release 6 reference sequence of the Drosophila melanogaster genome

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

Hoskins, Roger A.; Carlson, Joseph W.; Wan, Kenneth H.

Drosophila melanogaster plays an important role in molecular, genetic, and genomic studies of heredity, development, metabolism, behavior, and human disease. The initial reference genome sequence reported more than a decade ago had a profound impact on progress in Drosophila research, and improving the accuracy and completeness of this sequence continues to be important to further progress. We previously described improvement of the 117-Mb sequence in the euchromatic portion of the genome and 21 Mb in the heterochromatic portion, using a whole-genome shotgun assembly, BAC physical mapping, and clone-based finishing. Here, we report an improved reference sequence of the single-copy andmore » middle-repetitive regions of the genome, produced using cytogenetic mapping to mitotic and polytene chromosomes, clone-based finishing and BAC fingerprint verification, ordering of scaffolds by alignment to cDNA sequences, incorporation of other map and sequence data, and validation by whole-genome optical restriction mapping. These data substantially improve the accuracy and completeness of the reference sequence and the order and orientation of sequence scaffolds into chromosome arm assemblies. Representation of the Y chromosome and other heterochromatic regions is particularly improved. The new 143.9-Mb reference sequence, designated Release 6, effectively exhausts clone-based technologies for mapping and sequencing. Highly repeat-rich regions, including large satellite blocks and functional elements such as the ribosomal RNA genes and the centromeres, are largely inaccessible to current sequencing and assembly methods and remain poorly represented. In conclusion, further significant improvements will require sequencing technologies that do not depend on molecular cloning and that produce very long reads.« less

Scalable alignment and transfer of nanowires based on oriented polymer nanofibers.

PubMed

Yan, Shancheng; Lu, Lanxin; Meng, Hao; Huang, Ningping; Xiao, Zhongdang

2010-03-05

We develop a simple and scalable method based on oriented polymer nanofiber films for the parallel assembly and transfer of nanowires at high density. Nanowires dispersed in solution are aligned and selectively deposited at the central space of parallel nanochannels formed by the well-oriented nanofibers as a result of evaporation-induced flow and capillarity. A general contact printing method is used to realize the transfer of the nanowires from the donor nanofiber film to a receiver substrate. The mechanism, which involves ordered alignment of nanowires on oriented polymer nanofiber films, is also explored with an evaporation model of cylindrical droplets. The simplicity of the assembly and transfer, and the facile fabrication of large-area well-oriented nanofiber films, make the present method promising for the application of nanowires, especially for the disordered nanowires synthesized by solution chemistry.

Chiral signs of TPPS co-assemblies with chiral gelators: role of molecular and supramolecular chirality.

PubMed

Wang, Qiuling; Zhang, Li; Yang, Dong; Li, Tiesheng; Liu, Minghua

2016-10-13

A dianionic tetrakis(4-sulfonatophenyl)porphyrin (TPPS) self-assembled into J-aggregates when it co-assembled with a chiral cationic amphiphile via supramolecular gelation. The chiral signs of TPPS J aggregates followed the supramolecular chirality of amphiphilic assemblies rather than the molecular chirality of the amphiphile.

CAR: contig assembly of prokaryotic draft genomes using rearrangements.

PubMed

Lu, Chin Lung; Chen, Kun-Tze; Huang, Shih-Yuan; Chiu, Hsien-Tai

2014-11-28

Next generation sequencing technology has allowed efficient production of draft genomes for many organisms of interest. However, most draft genomes are just collections of independent contigs, whose relative positions and orientations along the genome being sequenced are unknown. Although several tools have been developed to order and orient the contigs of draft genomes, more accurate tools are still needed. In this study, we present a novel reference-based contig assembly (or scaffolding) tool, named as CAR, that can efficiently and more accurately order and orient the contigs of a prokaryotic draft genome based on a reference genome of a related organism. Given a set of contigs in multi-FASTA format and a reference genome in FASTA format, CAR can output a list of scaffolds, each of which is a set of ordered and oriented contigs. For validation, we have tested CAR on a real dataset composed of several prokaryotic genomes and also compared its performance with several other reference-based contig assembly tools. Consequently, our experimental results have shown that CAR indeed performs better than all these other reference-based contig assembly tools in terms of sensitivity, precision and genome coverage. CAR serves as an efficient tool that can more accurately order and orient the contigs of a prokaryotic draft genome based on a reference genome. The web server of CAR is freely available at http://genome.cs.nthu.edu.tw/CAR/ and its stand-alone program can also be downloaded from the same website.

Ultrafast shock compression of self-assembled monolayers: a molecular picture.

PubMed

Patterson, James E; Dlott, Dana D

2005-03-24

Simulations of self-assembled monolayers (SAMs) are performed to interpret experimental measurements of ultrafast approximately 1 GPa (volume compression deltaV approximately 0.1) planar shock compression dynamics probed by vibrational sum-frequency generation (SFG) spectroscopy (Lagutchev, A. S.; Patterson, J. E.; Huang, W.; Dlott, D. D. J. Phys. Chem. B 2005, 109, XXXX). The SAMs investigated are octadecanethiol (ODT) and pentadecanethiol (PDT) on Au(111) and Ag(111) substrates, and benzyl mercaptan (BMT) on Au(111). In the alkane SAMs, SFG is sensitive to the instantaneous orientation of the terminal methyl; in BMT it is sensitive to the phenyl orientation. Computed structures of alkane SAMs are in good agreement with experiment. In alkanes, the energies of gauche defects increase with increasing number and depth below the methyl plane, with the exception of ODT/Au where both single and double gauche defects at the two uppermost dihedrals have similar energies. Simulations of isothermal uniaxial compression of SAM lattices show that chain and methyl tilting is predominant in PDT/Au, ODT/Ag and PDT/Ag, whereas single and double gauche defect formation is predominant in ODT/Au. Time-resolved shock data showing transient SFG signal loss of ODT/Au and PDT/Au are fit by calculations of the terminal group orientations as a function of deltaV and their contributions to the SFG hyperpolarizability. The highly elastic response of PDT/Au results from shock-generated methyl and chain tilting. The viscoelastic response of ODT/Au results from shock generation of single and double gauche defects. Isothermal compression simulations help explain and fit the time dependence of shock spectra but generally underestimate the magnitude of SFG signal loss because they do not include effects of high-strain-rate dynamics and shock front and surface irregularities.

Adsorption of hydrophobin on different self-assembled monolayers: the role of the hydrophobic dipole and the electric dipole.

PubMed

Peng, Chunwang; Liu, Jie; Zhao, Daohui; Zhou, Jian

2014-09-30

In this work, the adsorptions of hydrophobin (HFBI) on four different self-assembled monolayers (SAMs) (i.e., CH3-SAM, OH-SAM, COOH-SAM, and NH2-SAM) were investigated by parallel tempering Monte Carlo and molecular dynamics simulations. Simulation results indicate that the orientation of HFBI adsorbed on neutral surfaces is dominated by a hydrophobic dipole. HFBI adsorbs on the hydrophobic CH3-SAM through its hydrophobic patch and adopts a nearly vertical hydrophobic dipole relative to the surface, while it is nearly horizontal when adsorbed on the hydrophilic OH-SAM. For charged SAM surfaces, HFBI adopts a nearly vertical electric dipole relative to the surface. HFBI has the narrowest orientation distribution on the CH3-SAM, and thus can form an ordered monolayer and reverse the wettability of the surface. For HFBI adsorption on charged SAMs, the adsorption strength weakens as the surface charge density increases. Compared with those on other SAMs, a larger area of the hydrophobic patch is exposed to the solution when HFBI adsorbs on the NH2-SAM. This leads to an increase of the hydrophobicity of the surface, which is consistent with the experimental results. The binding of HFBI to the CH3-SAM is mainly through hydrophobic interactions, while it is mediated through a hydration water layer near the surface for the OH-SAM. For the charged SAM surfaces, the adsorption is mainly induced by electrostatic interactions between the charged surfaces and the oppositely charged residues. The effect of a hydrophobic dipole on protein adsorption onto hydrophobic surfaces is similar to that of an electric dipole for charged surfaces. Therefore, the hydrophobic dipole may be applied to predict the probable orientations of protein adsorbed on hydrophobic surfaces.

Influence of molecular distortion on the exciton quenching for quaterthiophene-terminated self-assembled monolayers on Au(111)

NASA Astrophysics Data System (ADS)

Kato, Hiroyuki S.; Murakami, Yoshinari; Saitoh, Riyo; Osumi, Yuji; Okaue, Daijiro; Kiriyama, Yoshiaki; Ueba, Takahiro; Yamada, Takashi; Ie, Yutaka; Aso, Yoshio; Munakata, Toshiaki

2018-03-01

We have studied the dynamics of photoexcited electronic states for structure-specific alkanethiolate-based self-assembled monolayers (SAMs) on Au(111). At the even numbers of methylene units (n) in the alkylene chain, a molecular distortion due to strong interference between the end substituents is expected. Focused on this geometrical perturbation, here, we examine the influence of the molecular distortion on the quenching process of photoexcited quaterthiophene (4T)-terminated alkanethiolate SAMs (4TCnS-SAMs) for even n (= 6 and 8). The occupied and unoccupied electronic levels of 4TCnS-SAMs are specified by ultraviolet photoelectron spectroscopy (UPS) and two-photon photoemission (2PPE) spectroscopy, respectively. The quenching rate, i.e., lifetime (τn), of the photoexcited state for 4TCnS-SAMs is evaluated by the time-resolved 2PPE measurements. In comparison to the previously reported results for odd n [J. Phys. Chem. C 119 (2015) 7400-7407], we find that τn for even n is not in the middle of those for n ± 1 but close to that for n - 1, i.e., τ6 ≈ τ5 and τ8 ≈ τ7, in contrast to the negligible difference in the electronic levels for all n. By the examination of molecular configurations using scanning tunneling microscopy (STM) and infrared reflection absorption spectroscopy (IRAS), we elucidate the weak n dependence of the 4T group orientation and the n-parity-dependent conformation change of alkylene chain. We conclude that the n parity dependence of τn results from a structural distortion of the aliphatic alkylene chain, in which a skewed alkylene chain appears for even n, rather than the electronic modification of the aromatic 4T groups.

Modular Organization of Residue-Level Contacts Shapes the Selection Pressure on Individual Amino Acid Sites of Ribosomal Proteins.

PubMed

Mallik, Saurav; Kundu, Sudip

2017-04-01

Understanding the molecular evolution of macromolecular complexes in the light of their structure, assembly, and stability is of central importance. Here, we address how the modular organization of native molecular contacts shapes the selection pressure on individual residue sites of ribosomal complexes. The bacterial ribosomal complex is represented as a residue contact network where nodes represent amino acid/nucleotide residues and edges represent their van der Waals interactions. We find statistically overrepresented native amino acid-nucleotide contacts (OaantC, one amino acid contacts one or multiple nucleotides, internucleotide contacts are disregarded). Contact number is defined as the number of nucleotides contacted. Involvement of individual amino acids in OaantCs with smaller contact numbers is more random, whereas only a few amino acids significantly contribute to OaantCs with higher contact numbers. An investigation of structure, stability, and assembly of bacterial ribosome depicts the involvement of these OaantCs in diverse biophysical interactions stabilizing the complex, including high-affinity protein-RNA contacts, interprotein cooperativity, intersubunit bridge, packing of multiple ribosomal RNA domains, etc. Amino acid-nucleotide constituents of OaantCs with higher contact numbers are generally associated with significantly slower substitution rates compared with that of OaantCs with smaller contact numbers. This evolutionary rate heterogeneity emerges from the strong purifying selection pressure that conserves the respective amino acid physicochemical properties relevant to the stabilizing interaction with OaantC nucleotides. An analysis of relative molecular orientations of OaantC residues and their interaction energetics provides the biophysical ground of purifying selection conserving OaantC amino acid physicochemical properties. © The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Effect of metallic silver nanoparticles on the alignment and relaxation behaviour of liquid crystalline material in smectic C* phase

NASA Astrophysics Data System (ADS)

Vimal, Tripti; Kumar Gupta, Swadesh; Katiyar, Rohit; Srivastava, Atul; Czerwinski, Michal; Krup, Katarzyna; Kumar, Sandeep; Manohar, Rajiv

2017-09-01

The influence of silver nanoparticles dispersed in a Ferroelectric Liquid Crystal (FLC) on the properties of the resultant composite system has been investigated by thermal, electro-optical, and dielectric methods. We show that the concentration of thiol capped silver nanoparticles is a critical factor in governing the alignment of nanoparticles (NPs) in the host FLC. The orientation of NPs in composite samples affects the ordering of the LC (Liquid Crystal) phase and consequently changes the various phase transition temperatures of the host LC. Formation of self-assembled 2D (two dimensional) arrays of nanoparticles is observed for high concentration of dopant in the LC, oriented perpendicular to the direction of rubbing. We propose that the molecular interaction between the thiol capped NPs and LC molecules is the key factor behind such an arrangement of NPs. Orientation of NPs has affected the relaxation behaviour and various other material parameters, significantly. A noteworthy change in DC conductivity articulates our proposed idea of the formation of 2D array of NPs perpendicular to the direction of rubbing. This comprehensive study endorses the importance of dopant concentration in modifying the properties of the host LC material.

Solution processed nanogap organic diodes based on liquid crystalline materials

NASA Astrophysics Data System (ADS)

Wang, Yi-Fei; Iino, Hiroaki; Hanna, Jun-ichi

2017-09-01

Co-planar nanogap organic diodes were fabricated with smectic liquid crystalline materials of the benzothienobenzothiophene (BTBT) derivative by a spin-coating technique. A high rectification ratio of the order of 106 at ±3 V was achieved when a liquid crystalline material of 2,7-didecyl benzothieno[3,2-b][1]benzothiophene (10-BTBT-10) was used in a device configuration of Al/10-BTBT-10/pentafluorobenzenethiol-treated Au on a glass substrate, which was 4 orders higher than that of the device based on non-liquid crystalline materials of 2,7-dibutyl benzothieno[3,2-b][1]benzothiophene (4-BTBT-4) and BTBT. Similar results were also observed when another liquid crystalline material of ω, ω'-dioctylterthiophene (8-TTP-8) and a non-liquid crystalline material of terthiophene (TTP) were used. These improved rectifications can be ascribed to the self-assembly properties and controllable molecular orientation of liquid crystalline materials, which made uniform perpendicular oriented polycrystalline films favorable for superior charge transport in nano-channels.

Donor/Acceptor Molecular Orientation-Dependent Photovoltaic Performance in All-Polymer Solar Cells.

PubMed

Zhou, Ke; Zhang, Rui; Liu, Jiangang; Li, Mingguang; Yu, Xinhong; Xing, Rubo; Han, Yanchun

2015-11-18

The correlated donor/acceptor (D/A) molecular orientation plays a crucial role in solution-processed all-polymer solar cells in term of photovoltaic performance. For the conjugated polymers PTB7-th and P(NDI2OD-T2), the preferential molecular orientation of neat PTB7-th films kept face-on regardless of the properties of processing solvents. However, an increasing content of face-on molecular orientation in the neat P(NDI2OD-T2) films could be found by changing processing solvents from chloronaphthalene (CN) and o-dichlorobenzene (oDCB) to chlorobenzene (CB). Besides, the neat P(NDI2OD-T2) films also exhibited a transformation of preferential molecular orientation from face-on to edge-on when extending film drying time by casting in the same solution. Consequently, a distribution diagram of molecular orientation for P(NDI2OD-T2) films was depicted and the same trend could be observed for the PTB7-th/P(NDI2OD-T2) blend films. By manufacture of photovoltaic devices with blend films, the relationship between the correlated D/A molecular orientation and device performance was established. The short-circuit current (Jsc) of devices processed by CN, oDCB, and CB enhanced gradually from 1.24 to 8.86 mA/cm(2) with the correlated D/A molecular orientation changing from face-on/edge-on to face-on/face-on, which could be attributed to facile exciton dissociation at D/A interface with the same molecular orientation. Therefore, the power conversion efficiency (PCE) of devices processed by CN, oDCB, and CB improved from 0.53% to 3.52% ultimately.

Self-assembled nanogaps for molecular electronics.

PubMed

Tang, Qingxin; Tong, Yanhong; Jain, Titoo; Hassenkam, Tue; Wan, Qing; Moth-Poulsen, Kasper; Bjørnholm, Thomas

2009-06-17

A nanogap for molecular devices was realized using solution-based self-assembly. Gold nanorods were assembled to gold nanoparticle-coated conducting SnO2:Sb nanowires via thiol end-capped oligo(phenylenevinylene)s (OPVs). The molecular gap was easily created by the rigid molecule itself during self-assembly and the gap length was determined by the molecule length. The gold nanorods and gold nanoparticles, respectively covalently bonded at the two ends of the molecule, had very small dimensions, e.g. a width of approximately 20 nm, and hence were expected to minimize the screening effect. The ultra-long conducting SnO2:Sb nanowires provided the bridge to connect one of the electrodes of the molecular device (gold nanoparticle) to the external circuit. The tip of the atomic force microscope (AFM) was contacted onto the other electrode (gold nanorod) for the electrical measurement of the OPV device. The conductance measurement confirmed that the self-assembly of the molecules and the subsequent self-assembly of the gold nanorods was a feasible method for the fabrication of the nanogap of the molecular devices.

Nanopatterning of Surfaces with Monometallic and Heterobimetallic 1D Coordination Polymers: A Molecular Tectonics Approach at the Solid/Liquid Interface.

PubMed

El Garah, Mohamed; Marets, Nicolas; Mauro, Matteo; Aliprandi, Alessandro; Bonacchi, Sara; De Cola, Luisa; Ciesielski, Artur; Bulach, Véronique; Hosseini, Mir Wais; Samorì, Paolo

2015-07-08

The self-assembly of multiple molecular components into complex supramolecular architectures is ubiquitous in nature and constitutes one of the most powerful strategies to fabricate multifunctional nanomaterials making use of the bottom-up approach. When spatial confinement in two dimensions on a solid substrate is employed, this approach can be exploited to generate periodically ordered structures from suitably designed molecular tectons. In this study we demonstrate that physisorbed directional periodic arrays of monometallic or heterobimetallic coordination polymers can be generated on a highly oriented pyrolitic graphite surface by combinations of a suitably designed directional organic tecton or metallatecton based on a porphyrin or nickel(II) metalloporphyrin backbone bearing both a pyridyl unit and a terpyridyl unit acting as coordinating sites for CoCl2. The periodic architectures were visualized at the solid/liquid interface with a submolecular resolution by scanning tunneling microscopy and corroborated by combined density functional and time-dependent density functional theory calculations. The capacity to nanopattern the surface for the first time with two distinct metallic centers exhibiting different electronic and optical properties is a key step toward the bottom-up construction of robust multicomponent and, thus, multifunctional molecular nanostructures and nanodevices.

Directed block copolymer self-assembly implemented via surface-embedded electrets

NASA Astrophysics Data System (ADS)

Wu, Mei-Ling; Wang, Dong; Wan, Li-Jun

2016-02-01

Block copolymer (BCP) nanolithography is widely recognized as a promising complementary approach to circumvent the feature size limits of conventional photolithography. The directed self-assembly of BCP thin film to form ordered nanostructures with controlled orientation and localized pattern has been the key challenge for practical nanolithography applications. Here we show that BCP nanopatterns can be directed on localized surface electrets defined by electron-beam irradiation to realize diverse features in a simple, effective and non-destructive manner. Charged electrets can generate a built-in electric field in BCP thin film and induce the formation of perpendicularly oriented microdomain of BCP film. The electret-directed orientation control of BCP film can be either integrated with mask-based patterning technique or realized by electron-beam direct-writing method to fabricate microscale arbitrary lateral patterns down to single BCP cylinder nanopattern. The electret-directed BCP self-assembly could provide an alternative means for BCP-based nanolithography, with high resolution.

Structure Prediction of Self-Assembled Dye Aggregates from Cryogenic Transmission Electron Microscopy, Molecular Mechanics, and Theory of Optical Spectra.

PubMed

Friedl, Christian; Renger, Thomas; Berlepsch, Hans V; Ludwig, Kai; Schmidt Am Busch, Marcel; Megow, Jörg

2016-09-01

Cryogenic transmission electron microscopy (cryo-TEM) studies suggest that TTBC molecules self-assemble in aqueous solution to form single-walled tubes with a diameter of about 35 Å. In order to reveal the arrangement and mutual orientations of the individual molecules in the tube, we combine information from crystal structure data of this dye with a calculation of linear absorbance and linear dichroism spectra and molecular dynamics simulations. We start with wrapping crystal planes in different directions to obtain tubes of suitable diameter. This set of tube models is evaluated by comparing the resulting optical spectra with experimental data. The tubes that can explain the spectra are investigated further by molecular dynamics simulations, including explicit solvent molecules. From the trajectories of the most stable tube models, the short-range ordering of the dye molecules is extracted and the optimization of the structure is iteratively completed. The final structural model is a tube of rings with 6-fold rotational symmetry, where neighboring rings are rotated by 30° and the transition dipole moments of the chromophores form an angle of 74° with respect to the symmetry axis of the tube. This model is in agreement with cryo-TEM images and can explain the optical spectra, consisting of a sharp red-shifted J-band that is polarized parallel to to the symmetry axis of the tube and a broad blue-shifted H-band polarized perpendicular to this axis. The general structure of the homogeneous spectrum of this hybrid HJ-aggregate is described by an analytical model that explains the difference in redistribution of oscillator strength inside the vibrational manifolds of the J- and H-bands and the relative intensities and excitation energies of those bands. In addition to the particular system investigated here, the present methodology can be expected to aid the structure prediction for a wide range of self-assembled dye aggregates.

Self-Assembly of Hierarchical DNA Nanotube Architectures with Well-Defined Geometries.

PubMed

Jorgenson, Tyler D; Mohammed, Abdul M; Agrawal, Deepak K; Schulman, Rebecca

2017-02-28

An essential motif for the assembly of biological materials such as actin at the scale of hundreds of nanometers and beyond is a network of one-dimensional fibers with well-defined geometry. Here, we demonstrate the programmed organization of DNA filaments into micron-scale architectures where component filaments are oriented at preprogrammed angles. We assemble L-, T-, and Y-shaped DNA origami junctions that nucleate two or three micron length DNA nanotubes at high yields. The angles between the nanotubes mirror the angles between the templates on the junctions, demonstrating that nanoscale structures can control precisely how micron-scale architectures form. The ability to precisely program filament orientation could allow the assembly of complex filament architectures in two and three dimensions, including circuit structures, bundles, and extended materials.

Growth of pentacene on α -Al2O3 (0001) studied by in situ optical spectroscopy

NASA Astrophysics Data System (ADS)

Zhang, Lei; Fu, X.; Hohage, M.; Zeppenfeld, P.; Sun, L. D.

2017-09-01

The growth of pentacene thin films on a sapphire α -Al2O3 (0001) surface was investigated in situ using differential reflectance spectroscopy (DRS). Two different film structures are observed depending on the substrate temperature. If pentacene is deposited at room temperature, a wetting layer consisting of flat-lying molecules is formed after which upright-standing molecular layers with a herringbone structure start to grow. At low substrate temperature of 100 K, the long molecular axis of the pentacene molecules remains parallel to the surface plane throughout the entire growth regime up to rather large thicknesses. Heating thin films deposited at 100 K to room temperature causes the pentacene molecules beyond the wetting layer to stand up and assemble into a herringbone structure. Another interesting observation is the dewetting of the first flat-lying monolayer upon exposure to air, leading to the condensation of islands consisting of upright-standing molecules. Our results emphasize the interplay between growth kinetics and thermodynamics and its influence on the molecular orientation in organic thin films.

Cancer cell death induced by the intracellular self-assembly of an enzyme-responsive supramolecular gelator.

PubMed

Tanaka, Akiko; Fukuoka, Yuki; Morimoto, Yuka; Honjo, Takafumi; Koda, Daisuke; Goto, Masahiro; Maruyama, Tatsuo

2015-01-21

We report cancer cell death initiated by the intracellular molecular self-assembly of a peptide lipid, which was derived from a gelator precursor. The gelator precursor was designed to form nanofibers via molecular self-assembly, after cleavage by a cancer-related enzyme (matrix metalloproteinase-7, MMP-7), leading to hydrogelation. The gelator precursor exhibited remarkable cytotoxicity to five different cancer cell lines, while the precursor exhibited low cytotoxicity to normal cells. Cancer cells secrete excessive amounts of MMP-7, which converted the precursor into a supramolecular gelator prior to its uptake by the cells. Once inside the cells, the supramolecular gelator formed a gel via molecular self-assembly, exerting vital stress on the cancer cells. The present study thus describes a new drug where molecular self-assembly acts as the mechanism of cytotoxicity.

Molecular adsorption and multilayer growth of pentacene on Cu(100):Layer structure and energetics

NASA Astrophysics Data System (ADS)

Satta, M.; Iacobucci, S.; Larciprete, R.

2007-04-01

We used the partial charge tight binding method to perform a full structure optimization to determine equilibrium adsorption geometries, energetics, and local charge redistribution for molecular adsorption and multilayer growth of pentacene on Cu(100). We found that single molecule adsorption induces only a localized perturbation of the metal lattice which is limited to the topmost layers. At saturation coverage four stable topologies (Brick, Wave, Lines and Zigzag) were identified, all based on pentacene molecules lying flat on the metal surface and with the central phenyl ring adsorbed in top position. Only two (Brick and Wave) out of the four structures are able to sustain multilayer growth. In both cases, assembling beyond the second layer corresponds to a transition from the flat to a tilted geometry, in which the pentacenes adopt a face-plane-face arrangement leading to a herringbone structure. The energetics of the different structure are reported as a function of the molecular number density of the pentacene multilayer by calculating cohesive, stress, and electrostatic energies. The dominant tilted molecular orientation in the pentacene multilayer is in agreement with the average tilt angle of 65° between the molecular plane and the Cu surface derived by near edge x-ray absorption spectroscopy of a four monolayer pentacene film deposited on Cu(100).

A Novel Domain Assembly Routine for Creating Full-Length Models of Membrane Proteins from Known Domain Structures.

PubMed

Koehler Leman, Julia; Bonneau, Richard

2018-04-03

Membrane proteins composed of soluble and membrane domains are often studied one domain at a time. However, to understand the biological function of entire protein systems and their interactions with each other and drugs, knowledge of full-length structures or models is required. Although few computational methods exist that could potentially be used to model full-length constructs of membrane proteins, none of these methods are perfectly suited for the problem at hand. Existing methods require an interface or knowledge of the relative orientations of the domains or are not designed for domain assembly, and none of them are developed for membrane proteins. Here we describe the first domain assembly protocol specifically designed for membrane proteins that assembles intra- and extracellular soluble domains and the transmembrane domain into models of the full-length membrane protein. Our protocol does not require an interface between the domains and samples possible domain orientations based on backbone dihedrals in the flexible linker regions, created via fragment insertion, while keeping the transmembrane domain fixed in the membrane. For five examples tested, our method mp_domain_assembly, implemented in RosettaMP, samples domain orientations close to the known structure and is best used in conjunction with experimental data to reduce the conformational search space.

Choosing sides--asymmetric centriole and basal body assembly.

PubMed

Pearson, Chad G

2014-07-01

Centrioles and basal bodies (CBBs) are microtubule-rich cylindrical structures that nucleate and organize centrosomes and cilia, respectively. Despite their apparent ninefold rotational symmetry, the nine sets of triplet microtubules in CBBs possess asymmetries in their morphology and in the structures that associate with them. These asymmetries define the position of nascent CBB assembly, the orientation of ciliary beating, the orientation of spindle poles and the maintenance of cellular geometry. For some of these functions, the orientation of CBBs is first established during new CBB biogenesis when the daughter structure is positioned adjacent to the mother. The mother CBB organizes the surrounding environment that nascent CBBs are born into, thereby providing a nest for the new CBB to develop. Protists, including ciliates and algae, highlight the importance of this environment with the formation of asymmetrically placed scaffolds onto which new basal bodies assemble and are positioned. Recent studies illuminate the positioning of nascent centrioles relative to a modular pericentriolar material (PCM) environment and suggest that, like ciliates, centrosomes organize an immediate environment surrounding centrioles for their biogenesis and positioning. In this Commentary, I will explore the positioning of nascent CBB assembly as the first event in building cellular asymmetries and describe how the environment surrounding both basal bodies and centrioles may define asymmetric assembly. © 2014. Published by The Company of Biologists Ltd.

Choosing sides – asymmetric centriole and basal body assembly

PubMed Central

Pearson, Chad G.

2014-01-01

ABSTRACT Centrioles and basal bodies (CBBs) are microtubule-rich cylindrical structures that nucleate and organize centrosomes and cilia, respectively. Despite their apparent ninefold rotational symmetry, the nine sets of triplet microtubules in CBBs possess asymmetries in their morphology and in the structures that associate with them. These asymmetries define the position of nascent CBB assembly, the orientation of ciliary beating, the orientation of spindle poles and the maintenance of cellular geometry. For some of these functions, the orientation of CBBs is first established during new CBB biogenesis when the daughter structure is positioned adjacent to the mother. The mother CBB organizes the surrounding environment that nascent CBBs are born into, thereby providing a nest for the new CBB to develop. Protists, including ciliates and algae, highlight the importance of this environment with the formation of asymmetrically placed scaffolds onto which new basal bodies assemble and are positioned. Recent studies illuminate the positioning of nascent centrioles relative to a modular pericentriolar material (PCM) environment and suggest that, like ciliates, centrosomes organize an immediate environment surrounding centrioles for their biogenesis and positioning. In this Commentary, I will explore the positioning of nascent CBB assembly as the first event in building cellular asymmetries and describe how the environment surrounding both basal bodies and centrioles may define asymmetric assembly. PMID:24895399

Packed rod neutron shield for fast nuclear reactors

DOEpatents

Eck, John E.; Kasberg, Alvin H.

1978-01-01

A fast neutron nuclear reactor including a core and a plurality of vertically oriented neutron shield assemblies surrounding the core. Each assembly includes closely packed cylindrical rods within a polygonal metallic duct. The shield assemblies are less susceptible to thermal stresses and are less massive than solid shield assemblies, and are cooled by liquid coolant flow through interstices among the rods and duct.

Flow-oriented dynamic assembly algorithm in TCP over OBS networks

NASA Astrophysics Data System (ADS)

Peng, Shuping; Li, Zhengbin; He, Yongqi; Xu, Anshi

2008-11-01

OBS is envisioned as a promising infrastructure for the next generation optical network, and TCP is likely to be the dominant transport protocol in the next generation network. Therefore, it is necessary to evaluate the performance of TCP over OBS networks. The assembly at the ingress edge nodes will impact the network performance. There have been several Fixed Assembly Period (FAP) algorithms proposed. However, the assembly period in FAP is fixed, and it can not be adjusted according to the network condition. Moreover, in FAP, the packets from different TCP sources are assembled into one burst. In that case, if such a burst is dropped, the TCP windows of the corresponding sources will shrink and the throughput will be reduced. In this paper, we introduced a flow-oriented Dynamic Assembly Period (DAP) algorithm for TCP over OBS networks. Through comparing the previous and current burst lengths, DAP can track the variation of TCP window, and update the assembly period dynamically for the next assembly. The performance of DAP is evaluated over a single TCP connection and multiple connections, respectively. The simulation results show that DAP performs better than FAP at almost the whole range of burst dropping probability.

Preferred orientation of albumin adsorption on a hydrophilic surface from molecular simulation.

PubMed

Hsu, Hao-Jen; Sheu, Sheh-Yi; Tsay, Ruey-Yug

2008-12-01

In general, non-specific protein adsorption follows a two-step procedure, i.e. first adsorption onto a surface in native form, and a subsequent conformational change on the surface. In order to predict the subsequent conformational change, it is important to determine the preferred orientation of an adsorbed protein in the first step of the adsorption. In this work, a method based on finding the global minimum of the interaction potential energy of an adsorbed protein has been developed to delineate the preferred orientations for the adsorption of human serum albumin (HSA) on a model surface with a hydrophilic self-assembled monolayer (SAM). For computational efficiency, solvation effects were greatly simplified by only including the dampening of electrostatic effects while neglecting contributions due to the competition of water molecules for the functional groups on the surface. A contour map obtained by systematic rotation of a molecule in conjunction with perpendicular motion to the surface gives the minimum interaction energy of the adsorbed molecule at various adsorption orientations. Simulation results show that for an -OH terminated SAM surface, a "back-on" orientation of HSA is the preferred orientation. The projection area of this adsorption orientation corresponds with the "triangular-side-on" adsorption of a heart shaped HSA molecule. The method proposed herein is able to provide results which are consistent with those predicted by Monte Carlo (MC) simulations with a substantially less computing cost. The high computing efficiency of the current method makes it possible to be implemented as a design tool for the control of protein adsorption on surfaces; however, before this can be fully realized, these methods must be further developed to enable interaction free energy to be calculated in place of potential energy, along with a more realistic representation of solvation effects.

Tailored Surfaces/Assemblies for Molecular Plasmonics and Plasmonic Molecular Electronics.

PubMed

Lacroix, Jean-Christophe; Martin, Pascal; Lacaze, Pierre-Camille

2017-06-12

Molecular plasmonics uses and explores molecule-plasmon interactions on metal nanostructures for spectroscopic, nanophotonic, and nanoelectronic devices. This review focuses on tailored surfaces/assemblies for molecular plasmonics and describes active molecular plasmonic devices in which functional molecules and polymers change their structural, electrical, and/or optical properties in response to external stimuli and that can dynamically tune the plasmonic properties. We also explore an emerging research field combining molecular plasmonics and molecular electronics.

The A, C, G, and T of Genome Assembly.

PubMed

Wajid, Bilal; Sohail, Muhammad U; Ekti, Ali R; Serpedin, Erchin

2016-01-01

Genome assembly in its two decades of history has produced significant research, in terms of both biotechnology and computational biology. This contribution delineates sequencing platforms and their characteristics, examines key steps involved in filtering and processing raw data, explains assembly frameworks, and discusses quality statistics for the assessment of the assembled sequence. Furthermore, the paper explores recent Ubuntu-based software environments oriented towards genome assembly as well as some avenues for future research.

Development of self-assembled molecular structures on polymeric surfaces and their applications as ultrasonically responsive barrier coatings for on-demand, pulsatile drug delivery

NASA Astrophysics Data System (ADS)

Kwok, Connie Sau-Kuen

Nature in the form of DNA, proteins, and cells has the remarkable ability to interact with its environment by processing biological information through specific molecular recognition at the interface. As such, materials that are capable of triggering an appropriate biological response need to be engineered at the biomaterial surface. Chemically and structurally well-defined self-assembled monolayers (SAMs), biomimetics of the lipid bilayer in cell membranes, have been created and studied mostly on rigid metallic surfaces. This dissertation is motivated by the lack of methods to generate a molecularly designed surface for biomedical polymers and thus provides an enabling technology to engineer a polymeric surface precisely at a molecular and cellular level. To take this innovation one step further, we demonstrated that such self-assembled molecular structure coated on drug-containing polymeric devices could act as a stimulus-responsive barrier for controlled drug delivery. A simple, one-step procedure for generating ordered, crystalline methylene chains on polymeric surfaces via urethane linkages was successfully developed. The self-assemblies and molecular structures of these crystalline methylene chains are comparable to the SAM model surfaces, as evidenced by various surface characterization techniques (XPS, TOF-SIMS, and FTIR-ATR). For the first time, these self-assembled molecular structures are shown to function collectively as an ultrasound-responsive barrier membrane for pulsatile drug delivery, including delivery of low-molecular-weight ciprofloxacin and high-molecular-weight insulin. Encouraging results, based on the insulin-activated deoxyglucose uptakes in adipocytes, indicate that the released insulin remained biologically active. Both chemical and acoustic analyses suggest that the ultrasound-assisted release mechanism is primarily induced by transient cavitation, which causes temporary disruption of the self-assembled overlayer, and thus allows temporal release of the encapsulated drugs. In addition to acoustic energy, self-assembled surfaces experience order-disorder transition and have a transition temperature higher than body temperature if longer alkyl chains (C18) are used. The C18-assembled surface barrier membrane exhibits a relatively superior impermeable coating than the shorter C12 chains. The versatility of derivatizing the terminal groups of the self-assembled molecular structures is illustrated by attaching poly (ethyleneoxide) oligomers to the alkyl chains to minimize nonspecific protein adsorption. This study lays an important foundation for future work in conjugating other biomolecules to develop surface-based diagnostics and biomaterials. With much success, this original research work of forming self-assembled crystalline structures on synthetic materials still allows for numerous opportunities for new applications and possibly even more new discoveries.

Guided molecular self-assembly: a review of recent efforts

NASA Astrophysics Data System (ADS)

Huie, Jiyun C.

2003-04-01

This paper serves as an introductory review of significant and novel successes achieved in the fields of nanotechnology, particularly in the formation of nanostructures using guided molecular self-assembly methods. Self-assembly is a spontaneous process by which molecules and nanophase entities may materialize into organized aggregates or networks. Through various interactive mechanisms of self-assembly, such as electrostatics, chemistry, surface properties, and via other mediating agents, the technique proves indispensable to recent functional materials and device realizations. The discussion will extend to spontaneous and Langmuir-Blodgett formation of self-assembled monolayers on various substrates, and a number of different categories of self-assembly techniques based on the type of interaction exploited. Combinatorial techniques, known as soft lithography, of micro-contact printing and dip-pen nanolithography, which can be effectively used to up-size nanostructured molecular assemblies to submicrometer and micrometer scale patterns, will also be mentioned.

Interactive Computerized Video Orientation.

ERIC Educational Resources Information Center

Briesacker, Jeanie

In response to California State Assembly Bill (AB) 3, which requires the state's community colleges to implement orientations and other specified matriculation services, Fullerton College (FC) developed two orientation videos in 1989 for native speakers of English and English-as-a-Second Language (ESL) students. The videos were used by counselors…

Functional Nanostructured Materials Based on Polymerized Surfactant Liquid Crystal Assemblies Liquid Crystal Assemblies

NASA Astrophysics Data System (ADS)

Gin, Douglas

2003-03-01

The development of materials with controlled nanostructures is one of the most important new areas of scientific research in chemistry and engineering. Our research group has developed a novel approach for making nanostructured polymer materials with unique functional properties using liquid crystals as starting materials. In this approach, we design polymerizable organic building blocks based on lyotropic liquid crystals (LLCs) (i.e., amphiphiles or surfactants) that carry, or can accommodate, a functional property of general interest. Through appropriate molecular design, these monomers self-assemble in the presence of water into fluid, yet ordered phase-separated, water-hydrocarbon assemblies with predictable nanoscale geometries. The architectures of these LLC phases can range from stacked two-dimensional lamellae to hexagonally ordered cylindrical channels with uniform feature sizes in the 1-10 nm range. These LLC phases are then photopolymerized into robust polymer networks with preservation of their small-scale structures. This approach allows us to investigate the effect of nanometer-scale architecture on important bulk properties, as well as to engineer chemical environments on the nanometer-scale for several areas of application. In this talk, new functional materials based on the polymerization of the lyotropic inverted hexagonal phase will be presented as one example of our general approach. Issues in the design and photopolymerization of functional amphiphilic monomers that adopt this LC architecture will be discussed. More importantly, the use of the resulting nanostructured polymer networks in three areas of application will be presented: (1) as templates for the synthesis of functional nanocomposites; (2) as tunable heterogeneous catalysts, and (3) as nanoporous membrane and separation media. In particular, issues pertaining to the contribution of nanoscale architecture to the performance of these systems will be highlighted. Opportunities for tailoring the nanoscale chemical environment and architecture of these materials through molecular design will be presented. Finally, the development of methods for controlling macroscopic orientation through processing will also be discussed.

Quantitative computational models of molecular self-assembly in systems biology

PubMed Central

Thomas, Marcus; Schwartz, Russell

2017-01-01

Molecular self-assembly is the dominant form of chemical reaction in living systems, yet efforts at systems biology modeling are only beginning to appreciate the need for and challenges to accurate quantitative modeling of self-assembly. Self-assembly reactions are essential to nearly every important process in cell and molecular biology and handling them is thus a necessary step in building comprehensive models of complex cellular systems. They present exceptional challenges, however, to standard methods for simulating complex systems. While the general systems biology world is just beginning to deal with these challenges, there is an extensive literature dealing with them for more specialized self-assembly modeling. This review will examine the challenges of self-assembly modeling, nascent efforts to deal with these challenges in the systems modeling community, and some of the solutions offered in prior work on self-assembly specifically. The review concludes with some consideration of the likely role of self-assembly in the future of complex biological system models more generally. PMID:28535149

Quantitative computational models of molecular self-assembly in systems biology.

PubMed

Thomas, Marcus; Schwartz, Russell

2017-05-23

Molecular self-assembly is the dominant form of chemical reaction in living systems, yet efforts at systems biology modeling are only beginning to appreciate the need for and challenges to accurate quantitative modeling of self-assembly. Self-assembly reactions are essential to nearly every important process in cell and molecular biology and handling them is thus a necessary step in building comprehensive models of complex cellular systems. They present exceptional challenges, however, to standard methods for simulating complex systems. While the general systems biology world is just beginning to deal with these challenges, there is an extensive literature dealing with them for more specialized self-assembly modeling. This review will examine the challenges of self-assembly modeling, nascent efforts to deal with these challenges in the systems modeling community, and some of the solutions offered in prior work on self-assembly specifically. The review concludes with some consideration of the likely role of self-assembly in the future of complex biological system models more generally.

Self-Assembly and Crystallization of Hairy (f-Star) and DNA-Grafted Nanocubes

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

Knorowski, Christopher; Travesset, Alex

Nanoparticle superlattices are key to realizing many of the materials that will solve current technological challenges. Particularly important for their optical, mechanical or catalytic properties are superlattices of anisotropic (nonspherical) nanoparticles. The key challenge is how to program anisotropic nanoparticles to self-assemble into the relevant structures. In this Article, using numerical simulations, we show that “hairy” (f-star) or DNA grafted on nanocubes provides a general framework to direct the self-assembly into phases with crystalline, liquid crystalline, rotator, or noncrystalline phases with both long-range positional and orientational order. We discuss the relevance of these phases for engineering nanomaterials or micromaterials displayingmore » precise orientational order, realization of dry superlattices as well as for the field of programmed self-assembly of anisotropic nanoparticles in general.« less

Curcumin Binding to Beta Amyloid: A Computational Study.

PubMed

Rao, Praveen P N; Mohamed, Tarek; Teckwani, Karan; Tin, Gary

2015-10-01

Curcumin, a chemical constituent present in the spice turmeric, is known to prevent the aggregation of amyloid peptide implicated in the pathophysiology of Alzheimer's disease. While curcumin is known to bind directly to various amyloid aggregates, no systematic investigations have been carried out to understand its ability to bind to the amyloid aggregates including oligomers and fibrils. In this study, we constructed computational models of (i) Aβ hexapeptide (16) KLVFFA(21) octamer steric-zipper β-sheet assembly and (ii) full-length Aβ fibril β-sheet assembly. Curcumin binding in these models was evaluated by molecular docking and molecular dynamics (MD) simulation studies. In both the models, curcumin was oriented in a linear extended conformation parallel to fiber axis and exhibited better stability in the Aβ hexapeptide (16) KLVFFA(21) octamer steric-zipper model (Ebinding  = -10.05 kcal/mol) compared to full-length Aβ fibril model (Ebinding  = -3.47 kcal/mol). Analysis of MD trajectories of curcumin bound to full-length Aβ fibril shows good stability with minimum Cα-atom RMSD shifts. Interestingly, curcumin binding led to marked fluctuations in the (14) HQKLVFFA(21) region that constitute the fibril spine with RMSF values ranging from 1.4 to 3.6 Å. These results show that curcumin binding to Aβ shifts the equilibrium in the aggregation pathway by promoting the formation of non-toxic aggregates. © 2015 John Wiley & Sons A/S.

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

Li, Hongfei; Yang, Zhenhua; Pan, Cheng

Here, we report that the addition of a non-photoactive tertiary polymer phase in the binary bulk heterojunction (BHJ) polymer solar cell leads to a self-assembled columnar nanostructure, enhancing the charge mobilities and photovoltaic efficiency with surprisingly increased optimal active blend thicknesses over 300 nm, 3–4 times larger than that of the binary counterpart. Using the prototypical poly(3-hexylthiophene) (P3HT):fullerene blend as a model BHJ system, we discover that the inert poly(methyl methacrylate) (PMMA) added in the binary BHJ blend self-assembles into vertical columns, which not only template the phase segregation of electron acceptor fullerenes but also induce the out-of-plane rotation ofmore » the edge-on-orientated crystalline P3HT phase. Using complementary interrogation methods including neutron reflectivity, X-ray scattering, atomic force microscopy, transmission electron microscopy, and molecular dynamics simulations, we show that the enhanced charge transport originates from the more randomized molecular stacking of the P3HT phase and the spontaneous segregation of fullerenes at the P3HT/PMMA interface, driven by the high surface tension between the two polymeric components. The results demonstrate a potential method for increasing the thicknesses of high-performance polymer BHJ solar cells with improved photovoltaic efficiency, alleviating the burden of stringently controlling the ultrathin blend thickness during the roll-to-roll-type large-area manufacturing environment.« less

Understanding nucleotide-regulated FtsZ filament dynamics and the monomer assembly switch with large-scale atomistic simulations.

PubMed

Ramírez-Aportela, Erney; López-Blanco, José Ramón; Andreu, José Manuel; Chacón, Pablo

2014-11-04

Bacterial cytoskeletal protein FtsZ assembles in a head-to-tail manner, forming dynamic filaments that are essential for cell division. Here, we study their dynamics using unbiased atomistic molecular simulations from representative filament crystal structures. In agreement with experimental data, we find different filament curvatures that are supported by a nucleotide-regulated hinge motion between consecutive FtsZ monomers. Whereas GTP-FtsZ filaments bend and twist in a preferred orientation, thereby burying the nucleotide, the differently curved GDP-FtsZ filaments exhibit a heterogeneous distribution of open and closed interfaces between monomers. We identify a coordinated Mg(2+) ion as the key structural element in closing the nucleotide site and stabilizing GTP filaments, whereas the loss of the contacts with loop T7 from the next monomer in GDP filaments leads to open interfaces that are more prone to depolymerization. We monitored the FtsZ monomer assembly switch, which involves opening/closing of the cleft between the C-terminal domain and the H7 helix, and observed the relaxation of isolated and filament minus-end monomers into the closed-cleft inactive conformation. This result validates the proposed switch between the low-affinity monomeric closed-cleft conformation and the active open-cleft FtsZ conformation within filaments. Finally, we observed how the antibiotic PC190723 suppresses the disassembly switch and allosterically induces closure of the intermonomer interfaces, thus stabilizing the filament. Our studies provide detailed structural and dynamic insights into modulation of both the intrinsic curvature of the FtsZ filaments and the molecular switch coupled to the high-affinity end-wise association of FtsZ monomers.

Self-Assembled Polystyrene Beads for Templated Covalent Functionalization of Graphitic Substrates Using Diazonium Chemistry.

PubMed

Van Gorp, Hans; Walke, Peter; Bragança, Ana M; Greenwood, John; Ivasenko, Oleksandr; Hirsch, Brandon E; De Feyter, Steven

2018-04-11

A network of self-assembled polystyrene beads was employed as a lithographic mask during covalent functionalization reactions on graphitic surfaces to create nanocorrals for confined molecular self-assembly studies. The beads were initially assembled into hexagonal arrays at the air-liquid interface and then transferred to the substrate surface. Subsequent electrochemical grafting reactions involving aryl diazonium molecules created covalently bound molecular units that were localized in the void space between the nanospheres. Removal of the bead template exposed hexagonally arranged circular nanocorrals separated by regions of chemisorbed molecules. Small molecule self-assembly was then investigated inside the resultant nanocorrals using scanning tunneling microscopy to highlight localized confinement effects. Overall, this work illustrates the utility of self-assembly principles to transcend length scale gaps in the development of hierarchically patterned molecular materials.

Multi-Scale Responses of Liquid Crystals Triggered by Interfacial Assemblies of Cleavable Homopolymers.

PubMed

Kim, Young-Ki; Huang, Yuran; Tsuei, Michael; Wang, Xin; Gianneschi, Nathan C; Abbott, Nicholas L

2018-04-22

Liquid crystals (LCs) offer the basis of stimuli-responsive materials that can amplify targeted molecular events into macroscopic outputs. However, general and versatile design principles are needed to realize the full potential of these materials. To this end, we report the synthesis of two homopolymers with mesogenic side chains that can be cleaved upon exposure to either H 2 O 2 (polymer P1) or UV light (polymer P2). Optical measurements reveal that the polymers dissolve in bulk LC and spontaneously assemble at nematic LC-aqueous interfaces to impose a perpendicular orientation on the LCs. Subsequent addition of H 2 O 2 to the aqueous phase or exposure of the LC to UV was shown to trigger a surface-driven ordering transition to a planar orientation and an accompanying macroscopic optical output. Differences in the dynamics of the response to each stimulus are consistent with sequential processing of P1 at the LC-aqueous interface (H 2 O 2 ) and simultaneous transformation of P2 within the LC (UV). The versatility of the approach is demonstrated by creating stimuli-responsive LCs as films or microdroplets, and by dissolving mixtures of P1 and P2 into LCs to create LC materials that respond to two stimuli. Overall, our results validate a simple and generalizable approach to the rational design of polymers that can be used to program stimuli-responsiveness into LC materials. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Biocompatible Materials Based on Self-Assembling Peptides on Ti25Nb10Zr Alloy: Molecular Structure and Organization Investigated by Synchrotron Radiation Induced Techniques

PubMed Central

Franchi, Stefano; Braic, Mariana; Skála, Tomáš; Nováková, Jaroslava; Zamuner, Annj

2018-01-01

In this work, we applied advanced Synchrotron Radiation (SR) induced techniques to the study of the chemisorption of the Self Assembling Peptide EAbuK16, i.e., H-Abu-Glu-Abu-Glu-Abu-Lys-Abu-Lys-Abu-Glu-Abu-Glu-Abu-Lys-Abu-Lys-NH2 that is able to spontaneously aggregate in anti-parallel β-sheet conformation, onto annealed Ti25Nb10Zr alloy surfaces. This synthetic amphiphilic oligopeptide is a good candidate to mimic extracellular matrix for bone prosthesis, since its β-sheets stack onto each other in a multilayer oriented nanostructure with internal pores of 5–200 nm size. To prepare the biomimetic material, Ti25Nb10Zr discs were treated with aqueous solutions of EAbuK16 at different pH values. Here we present the results achieved by performing SR-induced X-ray Photoelectron Spectroscopy (SR-XPS), angle-dependent Near Edge X-ray Absorption Fine Structure (NEXAFS) spectroscopy, FESEM and AFM imaging on Ti25Nb10Zr discs after incubation with self-assembling peptide solution at five different pH values, selected deliberately to investigate the best conditions for peptide immobilization. PMID:29518968

Control of hydroxyapatite coating by self-assembled monolayers on titanium and improvement of osteoblast adhesion.

PubMed

Shen, Juan; Qi, Yongcheng; Jin, Bo; Wang, Xiaoyan; Hu, Yamin; Jiang, Qiying

2017-01-01

Self-assembly technique was applied to introduce functional groups and form hydroxyl-, amine-, and carboxyl-terminal self-assembled monolayers (SAMs). The SAMs were grafted onto titanium substrates to obtain a molecularly smooth functional surface. Subsequent hydrothermal crystal growth formed homogeneous and crack-free crystalline hydroxyapatite (HA) coatings on these substrates. AFM and XPS were used to characterize the SAM surfaces, and XRD, SEM, and TEM were used to characterize the HA coatings. Results show that highly crystalline, dense, and oriented HA coatings can be formed on the OH-, NH 2 -, and COOH-SAM surfaces. The SAM surface with -COOH exhibited stronger nucleating ability than that with -OH and -NH 2 . The nucleation and growth processes of HA coatings were effectively controlled by varying reaction time, pH, and temperature. By using this method, highly crystalline, dense, and adherent HA coatings were obtained. In addition, in vitro cell evaluation demonstrated that HA coatings improved cell adhesion as compared with pristine titanium substrate. The proposed method is considerably effective in introducing the HA coatings on titanium surfaces for various biomedical applications and further usage in other industries. © 2015 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 105B: 124-135, 2017. © 2015 Wiley Periodicals, Inc.

New self-assembly strategies for next generation lithography

NASA Astrophysics Data System (ADS)

Schwartz, Evan L.; Bosworth, Joan K.; Paik, Marvin Y.; Ober, Christopher K.

2010-04-01

Future demands of the semiconductor industry call for robust patterning strategies for critical dimensions below twenty nanometers. The self assembly of block copolymers stands out as a promising, potentially lower cost alternative to other technologies such as e-beam or nanoimprint lithography. One approach is to use block copolymers that can be lithographically patterned by incorporating a negative-tone photoresist as the majority (matrix) phase of the block copolymer, paired with photoacid generator and a crosslinker moiety. In this system, poly(α-methylstyrene-block-hydroxystyrene)(PαMS-b-PHOST), the block copolymer is spin-coated as a thin film, processed to a desired microdomain orientation with long-range order, and then photopatterned. Therefore, selfassembly of the block copolymer only occurs in select areas due to the crosslinking of the matrix phase, and the minority phase polymer can be removed to produce a nanoporous template. Using bulk TEM analysis, we demonstrate how the critical dimension of this block copolymer is shown to scale with polymer molecular weight using a simple power law relation. Enthalpic interactions such as hydrogen bonding are used to blend inorganic additives in order to enhance the etch resistance of the PHOST block. We demonstrate how lithographically patternable block copolymers might fit in to future processing strategies to produce etch-resistant self-assembled features at length scales impossible with conventional lithography.

The A, C, G, and T of Genome Assembly

PubMed Central

Wajid, Bilal; Sohail, Muhammad U.; Ekti, Ali R.; Serpedin, Erchin

2016-01-01

Genome assembly in its two decades of history has produced significant research, in terms of both biotechnology and computational biology. This contribution delineates sequencing platforms and their characteristics, examines key steps involved in filtering and processing raw data, explains assembly frameworks, and discusses quality statistics for the assessment of the assembled sequence. Furthermore, the paper explores recent Ubuntu-based software environments oriented towards genome assembly as well as some avenues for future research. PMID:27247941

Shingle assembly

DOEpatents

Dinwoodie, Thomas L.

2007-02-20

A barrier, such as a PV module, is secured to a base by a support to create a shingle assembly with a venting region defined between the barrier and base for temperature regulation. The first edge of one base may be interengageable with the second edge of an adjacent base to be capable of resisting first and second disengaging forces oriented perpendicular to the edges and along planes oriented parallel to and perpendicular to the base. A deflector may be used to help reduce wind uplift forces.

Optoelectronic functional materials based on alkylated-π molecules: self-assembled architectures and nonassembled liquids.

PubMed

Li, Hongguang; Choi, Jiyoung; Nakanishi, Takashi

2013-05-07

The engineering of single molecules into higher-order hierarchical assemblies is a current research focus in molecular materials chemistry. Molecules containing π-conjugated units are an important class of building blocks because their self-assembly is not only of fundamental interest, but also the key to fabricating functional systems for organic electronic and photovoltaic applications. Functionalizing the π-cores with "alkyl chains" is a common strategy in the molecular design that can give the system desirable properties, such as good solubility in organic solvents for solution processing. Moreover, the alkylated-π system can regulate the self-assembly behavior by fine-tuning the intermolecular forces. The optimally assembled structures can then exhibit advanced functions. However, while some general rules have been revealed, a comprehensive understanding of the function played by the attached alkyl chains is still lacking, and current methodology is system-specific in many cases. Better clarification of this issue requires contributions from carefully designed libraries of alkylated-π molecular systems in both self-assembly and nonassembly materialization strategies. Here, based on recent efforts toward this goal, we show the power of the alkyl chains in controlling the self-assembly of soft molecular materials and their resulting optoelectronic properties. The design of alkylated-C60 is selected from our recent research achievements, as the most attractive example of such alkylated-π systems. Some other closely related systems composed of alkyl chains and π-units are also reviewed to indicate the universality of the methodology. Finally, as a contrast to the self-assembled molecular materials, nonassembled, solvent-free, novel functional liquid materials are discussed. In doing so, a new journey toward the ultimate organic "soft" materials is introduced, based on alkylated-π molecular design.

Molecular switches and motors on surfaces.

PubMed

Pathem, Bala Krishna; Claridge, Shelley A; Zheng, Yue Bing; Weiss, Paul S

2013-01-01

Molecular switches and motors respond structurally, electronically, optically, and/or mechanically to external stimuli, testing and potentially enabling extreme miniaturization of optoelectronic devices, nanoelectromechanical systems, and medical devices. The assembly of motors and switches on surfaces makes it possible both to measure the properties of individual molecules as they relate to their environment and to couple function between assembled molecules. In this review, we discuss recent progress in assembling molecular switches and motors on surfaces, measuring static and dynamic structures, understanding switching mechanisms, and constructing functional molecular materials and devices. As demonstrative examples, we choose a representative molecule from three commonly studied classes including molecular switches, photochromic molecules, and mechanically interlocked molecules. We conclude by offering perspectives on the future of molecular switches and motors on surfaces.

Constructing a molecular theory of self-assembly: Interplay of ideas from surfactants and block copolymers.

PubMed

Nagarajan, Ramanathan

2017-06-01

Low molecular weight surfactants and high molecular weight block copolymers display analogous self-assembly behavior in solutions and at interfaces, generating nanoscale structures of different shapes. Understanding the link between the molecular structure of these amphiphiles and their self-assembly behavior has been the goal of theoretical studies. Despite the analogies between surfactants and block copolymers, models predicting their self-assembly behavior have evolved independent of one another, each overlooking the molecular feature considered critical to the other. In this review, we focus on the interplay of ideas pertaining to surfactants and block copolymers in three areas of self-assembly. First, we show how improved free energy models have evolved by applying ideas from surfactants to block copolymers and vice versa, giving rise to a unitary theoretical framework and better predictive capabilities for both classes of amphiphiles. Second we show that even though molecular packing arguments are often used to explain aggregate shape transitions resulting from self-assembly, the molecular packing considerations are more relevant in the case of surfactants whereas free energy criteria are relevant for block copolymers. Third, we show that even though the surfactant and block copolymer aggregates are small nanostructures, the size differences between them is significant enough to make the interfacial effects control the solubilization of molecules in surfactant micelles while the bulk interactions control the solubilization in block copolymer micelles. Finally, we conclude by identifying recent theoretical progress in adapting the micelle model to a wide variety of self-assembly phenomena and the challenges to modeling posed by emerging novel classes of amphiphiles with complex biological, inorganic or nanoparticle moieties. Published by Elsevier B.V.

Polymeric amphiphile branching leads to rare nanodisc shaped planar self-assemblies.

PubMed

Qu, Xiaozhong; Omar, Leila; Le, Thi Bich Hang; Tetley, Laurence; Bolton, Katherine; Chooi, Kar Wai; Wang, Wei; Uchegbu, Ijeoma F

2008-09-16

Self-assembly is fundamental to the biological function of cells and the fabrication of nanomaterials. However, the origin of the shape of various self-assemblies, such as the shape of cells, is not altogether clear. Polymeric, oligomeric, or low molecular weight amphiphiles are a rich source of nanomaterials, and controlling their self-assembly is the route to tailored nanosystems with specific functionalities. Here, we provide direct evidence that a particular molecular architecture, polymeric branching, leads to a rare form of self-assembly, the planar nanodisc. Cholesterol containing self-assemblies formed from amphiphilic linear or branched cetyl poly(ethylenimine) (Mn approximately 1000 Da) or amphiphilic cetyl poly(propylenimine) dendrimer derivatives (Mn approximately 2000 Da) show that branching, by reducing the hydrophilic headgroup area, alters the shape of the self-assemblies transforming closed 60 nm spherical bilayer vesicles to rare 50 nm x 10 nm planar bilayer discs. Increasing the hydrophilic headgroup area, by the inclusion of methoxy poly(ethylene glycol) moieties into the amphiphilic headgroup, transforms the planar discs to 100 nm spherical bilayer vesicles. This study provides insight into the key role played by molecular shape on molecular self-organization into rare nanodiscs.

Oriented molecular sieve membranes by heteroepitaxial growth.

PubMed

Jeong, Hae-Kwon; Krohn, John; Sujaoti, Khristina; Tsapatsis, Michael

2002-11-06

Heteroepitaxial growth of titanosilicates (ETS-10 and ETS-4) is reported. Using this heteroepitaxial growth, oriented ETS-10/-4 membranes have been fabricated, demonstrating a novel way to achieve preferred orientation of molecular sieve films.

Rigorous theory of molecular orientational nonlinear optics

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

Kwak, Chong Hoon, E-mail: chkwak@ynu.ac.kr; Kim, Gun Yeup

2015-01-15

Classical statistical mechanics of the molecular optics theory proposed by Buckingham [A. D. Buckingham and J. A. Pople, Proc. Phys. Soc. A 68, 905 (1955)] has been extended to describe the field induced molecular orientational polarization effects on nonlinear optics. In this paper, we present the generalized molecular orientational nonlinear optical processes (MONLO) through the calculation of the classical orientational averaging using the Boltzmann type time-averaged orientational interaction energy in the randomly oriented molecular system under the influence of applied electric fields. The focal points of the calculation are (1) the derivation of rigorous tensorial components of the effective molecularmore » hyperpolarizabilities, (2) the molecular orientational polarizations and the electronic polarizations including the well-known third-order dc polarization, dc electric field induced Kerr effect (dc Kerr effect), optical Kerr effect (OKE), dc electric field induced second harmonic generation (EFISH), degenerate four wave mixing (DFWM) and third harmonic generation (THG). We also present some of the new predictive MONLO processes. For second-order MONLO, second-order optical rectification (SOR), Pockels effect and difference frequency generation (DFG) are described in terms of the anisotropic coefficients of first hyperpolarizability. And, for third-order MONLO, third-order optical rectification (TOR), dc electric field induced difference frequency generation (EFIDFG) and pump-probe transmission are presented.« less

Talin determines the nanoscale architecture of focal adhesions.

PubMed

Liu, Jaron; Wang, Yilin; Goh, Wah Ing; Goh, Honzhen; Baird, Michelle A; Ruehland, Svenja; Teo, Shijia; Bate, Neil; Critchley, David R; Davidson, Michael W; Kanchanawong, Pakorn

2015-09-01

Insight into how molecular machines perform their biological functions depends on knowledge of the spatial organization of the components, their connectivity, geometry, and organizational hierarchy. However, these parameters are difficult to determine in multicomponent assemblies such as integrin-based focal adhesions (FAs). We have previously applied 3D superresolution fluorescence microscopy to probe the spatial organization of major FA components, observing a nanoscale stratification of proteins between integrins and the actin cytoskeleton. Here we combine superresolution imaging techniques with a protein engineering approach to investigate how such nanoscale architecture arises. We demonstrate that talin plays a key structural role in regulating the nanoscale architecture of FAs, akin to a molecular ruler. Talin diagonally spans the FA core, with its N terminus at the membrane and C terminus demarcating the FA/stress fiber interface. In contrast, vinculin is found to be dispensable for specification of FA nanoscale architecture. Recombinant analogs of talin with modified lengths recapitulated its polarized orientation but altered the FA/stress fiber interface in a linear manner, consistent with its modular structure, and implicating the integrin-talin-actin complex as the primary mechanical linkage in FAs. Talin was found to be ∼97 nm in length and oriented at ∼15° relative to the plasma membrane. Our results identify talin as the primary determinant of FA nanoscale organization and suggest how multiple cellular forces may be integrated at adhesion sites.

Intermolecular and interfacial forces: Elucidating molecular mechanisms using chemical force microscopy

NASA Astrophysics Data System (ADS)

Ashby, Paul David

Investigation into the origin of forces dates to the early Greeks. Yet, only in recent decades have techniques for elucidating the molecular origin of forces been developed. Specifically, Chemical Force Microscopy uses the high precision and nanometer scale probe of Atomic Force Microscopy to measure molecular and interfacial interactions. This thesis presents the development of many novel Chemical Force Microscopy techniques for measuring equilibrium and time-dependant force profiles of molecular interactions, which led to a greater understanding of the origin of interfacial forces in solution. In chapter 2, Magnetic Feedback Chemical Force Microscopy stiffens the cantilever for measuring force profiles between self-assembled monolayer (SAM) surfaces. Hydroxyl and carboxyl terminated SAMs produce long-range interactions that extend one or three nanometers into the solvent, respectively. In chapter 3, an ultra low noise AFM is produced through multiple modifications to the optical deflection detection system and signal processing electronics. In chapter 4, Brownian Force Profile Reconstruction is developed for accurate measurement of steep attractive interactions. Molecular ordering is observed for OMCTS, 1-nonanol, and water near flat surfaces. The molecular ordering of the solvent produces structural or solvation forces, providing insight into the orientation and possible solidification of the confined solvent. Seven molecular layers of OMCTS are observed but the oil remains fluid to the last layer. 1-nonanol strongly orders near the surface and becomes quasi-crystalline with four layers. Water is oriented by the surface and symmetry requires two layers of water (3.7 A) to be removed simultaneously. In chapter 5, electronic control of the cantilever Q (Q-control) is used to obtain the highest imaging sensitivity. In chapter 6, Energy Dissipation Chemical Force Microscopy is developed to investigate the time dependence and dissipative characteristics of SAM interfacial interactions in solution. Long-range adhesive forces for hydroxyl and carboxyl terminated SAM surfaces arise from solvent, not ionic, interactions. Exclusion of the solvent and contact between the SAM surfaces leads to rearrangement of the SAM headgroups. The isolation of the chemical and physical interfacial properties from the topography by Energy Dissipation Chemical Force Microscopy produces a new quantitative high-sensitivity imaging mode.

Water penetration/accommodation and phase behaviour of the neutral Langmuir monolayer at the air/water interface probed with sum frequency generation vibrational spectroscopy (SFG-VS).

PubMed

Zhang, Zhen; Zheng, De-Sheng; Guo, Yuan; Wang, Hong-Fei

2009-02-14

A strong and broad hydrogen bonded O-H band around 3520 cm(-1) is observed in the insoluble monolayer of the neutral liquid crystal molecules of 4''-n-pentyl-4-p-cyanobiphenyl (5CB) and 4''-n-octyl-4-p-cyanobiphenyl (8CB) throughout the whole surface density range, but not in the 4-pentyl-4'-cyanoterphenyl (5CT) monolayer, at the air/water interface. This novel spectral feature suggests the existence of an oriented water cluster species which has penetrated or accommodated into the Langmuir monolayer of the 8CB and 5CB molecules. This finding provided a molecular level mechanism for the stark difference in the phase behaviour between the CB and CT insoluble Langmuir monolayers at the air/water interface. It also calls for attention to the details of the specific water-surface interaction in mediating the structure and the phase behaviour of the molecular assemblies at the heterogeneous aqueous interfaces.

Freely suspended nanocomposite membranes as highly sensitive sensors

NASA Astrophysics Data System (ADS)

Jiang, Chaoyang; Markutsya, Sergiy; Pikus, Yuri; Tsukruk, Vladimir V.

2004-10-01

Highly sensitive sensor arrays are in high demand for prospective applications in remote sensing and imaging. Measuring microscopic deflections of compliant micromembranes and cantilevers is developing into one of the most versatile approaches for thermal, acoustic and chemical sensing. Here, we report on an innovative fabrication of compliant nanocomposite membranes with nanoscale thickness showing extraordinary sensitivity and dynamic range, which makes them candidates for a new generation of membrane-based sensor arrays. These nanomembranes with a thickness of 25-70 nm, which can be freely suspended over large (hundred micrometres) openings are fabricated with molecular precision by time-efficient, spin-assisted layer-by-layer assembly. They are designed as multilayered molecular composites made of a combination of polymeric monolayers and a metal nanoparticle intralayer. We demonstrate that these nanocomposite membranes possess unparalleled sensitivity and a unique autorecovering ability. The membrane nanostructure that is responsible for these outstanding properties combines multilayered polymer/nanoparticle organization, high polymer-chain orientation, and a pre-stretched state.

Surface force measurements and simulations of mussel-derived peptide adhesives on wet organic surfaces.

PubMed

Levine, Zachary A; Rapp, Michael V; Wei, Wei; Mullen, Ryan Gotchy; Wu, Chun; Zerze, Gül H; Mittal, Jeetain; Waite, J Herbert; Israelachvili, Jacob N; Shea, Joan-Emma

2016-04-19

Translating sticky biological molecules-such as mussel foot proteins (MFPs)-into synthetic, cost-effective underwater adhesives with adjustable nano- and macroscale characteristics requires an intimate understanding of the glue's molecular interactions. To help facilitate the next generation of aqueous adhesives, we performed a combination of surface forces apparatus (SFA) measurements and replica-exchange molecular dynamics (REMD) simulations on a synthetic, easy to prepare, Dopa-containing peptide (MFP-3s peptide), which adheres to organic surfaces just as effectively as its wild-type protein analog. Experiments and simulations both show significant differences in peptide adsorption on CH3-terminated (hydrophobic) and OH-terminated (hydrophilic) self-assembled monolayers (SAMs), where adsorption is strongest on hydrophobic SAMs because of orientationally specific interactions with Dopa. Additional umbrella-sampling simulations yield free-energy profiles that quantitatively agree with SFA measurements and are used to extract the adhesive properties of individual amino acids within the context of MFP-3s peptide adhesion, revealing a delicate balance between van der Waals, hydrophobic, and electrostatic forces.

Electron Transport through Porphyrin Molecular Junctions

NASA Astrophysics Data System (ADS)

Zhou, Qi

The goal of this work is to study the properties that would affect the electron transport through a porphyrin molecular junction. This work contributes to the field of electron transport in molecular junctions in the following 3 aspects. First of all, by carrying out experiments comparing the conductance of the iron (III) porphyrin (protected) and the free base porphyrin (protected), it is confirmed that the molecular energy level broadening and shifting occurs for porphyrin molecules when coupled with the metal electrodes, and this level broadening and shifting plays an important role in the electron transport through molecular junctions. Secondly, by carrying out an in-situ deprotection of the acetyl-protected free base porphyrin molecules, it is found out that the presence of acetyl groups reduces the conductance. Thirdly, by incorporating the Matrix-assisted laser desorption/ionization (MALDI) spectrum and the in-situ deprotection prior to formation of molecular junctions, it allows a more precise understanding of the molecules involved in the formation of molecular junctions, and therefore allows an accurate analysis of the conductance histogram. The molecules are prepared by self-assembly and the junctions are formed using a Scanning Tunneling Microscopy (STM) molecular break junction technique. The porphyrin molecules are characterized by MALDI in solution before self-assembly to a gold/mica substrate. The self-assembled monolayers (SAMs) of porphyrins on gold are characterized by Ultraviolet-visible (UV-Vis) reflection spectroscopy to confirm that the molecules are attached to the substrate. The SAMs are then characterized by Angle-Resolved X-ray photoelectron spectroscopy (ARXPS) to determine the thickness and the average molecular orientation of the molecular layer. The electron transport is measured by conductance-displacement (G-S) experiments under a given bias (-0.4V). The conductance value of a single molecule is identified by a statistical analysis over a large set of measurements. In this thesis, I focus on two factors that would affect the electron transport through the porphyrin molecules, namely, the metal ion center, and the deprotection of the end groups. The effect of metal ion center is studied by comparing the conductance of an iron (III) porphyrin (protected) to that of a free base porphyrin (protected). The in-situ deprotection of the molecules before forming the junctions is completed to study the effect of the molecular-electrode interaction. The first factor studied, that is, the metal ion center in the porphyrin molecule, show that the conductance for iron (III) porphyrin (protected) is 3.74 x10-5 G0, and the conductance for the free base porphyrin (protected) is 4.73x10-5 G0 , where G0 = e2 / pih = (25.8kO)-1 is the quantized unit of electrical conductance. Through our collaborative efforts, first principles calculations carried out by our collaborators for the molecular levels of an isolated molecule (without electrodes) show that the energy levels of an iron (III) porphyrin molecule are slightly shifted compared to that of the free base porphyrin. For the free base porphyrin, the highest occupied molecular orbital (HOMO) level (-4.952 eV) lies between the chemical potentials of the substrate (-4.7 eV) and the STM tip (-5.1 eV). This level serves as a channel for electron transport. For the iron (III) porphyrin, the HOMO is at -5.306 eV, which is not in between the chemical potentials of the substrate. Therefore, a significantly smaller conductance is expected for the iron (III) porphyrin compared to the conductance of a free base porphyrin, because of the lack of the electron transport channel. However, the conductance measured from G-S experiments is comparable, i.e. 3.74 x10-5 G0 for iron (III) porphyrin and 4.73x10-5 G0 for free base porphyrin. This suggests that the molecular energy level broadening and shifting occurs for porphyrin molecules when coupled with the metal electrodes, and this level broadening and shifting may significantly affect the electron transport through molecular junctions. The second factor studied, that is, the deprotection of the porphyrin end groups (acetylthio, -SCOCH3), was completed in-situ for the free base porphyrin through the reaction of the acetylthio with sulfuric acid at 35° Celsius for 3 hours. MALDI spectroscopy confirms that two additional deprotected porphyrin species are formed by deprotection, with protonated (MH+) molecular masses of 721 and 679, corresponding to a partially deprotected porphyrin (i.e. only one of the two end groups deprotected), and a fully deprotected porphyrin molecule. Along with the un-reacted acetyl protected porphyrin, a total of 3 porphyrin species are in the solution. This solution is used for self-assembly on a gold/mica surface. The thickness of the in-situ deprotected SAM is determined to be ˜1.7 nm, confirming a relatively upright molecular orientation (54.0°-63.5° between the substrate surface and the molecule), compared to a thickness of ˜1.5 nm for the protected SAM that has a more flat-lying molecular orientation (˜45.6° between the substrate surface and the molecule). From G-S measurements on SAMs prepared by in-situ deprotection, junctions with lower conductance steps at mid 10-5 G0 and junctions with higher conductance steps around 10-4 G 0 are observed. Supported by computational modeling from our collaborating research group, we associate the lower conductance steps to junctions based on the protected form of thiols at the tip-molecule interface, and the higher conductance steps to the deprotected form of the thiol contacts. We suggest that the reduced conductance in the protected porphyrin originates from the presence of the acetyl end groups (-COCH3), rather than from the elongation of the sulfur-gold (S-Au) bonds at the tip-molecule interface. By studying these two factors, I expect this work to provide insights into electron transport through molecules or metal-molecule-metal junctions, and in applications related to integrating molecules as functional units in electronic devices. Future work related to this thesis may include the molecular conductance based on reduction-oxidation (redox) properties of iron ligated porphyrins for the application of molecular switches and molecular memory elements.

Cofacial Assembly of Metallomacrocycles. A Molecular Engineering Approach to Electrically Conductive Polymers.

DTIC Science & Technology

1981-05-13

34molecular metals." THE COFACIAL ASSEMBLY STRATEGY Although the above molecular macrocycle, halogen cocrystalli - zation approach to the synthesis of...substitute various oxidizing quinones for halogens in the cocrystallization synthesis have failed because integrated stacK (Figure 2C,D) insulators are

Modulating protein behaviors on responsive surface by external electric fields: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Xie, Yun; Pan, Yufang; Zhang, Rong; Liang, Ying; Li, Zhanchao

2015-01-01

Molecular dynamics simulations were employed to investigate the modulation of protein behaviors on the electrically responsive zwitterionic phosphorylcholine self-assembled monolayers (PC-SAMs). Results show that PC-SAMs could sensitively respond to the applied electric fields and exhibit three states with different charge distributions, namely both the negatively charged phosphate groups and the positively charged choline groups are exposed to the solution in the absence of electric fields (state 1), phosphate groups exposed in the presence of positive electric fields (state 2), and choline groups exposed in the presence of negative electric fields (state 3). Under state 1, the adsorption of Cyt c on the PC-SAM is reversible and the orientations of Cyt c are randomly distributed. Under state 2, the adsorption of Cyt c is enhanced due to the electrostatic attractions between the exposed phosphate groups and the positively charged protein; when adsorbed on the PC-SAMs, Cyt c tends to adopt the orientation with the heme plane perpendicular to the surface plane, and the percentage of this orientation increases as the field strength rises up. Under state 3, the adsorption of Cyt c is retarded because of the electrostatic repulsions between the exposed choline groups and the protein; however, if the gaps between PC chains are large enough, Cyt c could insert into the PC-SAM and access the phosphate groups after overcoming a slight energy barrier. Under three states, the basic backbone structures of Cyt c are well kept within the simulation time since the conformation of Cyt c is mainly affected by the surface-generated electric fields, whose strengths are modulated by the external electric fields and are not strong enough to deform protein. The results indicate the possibility of regulating protein behaviors, including promoting or retarding protein adsorption and regulating protein orientations, on responsive surfaces by applying electric fields on the surfaces without worrying protein deformation, which may be helpful in the applications of protein separation and controlled drug delivery.

Delocalized versus localized excitations in the photoisomerization of azobenzene-functionalized alkanethiolate SAMs

NASA Astrophysics Data System (ADS)

Bronsch, Wibke; Moldt, Thomas; Boie, Larissa; Gahl, Cornelius; Weinelt, Martin

2017-12-01

Self-assembled monolayers of azobenzene-functionalized alkanethiolates form molecular ensembles with preferential orientation and significant excitonic coupling among the azobenzene chromophores. We have studied their optical switching with differential reflectance and two-photon-photoemission spectroscopy tuning the excitation wavelength through the excitonically broadened S2 absorption band. While the effective isomerization cross-section increases towards shorter wavelengths, the fraction of cis molecules in the photostationary state decreases. We attribute this observation to the absorption of the cis isomer in the SAM. The photoisomerization in the SAM thereby follows the behavior of non-interacting chromophores in solution, despite the formation of H-aggregates. Our study thus reveals that photoswitching occurs via localized excitations while strongly excitonically coupled, delocalized states do not contribute significantly.

Phases and Dynamics of Self-Assembled DNA Programmed Nanocubes

NASA Astrophysics Data System (ADS)

Knorowski, Christopher; Travesset, Alex

2013-03-01

Systems of Nanoparticles grafted with complementary DNA strands have been shown to self-assemble into an array of superlattices. In this talk, we extend our previous model, which successfully predicted equilibrium phases and dynamics of assembly for spherical Nanoparticles without fitting parameters, to the case of nanocubes. We show that the phase diagram consists of bcc and sc lattices, depending on DNA length. The bcc lattices are either rotator and orientational glass or cubatic. For temperatures above the DNA melting temperature, the system is equivalent to f-star polymer systems, and consist of bcc, also with rotator, orientational glass or cubatic orientational order as well as sc. We also provide a characterization of the dynamics, including the role of topological defects in crystal nucleation and growth. This work is funded by DOE through the Ames Lab under Contract DE-AC02-07CH11358. Most simulations are performed on the Exalted GPU cluster, which is funded by a grant from Iowa State University and Nvidia Corp.

Crops: a green approach toward self-assembled soft materials.

PubMed

Vemula, Praveen Kumar; John, George

2008-06-01

To date, a wide range of industrial materials such as solvents, fuels, synthetic fibers, and chemical products are being manufactured from petroleum resources. However, rapid depletion of fossil and petroleum resources is encouraging current and future chemists to orient their research toward designing safer chemicals, products, and processes from renewable feedstock with an increased awareness of environmental and industrial impact. Advances in genetics, biotechnology, process chemistry, and engineering are leading to a new manufacturing concept for converting renewable biomass to valuable fuels and products, generally known as the biorefinery concept. The swift integration of crop-based materials synthesis and biorefinery manufacturing technologies offers the potential for new advances in sustainable energy alternatives and biomaterials that will lead to a new manufacturing paradigm. This Account presents a novel and emerging concept of generating various forms of soft materials from crops (an alternate feedstock). In future research, developing biobased soft materials will be a fascinating yet demanding practice, which will have direct impact on industrial applications as an economically viable alternative. Here we discuss some remarkable examples of glycolipids generated from industrial byproducts such as cashew nut shell liquid, which upon self-assembly produced soft nanoarchitectures including lipid nanotubes, twisted/helical nanofibers, low-molecular-weight gels, and liquid crystals. Synthetic methods applied to a "chiral pool" of carbohydrates using the selectivity of enzyme catalysis yield amphiphilic products derived from biobased feedstock including amygdalin, trehalose, and vitamin C. This has been achieved with a lipase-mediated regioselective synthetic procedure to obtain such amphiphiles in quantitative yields. Amygdalin amphiphiles showed unique gelation behavior in a broad range of solvents such as nonpolar hexanes to polar aqueous solutions. Importantly, an enzyme triggered drug-delivery model for hydrophobic drugs was demonstrated by using these supramolecularly assembled hydrogels. Following a similar biocatalytic approach, vitamin C amphiphiles were synthesized with different hydrocarbon chain lengths, and their ability to self-assemble into molecular gels and liquid crystals has been studied in detail. Such biobased soft materials were successfully used to develop novel organic-inorganic hybrid materials by in situ synthesis of metal nanoparticles. The self-assembled soft materials were characterized by several spectroscopic techniques, UV-visible, infrared, and fluorescence spectrophotometers, as well as microscopic methods including polarized optical, confocal, scanning, and transmission electron microscopes, and thermal analysis. The molecular packing of the hierarchically assembled bilayer membranes was fully elucidated by X-ray analysis. We envision that the results summarized in this Account will encourage interdisciplinary collaboration between scientists in the fields of organic synthesis, soft materials research, and green chemistry to develop functional materials from underutilized crop-based renewable feedstock, with innovation driven both by material needs and environmentally benign design principles.

ABACAS: algorithm-based automatic contiguation of assembled sequences

PubMed Central

Assefa, Samuel; Keane, Thomas M.; Otto, Thomas D.; Newbold, Chris; Berriman, Matthew

2009-01-01

Summary: Due to the availability of new sequencing technologies, we are now increasingly interested in sequencing closely related strains of existing finished genomes. Recently a number of de novo and mapping-based assemblers have been developed to produce high quality draft genomes from new sequencing technology reads. New tools are necessary to take contigs from a draft assembly through to a fully contiguated genome sequence. ABACAS is intended as a tool to rapidly contiguate (align, order, orientate), visualize and design primers to close gaps on shotgun assembled contigs based on a reference sequence. The input to ABACAS is a set of contigs which will be aligned to the reference genome, ordered and orientated, visualized in the ACT comparative browser, and optimal primer sequences are automatically generated. Availability and Implementation: ABACAS is implemented in Perl and is freely available for download from http://abacas.sourceforge.net Contact: sa4@sanger.ac.uk PMID:19497936

Mechanisms of two-color laser-induced field-free molecular orientation.

PubMed

Spanner, Michael; Patchkovskii, Serguei; Frumker, Eugene; Corkum, Paul

2012-09-14

Two mechanisms of two-color (ω+2ω) laser-induced field-free molecular orientation, based on the hyperpolarizability and ionization depletion, are explored and compared. The CO molecule is used as a computational example. While the hyperpolarizability mechanism generates small amounts of orientation at intensities below the ionization threshold, ionization depletion quickly becomes the dominant mechanism as soon as ionizing intensities are reached. Only the ionization mechanism leads to substantial orientation (e.g., on the order of ≳0.1). For intensities typical of laser-induced molecular alignment and orientation experiments, the two mechanisms lead to robust, characteristic timings of the field-free orientation wave-packet revivals relative to the alignment revivals and the revival time. The revival timings can be used to detect the active orientation mechanism experimentally.

Investigating the relationship between changes in collagen fiber orientation during skin aging and collagen/water interactions by polarized-FTIR microimaging.

PubMed

Eklouh-Molinier, Christophe; Happillon, Teddy; Bouland, Nicole; Fichel, Caroline; Diébold, Marie-Danièle; Angiboust, Jean-François; Manfait, Michel; Brassart-Pasco, Sylvie; Piot, Olivier

2015-09-21

Upon chronological aging, human skin undergoes structural and molecular modifications, especially at the level of type I collagen. This macromolecule is one of the main dermal structural proteins and presents several age-related alterations. It exhibits a triple helical structure and assembles itself to form fibrils and fibers. In addition, water plays an important role in stabilizing the collagen triple helix by forming hydrogen-bonds between collagen residues. However, the influence of water on changes of dermal collagen fiber orientation with age has not been yet understood. Polarized-Fourier Transform Infrared (P-FTIR) imaging is an interesting biophotonic approach to determine in situ the orientation of type I collagen fibers, as we have recently shown by comparing skin samples of different ages. In this work, P-FTIR spectral imaging was performed on skin samples from two age groups (35- and 38-year-old on the one hand, 60- and 66-year-old on the other hand), and our analyses were focused on the effect of H2O/D2O substitution. Spectral data were processed with fuzzy C-means (FCM) clustering in order to distinguish different orientations of collagen fibers. We demonstrated that the orientation was altered with aging, and that D2O treatment, affecting primarily highly bound water molecules, is more marked for the youngest skin samples. Collagen-bound water-related spectral markers were also highlighted. Our results suggest a weakening of water/collagen interactions with age. This non-destructive and label-free methodology allows us to understand better the importance of bound water in collagen fiber orientation alterations occurring with skin aging. Obtaining such structural information could find benefits in dermatology as well as in cosmetics.

Controlling Protein Surface Orientation by Strategic Placement of Oligo-Histidine Tags

PubMed Central

2017-01-01

We report oriented immobilization of proteins using the standard hexahistidine (His6)-Ni2+:NTA (nitrilotriacetic acid) methodology, which we systematically tuned to give control of surface coverage. Fluorescence microscopy and surface plasmon resonance measurements of self-assembled monolayers (SAMs) of red fluorescent proteins (TagRFP) showed that binding strength increased by 1 order of magnitude for each additional His6-tag on the TagRFP proteins. All TagRFP variants with His6-tags located on only one side of the barrel-shaped protein yielded a 1.5 times higher surface coverage compared to variants with His6-tags on opposite sides of the so-called β-barrel. Time-resolved fluorescence anisotropy measurements supported by polarized infrared spectroscopy verified that the orientation (and thus coverage and functionality) of proteins on surfaces can be controlled by strategic placement of a His6-tag on the protein. Molecular dynamics simulations show how the differently tagged proteins reside at the surface in “end-on” and “side-on” orientations with each His6-tag contributing to binding. Also, not every dihistidine subunit in a given His6-tag forms a full coordination bond with the Ni2+:NTA SAMs, which varied with the position of the His6-tag on the protein. At equal valency but different tag positions on the protein, differences in binding were caused by probing for Ni2+:NTA moieties and by additional electrostatic interactions between different fractions of the β-barrel structure and charged NTA moieties. Potential of mean force calculations indicate there is no specific single-protein interaction mode that provides a clear preferential surface orientation, suggesting that the experimentally measured preference for the end-on orientation is a supra-protein, not a single-protein, effect. PMID:28850777

Assembly of acid-functionalized single-walled carbon nanotubes at oil/water interfaces.

PubMed

Feng, Tao; Hoagland, David A; Russell, Thomas P

2014-02-04

The efficient segregation of water-soluble, acid-functionalized, single-walled carbon nanotubes (SWCNTs) at the oil/water interface was induced by dissolving low-molecular-weight amine-terminated polystyrene (PS-NH2) in the oil phase. Salt-bridge interactions between carboxylic acid groups of SWCNTs and amine groups of PS drove the assembly of SWCNTs at the interface, monitored by pendant drop tensiometry and laser scanning confocal microscopy. The impact of PS end-group functionality, PS and SWCNT concentrations, and the degree of SWCNT acid modification on the interfacial activity was assessed, and a sharp drop in interfacial tension was observed above a critical SWCNT concentration. Interfacial tensions were low enough to support stable oil/water emulsions. Further experiments, including potentiometric titrations and the replacement of SWCNTs by other carboxyl-containing species, demonstrated that the interfacial tension drop reflects the loss of SWCNT charge as the pH falls near/below the intrinsic carboxyl dissociation constant; species lacking multivalent carboxylic acid groups are inactive. The trapped SWCNTs appear to be neither ordered nor oriented.

Two-dimensional network stability of nucleobases and amino acids on graphite under ambient conditions: adenine, L-serine and L-tyrosine.

PubMed

Bald, Ilko; Weigelt, Sigrid; Ma, Xiaojing; Xie, Pengyang; Subramani, Ramesh; Dong, Mingdong; Wang, Chen; Mamdouh, Wael; Wang, Jianguo; Besenbacher, Flemming

2010-04-14

We have investigated the stability of two-dimensional self-assembled molecular networks formed upon co-adsorption of the DNA base, adenine, with each of the amino acids, L-serine and L-tyrosine, on a highly oriented pyrolytic graphite (HOPG) surface by drop-casting from a water solution. L-serine and L-tyrosine were chosen as model systems due to their different interaction with the solvent molecules and the graphite substrate, which is reflected in a high and low solubility in water, respectively, compared with adenine. Combined scanning tunneling microscopy (STM) measurements and density functional theory (DFT) calculations show that the self-assembly process is mainly driven by the formation of strong adenine-adenine hydrogen bonds. We find that pure adenine networks are energetically more stable than networks built up of either pure L-serine, pure L-tyrosine or combinations of adenine with L-serine or L-tyrosine, and that only pure adenine networks are stable enough to be observable by STM under ambient conditions.

Self-assembly of Janus particles into helices with tunable pitch

NASA Astrophysics Data System (ADS)

Fernández, M. Sobrino; Misko, V. R.; Peeters, F. M.

2015-10-01

Janus particles present an important class of building blocks for directional assembly. These are compartmentalized colloids with two different hemispheres. In this work we consider a three-dimensional model of Janus spheres that contain one hydrophobic and one charged hemisphere. Using molecular dynamics simulations, we study the morphology of these particles when confined in a channel-like environment. The interplay between the attractive and repulsive forces on each particle gives rise to a rich phase space where the relative orientation of each particle plays a dominant role in the formation of large-scale clusters. The interest in this system is primarily due to the fact that it could give a better understanding of the mechanisms of the formation of polar membranes. A variety of ordered membranelike morphologies is found consisting of single and multiple connected chain configurations. The helicity of these chains can be chosen by simply changing the salt concentration of the solution. Special attention is given to the formation of Bernal spirals. These helices are composed of regular tetrahedra and are known to exhibit nontrivial translational and rotational symmetry.

Self-Assembled Structures of Benzoic Acid on Au(111) Surface

NASA Astrophysics Data System (ADS)

Vu, Thu-Hien; Wandlowski, Thomas

2017-06-01

Electrochemical scanning tunneling microscopy combined with cyclic voltammetry were employed to explore the self-assembly of benzoic acid (BA) on a Au(111) substrate surface in a 0.1-M HClO4 solution. At the negatively charged surface, BA molecules form two highly ordered physisorbed adlayers with their phenyl rings parallel to the substrate surface. High-resolution scanning tunneling microscopy images reveal the packing arrangement and internal molecular structures. The striped pattern and zigzag structure of the BA adlayers are composed of parallel rows of dimers, in which two BA molecules are bound through a pair of O-H···O hydrogen bonds. Increasing the electrode potential further to positive charge densities of Au(111) leads to the desorption of the physisorbed hydrogen-bonded networks and the formation of a chemisorbed adlayer. BA molecules change their orientation from planar to upright fashion, which is accompanied by the deprotonation of the carboxyl group. Furthermore, potential-induced formation and dissolution of BA adlayers were also investigated. Structural transitions between the various types of ordered adlayers occur according to a nucleation and growth mechanism.

Hygrothermal Anaylsis of Wood-Frame Wall Assemblies in a Mixed-Humid Climate

Treesearch

Samuel V. Glass

2013-01-01

This study uses a one-dimensional hygrothermal model to investigate the moisture performance of 10 residential wood-frame wall assemblies in a representative mixed-humid climate location of Baltimore, Maryland (climate zone 4A). All the assemblies include oriented strandboard (OSB) sheathing and vinyl siding. The walls differ in stud cavity thickness, level of cavity...

Embedded sensor having an identifiable orientation

DOEpatents

Bennett, Thomas E.; Nelson, Drew V.

2002-01-01

An apparatus and method is described wherein a sensor, such as a mechanical strain sensor, embedded in a fiber core, is "flagged" to identify a preferred orientation of the sensor. The identifying "flag" is a composite material, comprising a plurality of non-woven filaments distributed in a resin matrix, forming a small planar tab. The fiber is first subjected to a stimulus to identify the orientation providing the desired signal response, and then sandwiched between first and second layers of the composite material. The fiber, and therefore, the sensor orientation is thereby captured and fixed in place. The process for achieving the oriented fiber includes, after identifying the fiber orientation, carefully laying the oriented fiber onto the first layer of composite, moderately heating the assembled layer for a short period in order to bring the composite resin to a "tacky" state, heating the second composite layer as the first, and assembling the two layers together such that they merge to form a single consolidated block. The consolidated block achieving a roughly uniform distribution of composite filaments near the embedded fiber such that excess resin is prevented from "pooling" around the periphery of the fiber.

Self-Assembly of Topological Solitons and Functional Nanoparticles in Liquid Crystals

NASA Astrophysics Data System (ADS)

Ackerman, Paul Jeffrey

As a result of their intrinsic orientational order, soft elasticity, and facile response to external stimuli, liquid crystals (LCs) provide a rich environment for both fundamental science and viable technological applications. In this thesis I explore the emergent properties of confinement-frustrated chiral nematic LCs and nanoparticle-LC composites. Due to a complex free energy landscape, con- fined LCs exhibit a large number of local and global energy minima and can facilitate self-assembly of many types of topological solitons. These localized configurations of molecular orientation field are useful for technological applications, have properties that are enhanced by colloidal inclusions and enable the fundamental studies of nanoparticle interactions. Experimental and numerical ex- ploration of these topologically nontrivial solitons may influence the experimental realization of their analogs in physical systems ranging from elementary particles to cosmology. The delicate interplay of topology, chirality and confinement of LCs can enable spontaneous or optical vortex initiated self-assembly of solitons. In turn, the optical generation and patterning of reconfigurable LC solitons can enable the production of optical vortices in laser beams, demon- strating hierarchical control of defects in matter and light with potential technological applications. The elasticity and facile response of LCs to applied fields facilitates the self-assembly of crystals and chains of solitons, giant electrostriction, as well as electrically driven nonequilibrium dynamics in the form of reversible directional motion of stable defect pairs. Concepts of chirality and topo- logical invariants, such as Hopf index and Skyrmion number, are invoked to examine and classify a variety of spatial solitons, including Skyrmions, Hopfions, and torons, as well as to analyze the role of chirality and the unexpected observation of twist handedness reversal that enables soliton stability. By introducing colloidal particles to the confined chiral LCs, we probe how new composite material properties can emerge spontaneously or be pre-designed and then probed by combining the facile response of the LC host and the unique properties of nanoparticles. This allows us to achieve polar ferromagnetic response in chiral ferromagnetic LC colloids as well as to probe plasmon- exciton interactions through controlling metal and semiconductor quantum dot nanoparticles within topological defects.

Perpendicular Orientation Control without Interfacial Treatment of RAFT-Synthesized High-χ Block Copolymer Thin Films with Sub-10 nm Features Prepared via Thermal Annealing.

PubMed

Nakatani, Ryuichi; Takano, Hiroki; Chandra, Alvin; Yoshimura, Yasunari; Wang, Lei; Suzuki, Yoshinori; Tanaka, Yuki; Maeda, Rina; Kihara, Naoko; Minegishi, Shinya; Miyagi, Ken; Kasahara, Yuusuke; Sato, Hironobu; Seino, Yuriko; Azuma, Tsukasa; Yokoyama, Hideaki; Ober, Christopher K; Hayakawa, Teruaki

2017-09-20

In this study, a series of perpendicular lamellae-forming poly(polyhedral oligomeric silsesquioxane methacrylate-block-2,2,2-trifluoroethyl methacrylate)s (PMAPOSS-b-PTFEMAs) was developed based on the bottom-up concept of creating a simple yet effective material by tailoring the chemical properties and molecular composition of the material. The use of silicon (Si)-containing hybrid high-χ block copolymers (BCPs) provides easy access to sub-10 nm feature sizes. However, as the surface free energies (SFEs) of Si-containing polymers are typically vastly lower than organic polymers, this tends to result in the selective segregation of the inorganic block onto the air interface and increased difficulty in controlling the BCP orientation in thin films. Therefore, by balancing the SFEs between the organic and inorganic blocks through the use of poly(2,2,2-trifluoroethyl methacrylate) (PTFEMA) on the organic block, a polymer with an SFE similar to Si-containing polymers, orientation control of the BCP domains in thin films becomes much simpler. Herein, perpendicularly oriented BCP thin films with a χ eff value of 0.45 were fabricated using simple spin-coating and thermal annealing processes under ambient conditions. The thin films displayed a minimum domain size of L 0 = 11 nm, as observed via atomic force microscopy (AFM), scanning electron microscopy (SEM), and transmission electron microscopy (TEM). Furthermore, directed self-assembly (DSA) of the BCP on a topographically prepatterned substrate using the grapho-epitaxy method was used to successfully obtain perpendicularly oriented lamellae with a half pitch size of ca. 8 nm.

Investigating the effects of peptoid substitutions in self-assembly of Fmoc-diphenylalanine derivatives.

PubMed

Rajbhandary, Annada; Nilsson, Bradley L

2017-03-01

Low molecular weight agents that undergo self-assembly into fibril networks with hydrogel properties are promising biomaterials. Most low molecular weight hydrogelators are discovered empirically or serendipitously due to imperfect understanding of the mechanisms of self-assembly, the packing structure of self-assembled materials, and how the self-assembly process corresponds to emergent hydrogelation. Herein, the mechanisms of self-assembly and hydrogelation of N-fluorenylmethoxycarbonyl diphenylalanine (Fmoc-PhePhe), a well-studied low molecular weight hydrogelator, is probed by systematic comparison with derivatives in which Phe residues are replaced by corresponding N-benzyl glycine peptoid (Nphe) analogs. Peptoids are peptidomimetics that shift display of side chain functionality from the α-carbon to the terminal nitrogen. This alters the hydrogen bonding capacity, the side chain presentation geometry, amide cis/trans isomerization equilibrium, and β-sheet potential of the peptoid relative to the corresponding amino acid in the context of peptidic polymers. It was found that amino acid/peptoid hybrids Fmoc-Phe-Nphe and Fmoc-Nphe-Phe have altered fibril self-assembly propensity and reduced hydrogelation capacity relative to the parent dipeptide, and that fibril self-assembly of the dipeptoid, Fmoc-Nphe-Nphe, is completely curtailed. These findings provide insight into the potential of low molecular weight peptoids and peptide/peptoid hybrids as hydrogelation agents and illuminate the importance of hydrogen bonding and π-π interaction geometry in facilitating self-assembly of Fmoc-Phe-Phe. © 2016 Wiley Periodicals, Inc.

Competitive chiral induction in a 2D molecular assembly: Intrinsic chirality versus coadsorber-induced chirality.

PubMed

Chen, Ting; Li, Shu-Ying; Wang, Dong; Wan, Li-Jun

2017-11-01

Noncovalently introducing stereogenic information is a promising approach to embed chirality in achiral molecular systems. However, the interplay of the noncovalently introduced chirality with the intrinsic chirality of molecules or molecular aggregations has rarely been addressed. We report a competitive chiral expression of the noncovalent interaction-mediated chirality induction and the intrinsic stereogenic center-controlled chirality induction in a two-dimensional (2D) molecular assembly at the liquid/solid interface. Two enantiomorphous honeycomb networks are formed by the coassembly of an achiral 5-(benzyloxy)isophthalic acid (BIC) derivative and 1-octanol at the liquid/solid interface. The preferential formation of the globally homochiral assembly can be achieved either by using the chiral analog of 1-octanol, ( S )-6-methyl-1-octanol, as a chiral coadsorber to induce chirality to the BIC assembly via noncovalent hydrogen bonding or by covalently linking a chiral center in the side chain of BIC. Both the chiral coadsorber and the intrinsically chiral BIC derivative can act as a chiral seeds to induce a preferred handedness in the assembly of the achiral BIC derivatives. Furthermore, the noncovalent interaction-mediated chirality induction can restrain or even overrule the manifestation of the intrinsic chirality of the BIC molecule and dominate the handedness of the 2D molecular coassembly. This study provides insight into the interplay of intrinsically chiral centers and external chiral coadsorbers in the chiral induction, transfer, and amplification processes of 2D molecular assembly.

Competitive chiral induction in a 2D molecular assembly: Intrinsic chirality versus coadsorber-induced chirality

PubMed Central

Chen, Ting; Li, Shu-Ying; Wang, Dong; Wan, Li-Jun

2017-01-01

Noncovalently introducing stereogenic information is a promising approach to embed chirality in achiral molecular systems. However, the interplay of the noncovalently introduced chirality with the intrinsic chirality of molecules or molecular aggregations has rarely been addressed. We report a competitive chiral expression of the noncovalent interaction–mediated chirality induction and the intrinsic stereogenic center–controlled chirality induction in a two-dimensional (2D) molecular assembly at the liquid/solid interface. Two enantiomorphous honeycomb networks are formed by the coassembly of an achiral 5-(benzyloxy)isophthalic acid (BIC) derivative and 1-octanol at the liquid/solid interface. The preferential formation of the globally homochiral assembly can be achieved either by using the chiral analog of 1-octanol, (S)-6-methyl-1-octanol, as a chiral coadsorber to induce chirality to the BIC assembly via noncovalent hydrogen bonding or by covalently linking a chiral center in the side chain of BIC. Both the chiral coadsorber and the intrinsically chiral BIC derivative can act as a chiral seeds to induce a preferred handedness in the assembly of the achiral BIC derivatives. Furthermore, the noncovalent interaction–mediated chirality induction can restrain or even overrule the manifestation of the intrinsic chirality of the BIC molecule and dominate the handedness of the 2D molecular coassembly. This study provides insight into the interplay of intrinsically chiral centers and external chiral coadsorbers in the chiral induction, transfer, and amplification processes of 2D molecular assembly. PMID:29119137

Cooperative synchronized assemblies enhance orientation discrimination.

PubMed

Samonds, Jason M; Allison, John D; Brown, Heather A; Bonds, A B

2004-04-27

There is no clear link between the broad tuning of single neurons and the fine behavioral capabilities of orientation discrimination. We recorded from populations of cells in the cat visual cortex (area 17) to examine whether the joint activity of cells can support finer discrimination than found in individual responses. Analysis of joint firing yields a substantial advantage (i.e., cooperation) in fine-angle discrimination. This cooperation increases to more considerable levels as the population of an assembly is increased. The cooperation in a population of six cells provides encoding of orientation with an information advantage that is at least 2-fold in terms of requiring either fewer cells or less time than independent coding. This cooperation suggests that correlated or synchronized activity can increase information.

Crystallization and Microphase Separation in Chiral Block Copolymers

NASA Astrophysics Data System (ADS)

Ho, Rong-Ming

2012-02-01

Block copolymers composed of chiral entities, denoted as chiral block copolymers (BCP*s), were designed to fabricate helical architectures from self-assembly. A helical phase (denoted H*) was discovered in the self-assembly of poly(styrene)-b-poly(L-lactide) (PS-PLLA) BCPs*. To examine the phase behavior of the PS-PLLA, self-assembled superstructures resulting from the competition between crystallization and microphase separation of the PS-PLLA in solution were examined. A kinetically controlled process by changing non-solvent addition rate was utilized to control the BCP* self-assembly. Single-crystal lozenge lamellae were obtained by the slow self-assembly (i.e., slow non-solvent addition rate) of PS-PLLA whereas amorphous helical ribbon superstructures were obtained from the fast self-assembly (i.e., fast non-solvent addition rate). As a result, the formation of helical architectures from the self-assembly of the PS-PLLA reflects the impact of chirality on microphase separation, but the chiral effect might be overwhelmed by crystallization. Consequently, various crystalline PS-PLLA nanostructures in bulk were obtained by controlling the crystallization temperature of PLLA (Tc,PLLA) at which crystalline helices and crystalline cylinders occur while Tc,PLLA=x Tg,PS, respectively. Anisotropic arrangement of the PLLA crystallites grown within the microdomains was identified. The formation of this exclusive crystalline growth is attributed to the spatial confinement effect for crystallization. While Tc,PLLA=x Tg,PS, the preferential growth may modulate the curvature of microdomains by shifting the molecular chains to access the fast path for crystalline growth due to the increase in chain mobility. As a result, a spring-like behavior of the helical nanostructure can be driven by crystallization so as to dictate the transformation of helices and to result in crystalline cylinders.

Self-Assembly Behavior of Amphiphilic Janus Dendrimers in Water: A Combined Experimental and Coarse-Grained Molecular Dynamics Simulation Approach.

PubMed

Elizondo-García, Mariana E; Márquez-Miranda, Valeria; Araya-Durán, Ingrid; Valencia-Gallegos, Jesús A; González-Nilo, Fernando D

2018-04-21

Amphiphilic Janus dendrimers (JDs) are repetitively branched molecules with hydrophilic and hydrophobic components that self-assemble in water to form a variety of morphologies, including vesicles analogous to liposomes with potential pharmaceutical and medical application. To date, the self-assembly of JDs has not been fully investigated thus it is important to gain insight into its mechanism and dependence on JDs’ molecular structure. In this study, the aggregation behavior in water of a second-generation bis-MPA JD was evaluated using experimental and computational methods. Dispersions of JDs in water were carried out using the thin-film hydration and ethanol injection methods. Resulting assemblies were characterized by dynamic light scattering, confocal microscopy, and atomic force microscopy. Furthermore, a coarse-grained molecular dynamics (CG-MD) simulation was performed to study the mechanism of JDs aggregation. The obtaining of assemblies in water with no interdigitated bilayers was confirmed by the experimental characterization and CG-MD simulation. Assemblies with dendrimersome characteristics were obtained using the ethanol injection method. The results of this study establish a relationship between the molecular structure of the JD and the properties of its aggregates in water. Thus, our findings could be relevant for the design of novel JDs with tailored assemblies suitable for drug delivery systems.

A Structural Model for the Single-Stranded DNA Genome of Filamentous Bacteriophage Pf1†

PubMed Central

Tsuboi, Masamichi; Tsunoda, Masaru; Overman, Stacy A.; Benevides, James M.; Thomas, George J.

2010-01-01

The filamentous bacteriophage Pf1, which infects strain PAK of Pseudomonas aeruginosa, is a flexible filament (~2000 × 6.5 nm) consisting of a covalently closed DNA loop of 7349 nucleotides sheathed by 7350 copies of a 46-residue α-helical subunit. The subunit α-helices, which are inclined at a small average angle (~16°) from the virion axis, are arranged compactly around the DNA core. Orientations of the Pf1 DNA nucleotides with respect to the filament axis are not known. In this work we report and interpret the polarized Raman spectra of oriented Pf1 filaments. We demonstrate that the polarizations of DNA Raman band intensities establish that the nucleotide bases of packaged Pf1 DNA are well ordered within the virion and that the base planes are positioned close to parallel to the filament axis. The present results are combined with a previously proposed projection of the intraviral path of Pf1 DNA (1) to develop a novel molecular model for the Pf1 assembly. PMID:20078135

Metal dependent motif transition in a self-assembled monolayer of bipyridine derivatives via coordination: An STM study.

PubMed

Wang, Yi; Yuan, Qunhui; Xu, Hongbo; Zhu, Xuefeng; Gan, Wei

2016-07-21

Low-dimensional molecular motifs with diversity developed via the on-surface chemistry are attracting growing interest for their potential in advanced nanofabrication. In this work, scanning tunneling microscopy was employed to investigate the in situ and ex situ metal coordinations between 4,4'-ditetradecyl-2,2'-bipyridine (bpy) and Zn(ii) or Cu(ii) ions at a highly oriented pyrolytic graphite (HOPG)/1-phenyloctane interface under ambient conditions. The results demonstrate that the bpy adopts a flat-lying orientation with its substituted alkyl chains in a tail-to-tail arrangement in a bpy monolayer. For the in situ coordination, the bpy/Zn(ii) and bpy/Cu(ii) complexes are aligned in edge-on fashions, wherein the bpy stands vertically on the HOPG surface and interdigitates at the alkyl chains. In the two-dimensional arrays of ex situ coordinated complexes, metal dependent motifs have been observed with Zn(ii) and Cu(ii), wherein the bipyridine moieties are parallel to the graphite surface. These results suggest that the desired on-surface coordination architectures may be achieved by the intentional selection of the metal centers.

Alignment between Protostellar Outflows and Filamentary Structure

NASA Astrophysics Data System (ADS)

Stephens, Ian W.; Dunham, Michael M.; Myers, Philip C.; Pokhrel, Riwaj; Sadavoy, Sarah I.; Vorobyov, Eduard I.; Tobin, John J.; Pineda, Jaime E.; Offner, Stella S. R.; Lee, Katherine I.; Kristensen, Lars E.; Jørgensen, Jes K.; Goodman, Alyssa A.; Bourke, Tyler L.; Arce, Héctor G.; Plunkett, Adele L.

2017-09-01

We present new Submillimeter Array (SMA) observations of CO(2-1) outflows toward young, embedded protostars in the Perseus molecular cloud as part of the Mass Assembly of Stellar Systems and their Evolution with the SMA (MASSES) survey. For 57 Perseus protostars, we characterize the orientation of the outflow angles and compare them with the orientation of the local filaments as derived from Herschel observations. We find that the relative angles between outflows and filaments are inconsistent with purely parallel or purely perpendicular distributions. Instead, the observed distribution of outflow-filament angles are more consistent with either randomly aligned angles or a mix of projected parallel and perpendicular angles. A mix of parallel and perpendicular angles requires perpendicular alignment to be more common by a factor of ˜3. Our results show that the observed distributions probably hold regardless of the protostar’s multiplicity, age, or the host core’s opacity. These observations indicate that the angular momentum axis of a protostar may be independent of the large-scale structure. We discuss the significance of independent protostellar rotation axes in the general picture of filament-based star formation.

Realization of Molecular-Based Transistors.

PubMed

Richter, Shachar; Mentovich, Elad; Elnathan, Roey

2018-06-06

Molecular-based devices are widely considered as significant candidates to play a role in the next generation of "post-complementary metal-oxide-semiconductor" devices. In this context, molecular-based transistors: molecular junctions that can be electrically gated-are of particular interest as they allow new modes of operation. The properties of molecular transistors composed of a single- or multimolecule assemblies, focusing on their practicality as real-world devices, concerning industry demands and its roadmap are compared. Also, the capability of the gate electrode to modulate the molecular transistor characteristics efficiently is addressed, showing that electrical gating can be easily facilitated in single molecular transistors and that gating of transistor composed of molecular assemblies is possible if the device is formed vertically. It is concluded that while the single-molecular transistor exhibits better performance on the lab-scale, its realization faces signifacant challenges when compared to those faced by transistors composed of a multimolecule assembly. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Multidimensional Self-Assembled Structures of Alkylated Cellulose Oligomers Synthesized via in Vitro Enzymatic Reactions.

PubMed

Yataka, Yusuke; Sawada, Toshiki; Serizawa, Takeshi

2016-10-04

The self-assembly of biomolecules into highly ordered nano-to-macroscale structures is essential in the construction of biological tissues and organs. A variety of biomolecular assemblies composed of nucleic acids, peptides, and lipids have been used as molecular building units for self-assembled materials. However, crystalline polysaccharides have rarely been utilized in self-assembled materials. In this study, we describe multidimensional self-assembled structures of alkylated cellulose oligomers synthesized via in vitro enzymatic reactions. We found that the alkyl chain length drastically affected the assembled morphologies and allomorphs of cellulose moieties. The modulation of the intermolecular interactions of cellulose oligomers by alkyl substituents was highly effective at controlling their assembly into multidimensional structures. This study proposes a new potential of crystalline oligosaccharides for structural components of molecular assemblies with controlled morphologies and crystal structures.

Controlling Molecular Ordering in Solution-State Conjugated Polymers

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

Zhu, Jiahua; Han, Youngkyu; Kumar, Rajeev

Rationally encoding molecular interactions that can control the assembly structure and functional expression in solution of conjugated polymers holds great potential for enabling optimal organic optoelectronic and sensory materials. In this work, we show that thermally-controlled and surfactant-guided assembly of water-soluble conjugated polymers in aqueous solution is a simple and effective strategy to generate optoelectronic materials with desired molecular ordering. We have studied a conjugated polymer consisting of a hydrophobic thiophene backbone and hydrophilic, thermo-responsive ethylene oxide side groups, which shows a step-wise, multi-dimensional assembly in water. By incorporating the polymer into phase-segregated domains of an amphiphilic surfactant in solution,more » we demonstrate that both chain conformation and degree of molecular ordering of the conjugated polymer can be tuned in hexagonal, micellar and lamellar phases of the surfactant solution. The controlled molecular ordering in conjugated polymer assembly is demonstrated as a key factor determining the electronic interaction and optical function.« less

Controlling Molecular Ordering in Solution-State Conjugated Polymers

DOE PAGES

Zhu, Jiahua; Han, Youngkyu; Kumar, Rajeev; ...

2015-07-17

Rationally encoding molecular interactions that can control the assembly structure and functional expression in solution of conjugated polymers holds great potential for enabling optimal organic optoelectronic and sensory materials. In this work, we show that thermally-controlled and surfactant-guided assembly of water-soluble conjugated polymers in aqueous solution is a simple and effective strategy to generate optoelectronic materials with desired molecular ordering. We have studied a conjugated polymer consisting of a hydrophobic thiophene backbone and hydrophilic, thermo-responsive ethylene oxide side groups, which shows a step-wise, multi-dimensional assembly in water. By incorporating the polymer into phase-segregated domains of an amphiphilic surfactant in solution,more » we demonstrate that both chain conformation and degree of molecular ordering of the conjugated polymer can be tuned in hexagonal, micellar and lamellar phases of the surfactant solution. The controlled molecular ordering in conjugated polymer assembly is demonstrated as a key factor determining the electronic interaction and optical function.« less

Enhancing the Activity of Peptide-Based Artificial Hydrolase with Catalytic Ser/His/Asp Triad and Molecular Imprinting.

PubMed

Wang, Mengfan; Lv, Yuqi; Liu, Xiaojing; Qi, Wei; Su, Rongxin; He, Zhimin

2016-06-08

In this study, an artificial hydrolase was developed by combining the catalytic Ser/His/Asp triad with N-fluorenylmethoxycarbonyl diphenylalanine (Fmoc-FF), followed by coassembly of the peptides into nanofibers (CoA-HSD). The peptide-based nanofibers provide an ideal supramolecular framework to support the functional groups. Compared with the self-assembled catalytic nanofibers (SA-H), which contain only the catalytic histidine residue, the highest activity of CoA-HSD occurs when histidine, serine, and aspartate residues are at a ratio of 40:1:1. This indicates that the well-ordered nanofiber structure and the synergistic effects of serine and aspartate residues contribute to the enhancement in activity. Additionally, for the first time, molecular imprinting was applied to further enhance the activity of the peptide-based artificial enzyme (CoA-HSD). p-NPA was used as the molecular template to arrange the catalytic Ser/His/Asp triad residues in the proper orientation. As a result, the activity of imprinted coassembled CoA-HSD nanofibers is 7.86 times greater than that of nonimprinted CoA-HSD and 13.48 times that of SA-H.

The influence of molecular mobility on the properties of networks of gold nanoparticles and organic ligands

PubMed Central

Kamalakar, M Venkata; Prendergast, Úna; Kübel, Christian; Lemma, Tibebe; Dayen, Jean-François

2014-01-01

Summary We prepare and investigate two-dimensional (2D) single-layer arrays and multilayered networks of gold nanoparticles derivatized with conjugated hetero-aromatic molecules, i.e., S-(4-{[2,6-bipyrazol-1-yl)pyrid-4-yl]ethynyl}phenyl)thiolate (herein S-BPP), as capping ligands. These structures are fabricated by a combination of self-assembly and microcontact printing techniques, and are characterized by electron microscopy, UV–visible spectroscopy and Raman spectroscopy. Selective binding of the S-BPP molecules to the gold nanoparticles through Au–S bonds is found, with no evidence for the formation of N–Au bonds between the pyridine or pyrazole groups of BPP and the gold surface. Subtle, but significant shifts with temperature of specific Raman S-BPP modes are also observed. We attribute these to dynamic changes in the orientation and/or increased mobility of the molecules on the gold nanoparticle facets. As for their conductance, the temperature-dependence for S-BPP networks differs significantly from standard alkanethiol-capped networks, especially above 220 K. Relating the latter two observations, we propose that dynamic changes in the molecular layers effectively lower the molecular tunnel barrier for BPP-based arrays at higher temperatures. PMID:25383278

The influence of molecular mobility on the properties of networks of gold nanoparticles and organic ligands.

PubMed

Devid, Edwin J; Martinho, Paulo N; Kamalakar, M Venkata; Prendergast, Úna; Kübel, Christian; Lemma, Tibebe; Dayen, Jean-François; Keyes, Tia E; Doudin, Bernard; Ruben, Mario; van der Molen, Sense Jan

2014-01-01

We prepare and investigate two-dimensional (2D) single-layer arrays and multilayered networks of gold nanoparticles derivatized with conjugated hetero-aromatic molecules, i.e., S-(4-{[2,6-bipyrazol-1-yl)pyrid-4-yl]ethynyl}phenyl)thiolate (herein S-BPP), as capping ligands. These structures are fabricated by a combination of self-assembly and microcontact printing techniques, and are characterized by electron microscopy, UV-visible spectroscopy and Raman spectroscopy. Selective binding of the S-BPP molecules to the gold nanoparticles through Au-S bonds is found, with no evidence for the formation of N-Au bonds between the pyridine or pyrazole groups of BPP and the gold surface. Subtle, but significant shifts with temperature of specific Raman S-BPP modes are also observed. We attribute these to dynamic changes in the orientation and/or increased mobility of the molecules on the gold nanoparticle facets. As for their conductance, the temperature-dependence for S-BPP networks differs significantly from standard alkanethiol-capped networks, especially above 220 K. Relating the latter two observations, we propose that dynamic changes in the molecular layers effectively lower the molecular tunnel barrier for BPP-based arrays at higher temperatures.

Influence of Molecular Shape on the Thermal Stability and Molecular Orientation of Vapor-Deposited Organic Semiconductors

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

Walters, Diane M; Antony, Lucas; de Pablo, Juan

High thermal stability and anisotropic molecular orientation enhance the performance of vapor-deposited organic semiconductors, but controlling these properties is a challenge in amorphous materials. To understand the influence of molecular shape on these properties, vapor-deposited glasses of three disk-shaped molecules were prepared. For all three systems, enhanced thermal stability is observed for glasses prepared over a wide range of substrate temperatures and anisotropic molecular orientation is observed at lower substrate temperatures. For two of the disk-shaped molecules, atomistic simulations of thin films were also performed and anisotropic molecular orientation was observed at the equilibrium liquid surface. We find that themore » structure and thermal stability of these vapor-deposited glasses results from high surface mobility and partial equilibration toward the structure of the equilibrium liquid surface during the deposition process. For the three molecules studied, molecular shape is a dominant factor in determining the anisotropy of vapor-deposited glasses.« less

The space station assembly phase: Flight telerobotic servicer feasibility, volume 1

NASA Technical Reports Server (NTRS)

Smith, Jeffrey H.; Gyamfi, Max A.; Volkmer, Kent; Zimmerman, Wayne F.

1987-01-01

The question is addressed which was raised by the Critical Evaluation Task Force (CETF) analysis of the space station: if a Flight Telerobotic Servicer (FTS) of a given technical risk could be built for use during space station assembly, could it save significant extravehicular (EVA) resources. Key issues and trade-offs associated with using an FTS to aid in space station assembly phase tasks such as construction and servicing are identified. A methodology is presented that incorporates assessment of candidate assembly phase tasks, telerobotics performance capabilities, development costs, operational constraints (STS and proximity operations), maintenance, attached payloads, and polar platforms. A discussion of the issues is presented with focus on potential FTS roles: (1) as a research-oriented test bed to learn more about space usage of telerobotics; (2) as a research-based test bed with an experimental demonstration orientation and limited assembly and servicing applications; or (3) as an operational system to augment EVA, to aid the construction of the space station, and to reduce the programmatic (schedule) risk by increasing the flexibility of mission operations. During the course of the study, the baseline configuration was modified into Phase 1 (a station assembled in 12 flights), and Phase 2 (a station assembled over a 30 flight period) configuration.

Organization of inorganic nanomaterials via programmable DNA self-assembly and peptide molecular recognition.

PubMed

Carter, Joshua D; LaBean, Thomas H

2011-03-22

An interesting alternative to top-down nanofabrication is to imitate biology, where nanoscale materials frequently integrate organic molecules for self-assembly and molecular recognition with ordered, inorganic minerals to achieve mechanical, sensory, or other advantageous functions. Using biological systems as inspiration, researchers have sought to mimic the nanoscale composite materials produced in nature. Here, we describe a combination of self-assembly, molecular recognition, and templating, relying on an oligonucleotide covalently conjugated to a high-affinity gold-binding peptide. After integration of the peptide-coupled DNA into a self-assembling superstructure, the templated peptides recognize and bind gold nanoparticles. In addition to providing new ways of building functional multinanoparticle systems, this work provides experimental proof that a single peptide molecule is sufficient for immobilization of a nanoparticle. This molecular construction strategy, combining DNA assembly and peptide recognition, can be thought of as programmable, granular, artificial biomineralization. We also describe the important observation that the addition of 1-2% Tween 20 surfactant to the solution during gold particle binding allows the gold nanoparticles to remain soluble within the magnesium-containing DNA assembly buffer under conditions that usually lead to the aggregation and precipitation of the nanoparticles.

SCARF: maximizing next-generation EST assemblies for evolutionary and population genomic analyses.

PubMed

Barker, Michael S; Dlugosch, Katrina M; Reddy, A Chaitanya C; Amyotte, Sarah N; Rieseberg, Loren H

2009-02-15

Scaffolded and Corrected Assembly of Roche 454 (SCARF) is a next-generation sequence assembly tool for evolutionary genomics that is designed especially for assembling 454 EST sequences against high-quality reference sequences from related species. The program was created to knit together 454 contigs that do not assemble during traditional de novo assembly, using a reference sequence library to orient the 454 sequences. SCARF is freely available at http://msbarker.com/software.htm, and is released under the open source GPLv3 license (http://www.opensource.org/licenses/gpl-3.0.html.

Noncontact orientation of objects in three-dimensional space using magnetic levitation

PubMed Central

Subramaniam, Anand Bala; Yang, Dian; Yu, Hai-Dong; Nemiroski, Alex; Tricard, Simon; Ellerbee, Audrey K.; Soh, Siowling; Whitesides, George M.

2014-01-01

This paper describes several noncontact methods of orienting objects in 3D space using Magnetic Levitation (MagLev). The methods use two permanent magnets arranged coaxially with like poles facing and a container containing a paramagnetic liquid in which the objects are suspended. Absent external forcing, objects levitating in the device adopt predictable static orientations; the orientation depends on the shape and distribution of mass within the objects. The orientation of objects of uniform density in the MagLev device shows a sharp geometry-dependent transition: an analytical theory rationalizes this transition and predicts the orientation of objects in the MagLev device. Manipulation of the orientation of the levitating objects in space is achieved in two ways: (i) by rotating and/or translating the MagLev device while the objects are suspended in the paramagnetic solution between the magnets; (ii) by moving a small external magnet close to the levitating objects while keeping the device stationary. Unlike mechanical agitation or robotic selection, orienting using MagLev is possible for objects having a range of different physical characteristics (e.g., different shapes, sizes, and mechanical properties from hard polymers to gels and fluids). MagLev thus has the potential to be useful for sorting and positioning components in 3D space, orienting objects for assembly, constructing noncontact devices, and assembling objects composed of soft materials such as hydrogels, elastomers, and jammed granular media. PMID:25157136

Noncontact orientation of objects in three-dimensional space using magnetic levitation.

PubMed

Subramaniam, Anand Bala; Yang, Dian; Yu, Hai-Dong; Nemiroski, Alex; Tricard, Simon; Ellerbee, Audrey K; Soh, Siowling; Whitesides, George M

2014-09-09

This paper describes several noncontact methods of orienting objects in 3D space using Magnetic Levitation (MagLev). The methods use two permanent magnets arranged coaxially with like poles facing and a container containing a paramagnetic liquid in which the objects are suspended. Absent external forcing, objects levitating in the device adopt predictable static orientations; the orientation depends on the shape and distribution of mass within the objects. The orientation of objects of uniform density in the MagLev device shows a sharp geometry-dependent transition: an analytical theory rationalizes this transition and predicts the orientation of objects in the MagLev device. Manipulation of the orientation of the levitating objects in space is achieved in two ways: (i) by rotating and/or translating the MagLev device while the objects are suspended in the paramagnetic solution between the magnets; (ii) by moving a small external magnet close to the levitating objects while keeping the device stationary. Unlike mechanical agitation or robotic selection, orienting using MagLev is possible for objects having a range of different physical characteristics (e.g., different shapes, sizes, and mechanical properties from hard polymers to gels and fluids). MagLev thus has the potential to be useful for sorting and positioning components in 3D space, orienting objects for assembly, constructing noncontact devices, and assembling objects composed of soft materials such as hydrogels, elastomers, and jammed granular media.

Fluorescent J-aggregates of core-substituted perylene bisimides: studies on structure-property relationship, nucleation-elongation mechanism, and sergeants-and-soldiers principle.

PubMed

Kaiser, Theo E; Stepanenko, Vladimir; Würthner, Frank

2009-05-20

A series of highly soluble and fluorescent, at core tetraaryloxy-substituted and in imide positions hydrogen atom containing perylene bisimide (PBI) dyes 1a-e with varying peripheral side chains have been synthesized and thoroughly characterized. The self-assembly of these PBIs has been studied in detail by UV/vis, linear dichroism (LD) and circular dichroism (CD) spectroscopy, and scanning probe microscopy (AFM, STM). These studies revealed that the present PBIs self-assemble into extended double string cables, which consist of two hydrogen-bonded supramolecular polymeric chains of densely packed and strongly excitonically coupled PBI chromophores, providing highly fluorescent J-aggregates. The aggregation strength ("melting" temperature) and the fluorescence properties of these J-aggregates are dependent on the number and chain length of the peripheral alkoxy substituents, thus revealing a structure-property relationship. In contrast to previously reported assemblies of PBIs, for which the aggregation process is described by the isodesmic (or equal K) model, a cooperative nucleation-elongation mechanism applies for the aggregation of the present assemblies as revealed by concentration-dependent UV/vis absorption studies with the chiral PBI 1e, providing equilibrium constants for dimerization (= nucleation) of K(2) = 13 +/- 11 L mol(-1) and for elongation of K = 2.3 +/- 0.1 x 10(6) L mol(-1) in methylcyclohexane (MCH). LD spectroscopic measurements have been performed to analyze the orientation of the monomers within the aggregates. The nonlinearity of chiral amplification in PBI aggregates directed by sergeants-and-soldiers principle has been elucidated by coaggregation experiments of different PBI dyes using CD spectroscopy. The dimensions as well as the molecular arrangement of the monomeric units in assemblies have been explored by atomic force microscopy (AFM) and scanning tunneling microscopy (STM).

Unidirectional self-assembly of soft templated mesoporous carbons by zone annealing

NASA Astrophysics Data System (ADS)

Xue, Jiachen; Singh, Gurpreet; Qiang, Zhe; Karim, Alamgir; Vogt, Bryan D.

2013-08-01

Surfactant or block copolymer-templated mesoporous films have been extensively explored, but achieving mesostructure coherence and unidirectional orientation over macroscopic dimensions has remained quite challenging for these self-assembled systems. Here, we extend the concepts associated with zone refinement of crystalline materials to soft templated mesoporous carbon films based on the cooperative assembly of commercial non-ionic surfactants (block copolymers) and phenolic resin oligomers (resol) to provide macroscopic alignment of both cubic (FDU-16) and hexagonal (FDU-15) mesostructures. The average orientation of these mesophases is determined from rotation grazing incidence small angle X-ray scattering (GISAXS) measurements. For FDU-15 templated by Pluronic P123, the orientation factor for the zone-annealed film is 0.98 based on the average of the second Legendre polynomial, but this orientation deteriorates significantly during carbonization. Notably, a thermal stabilization step following zone annealing preserves the orientation of the mesostructure during carbonization. The orientation factor for an isotropic cubic structure (FDU-16 templated by Pluronic F127) is only 0.48 (based on the 111 reflection with incident angle 0.15°) for the same zone annealing protocol, but this illustrates the versatility of zone annealing to different mesostructures. Unexpectedly, zone annealing of FDU-15 templated by Pluronic F127 leads to stabilization of the mesostructure through carbonization, whereas this structure collapses fully during carbonization even after extended oven annealing; despite no clear macroscopic orientation of the cylindrical mesostructure from zone annealing. Thermal zone annealing provides a simple methodology to produce highly ordered and macroscopically oriented stable mesoporous carbon films, but the efficacy is strongly tied to the mobility of the template during the zone annealing.Surfactant or block copolymer-templated mesoporous films have been extensively explored, but achieving mesostructure coherence and unidirectional orientation over macroscopic dimensions has remained quite challenging for these self-assembled systems. Here, we extend the concepts associated with zone refinement of crystalline materials to soft templated mesoporous carbon films based on the cooperative assembly of commercial non-ionic surfactants (block copolymers) and phenolic resin oligomers (resol) to provide macroscopic alignment of both cubic (FDU-16) and hexagonal (FDU-15) mesostructures. The average orientation of these mesophases is determined from rotation grazing incidence small angle X-ray scattering (GISAXS) measurements. For FDU-15 templated by Pluronic P123, the orientation factor for the zone-annealed film is 0.98 based on the average of the second Legendre polynomial, but this orientation deteriorates significantly during carbonization. Notably, a thermal stabilization step following zone annealing preserves the orientation of the mesostructure during carbonization. The orientation factor for an isotropic cubic structure (FDU-16 templated by Pluronic F127) is only 0.48 (based on the 111 reflection with incident angle 0.15°) for the same zone annealing protocol, but this illustrates the versatility of zone annealing to different mesostructures. Unexpectedly, zone annealing of FDU-15 templated by Pluronic F127 leads to stabilization of the mesostructure through carbonization, whereas this structure collapses fully during carbonization even after extended oven annealing; despite no clear macroscopic orientation of the cylindrical mesostructure from zone annealing. Thermal zone annealing provides a simple methodology to produce highly ordered and macroscopically oriented stable mesoporous carbon films, but the efficacy is strongly tied to the mobility of the template during the zone annealing. Electronic supplementary information (ESI) available: GISAXS profiles for the FDU-15-F127 at φ = 0° and φ = 90° is included along with 2D GISAXS data for all azimuthal data associated with FDU-15-P123 to illustrate the azimuthal dependence on the diffraction patterns. See DOI: 10.1039/c3nr02821f

Orientation-controlled parallel assembly at the air-water interface

NASA Astrophysics Data System (ADS)

Park, Kwang Soon; Hao Hoo, Ji; Baskaran, Rajashree; Böhringer, Karl F.

2012-10-01

This paper presents an experimental and theoretical study with statistical analysis of a high-yield, orientation-specific fluidic self-assembly process on a preprogrammed template. We demonstrate self-assembly of thin (less than few hundred microns in thickness) parts, which is vital for many applications in miniaturized platforms but problematic for today's pick-and-place robots. The assembly proceeds row-by-row as the substrate is pulled up through an air-water interface. Experiments and analysis are presented with an emphasis on the combined effect of controlled surface waves and magnetic force. For various gap values between a magnet and Ni-patterned parts, magnetic force distributions are generated using Monte Carlo simulation and employed to predict assembly yield. An analysis of these distributions shows that a gradual decline in yield following the probability density function can be expected with degrading conditions. The experimentally determined critical magnetic force is in good agreement with a derived value from a model of competing forces acting on a part. A general set of design guidelines is also presented from the developed model and experimental data.

A Generic Self-Assembly Process in Microcompartments and Synthetic Protein Nanotubes.

PubMed

Uddin, Ismail; Frank, Stefanie; Warren, Martin J; Pickersgill, Richard W

2018-05-01

Bacterial microcompartments enclose a biochemical pathway and reactive intermediate within a protein envelope formed by the shell proteins. Herein, the orientation of the propanediol-utilization (Pdu) microcompartment shell protein PduA in bacterial microcompartments and in synthetic nanotubes, and the orientation of PduB in synthetic nanotubes are revealed. When produced individually, PduA hexamers and PduB trimers, tessellate to form flat sheets in the crystal, or they can self-assemble to form synthetic protein nanotubes in solution. Modelling the orientation of PduA in the 20 nm nanotube so as to preserve the shape complementarity and key interactions seen in the crystal structure suggests that the concave surface of the PduA hexamer faces out. This orientation is confirmed experimentally in synthetic nanotubes and in the bacterial microcompartment produced in vivo. The PduB nanotubes described here have a larger diameter, 63 nm, with the concave surface of the trimer again facing out. The conserved concave surface out characteristic of these nano-structures reveals a generic assembly process that causes the interface between adjacent subunits to bend in a common direction that optimizes shape complementarity and minimizes steric clashes. This understanding underpins engineering strategies for the biotechnological application of protein nanotubes. © 2018 The Authors. Published by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Watching Nanoscale Self-Assembly Kinetics of Gold Prisms in Liquids

NASA Astrophysics Data System (ADS)

Kim, Juyeong; Ou, Zihao; Jones, Matthew R.; Chen, Qian

We use liquid-phase transmission electron microscopy to watch self-assembly of gold triangular prisms into polymer-like structures. The in situ dynamics monitoring enabled by liquid-phase transmission electron microscopy, single nanoparticle tracking, and the marked conceptual similarity between molecular reactions and nanoparticle self-assembly combined elucidate the following mechanistic understanding: a step-growth polymerization based assembly statistics, kinetic pathways sampling particle curvature dependent energy minima and their interconversions, and directed assembly into polymorphs (linear or cyclic chains) through in situ modulation of the prism bonding geometry. Our study bridges the constituent kinetics on the molecular and nanoparticle length scales, which enriches the design rules in directed self-assembly of anisotropic nanoparticles.

Characterization and kinetics of surface functionalization and binding of biologically and chemically significant molecules

NASA Astrophysics Data System (ADS)

Steiner, Rachel

The purpose of this project is to investigate intermolecular interactions of organic molecular assemblies. By understanding the structure and physical interactions in these assemblies, we gain insights into practical applications for nanoscale systems built upon these surface structures. It is possible for organic chemists to create many forms of modified organic molecules, functionalizing them with specific reactive end groups. Through surface functionalization, enabling covalent or highly associative binding, it is possible to create ordered molecular assemblies of these molecules. Scientists can study the nature of this structure and the intermolecular interactions through spectroscopic, optical, and scattering experiments. To understand the self-assembly process in molecular systems, we preliminarily created monolayer films on silica substrates with a variety of organic molecules. In particular, we functionalized silica substrates with hydroxyl groups and covalently bound acid chloride functionalized aromatic compounds, with and without an underlying adhesion layer of 3-aminopropyltriethoxysilane. We characterized the monolayer assemblies with ellipsometry, UV-vis absorption spectroscopy, FTIR spectroscopy, and fluorescence/photoemission spectroscopy, obtaining a quantitative measure of the molecular surface coverage. In order to understand the nature of these molecular assemblies, we also pursued an in-depth kinetic study to control and optimize the monolayer formation process. Through use of UV-vis spectroscopy, we determined that the monolayer formation can best be modeled with diffusion-limited Langmuir kinetics. Specifically, we concluded that for anthracene acid chloride in dichloromethane the average diffusion coefficient was 1.6x10-7 cm2/sec. Additionally, we find we are able to achieve surface coverages of approximately 2x1014 molecules/cm2. Having established the ability to create ordered molecular assemblies, through surface functionalization, enabling covalent or highly associative binding, we continued to explore the field of molecular assemblies by studying the binding and structure of molecules to carbon nanostructures. Previous studies have shown that alkyl side chains and aromatic compounds, such as pyrene, will bind non-covalently to the sidewalls of carbon nanotubes through pi-pi interactions. We explored functionalization of carbon nanotubes and graphene by using microscopy to examine the adsorption of biomolecules onto nanotube sidewalls and graphene.

Self-assembled squares and triangles by simultaneous hydrogen bonding and metal coordination.

PubMed

Marshall, Laura J; de Mendoza, Javier

2013-04-05

Through the combination of hydrogen bonding and metal-templated self-assembly, molecular squares and molecular triangles are observed in chloroform solution upon the complexation of hydrogen-bonded dimers of para-pyridyl-substituted 2-ureido-4-[1H]-pyrimidinone (UPy) and an appropriate cis-substituted palladium complex. Molecular modeling studies and NMR analysis confirmed the presence of two distinct structures in solution: the tubular structure of the molecular square and propeller-bowl structure of the molecular triangle.

Programming molecular self-assembly of intrinsically disordered proteins containing sequences of low complexity

NASA Astrophysics Data System (ADS)

Simon, Joseph R.; Carroll, Nick J.; Rubinstein, Michael; Chilkoti, Ashutosh; López, Gabriel P.

2017-06-01

Dynamic protein-rich intracellular structures that contain phase-separated intrinsically disordered proteins (IDPs) composed of sequences of low complexity (SLC) have been shown to serve a variety of important cellular functions, which include signalling, compartmentalization and stabilization. However, our understanding of these structures and our ability to synthesize models of them have been limited. We present design rules for IDPs possessing SLCs that phase separate into diverse assemblies within droplet microenvironments. Using theoretical analyses, we interpret the phase behaviour of archetypal IDP sequences and demonstrate the rational design of a vast library of multicomponent protein-rich structures that ranges from uniform nano-, meso- and microscale puncta (distinct protein droplets) to multilayered orthogonally phase-separated granular structures. The ability to predict and program IDP-rich assemblies in this fashion offers new insights into (1) genetic-to-molecular-to-macroscale relationships that encode hierarchical IDP assemblies, (2) design rules of such assemblies in cell biology and (3) molecular-level engineering of self-assembled recombinant IDP-rich materials.

Subtle balance of tropoelastin molecular shape and flexibility regulates dynamics and hierarchical assembly.

PubMed

Yeo, Giselle C; Tarakanova, Anna; Baldock, Clair; Wise, Steven G; Buehler, Markus J; Weiss, Anthony S

2016-02-01

The assembly of the tropoelastin monomer into elastin is vital for conferring elasticity on blood vessels, skin, and lungs. Tropoelastin has dual needs for flexibility and structure in self-assembly. We explore the structure-dynamics-function interplay, consider the duality of molecular order and disorder, and identify equally significant functional contributions by local and global structures. To study these organizational stratifications, we perturb a key hinge region by expressing an exon that is universally spliced out in human tropoelastins. We find a herniated nanostructure with a displaced C terminus and explain by molecular modeling that flexible helices are replaced with substantial β sheets. We see atypical higher-order cross-linking and inefficient assembly into discontinuous, thick elastic fibers. We explain this dysfunction by correlating local and global structural effects with changes in the molecule's assembly dynamics. This work has general implications for our understanding of elastomeric proteins, which balance disordered regions with defined structural modules at multiple scales for functional assembly.

Mesoscale Graphene-like Honeycomb Mono- and Multilayers Constructed via Self-Assembly of Coclusters.

PubMed

Hou, Xue-Sen; Zhu, Guo-Long; Ren, Li-Jun; Huang, Zi-Han; Zhang, Rui-Bin; Ungar, Goran; Yan, Li-Tang; Wang, Wei

2018-02-07

Honeycomb structure endows graphene with extraordinary properties. But could a honeycomb monolayer superlattice also be generated via self-assembly of colloids or nanoparticles? Here we report the construction of mono- and multilayer molecular films with honeycomb structure that can be regarded as self-assembled artificial graphene (SAAG). We construct fan-shaped molecular building blocks by covalently connecting two kinds of clusters, one polyoxometalate and four polyhedral oligomeric silsesquioxanes. The precise shape control enables these complex molecules to self-assemble into a monolayer 2D honeycomb superlattice that mirrors that of graphene but on the mesoscale. The self-assembly of the SAAG was also reproduced via coarse-grained molecular simulations of a fan-shaped building block. It revealed a hierarchical process and the key role of intermediate states in determining the honeycomb structure. Experimental images also show a diversity of bi- and trilayer stacking modes. The successful creation of SAAG and its stacks opens up prospects for the preparation of novel self-assembled nanomaterials with unique properties.

Effect of orientation on deformation behavior of Fe nanowires: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Sainath, G.; Srinivasan, V. S.; Choudhary, B. K.; Mathew, M. D.; Jayakumar, T.

2014-04-01

Molecular dynamics simulations have been carried out to study the effect of crystal orientation on tensile deformation behaviour of single crystal BCC Fe nanowires at 10 K. Two nanowires with an initial orientation of <100>/{100} and <110>/{111} have been chosen for this study. The simulation results show that the deformation mechanisms varied with crystal orientation. The nanowire with an initial orientation of <100>/{100} deforms predominantly by twinning mechanism, whereas the nanowire oriented in <110>/{111}, deforms by dislocation plasticity. In addition, the single crystal oriented in <110>/{111} shows higher strength and elastic modulus than <100>/{100} oriented nanowire.

Probing molecular orientation of P3HT nanofibers in fiber-based organic solar cells

NASA Astrophysics Data System (ADS)

Yoon, Sangcheol; Han, Yaeeun; Hwang, Inchan

2018-01-01

Molecular orientation of conjugated polymers plays a key role in exciton generation/separation and charge transport, and thus significantly influence photovoltaic devices. Herein, we fabricated fiber-based organic solar cells and investigated the photovoltaic parameters with different diameters of fibers and PCBM diffusion. The open-circuit voltage that varies with molecular orientation whether it is face-on or edge-on was observed to differ. The investigation of the open-circuit voltage dependence reveals that thick fibers have core/shell like structures with different orientations. Thick fibers have face-on in the core and edge-on orientations in the shell. The face-on orientations are not preferentially formed in thin fibers, but the PCBM diffusion can induce face-on orientations that exist within the intermixed phase. Our results may shed a light on better understanding on fiber-based solar cells and suggest a way toward improving photovoltaic efficiency. [Figure not available: see fulltext.

Highly luminescent colloidal nanoplates of perovskite cesium lead halide and their oriented assemblies

DOE PAGES

Bekenstein, Yehonadav; Koscher, Brent A.; Eaton, Samuel W.; ...

2015-12-15

Anisotropic colloidal quasi-two-dimensional nanoplates (NPLs) hold great promise as functional materials due to their combination of low dimensional optoelectronic properties and versatility through colloidal synthesis. Recently, lead-halide perovskites have emerged as important optoelectronic materials with excellent efficiencies in photovoltaic and light-emitting applications. Here we report the synthesis of quantum confined all inorganic cesium lead halide nanoplates in the perovskite crystal structure that are also highly luminescent (PLQY 84%). The controllable self-assembly of nanoplates either into stacked columnar phases or crystallographic-oriented thin-sheet structures is demonstrated. Furthermore, the broad accessible emission range, high native quantum yields, and ease of self-assembly make perovskitemore » NPLs an ideal platform for fundamental optoelectronic studies and the investigation of future devices.« less

Effect of Time and Deposition Method on Quality of Phosphonic Acid Modifier Self-Assembled Monolayers on Indium Zinc Oxide

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

Sang, Lingzi; Knesting, Kristina M.; Bulusu, Anuradha

Phosphonic acid (PA) self-assembled monolayers (SAMs) are utilized at critical interfaces between transparent conductive oxides (TCO) and organic active layers in organic photovoltaic devices (OPVs). The effects of PA deposition method and time on the formation of close-packed, high-quality monolayers is investigated here for SAMs fabricated by solution deposition, micro-contact printing, and spray coating. The solution deposition isotherm for pentafluorinated benzylphosphonic acid (F5BnPA) on indium-doped zinc oxide (IZO) is studied using polarization modulation-infrared reflection-absorption spectroscopy (PM-IRRAS) at room temperature as a model PA/IZO system. Fast surface adsorption occurs within the first min; however, well-oriented high-quality SAMs are reached only aftermore » -48 h, presumably through a continual process of molecular adsorption/desorption and monolayer filling accompanied by molecular reorientation. Two other rapid, soak-free deposition techniques, micro-contact printing and spray coating, are also explored. SAM quality is compared for deposition of phenyl phosphonic acid (PPA), F13-octylphosphonic acid (F13OPA), and pentafluorinated benzyl phosphonic acid (F5BnPA) by solution deposition, micro-contact printing and spray coating using PM-IRRAS. In contrast to micro-contact printing and spray coating techniques, 48-168 h solution deposition at both room temperature and 70 degrees C result in contamination- and surface etch-free close-packed monolayers with good reproducibility. SAMs fabricated by micro-contact printing and spray coating are much less well ordered.« less

Ultrafast electron transfer at organic semiconductor interfaces: Importance of molecular orientation

DOE PAGES

Ayzner, Alexander L.; Nordlund, Dennis; Kim, Do -Hwan; ...

2014-12-04

Much is known about the rate of photoexcited charge generation in at organic donor/acceptor (D/A) heterojunctions overaged over all relative arrangements. However, there has been very little experimental work investigating how the photoexcited electron transfer (ET) rate depends on the precise relative molecular orientation between D and A in thin solid films. This is the question that we address in this work. We find that the ET rate depends strongly on the relative molecular arrangement: The interface where the model donor compound copper phthalocyanine is oriented face-on with respect to the fullerene C 60 acceptor yields a rate that ismore » approximately 4 times faster than that of the edge-on oriented interface. Our results suggest that the D/A electronic coupling is significantly enhanced in the face-on case, which agrees well with theoretical predictions, underscoring the importance of controlling the relative interfacial molecular orientation.« less

Carrier-envelope phase-dependent field-free molecular orientation

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

Shu Chuancun; Yuan Kaijun; Hu Wenhui

2009-07-15

We present a strategy to achieve carrier-envelope phase-dependent field-free molecular orientation with the use of carrier-envelope phase (CEP) stabilization and asymmetric few-cycle terahertz (THz) laser pulses. The calculations are performed on the LiH molecule by an exact solution of the full time-dependent Schroedinger equation including both the vibrational and the rotational degrees of freedom. Our calculations show that an efficient field-free molecular orientation can be obtained even at considerable temperatures. Moreover, we find a simple dependence of the field-free orientation on the CEP, which implies that the CEP becomes an important parameter for control of molecular orientation. More importantly, themore » realization of this scenario is appealing based on the fact that the intense few-cycle THz pulse with duration as short as a few optical cycles is available as a research tool.« less

Molecular orientation in a dielectric liquid-vapor interphase

NASA Astrophysics Data System (ADS)

Chacón, E.; Mederos, L.; Navascués, G.; Tarazona, P.

1985-04-01

The density functional theory of Chacón et al. is used to study the molecular orientation in an interphase of a weak dipolar fluid. Explicit expressions are obtained using standard perturbation techniques. Molecular orientation, local susceptibility, and the Gibbsean surface susceptibility are evaluated for a Stockmayer model of dipolar fluid. The effect of the surface structure on the bulk ferroelectric transition is discussed in the light of the present theory and the numerical results.

Orientations of nonlocal vibrational modes from combined experimental and theoretical sum frequency spectroscopy

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

Chase, Hilary M.; Chen, Shunli; Fu, Li

2017-09-01

Inferring molecular orientations from vibrational sum frequency generation (SFG) spectra is challenging in polarization combinations that result in low signal intensities, or when the local point group symmetry approximation fails. While combining experiments with density functional theory (DFT) could overcome this problem, the scope of the combined method has yet to be established. Here, we assess its feasibility of determining the distributions of molecular orientations for one monobasic ester, two epoxides and three alcohols at the vapor/fused silica interface. We find that molecular orientations of nonlocal vibrational modes cannot be determined using polarization-resolved SFG measurements alone.

Rational Design of Molecular Gelator - Solvent Systems Guided by Solubility Parameters

NASA Astrophysics Data System (ADS)

Lan, Yaqi

Self-assembled architectures, such as molecular gels, have attracted wide interest among chemists, physicists and engineers during the past decade. However, the mechanism behind self-assembly remains largely unknown and no capability exists to predict a priori whether a small molecule will gelate a specific solvent or not. The process of self-assembly, in molecular gels, is intricate and must balance parameters influencing solubility and those contrasting forces that govern epitaxial growth into axially symmetric elongated aggregates. Although the gelator-gelator interactions are of paramount importance in understanding gelation, the solvent-gelator specific (i.e., H-bonding) and nonspecific (dipole-dipole, dipole-induced and instantaneous dipole induced forces) intermolecular interactions are equally important. Solvent properties mediate the self-assembly of molecular gelators into their self-assembled fibrillar networks. Herein, solubility parameters of solvents, ranging from partition coefficients (logP), to Henry's law constants (HLC), to solvatochromic ET(30) parameters, to Kamlet-Taft parameters (beta, alpha and pi), to Hansen solubility parameters (deltap, deltad, deltah), etc., are correlated with the gelation ability of numerous classes of molecular gelators. Advanced solvent clustering techniques have led to the development of a priori tools that can identify the solvents that will be gelled and not gelled by molecular gelators. These tools will greatly aid in the development of novel gelators without solely relying on serendipitous discoveries.

Light-Induced Conversion of Chemical Permeability to Enhance Electron and Molecular Transfer in Nanoscale Assemblies

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

Balgley, Renata; de Ruiter, Graham; Evmenenko, Guennadi

In this paper, we demonstrate how photochemically enhancing the permeability of metal–organic assemblies results in a significant enhancement of the electrochemical activity of metal complexes located within the assembly. The molecular assemblies consist of different layers of redox-active metal complexes ([M(mbpy-py)3][PF6]2; M = Ru or Os) that are separated by redox-inactive spacers consisting of 1,4-bis[2-(4-pyridyl)ethenyl]benzene (BPEB) and PdCl2 of variable thicknesses (0–13.4 nm). UV-irradiation (λ = 254 nm) of our assemblies induces a photochemical reaction in the redox-inactive spacer increasing the permeability of the assembly. The observed increase was evident by trapping organic (nBu4NBF4) and inorganic (NiCl2) salts inside themore » assemblies, and by evaluating the electrochemical response of quinones absorbed inside the molecular assemblies before and after UV irradiation. The increase in permeability is reflected by higher currents and a change in the directionality of electron transfer, i.e., from mono- to bidirectional, between the redox-active metal complexes and the electrode surface. The supramolecular structure of the assemblies dominates the overall electron transfer properties and overrules possible electron transfer mediated by the extensive π-conjugation of its individual organic components.« less

Oriented antibody immobilization on self-assembled monolayers applied as impedance biosensors

NASA Astrophysics Data System (ADS)

Tsugimura, Kaiki; Ohnuki, Hitoshi; Wu, Haiyun; Endo, Hideaki; Tsuya, Daiju; Izumi, Mitsuru

2017-11-01

Oriented immobilization of antibodies on a sensor chip is crucial for enhancing both the sensitivity and antigen-binding capacity of immunosensors. Here, we report a comparative study of the effect of oriented and random antibody immobilization on the binding efficiency by electrochemical impedance spectroscopy (EIS). Oriented immobilization of anti-myoglobin immunoglobulin G (anti-Myo IgG) was achieved by bonding to an Fc receptor of protein G (PrG) on a self-assembled monolayer (SAM), which results in the myoglobin (Myo) binding sites being exposed outside the sensing surface. Random immobilization of anti-Myo IgG was achieved by direct covalent attachment to the SAM surface. Both immobilizations were applied to interdigitated electrodes to enhance the electrochemical signal, and the Myo biosensor performance was then evaluated by a series of EIS measurements. We found that (i) the rate of the normalized charge transfer resistance for the oriented sample was 3 times higher than that for the random sample and (ii) the detection limit was 0.001 ng/mL, which is the lowest recorded detection limit among Myo immunosensors based on EIS. These findings indicate that oriented antibody immobilization is crucial for preparing highly sensitive EIS-based biosensors.

Photoresponse of supramolecular self-assembled networks on graphene-diamond interfaces.

PubMed

Wieghold, Sarah; Li, Juan; Simon, Patrick; Krause, Maximilian; Avlasevich, Yuri; Li, Chen; Garrido, Jose A; Heiz, Ueli; Samorì, Paolo; Müllen, Klaus; Esch, Friedrich; Barth, Johannes V; Palma, Carlos-Andres

2016-02-25

Nature employs self-assembly to fabricate the most complex molecularly precise machinery known to man. Heteromolecular, two-dimensional self-assembled networks provide a route to spatially organize different building blocks relative to each other, enabling synthetic molecularly precise fabrication. Here we demonstrate optoelectronic function in a near-to-monolayer molecular architecture approaching atomically defined spatial disposition of all components. The active layer consists of a self-assembled terrylene-based dye, forming a bicomponent supramolecular network with melamine. The assembly at the graphene-diamond interface shows an absorption maximum at 740 nm whereby the photoresponse can be measured with a gallium counter electrode. We find photocurrents of 0.5 nA and open-circuit voltages of 270 mV employing 19 mW cm(-2) irradiation intensities at 710 nm. With an ex situ calculated contact area of 9.9 × 10(2) μm(2), an incident photon to current efficiency of 0.6% at 710 nm is estimated, opening up intriguing possibilities in bottom-up optoelectronic device fabrication with molecular resolution.

Molecular Origins of Thermal Transitions in Polyelectrolyte Assemblies

NASA Astrophysics Data System (ADS)

Yildirim, Erol; Zhang, Yanpu; Antila, Hanne S.; Lutkenhaus, Jodie L.; Sammalkorpi, Maria; Aalto Team; Texas A&M Team

2015-03-01

Polyelectrolyte (PE) multilayers and complexes formed from oppositely charged polymers can exhibit extraordinary superhydrophobicity, mechanical strength and responsiveness resulting in applications ranging functional membranes, optics, sensors and drug delivery. Depending on the assembly conditions, PE assemblies may undergo a thermal transition from glassy to soft behavior under heating. Our earlier work using thermal analysis measurements shows a distinct thermal transition for PE layer-by-layer (LbL) systems assembled with added salt but no analogous transition in films assembled without added salt or dry systems. These findings raise interesting questions on the nature of the thermal transition; here, we explore its molecular origins through characterization of the PE aggregates by temperature-controlled all-atom molecular dynamics simulations. We show via molecular simulations the thermal transition results from the existence of an LCST (lower critical solution temperature) in the PE systems: the diffusion behavior, hydrogen bond formation, and bridging capacity of water molecules plasticizing the complex changes at the transition temperature. We quantify the behavior, map its chemistry specificity through comparison of strongly and weakly charged PE complexes, and connect the findings to our interrelated QCM-D experiments.

Photoresponse of supramolecular self-assembled networks on graphene–diamond interfaces

PubMed Central

Wieghold, Sarah; Li, Juan; Simon, Patrick; Krause, Maximilian; Avlasevich, Yuri; Li, Chen; Garrido, Jose A.; Heiz, Ueli; Samorì, Paolo; Müllen, Klaus; Esch, Friedrich; Barth, Johannes V.; Palma, Carlos-Andres

2016-01-01

Nature employs self-assembly to fabricate the most complex molecularly precise machinery known to man. Heteromolecular, two-dimensional self-assembled networks provide a route to spatially organize different building blocks relative to each other, enabling synthetic molecularly precise fabrication. Here we demonstrate optoelectronic function in a near-to-monolayer molecular architecture approaching atomically defined spatial disposition of all components. The active layer consists of a self-assembled terrylene-based dye, forming a bicomponent supramolecular network with melamine. The assembly at the graphene-diamond interface shows an absorption maximum at 740 nm whereby the photoresponse can be measured with a gallium counter electrode. We find photocurrents of 0.5 nA and open-circuit voltages of 270 mV employing 19 mW cm−2 irradiation intensities at 710 nm. With an ex situ calculated contact area of 9.9 × 102 μm2, an incident photon to current efficiency of 0.6% at 710 nm is estimated, opening up intriguing possibilities in bottom-up optoelectronic device fabrication with molecular resolution. PMID:26911248

Reversible and oriented immobilization of ferrocene-modified proteins.

PubMed

Yang, Lanti; Gomez-Casado, Alberto; Young, Jacqui F; Nguyen, Hoang D; Cabanas-Danés, Jordi; Huskens, Jurriaan; Brunsveld, Luc; Jonkheijm, Pascal

2012-11-21

Adopting supramolecular chemistry for immobilization of proteins is an attractive strategy that entails reversibility and responsiveness to stimuli. The reversible and oriented immobilization and micropatterning of ferrocene-tagged yellow fluorescent proteins (Fc-YFPs) onto β-cyclodextrin (βCD) molecular printboards was characterized using surface plasmon resonance (SPR) spectroscopy and fluorescence microscopy in combination with electrochemistry. The proteins were assembled on the surface through the specific supramolecular host-guest interaction between βCD and ferrocene. Application of a dynamic covalent disulfide lock between two YFP proteins resulted in a switch from monovalent to divalent ferrocene interactions with the βCD surface, yielding a more stable protein immobilization. The SPR titration data for the protein immobilization were fitted to a 1:1 Langmuir-type model, yielding K(LM) = 2.5 × 10(5) M(-1) and K(i,s) = 1.2 × 10(3) M(-1), which compares favorably to the intrinsic binding constant presented in the literature for the monovalent interaction of ferrocene with βCD self-assembled monolayers. In addition, the SPR binding experiments were qualitatively simulated, confirming the binding of Fc-YFP in both divalent and monovalent fashion to the βCD monolayers. The Fc-YFPs could be patterned on βCD surfaces in uniform monolayers, as revealed using fluorescence microscopy and atomic force microscopy measurements. Both fluorescence microscopy imaging and SPR measurements were carried out with the in situ capability to perform cyclic voltammetry and chronoamperometry. These studies emphasize the repetitive desorption and adsorption of the ferrocene-tagged proteins from the βCD surface upon electrochemical oxidation and reduction, respectively.

On the predictability of the orientation of protein domains joined by a spanning alpha-helical linker.

PubMed

Lai, Yen-Ting; Jiang, Lin; Chen, Wuyang; Yeates, Todd O

2015-11-01

Connecting proteins together in prescribed geometric arrangements is an important element in new areas of biomolecular design. In this study, we characterize the degree of three-dimensional orientational control that can be achieved when two protein domains that have alpha-helical termini are joined using an alpha-helical linker. A fusion between naturally oligomeric protein domains was designed in this fashion with the intent of creating a self-assembling 12-subunit tetrahedral protein cage. While the designed fusion protein failed to assemble into a tetrahedral cage in high yield, a series of crystal structures showed that the two fused components were indeed bridged by an intact alpha helix, although the fusion protein was distorted from the intended ideal configuration by bending of the helix, ranging from 7 to 35°. That range of deviation in orientation creates challenges for designing large, perfectly symmetric protein assemblies, although it should offer useful outcomes for other less geometrically demanding applications in synthetic biology. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Curvature-driven capillary migration and assembly of rod-like particles

PubMed Central

Cavallaro, Marcello; Botto, Lorenzo; Lewandowski, Eric P.; Wang, Marisa; Stebe, Kathleen J.

2011-01-01

Capillarity can be used to direct anisotropic colloidal particles to precise locations and to orient them by using interface curvature as an applied field. We show this in experiments in which the shape of the interface is molded by pinning to vertical pillars of different cross-sections. These interfaces present well-defined curvature fields that orient and steer particles along complex trajectories. Trajectories and orientations are predicted by a theoretical model in which capillary forces and torques are related to Gaussian curvature gradients and angular deviations from principal directions of curvature. Interface curvature diverges near sharp boundaries, similar to an electric field near a pointed conductor. We exploit this feature to induce migration and assembly at preferred locations, and to create complex structures. We also report a repulsive interaction, in which microparticles move away from planar bounding walls along curvature gradient contours. These phenomena should be widely useful in the directed assembly of micro- and nanoparticles with potential application in the fabrication of materials with tunable mechanical or electronic properties, in emulsion production, and in encapsulation. PMID:22184218

Making Macroscopic Assemblies of Aligned Carbon Nanotubes

NASA Technical Reports Server (NTRS)

Smalley, Richard E.; Colbert, Daniel T.; Smith, Ken A.; Walters, Deron A.; Casavant, Michael J.; Qin, Xiaochuan; Yakobson, Boris; Hauge, Robert H.; Saini, Rajesh Kumar; Chiung, Wan-Ting;

Free-standing supramolecular hydrogel objects by reaction-diffusion

PubMed Central

Lovrak, Matija; Hendriksen, Wouter E. J.; Maity, Chandan; Mytnyk, Serhii; van Steijn, Volkert; Eelkema, Rienk; van Esch, Jan H.

2017-01-01

Self-assembly provides access to a variety of molecular materials, yet spatial control over structure formation remains difficult to achieve. Here we show how reaction–diffusion (RD) can be coupled to a molecular self-assembly process to generate macroscopic free-standing objects with control over shape, size, and functionality. In RD, two or more reactants diffuse from different positions to give rise to spatially defined structures on reaction. We demonstrate that RD can be used to locally control formation and self-assembly of hydrazone molecular gelators from their non-assembling precursors, leading to soft, free-standing hydrogel objects with sizes ranging from several hundred micrometres up to centimeters. Different chemical functionalities and gradients can easily be integrated in the hydrogel objects by using different reactants. Our methodology, together with the vast range of organic reactions and self-assembling building blocks, provides a general approach towards the programmed fabrication of soft microscale objects with controlled functionality and shape. PMID:28580948

A highly oriented hybrid microarray modified electrode fabricated by a template-free method for ultrasensitive electrochemical DNA recognition

NASA Astrophysics Data System (ADS)

Shi, Lei; Chu, Zhenyu; Dong, Xueliang; Jin, Wanqin; Dempsey, Eithne

2013-10-01

Highly oriented growth of a hybrid microarray was realized by a facile template-free method on gold substrates for the first time. The proposed formation mechanism involves an interfacial structure-directing force arising from self-assembled monolayers (SAMs) between gold substrates and hybrid crystals. Different SAMs and variable surface coverage of the assembled molecules play a critical role in the interfacial directing forces and influence the morphologies of hybrid films. A highly oriented hybrid microarray was formed on the highly aligned and vertical SAMs of 1,4-benzenedithiol molecules with rigid backbones, which afforded an intense structure-directing power for the oriented growth of hybrid crystals. Additionally, the density of the microarray could be adjusted by controlling the surface coverage of assembled molecules. Based on the hybrid microarray modified electrode with a large specific area (ca. 10 times its geometrical area), a label-free electrochemical DNA biosensor was constructed for the detection of an oligonucleotide fragment of the avian flu virus H5N1. The DNA biosensor displayed a significantly low detection limit of 5 pM (S/N = 3), a wide linear response from 10 pM to 10 nM, as well as excellent selectivity, good regeneration and high stability. We expect that the proposed template-free method can provide a new reference for the fabrication of a highly oriented hybrid array and the as-prepared microarray modified electrode will be a promising paradigm in constructing highly sensitive and selective biosensors.Highly oriented growth of a hybrid microarray was realized by a facile template-free method on gold substrates for the first time. The proposed formation mechanism involves an interfacial structure-directing force arising from self-assembled monolayers (SAMs) between gold substrates and hybrid crystals. Different SAMs and variable surface coverage of the assembled molecules play a critical role in the interfacial directing forces and influence the morphologies of hybrid films. A highly oriented hybrid microarray was formed on the highly aligned and vertical SAMs of 1,4-benzenedithiol molecules with rigid backbones, which afforded an intense structure-directing power for the oriented growth of hybrid crystals. Additionally, the density of the microarray could be adjusted by controlling the surface coverage of assembled molecules. Based on the hybrid microarray modified electrode with a large specific area (ca. 10 times its geometrical area), a label-free electrochemical DNA biosensor was constructed for the detection of an oligonucleotide fragment of the avian flu virus H5N1. The DNA biosensor displayed a significantly low detection limit of 5 pM (S/N = 3), a wide linear response from 10 pM to 10 nM, as well as excellent selectivity, good regeneration and high stability. We expect that the proposed template-free method can provide a new reference for the fabrication of a highly oriented hybrid array and the as-prepared microarray modified electrode will be a promising paradigm in constructing highly sensitive and selective biosensors. Electronic supplementary information (ESI) available: Four-probe method for determining the conductivity of the hybrid crystal (Fig. S1); stability comparisons of the hybrid films (Fig. S2); FESEM images of the hybrid microarray (Fig. S3); electrochemical characterizations of the hybrid films (Fig. S4); DFT simulations (Fig. S5); cross-sectional FESEM image of the hybrid microarray (Fig. S6); regeneration and stability tests of the DNA biosensor (Fig. S7). See DOI: 10.1039/c3nr03097k

Reprogrammable Assembly of Molecular Motor on Solid Surfaces via Dynamic Bonds.

PubMed

Yu, Li; Sun, Jian; Wang, Qian; Guan, Yan; Zhou, Le; Zhang, Jingxuan; Zhang, Lanying; Yang, Huai

2017-06-01

Controllable assembly of molecular motors on solid surfaces is a fundamental issue for providing them to perform physical tasks. However, it can hardly be achieved by most previous methods due to their inherent limitations. Here, a general strategy is designed for the reprogrammable assembly of molecular motors on solid surfaces based on dynamic bonds. In this method, molecular motors with disulfide bonds can be remotely, reversibly, and precisely attached to solid surfaces with disulfide bonds, regardless of their chemical composition and microstructure. More importantly, it not only allows encoding geometric information referring to a pattern of molecular motors, but also enables erasing and re-encoding of geometric information via hemolytic photocleavage and recombination of disulfide bonds. Thus, solid surfaces can be regarded as "computer hardware", where molecular motors can be reformatted and reprogramed as geometric information. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Coalescence and Collisions of Gold Nanoparticles

PubMed Central

Antúnez-García, Joel; Mejía-Rosales, Sergio; Pérez-Tijerina, Eduardo; Montejano-Carrizales, Juan Martín; José-Yacamán, Miguel

2011-01-01

We study the assembling of small gold clusters subject to collisions and close contact coalescence by using molecular dynamics simulations to simulate events that occur typically in the sputtering process of synthesis. Our results support the notion that the kinetics of coalescence processes strongly determine the geometry and structure of the final particle. While impact velocities, relative orientations, and the initial shape of the interacting particles are unlikely to strictly determine the structural details of the newly formed particle, we found that high initial temperatures and/or impact velocities increase the probability of appearance of icosahedral-like structures, Wulff polyhedra are likely to be formed as a product of the interactions between nanospheres, while the appearance of fcc particles of approximately cuboctahedral shape is mainly due to the interaction between icosahedra. PMID:28879995

Coalescence and Collisions of Gold Nanoparticles.

PubMed

Antúnez-García, Joel; Mejía-Rosales, Sergio; Pérez-Tijerina, Eduardo; Montejano-Carrizales, Juan Martín; José-Yacamán, Miguel

2011-01-28

We study the assembling of small gold clusters subject to collisions and close contact coalescence by using molecular dynamics simulations to simulate events that occur typically in the sputtering process of synthesis. Our results support the notion that the kinetics of coalescence processes strongly determine the geometry and structure of the final particle. While impact velocities, relative orientations, and the initial shape of the interacting particles are unlikely to strictly determine the structural details of the newly formed particle, we found that high initial temperatures and/or impact velocities increase the probability of appearance of icosahedral-like structures, Wulff polyhedra are likely to be formed as a product of the interactions between nanospheres, while the appearance of fcc particles of approximately cuboctahedral shape is mainly due to the interaction between icosahedra.

How cholesterol constrains glycolipid conformation for optimal recognition of Alzheimer's beta amyloid peptide (Abeta1-40).

PubMed

Yahi, Nouara; Aulas, Anaïs; Fantini, Jacques

2010-02-05

Membrane lipids play a pivotal role in the pathogenesis of Alzheimer's disease, which is associated with conformational changes, oligomerization and/or aggregation of Alzheimer's beta-amyloid (Abeta) peptides. Yet conflicting data have been reported on the respective effect of cholesterol and glycosphingolipids (GSLs) on the supramolecular assembly of Abeta peptides. The aim of the present study was to unravel the molecular mechanisms by which cholesterol modulates the interaction between Abeta(1-40) and chemically defined GSLs (GalCer, LacCer, GM1, GM3). Using the Langmuir monolayer technique, we show that Abeta(1-40) selectively binds to GSLs containing a 2-OH group in the acyl chain of the ceramide backbone (HFA-GSLs). In contrast, Abeta(1-40) did not interact with GSLs containing a nonhydroxylated fatty acid (NFA-GSLs). Cholesterol inhibited the interaction of Abeta(1-40) with HFA-GSLs, through dilution of the GSL in the monolayer, but rendered the initially inactive NFA-GSLs competent for Abeta(1-40) binding. Both crystallographic data and molecular dynamics simulations suggested that the active conformation of HFA-GSL involves a H-bond network that restricts the orientation of the sugar group of GSLs in a parallel orientation with respect to the membrane. This particular conformation is stabilized by the 2-OH group of the GSL. Correspondingly, the interaction of Abeta(1-40) with HFA-GSLs is strongly inhibited by NaF, an efficient competitor of H-bond formation. For NFA-GSLs, this is the OH group of cholesterol that constrains the glycolipid to adopt the active L-shape conformation compatible with sugar-aromatic CH-pi stacking interactions involving residue Y10 of Abeta(1-40). We conclude that cholesterol can either inhibit or facilitate membrane-Abeta interactions through fine tuning of glycosphingolipid conformation. These data shed some light on the complex molecular interplay between cell surface GSLs, cholesterol and Abeta peptides, and on the influence of this molecular ballet on Abeta-membrane interactions.

Amperometric biosensor for Salmonella typhimurium detection in milk

USDA-ARS?s Scientific Manuscript database

This paper reports an amperometric biosensor for rapid and sensitive Salmonella Typhimurium detection in milk. The biosensor was assembled from the self-assembled monolayers technique on a gold surface. In this device, polyclonal antibodies were oriented by protein A. The biosensor structure was cha...

DNA-templated photonic arrays and assemblies: design principles and future opportunities.

PubMed

Su, Wu; Bonnard, Vanessa; Burley, Glenn A

2011-07-11

Molecular photonics is a rapidly developing and multi-disciplinary field of research involving the construction of molecular assemblies comprising photoactive building blocks that are responsive to a light stimulus. A salient challenge in this field is the controlled assembly of these building blocks with nanoscale precision. DNA exhibits considerable promise as an architecture for the templated assembly of photoactive materials. In this Concept Article we describe the progress that has been made in the area of DNA photonics, in which DNA acts as a platform for the construction of optoelectronic assemblies, thin films and devices. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Control of liquid crystal molecular orientation using ultrasound vibration

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

Taniguchi, Satoki; Wave Electronics Research Center, Doshisha University, 1-3 Tataramiyakodani, Kyotanabe, Kyoto 610-0321; Koyama, Daisuke

2016-03-07

We propose a technique to control the orientation of nematic liquid crystals using ultrasound and investigate the optical characteristics of the oriented samples. An ultrasonic liquid crystal cell with a thickness of 5–25 μm and two ultrasonic lead zirconate titanate transducers was fabricated. By exciting the ultrasonic transducers, the flexural vibration modes were generated on the cell. An acoustic radiation force to the liquid crystal layer was generated, changing the molecular orientation and thus the light transmission. By modulating the ultrasonic driving frequency and voltage, the spatial distribution of the molecular orientation of the liquid crystals could be controlled. The distributionmore » of the transmitted light intensity depends on the thickness of the liquid crystal layer because the acoustic field in the liquid crystal layer is changed by the orientational film.« less

Self-Assembly of Organic Ferroelectrics by Evaporative Dewetting: A Case of β-Glycine.

PubMed

Seyedhosseini, Ensieh; Romanyuk, Konstantin; Vasileva, Daria; Vasilev, Semen; Nuraeva, Alla; Zelenovskiy, Pavel; Ivanov, Maxim; Morozovska, Anna N; Shur, Vladimir Ya; Lu, Haidong; Gruverman, Alexei; Kholkin, Andrei L

2017-06-14

Self-assembly of ferroelectric materials attracts significant interest because it offers a promising fabrication route to novel structures useful for microelectronic devices such as nonvolatile memories, integrated sensors/actuators, or energy harvesters. In this work, we demonstrate a novel approach for self-assembly of organic ferroelectrics (as exemplified by ferroelectric β-glycine) using evaporative dewetting, which allows forming quasi-regular arrays of nano- and microislands with preferred orientation of polarization axes. Surprisingly, self-assembled islands are crystallographically oriented in a radial direction from the center of organic "grains" formed during dewetting process. The kinetics of dewetting process follows the t -1/2 law, which is responsible for the observed polygon shape of the grain boundaries and island coverage as a function of radial position. The polarization in ferroelectric islands of β-glycine is parallel to the substrate and switchable under a relatively small dc voltage applied by the conducting tip of piezoresponse force microscope. Significant size effect on polarization is observed and explained within the Landau-Ginzburg-Devonshire phenomenological formalism.

Construction and direct electrochemistry of orientation controlled laccase electrode

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

Li, Ying; Zhang, Jiwei; Huang, Xirong, E-mail: xrhuang@sdu.edu.cn

2014-03-28

Highlights: • A recombinant laccase with Cys-6×His tag at the N or C terminus was generated. • Orientation controlled laccase electrodes were constructed via self assembly. • The electrochemical behavior of laccase electrodes was orientation dependent. • The C terminus tagged laccase was better for bioelectrocatalytic reduction of O{sub 2}. - Abstract: A laccase has multiple redox centres. Chemisorption of laccases on a gold electrode through a polypeptide tag introduced at the protein surface provides an isotropic orientation of laccases on the Au surface, which allows the orientation dependent study of the direct electrochemistry of laccase. In this paper, usingmore » genetic engineering technology, two forms of recombinant laccase which has Cys-6×His tag at the N or C terminus were generated. Via the Au-S linkage, the recombinant laccase was assembled orientationally on gold electrode. A direct electron transfer and a bioelectrocatalytic activity toward oxygen reduction were observed on the two orientation controlled laccase electrodes, but their electrochemical behaviors were found to be quite different. The orientation of laccase on the gold electrode affects both the electron transfer pathway and the electron transfer efficiency of O{sub 2} reduction. The present study is helpful not only to the in-depth understanding of the direct electrochemistry of laccase, but also to the development of laccase-based biofuel cells.« less

Magnetic moment enhancement and spin polarization switch of the manganese phthalocyanine molecule on an IrMn(100) surface

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

Sun, X.; National Institute for Materials Science, 1-2-1 Sengen, Tsukuba 305-0047; Wang, B.

2014-07-21

The geometric, electronic, and magnetic structures of a manganese phthalocyanine (MnPc) molecule on an antiferromagnetic IrMn(100) surface are studied by density functional theory calculations. Two kinds of orientation of the adsorbed MnPc molecule are predicted to coexist due to molecular self-assembly on the surface—a top-site geometry with the Mn–N bonds aligned along the 〈100〉 direction, and a hollow-site orientation in which the Mn–N bonds are parallel to the 〈110〉 direction. The MnPc molecule is antiferromagnetically coupled to the substrate at the top site with a slight reduction in the magnetic moment of the Mn atom of the MnPc molecule (Mn{submore » mol}). In contrast, the magnetic moment of the Mn{sub mol} is enhanced to 4.28 μB at the hollow site, a value larger than that in the free MnPc molecule (3.51 μB). Molecular distortion induced by adsorption is revealed to be responsible for the enhancement of the magnetic moment. Furthermore, the spin polarization of the Mn{sub mol} atom at around the Fermi level is found to change from negative to positive through an elongation of the Mn–N bonds of the MnPc. We propose that a reversible switch of the low/high magnetic moment and negative/positive spin polarization might be realized through some mechanical engineering methods.« less

Molecular and supramolecular control of the work function of an inorganic electrode with self-assembled monolayer of umbrella-shaped fullerene derivatives.

PubMed

Lacher, Sebastian; Matsuo, Yutaka; Nakamura, Eiichi

2011-10-26

The surface properties of inorganic substrates can be altered by coating with organic molecules, which may result in the improvement of the properties suitable for electronic or biological applications. This article reports a systematic experimental study on the influence of the molecular and supramolecular properties of umbrella-shaped penta(organo)[60]fullerene derivatives, and on the work function and the water contact angle of indium-tin oxide (ITO) and gold surfaces. We could relate these macroscopic characteristics to single-molecular level properties, such as ionization potential and molecular dipole. The results led us to conclude that the formation of a SAM of a polar compound generates an electronic field through intermolecular interaction of the molecular charges, and this field makes the overall dipole of the SAM much smaller than the one expected from the simple sum of the dipoles of all molecules in the SAM. This effect, which was called depolarization and previously discussed theoretically, is now quantitatively probed by experiments. The important physical properties in surface science such as work function, ionization potential, and water contact angles have been mutually correlated at the level of molecular structures and molecular orientations on the substrate surface. We also found that the SAMs on ITO and gold operate under the same principle except that the "push-back" effect operates specifically for gold. The study also illustrates the ability of the photoelectron yield spectroscopy technique to rapidly measure the work function of a SAM-covered substrate and the ionization potential value of a molecule on the surface.

Nuclear core and fuel assemblies

DOEpatents

Downs, Robert E.

1981-01-01

A fast flux nuclear core of a plurality of rodded, open-lattice assemblies having a rod pattern rotated relative to a rod support structure pattern. Elongated fuel rods are oriented on a triangular array and laterally supported by grid structures positioned along the length of the assembly. Initial inter-assembly contact is through strongbacks at the corners of the support pattern and peripheral fuel rods between adjacent assemblies are nested so as to maintain a triangular pitch across a clearance gap between the other portions of adjacent assemblies. The rod pattern is rotated relative to the strongback support pattern by an angle .alpha. equal to sin .sup.-1 (p/2c), where p is the intra-assembly rod pitch and c is the center-to-center spacing among adjacent assemblies.

Tilt assembly for tracking solar collector assembly

DOEpatents

Almy, Charles; Peurach, John; Sandler, Reuben

2012-01-24

A tilt assembly is used with a solar collector assembly of the type comprising a frame, supporting a solar collector, for movement about a tilt axis by pivoting a drive element between first and second orientations. The tilt assembly comprises a drive element coupler connected to the drive element and a driver, the driver comprising a drive frame, a drive arm and a drive arm driver. The drive arm is mounted to the drive frame for pivotal movement about a drive arm axis. Movement on the drive arm mimics movement of the drive element. Drive element couplers can extend in opposite directions from the outer portion of the drive arm, whereby the assembly can be used between adjacent solar collector assemblies in a row of solar collector assemblies.

The influence of polymer architecture on the assembly of poly(ethylene oxide) grafted C60 fullerene clusters in aqueous solution: a molecular dynamics simulation study.

PubMed

Hooper, Justin B; Bedrov, Dmitry; Smith, Grant D

2009-03-28

The effect of polymer architecture on the aggregation behavior of C60 fullerenes tethered with a single chain of poly(ethylene oxide) (PEO) in aqueous solution has been investigated using coarse-grained, implicit solvent molecular dynamics simulations. The PEO-grafted fullerenes were comprised of a single tether of 60 repeat units represented as a linear polymer, a three-arm star (20 repeat units/arm) or a six-arm star (10 repeat units/arm). Additionally, the influence of arm length on self-assembly of the PEO-fullerene conjugates was investigated for the three-arm stars. Self-assembly is driven by favorable fullerene-fullerene and fullerene-PEO interactions. Our simulations reveal that it should be possible to control the size and geometry of the self-assembled fullerene aggregates in water through variation of PEO architecture and PEO molecular weight. We found that aggregate size and shape could be understood qualitatively in terms of the packing parameter concept that has been employed for diblock polymer and surfactant self-assembly. Higher molecular weight PEO (longer arms) and more compact PEO (more arms for the same molecular weight) resulted in greater steric repulsion between fullerenes, engendering greater aggregate surface curvature and hence the formation of smaller, more spherically shaped aggregates. Finally, weak attractive interactions between PEO and the fullerenes were found to play an important role in determining aggregate shape, size and the dynamics of self-assembly.

Assembling of G-strands into novel tetra-molecular parallel G4-DNA nanostructures using avidin-biotin recognition.

PubMed

Borovok, Natalia; Iram, Natalie; Zikich, Dragoslav; Ghabboun, Jamal; Livshits, Gideon I; Porath, Danny; Kotlyar, Alexander B

2008-09-01

We describe a method for the preparation of novel long (hundreds of nanometers), uniform, inter-molecular G4-DNA molecules composed of four parallel G-strands. The only long continuous G4-DNA reported so far are intra-molecular structures made of a single G-strand. To enable a tetra-molecular assembly of the G-strands we developed a novel approach based on avidin-biotin biological recognition. The steps of the G4-DNA production include: (i) Enzymatic synthesis of long poly(dG)-poly(dC) molecules with biotinylated poly(dG)-strand; (ii) Formation of a complex between avidin-tetramer and four biotinylated poly(dG)-poly(dC) molecules; (iii) Separation of the poly(dC) strands from the poly(dG)-strands, which are connected to the avidin; (iv) Assembly of the four G-strands attached to the avidin into tetra-molecular G4-DNA. The average contour length of the formed structures, as measured by AFM, is equal to that of the initial poly(dG)-poly(dC) molecules, suggesting a tetra-molecular mechanism of the G-strands assembly. The height of tetra-molecular G4-nanostructures is larger than that of mono-molecular G4-DNA molecules having similar contour length. The CD spectra of the tetra- and mono-molecular G4-DNA are markedly different, suggesting different structural organization of these two types of molecules. The tetra-molecular G4-DNA nanostructures showed clear electrical polarizability. This suggests that they may be useful for molecular electronics.

Magnetic-graphitic-nanocapsule templated diacetylene assembly and photopolymerization for sensing and multicoded anti-counterfeiting

NASA Astrophysics Data System (ADS)

Nie, Xiang-Kun; Xu, Yi-Ting; Song, Zhi-Ling; Ding, Ding; Gao, Feng; Liang, Hao; Chen, Long; Bian, Xia; Chen, Zhuo; Tan, Weihong

2014-10-01

Molecular self-assembly, a process to design molecular entities to aggregate into desired structures, represents a promising bottom-up route towards precise construction of functional systems. Here we report a multifunctional, self-assembled system based on magnetic-graphitic-nanocapsule (MGN) templated diacetylene assembly and photopolymerization. The as-prepared assembly system maintains the unique color and fluorescence change properties of the polydiacetylene (PDA) polymers, while also pursues the superior Raman, NIR, magnetic and superconducting properties from the MGN template. Based on both fluorescence and magnetic resonance imaging (MRI) T2 relaxivity, the MGN@PDA system could efficiently monitor the pH variations which could be used as a pH sensor. The MGN@PDA system further demonstrates potential as unique ink for anti-counterfeiting applications. Reversible color change, strong and unique Raman scattering and fluorescence emission, sensitive NIR thermal response, and distinctive magnetic properties afford this assembly system with multicoded anti-counterfeiting capabilities.Molecular self-assembly, a process to design molecular entities to aggregate into desired structures, represents a promising bottom-up route towards precise construction of functional systems. Here we report a multifunctional, self-assembled system based on magnetic-graphitic-nanocapsule (MGN) templated diacetylene assembly and photopolymerization. The as-prepared assembly system maintains the unique color and fluorescence change properties of the polydiacetylene (PDA) polymers, while also pursues the superior Raman, NIR, magnetic and superconducting properties from the MGN template. Based on both fluorescence and magnetic resonance imaging (MRI) T2 relaxivity, the MGN@PDA system could efficiently monitor the pH variations which could be used as a pH sensor. The MGN@PDA system further demonstrates potential as unique ink for anti-counterfeiting applications. Reversible color change, strong and unique Raman scattering and fluorescence emission, sensitive NIR thermal response, and distinctive magnetic properties afford this assembly system with multicoded anti-counterfeiting capabilities. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr03837a

In Vivo Orientation of Single Myosin Lever Arms in Zebrafish Skeletal Muscle

PubMed Central

Sun, Xiaojing; Ekker, Stephen C.; Shelden, Eric A.; Takubo, Naoko; Wang, Yihua; Burghardt, Thomas P.

2014-01-01

Cardiac and skeletal myosin assembled in the muscle lattice power contraction by transducing ATP free energy into the mechanical work of moving actin. Myosin catalytic/lever-arm domains comprise the transduction/mechanical coupling machinery that move actin by lever-arm rotation. In vivo, myosin is crowded and constrained by the fiber lattice as side chains are mutated and otherwise modified under normal, diseased, or aging conditions that collectively define the native myosin environment. Single-myosin detection uniquely defines bottom-up characterization of myosin functionality. The marriage of in vivo and single-myosin detection to study zebrafish embryo models of human muscle disease is a multiscaled technology that allows one-to-one registration of a selected myosin molecular alteration with muscle filament-sarcomere-cell-fiber-tissue-organ- and organism level phenotypes. In vivo single-myosin lever-arm orientation was observed at superresolution using a photoactivatable-green-fluorescent-protein (PAGFP)-tagged myosin light chain expressed in zebrafish skeletal muscle. By simultaneous observation of multiphoton excitation fluorescence emission and second harmonic generation from myosin, we demonstrated tag specificity for the lever arm. Single-molecule detection used highly inclined parallel beam illumination and was verified by quantized photoactivation and photobleaching. Single-molecule emission patterns from relaxed muscle in vivo provided extensive superresolved dipole orientation constraints that were modeled using docking scenarios generated for the myosin (S1) and GFP crystal structures. The dipole orientation data provided sufficient constraints to estimate S1/GFP coordination. The S1/GFP coordination in vivo is rigid and the lever-arm orientation distribution is well-ordered in relaxed muscle. For comparison, single myosins in relaxed permeabilized porcine papillary muscle fibers indicated slightly differently oriented lever arms and rigid S1/GFP coordination. Lever arms in both muscles indicated one preferred spherical polar orientation and widely distributed azimuthal orientations relative to the fiber symmetry axis. Cardiac myosin is more radially displaced from the fiber axis. Probe rigidity implies the PAGFP tag reliably indicates cross-bridge orientation in situ and in vivo. PMID:25229148

High-confidence coding and noncoding transcriptome maps

PubMed Central

2017-01-01

The advent of high-throughput RNA sequencing (RNA-seq) has led to the discovery of unprecedentedly immense transcriptomes encoded by eukaryotic genomes. However, the transcriptome maps are still incomplete partly because they were mostly reconstructed based on RNA-seq reads that lack their orientations (known as unstranded reads) and certain boundary information. Methods to expand the usability of unstranded RNA-seq data by predetermining the orientation of the reads and precisely determining the boundaries of assembled transcripts could significantly benefit the quality of the resulting transcriptome maps. Here, we present a high-performing transcriptome assembly pipeline, called CAFE, that significantly improves the original assemblies, respectively assembled with stranded and/or unstranded RNA-seq data, by orienting unstranded reads using the maximum likelihood estimation and by integrating information about transcription start sites and cleavage and polyadenylation sites. Applying large-scale transcriptomic data comprising 230 billion RNA-seq reads from the ENCODE, Human BodyMap 2.0, The Cancer Genome Atlas, and GTEx projects, CAFE enabled us to predict the directions of about 220 billion unstranded reads, which led to the construction of more accurate transcriptome maps, comparable to the manually curated map, and a comprehensive lncRNA catalog that includes thousands of novel lncRNAs. Our pipeline should not only help to build comprehensive, precise transcriptome maps from complex genomes but also to expand the universe of noncoding genomes. PMID:28396519

Cellulose microfibrils: visualization of biosynthetic and orienting complexes in association with the plasma membrane.

PubMed

Brown, R M; Montezinos, D

1976-01-01

Cellulose microfibril biosynthesis, assembly, and orientation in the unicellular green alga, Oocystis, is visualized in association with a linear enzyme complex embedded in the B face of the plasma membrane. Granule bands of the A face and complementary ridges of the B face are postulated to assist in the orientation of recently synthesized microfibrils. A model for microfibril synthesis and orientation is proposed and correlated with current hypotheses regarding cellulose biosynthesis in higher plants.

Substrate temperature controls molecular orientation in two-component vapor-deposited glasses

DOE PAGES

Jiang, J.; Walters, D. M.; Zhou, D.; ...

2016-02-22

Vapor-deposited glasses can be anisotropic and molecular orientation is important for organic electronics applications. In organic light emitting diodes (OLEDs), for example, the orientation of dye molecules in two-component emitting layers significantly influences emission efficiency. Here we investigate how substrate temperature during vapor deposition influences the orientation of dye molecules in a model two-component system. We determine the average orientation of a linear blue light emitter 1,4-di-[4-( N,N-diphenyl)amino]styrylbenzene (DSA-Ph) in mixtures with aluminum-tris(8-hydroxyquinoline) (Alq 3) by spectroscopic ellipsometry and IR dichroism. We find that molecular orientation is controlled by the ratio of the substrate temperature during deposition and the glassmore » transition temperature of the mixture. Furthermore, these findings extend recent results for single component vapor-deposited glasses and suggest that, during vapor deposition, surface mobility allows partial equilibration towards orientations preferred at the free surface of the equilibrium liquid.« less

Pre-Assembly of Near-Infrared Fluorescent Multivalent Molecular Probes for Biological Imaging.

PubMed

Peck, Evan M; Battles, Paul M; Rice, Douglas R; Roland, Felicia M; Norquest, Kathryn A; Smith, Bradley D

2016-05-18

A programmable pre-assembly method is described and shown to produce near-infrared fluorescent molecular probes with tunable multivalent binding properties. The modular assembly process threads one or two copies of a tetralactam macrocycle onto a fluorescent PEGylated squaraine scaffold containing a complementary number of docking stations. Appended to the macrocycle periphery are multiple copies of a ligand that is known to target a biomarker. The structure and high purity of each threaded complex was determined by independent spectrometric methods and also by gel electrophoresis. Especially helpful were diagnostic red-shift and energy transfer features in the absorption and fluorescence spectra. The threaded complexes were found to be effective multivalent molecular probes for fluorescence microscopy and in vivo fluorescence imaging of living subjects. Two multivalent probes were prepared and tested for targeting of bone in mice. A pre-assembled probe with 12 bone-targeting iminodiacetate ligands produced more bone accumulation than an analogous pre-assembled probe with six iminodiacetate ligands. Notably, there was no loss in probe fluorescence at the bone target site after 24 h in the living animal, indicating that the pre-assembled fluorescent probe maintained very high mechanical and chemical stability on the skeletal surface. The study shows how this versatile pre-assembly method can be used in a parallel combinatorial manner to produce libraries of near-infrared fluorescent multivalent molecular probes for different types of imaging and diagnostic applications, with incremental structural changes in the number of targeting groups, linker lengths, linker flexibility, and degree of PEGylation.

Self-assembly and continuous growth of hexagonal graphene flakes on liquid Cu

NASA Astrophysics Data System (ADS)

Cho, Seong-Yong; Kim, Min-Sik; Kim, Minsu; Kim, Ki-Ju; Kim, Hyun-Mi; Lee, Do-Joong; Lee, Sang-Hoon; Kim, Ki-Bum

2015-07-01

Graphene growth on liquid Cu has received great interest, owing to the self-assembly behavior of hexagonal graphene flakes with aligned orientation and to the possibility of forming a single grain of graphene through a commensurate growth of these graphene flakes. Here, we propose and demonstrate a two-step growth process which allows the formation of self-assembled, completely continuous graphene on liquid Cu. After the formation of full coverage on the liquid Cu, grain boundaries were revealed via selective hydrogen etching and the original grain boundaries were clearly resolved. This result indicates that, while the flakes self-assembled with the same orientation, there still remain structural defects, gaps and voids that were not resolved by optical microscopy or scanning electron microscopy. To overcome this limitation, the two-step growth process was employed, consisting of a sequential process of a normal single-layer graphene growth and self-assembly process with a low carbon flux, followed by the final stage of graphene growth at a high degree of supersaturation with a high carbon flux. Continuity of the flakes was verified via hydrogen etching and a NaCl-assisted oxidation process, as well as by measuring the electrical properties of the graphene grown by the two-step process. Two-step growth can provide a continuous graphene layer, but commensurate stitching should be further studied.Graphene growth on liquid Cu has received great interest, owing to the self-assembly behavior of hexagonal graphene flakes with aligned orientation and to the possibility of forming a single grain of graphene through a commensurate growth of these graphene flakes. Here, we propose and demonstrate a two-step growth process which allows the formation of self-assembled, completely continuous graphene on liquid Cu. After the formation of full coverage on the liquid Cu, grain boundaries were revealed via selective hydrogen etching and the original grain boundaries were clearly resolved. This result indicates that, while the flakes self-assembled with the same orientation, there still remain structural defects, gaps and voids that were not resolved by optical microscopy or scanning electron microscopy. To overcome this limitation, the two-step growth process was employed, consisting of a sequential process of a normal single-layer graphene growth and self-assembly process with a low carbon flux, followed by the final stage of graphene growth at a high degree of supersaturation with a high carbon flux. Continuity of the flakes was verified via hydrogen etching and a NaCl-assisted oxidation process, as well as by measuring the electrical properties of the graphene grown by the two-step process. Two-step growth can provide a continuous graphene layer, but commensurate stitching should be further studied. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr03352g

Assembly/Disassembly of DNA-Au Nanoparticles: A Strategy of Intervention

DOE PAGES

Lim, I-Im S.; Wang, Lingyan; Chandrachud, Uma; ...

2008-01-01

This report describes the viability of a strategy for manipulating the assembly/disassembly processes of DNA-Au nanoparticles by molecular intervention. Using the temperature-induced assembly and disassembly processes of DNAs and gold nanoparticles as a model system, the introduction of a molecular recognition probe is demonstrated to lead to the intervention of the assembly/disassembly processes depending on its specific biorecognition. This process can be detected by monitoring the change in the optical properties of gold nanoparticles and their DNA assemblies. Implications of the preliminary results to exploration of the resulting nanostructures for fine-tuning of the interfacial reactivities in DNA-based bioassays and biomaterialmore » engineering are also discussed.« less

DNA-linked NanoParticle Lattices with Diamond Symmetry: Stability, Shape and Optical Properties

NASA Astrophysics Data System (ADS)

Emamy, Hamed; Tkachenko, Alexei; Gang, Oleg; Starr, Francis

The linking of nanoparticles (NP) by DNA has been proven to be an effective means to create NP lattices with specific order. Lattices with diamond symmetry are predicted to offer novel photonic properties, but self-assembly of such lattices has proven to be challenging due to the low packing fraction, sensitivity to bond orientation, and local heterogeneity. Recently, we reported an approach to create diamond NP lattices based on the association between anisotropic particles with well-defined tetravalent DNA binding topology and isotropically functionalized NP. Here, we use molecular dynamics simulations to evaluate the Gibbs free energy of these lattices, and thereby determine the stability of these lattices as a function of NP size and DNA stiffness. We also predict the equilibrium shape for the cubic diamond crystallite using the Wulff construction method. Specifically, we predict the equilibrium shape using the surface energy for different crystallographic planes. We evaluate surface energy directly form molecular dynamics simulation, which we correlate with theoretical estimates from the expected number of broken DNA bonds along a facet. Furthermore we study the optical properties of this structure, e.g optical bandgap.

Surface force measurements and simulations of mussel-derived peptide adhesives on wet organic surfaces

PubMed Central

Levine, Zachary A.; Rapp, Michael V.; Wei, Wei; Mullen, Ryan Gotchy; Wu, Chun; Zerze, Gül H.; Mittal, Jeetain; Waite, J. Herbert; Israelachvili, Jacob N.; Shea, Joan-Emma

2016-01-01

Translating sticky biological molecules—such as mussel foot proteins (MFPs)—into synthetic, cost-effective underwater adhesives with adjustable nano- and macroscale characteristics requires an intimate understanding of the glue’s molecular interactions. To help facilitate the next generation of aqueous adhesives, we performed a combination of surface forces apparatus (SFA) measurements and replica-exchange molecular dynamics (REMD) simulations on a synthetic, easy to prepare, Dopa-containing peptide (MFP-3s peptide), which adheres to organic surfaces just as effectively as its wild-type protein analog. Experiments and simulations both show significant differences in peptide adsorption on CH3-terminated (hydrophobic) and OH-terminated (hydrophilic) self-assembled monolayers (SAMs), where adsorption is strongest on hydrophobic SAMs because of orientationally specific interactions with Dopa. Additional umbrella-sampling simulations yield free-energy profiles that quantitatively agree with SFA measurements and are used to extract the adhesive properties of individual amino acids within the context of MFP-3s peptide adhesion, revealing a delicate balance between van der Waals, hydrophobic, and electrostatic forces. PMID:27036002

Interfacial growth of large-area single-layer metal-organic framework nanosheets

PubMed Central

Makiura, Rie; Konovalov, Oleg

2013-01-01

The air/liquid interface is an excellent platform to assemble two-dimensional (2D) sheets of materials by enhancing spontaneous organizational features of the building components and encouraging large length scale in-plane growth. We have grown 2D molecularly-thin crystalline metal-organic-framework (MOF) nanosheets composed of porphyrin building units and metal-ion joints (NAFS-13) under operationally simple ambient conditions at the air/liquid interface. In-situ synchrotron X-ray diffraction studies of the formation process performed directly at the interface were employed to optimize the NAFS-13 growth protocol leading to the development of a post-injection method –post-injection of the metal connectors into the water subphase on whose surface the molecular building blocks are pre-oriented– which allowed us to achieve the formation of large-surface area morphologically-uniform preferentially-oriented single-layer nanosheets. The growth of such large-size high-quality sheets is of interest for the understanding of the fundamental physical/chemical properties associated with ultra-thin sheet-shaped materials and the realization of their use in applications. PMID:23974345

49 CFR 572.199 - Pelvis iliac.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 49 Transportation 7 2011-10-01 2011-10-01 false Pelvis iliac. 572.199 Section 572.199... Dummy, Small Adult Female § 572.199 Pelvis iliac. (a) The iliac is part of the lower torso assembly... assembled dummy (drawing 180-0000). The dummy is equipped with a laterally oriented pelvis accelerometer as...

49 CFR 572.199 - Pelvis iliac.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 7 2010-10-01 2010-10-01 false Pelvis iliac. 572.199 Section 572.199... Dummy, Small Adult Female § 572.199 Pelvis iliac. (a) The iliac is part of the lower torso assembly... assembled dummy (drawing 180-0000). The dummy is equipped with a laterally oriented pelvis accelerometer as...

49 CFR 572.199 - Pelvis iliac.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 49 Transportation 7 2012-10-01 2012-10-01 false Pelvis iliac. 572.199 Section 572.199... Dummy, Small Adult Female § 572.199 Pelvis iliac. (a) The iliac is part of the lower torso assembly... assembled dummy (drawing 180-0000). The dummy is equipped with a laterally oriented pelvis accelerometer as...

49 CFR 572.142 - Head assembly and test procedure.

Code of Federal Regulations, 2010 CFR

2010-10-01

... acceleration versus time history curve shall be unimodal, and the oscillations occurring after the main pulse... for testing. (3) Suspend the head assembly with its midsagittal plane in vertical orientation as shown... head in transverse alignment with the CG, shall be used to ensure that the head transverse plane is...

Crankshafts: using simple, flat C2h-symmetric molecules to direct the assembly of chiral 2D nanopatterns.

PubMed

Zhou, Hui; Wuest, James D

2013-06-18

Linear D2h-symmetric bisisophthalic acids 1 and 2 and related substances have well-defined flattened structures, high affinities for graphite, and strong abilities to engage in specific intermolecular interactions. Their adsorption produces characteristic nanopatterns that reveal how 2D molecular organization can be controlled by reliable interadsorbate interactions such as hydrogen bonds when properly oriented by molecular geometry. In addition, the behavior of these compounds shows how large-scale organization can be obstructed by programming molecules to associate strongly according to competing motifs that have similar stability and can coexist smoothly without creating significant defects. Analogous new bisisophthalic acids 3a and 4a have similar associative properties, and their unique C2h-symmetric crankshaft geometry gives them the added ability to probe the poorly understood effect of chirality on molecular organization. Their adsorption shows how nanopatterns composed predictably of a single enantiomer can be obtained by depositing molecules that can respect established rules of association only by accepting neighbors of the same configuration. In addition, an analysis of the adsorption of crankshaft compounds 3a and 4a and their derivatives by STM reveals directly on the molecular level how kinetics and thermodynamics compete to control the crystallization of chiral compounds. In such ways, detailed studies of the adsorption of properly designed compounds on surfaces are proving to be a powerful way to discover and test rules that broadly govern molecular organization in both 2D and 3D.

3D metamaterial absorber for attomole molecular detection (Conference Presentation)

NASA Astrophysics Data System (ADS)

Tanaka, Takuo; Ishikawa, Atsushi

2016-09-01

3D Metamaterial absorber was used for a background-suppressed surface-enhanced molecular detection technique. By utilizing the resonant coupling of plasmonic modes of a metamaterial absorber and infrared (IR) vibrational modes of a self-assembled monolayer (SAM), attomole level molecular sensitivity was experimentally demonstrated. IR absorption spectroscopy of molecular vibrations is of importance in chemical, material, medical science and so on, since it provides essential information of the molecular structure, composition, and orientation. In the vibrational spectroscopic techniques, in addition to the weak signals from the molecules, strong background degrades the signal-to-noise ratio, and suppression of the background is crucial for the further improvement of the sensitivity. Here, we demonstrate low-background resonant Surface enhanced IR absorption (SEIRA) by using the metamaterial IR absorber that offers significant background suppression as well as plasmonic enhancement. The fabricated metamaterial consisted of 1D array of Au micro-ribbons on a thick Au film separated by a transparent gap layer made of MgF2. The surface structures were designed to exhibit an anomalous IR absorption at 3000 cm-1, which spectrally overlapped with C-H stretching vibrational modes. 16-Mercaptohexadecanoic acid (16-MHDA) was used as a test molecule, which formed a 2-nm thick SAM with their thiol head-group chemisorbed on the Au surface. In the FTIR measurements, the symmetric and asymmetric C-H stretching modes were clearly observed as reflection peaks within a broad plasmonic absorption of the metamaterial.

The effect of the molecular orientation on the release of antimicrobial substances from uniaxially drawn polymer matrixes.

PubMed

Iconomopoulou, S M; Voyiatzis, G A

2005-03-21

A new method of controlled release of low molecular weight biocides incorporated in polymer matrixes is described. The molecular orientation of uniaxially drawn biocide doped polymer films is suggested as a significant parameter for controlled release monitoring. Triclosan, a well-established widespread antibacterial agent, has been incorporated into high density polyethylene (HDPE) films that have been subsequently uniaxially drawn at different draw ratios. The molecular orientation developed was estimated utilizing polarized mu-Raman spectra. Biocide incorporated polymer films, drawn at different draw ratios, have been immersed in ethanol-water solutions (EtOH) and in physiological saline. The release of Triclosan out of the polymer matrix was probed with UV-Vis absorption spectroscopy for a period of time up to 15 months. In all cases, although the film surface of the drawn samples exposed to the liquid solution was higher than the undrawn one, the relevant release rate from the drawn specimens was lower than the non-stretched samples depending on the molecular orientation developed during the drawing process. A note is made of the fact that no significant molecular orientation relaxation of the polyethylene films has been observed even after such a long time of immersion of the drawn films in the liquid solutions.

Self-assembly of coiled coil peptides into nanoparticles vs 2-d plates: effects of assembly pathway

NASA Astrophysics Data System (ADS)

Kim, Kyunghee; Pochan, Darrin

Molecular solution assembly, or self-assembly, is a process by which ordered nanostructures or patterns are formed by non-covalent interactions during assembly. Biomimicry, the use of bioinspired molecules or biologically relevant materials, is an important area of self-assembly research with peptides serving a critical role as molecular tools. The morphology of peptide assemblies can be controlled by adjusting solution conditions such as the concentration of peptides, the temperature, and pH. Herein, spherical nanostructures, which have potential for creating an encapsulation system, are formed by self-assembly when coiled coil peptides are combined in solution. These peptides are homotrimeric and heterodimeric coiled-coil bundles and the homotrimer is connected with each of heterodimer through their external surfaces via disulfide bonds. The resultant covalent constructs could co-assemble into complementary trimeric hubs, respectively. The two peptide constructs are directly mixed and assembled in solution in order to produce either spherical particles or 2-d plates depending on the solution conditions and kinetic pathway of assembly. In particular, structural changes of the self-assembled peptides are explored by control of the thermal history of the assembly solution.

Sequencing and De Novo Assembly of the Toxicodendron radicans (Poison Ivy) Transcriptome

PubMed Central

Kim, Gunjune

2017-01-01

Contact with poison ivy plants is widely dreaded because they produce a natural product called urushiol that is responsible for allergenic contact delayed-dermatitis symptoms lasting for weeks. For this reason, the catchphrase most associated with poison ivy is “leaves of three, let it be”, which serves the purpose of both identification and an appeal for avoidance. Ironically, despite this notoriety, there is a dearth of specific knowledge about nearly all other aspects of poison ivy physiology and ecology. As a means of gaining a more molecular-oriented understanding of poison ivy physiology and ecology, Next Generation DNA sequencing technology was used to develop poison ivy root and leaf RNA-seq transcriptome resources. De novo assembled transcriptomes were analyzed to generate a core set of high quality expressed transcripts present in poison ivy tissue. The predicted protein sequences were evaluated for similarity to SwissProt homologs and InterProScan domains, as well as assigned both GO terms and KEGG annotations. Over 23,000 simple sequence repeats were identified in the transcriptome, and corresponding oligo nucleotide primer pairs were designed. A pan-transcriptome analysis of existing Anacardiaceae transcriptomes revealed conserved and unique transcripts among these species. PMID:29125533

Sequencing and De Novo Assembly of the Toxicodendron radicans (Poison Ivy) Transcriptome.

PubMed

Weisberg, Alexandra J; Kim, Gunjune; Westwood, James H; Jelesko, John G

2017-11-10

Contact with poison ivy plants is widely dreaded because they produce a natural product called urushiol that is responsible for allergenic contact delayed-dermatitis symptoms lasting for weeks. For this reason, the catchphrase most associated with poison ivy is "leaves of three, let it be", which serves the purpose of both identification and an appeal for avoidance. Ironically, despite this notoriety, there is a dearth of specific knowledge about nearly all other aspects of poison ivy physiology and ecology. As a means of gaining a more molecular-oriented understanding of poison ivy physiology and ecology, Next Generation DNA sequencing technology was used to develop poison ivy root and leaf RNA-seq transcriptome resources. De novo assembled transcriptomes were analyzed to generate a core set of high quality expressed transcripts present in poison ivy tissue. The predicted protein sequences were evaluated for similarity to SwissProt homologs and InterProScan domains, as well as assigned both GO terms and KEGG annotations. Over 23,000 simple sequence repeats were identified in the transcriptome, and corresponding oligo nucleotide primer pairs were designed. A pan-transcriptome analysis of existing Anacardiaceae transcriptomes revealed conserved and unique transcripts among these species.

Submolecular Gates Self-Assemble for Hot-Electron Transfer in Proteins.

PubMed

Filip-Granit, Neta; Goldberg, Eran; Samish, Ilan; Ashur, Idan; van der Boom, Milko E; Cohen, Hagai; Scherz, Avigdor

2017-07-27

Redox reactions play key roles in fundamental biological processes. The related spatial organization of donors and acceptors is assumed to undergo evolutionary optimization facilitating charge mobilization within the relevant biological context. Experimental information from submolecular functional sites is needed to understand the organization strategies and driving forces involved in the self-development of structure-function relationships. Here we exploit chemically resolved electrical measurements (CREM) to probe the atom-specific electrostatic potentials (ESPs) in artificial arrays of bacteriochlorophyll (BChl) derivatives that provide model systems for photoexcited (hot) electron donation and withdrawal. On the basis of computations we show that native BChl's in the photosynthetic reaction center (RC) self-assemble at their ground-state as aligned gates for functional charge transfer. The combined computational and experimental results further reveal how site-specific polarizability perpendicular to the molecular plane enhances the hot-electron transport. Maximal transport efficiency is predicted for a specific, ∼5 Å, distance above the center of the metalized BChl, which is in remarkably close agreement with the distance and mutual orientation of corresponding native cofactors. These findings provide new metrics and guidelines for analysis of biological redox centers and for designing charge mobilizing machines such as artificial photosynthesis.

Molecular dynamics simulations on PGLa using NMR orientational constraints.

PubMed

Sternberg, Ulrich; Witter, Raiker

2015-11-01

NMR data obtained by solid state NMR from anisotropic samples are used as orientational constraints in molecular dynamics simulations for determining the structure and dynamics of the PGLa peptide within a membrane environment. For the simulation the recently developed molecular dynamics with orientational constraints technique (MDOC) is used. This method introduces orientation dependent pseudo-forces into the COSMOS-NMR force field. Acting during a molecular dynamics simulation these forces drive molecular rotations, re-orientations and folding in such a way that the motional time-averages of the tensorial NMR properties are consistent with the experimentally measured NMR parameters. This MDOC strategy does not depend on the initial choice of atomic coordinates, and is in principle suitable for any flexible and mobile kind of molecule; and it is of course possible to account for flexible parts of peptides or their side-chains. MDOC has been applied to the antimicrobial peptide PGLa and a related dimer model. With these simulations it was possible to reproduce most NMR parameters within the experimental error bounds. The alignment, conformation and order parameters of the membrane-bound molecule and its dimer were directly derived with MDOC from the NMR data. Furthermore, this new approach yielded for the first time the distribution of segmental orientations with respect to the membrane and the order parameter tensors of the dimer systems. It was demonstrated the deuterium splittings measured at the peptide to lipid ratio of 1/50 are consistent with a membrane spanning orientation of the peptide.

Microstructure of cotton fibrous assemblies based on computed tomography

NASA Astrophysics Data System (ADS)

Jing, Hui; Yu, Weidong

2017-12-01

This paper describes for the first time the analysis of inner microstructure of cotton fibrous assemblies using computed tomography. Microstructure parameters such as packing density, fractal dimension as well as porosity including open porosity, closed porosity and total porosity are calculated based on 2D data from computed tomography. Values of packing density and fractal dimension are stable in random oriented fibrous assemblies, and there exists a satisfactory approximate linear relationship between them. Moreover, poles analysis indicates that porosity represents the tightness of fibrous assemblies and open poles are main existence.

Formation of hydroxyl-functionalized stilbenoid molecular sieves at the liquid/solid interface on top of a 1-decanol monolayer.

PubMed

Bellec, Amandine; Arrigoni, Claire; Douillard, Ludovic; Fiorini-Debuisschert, Céline; Mathevet, Fabrice; Kreher, David; Attias, André-Jean; Charra, Fabrice

2014-10-31

Specific molecular tectons can be designed to form molecular sieves through self-assembly at the solid-liquid interface. After demonstrating a model tecton bearing apolar alkyl chains, we then focus on a modified structure involving asymmetric functionalization of some alkyl chains with polar hydroxyl groups in order to get chemical selectivity in the sieving. As the formation of supramolecular self-assembled networks strongly depends on molecule-molecule, molecule-substrate and molecule-solvent interactions, we compared the tectons' self-assembly on graphite for two types of solvent. We demonstrate the possibility to create hydroxylated stilbenoid molecular sieves by using 1-decanol as a solvent. Interestingly, with this solvent, the porous network is developed on top of a 1-decanol monolayer.

Influence of Molecular Shape on Molecular Orientation and Stability of Vapor-Deposited Organic Semiconductors

NASA Astrophysics Data System (ADS)

Walters, Diane M.; Johnson, Noah D.; Ediger, M. D.

Physical vapor deposition is commonly used to prepare active layers in organic electronics. Recently, it has been shown that molecular orientation and packing can be tuned by changing the substrate temperature during deposition, while still producing macroscopically homogeneous films. These amorphous materials can be highly anisotropic when prepared with low substrate temperatures, and they can exhibit exceptional kinetic stability; films retain their favorable packing when heated to high temperatures. Here, we study the influence of molecular shape on molecular orientation and stability. We investigate disc-shaped molecules, such as TCTA and m-MTDATA, nearly spherical molecules, such as Alq3, and linear molecules covering a broad range of aspect ratios, such as p-TTP and BSB-Cz. Disc-shaped molecules have preferential horizontal orientation when deposited at low substrate temperatures, and their orientation can be tuned by changing the substrate temperature. Alq3 forms stable, amorphous films that are optically isotropic when vapor deposited over a broad range of substrate temperatures. This work may guide the choice of material and deposition conditions for vapor-deposited films used in organic electronics and allow for more efficient devices to be fabricated.

Tunable molecular orientation and elevated thermal stability of vapor-deposited organic semiconductors

PubMed Central

Walters, Diane M.; Lyubimov, Ivan; de Pablo, Juan J.; Ediger, M. D.

2015-01-01

Physical vapor deposition is commonly used to prepare organic glasses that serve as the active layers in light-emitting diodes, photovoltaics, and other devices. Recent work has shown that orienting the molecules in such organic semiconductors can significantly enhance device performance. We apply a high-throughput characterization scheme to investigate the effect of the substrate temperature (Tsubstrate) on glasses of three organic molecules used as semiconductors. The optical and material properties are evaluated with spectroscopic ellipsometry. We find that molecular orientation in these glasses is continuously tunable and controlled by Tsubstrate/Tg, where Tg is the glass transition temperature. All three molecules can produce highly anisotropic glasses; the dependence of molecular orientation upon substrate temperature is remarkably similar and nearly independent of molecular length. All three compounds form “stable glasses” with high density and thermal stability, and have properties similar to stable glasses prepared from model glass formers. Simulations reproduce the experimental trends and explain molecular orientation in the deposited glasses in terms of the surface properties of the equilibrium liquid. By showing that organic semiconductors form stable glasses, these results provide an avenue for systematic performance optimization of active layers in organic electronics. PMID:25831545

Metamaterial absorber for molecular detection and identification (Conference Presentation)

NASA Astrophysics Data System (ADS)

Tanaka, Takuo

2017-03-01

Metamaterial absorber was used for a background-suppressed surface-enhanced molecular detection technique. By utilizing the resonant coupling between plasmonic modes of a metamaterial absorber and infrared (IR) vibrational modes of a self-assembled monolayer (SAM), attomole level molecular sensitivity was experimentally demonstrated. IR absorption spectroscopy of molecular vibrations is of importance in chemical, material, medical science and so on, since it provides essential information of the molecular structure, composition, and orientation. In the vibrational spectroscopic techniques, in addition to the weak signals from the molecules, strong background degrades the signal-to-noise ratio, and suppression of the background is crucial for the further improvement of the sensitivity. Here, we demonstrate low-background resonant Surface enhanced IR absorption (SEIRA) by using the metamaterial IR absorber that offers significant background suppression as well as plasmonic enhancement. By using mask-less laser lithography technique, metamaterial absorber which consisted of 1D array of Au micro-ribbons on a thick Au film separated by a transparent gap layer made of MgF2 was fabricated. This metamaterial structure was designed to exhibit an anomalous IR absorption at 3000 cm-1, which spectrally overlapped with C-H stretching vibrational modes. 16-Mercaptohexadecanoic acid (16-MHDA) was used as a test molecule, which formed a 2-nm thick SAM with their thiol head-group chemisorbed on the Au surface. In the FTIR measurements, the symmetric and asymmetric C-H stretching modes were clearly observed as reflection peaks within a broad plasmonic absorption of the metamaterial, and 1.8 attomole molecular sensitivity was experimentally demonstrated.

Gibbs–Thomson Effect in Planar Nanowires: Orientation and Doping Modulated Growth

DOE PAGES

Shen, Youde; Chen, Renjie; Yu, Xuechao; ...

2016-06-02

Epitaxy-enabled bottom-up synthesis of self-assembled planar nanowires via the vapor–liquid–solid mechanism is an emerging and promising approach toward large-scale direct integration of nanowire-based devices without postgrowth alignment. In this paper, by examining large assemblies of indium tin oxide nanowires on yttria-stabilized zirconia substrate, we demonstrate for the first time that the growth dynamics of planar nanowires follows a modified version of the Gibbs–Thomson mechanism, which has been known for the past decades to govern the correlations between thermodynamic supersaturation, growth speed, and nanowire morphology. Furthermore, the substrate orientation strongly influences the growth characteristics of epitaxial planar nanowires as opposed tomore » impact at only the initial nucleation stage in the growth of vertical nanowires. The rich nanowire morphology can be described by a surface-energy-dependent growth model within the Gibbs–Thomson framework, which is further modulated by the tin doping concentration. Our experiments also reveal that the cutoff nanowire diameter depends on the substrate orientation and decreases with increasing tin doping concentration. Finally, these results enable a deeper understanding and control over the growth of planar nanowires, and the insights will help advance the fabrication of self-assembled nanowire devices.« less

Gibbs-Thomson Effect in Planar Nanowires: Orientation and Doping Modulated Growth.

PubMed

Shen, Youde; Chen, Renjie; Yu, Xuechao; Wang, Qijie; Jungjohann, Katherine L; Dayeh, Shadi A; Wu, Tom

2016-07-13

Epitaxy-enabled bottom-up synthesis of self-assembled planar nanowires via the vapor-liquid-solid mechanism is an emerging and promising approach toward large-scale direct integration of nanowire-based devices without postgrowth alignment. Here, by examining large assemblies of indium tin oxide nanowires on yttria-stabilized zirconia substrate, we demonstrate for the first time that the growth dynamics of planar nanowires follows a modified version of the Gibbs-Thomson mechanism, which has been known for the past decades to govern the correlations between thermodynamic supersaturation, growth speed, and nanowire morphology. Furthermore, the substrate orientation strongly influences the growth characteristics of epitaxial planar nanowires as opposed to impact at only the initial nucleation stage in the growth of vertical nanowires. The rich nanowire morphology can be described by a surface-energy-dependent growth model within the Gibbs-Thomson framework, which is further modulated by the tin doping concentration. Our experiments also reveal that the cutoff nanowire diameter depends on the substrate orientation and decreases with increasing tin doping concentration. These results enable a deeper understanding and control over the growth of planar nanowires, and the insights will help advance the fabrication of self-assembled nanowire devices.

Mechanisms of nuclear pore complex assembly - two different ways of building one molecular machine.

PubMed

Otsuka, Shotaro; Ellenberg, Jan

2018-02-01

The nuclear pore complex (NPC) mediates all macromolecular transport across the nuclear envelope. In higher eukaryotes that have an open mitosis, NPCs assemble at two points in the cell cycle: during nuclear assembly in late mitosis and during nuclear growth in interphase. How the NPC, the largest nonpolymeric protein complex in eukaryotic cells, self-assembles inside cells remained unclear. Recent studies have started to uncover the assembly process, and evidence has been accumulating that postmitotic and interphase NPC assembly use fundamentally different mechanisms; the duration, structural intermediates, and regulation by molecular players are different and different types of membrane deformation are involved. In this Review, we summarize the current understanding of these two modes of NPC assembly and discuss the structural and regulatory steps that might drive the assembly processes. We furthermore integrate understanding of NPC assembly with the mechanisms for rapid nuclear growth in embryos and, finally, speculate on the evolutionary origin of the NPC implied by the presence of two distinct assembly mechanisms. © 2017 The Authors. FEBS Letters published by John Wiley & Sons Ltd on behalf of Federation of European Biochemical Societies.

Membrane Protein Incorporation into Nano-Bioelectronics: An insight into Rhodopsin Controlled SiNW-FET Devices

NASA Astrophysics Data System (ADS)

Tunuguntla, Ramya

Biological systems use different energy sources to interact with their environments by creating ion gradients, membrane electric potentials, or a proton motive force to accomplish strikingly complex tasks on the nanometer length scale, such as energy harvesting, and whole organism replication. Most of this activity involves a vast arsenal of active and passive ion channels, membrane receptors and ion pumps that mediate complex and precise transport across biological membranes. Despite the remarkable rate of progress exhibited by modern microelectronic devices, they still cannot compete with the efficiency and precision of biological systems on the component level. At the same time, the sophistication of these molecular machines provides an excellent opportunity to use them in hybrid bioelectronic devices where such a combination could deliver enhanced electronic functionality and enable seamless bi-directional interfaces between man-made and biological assemblies. Artificial membrane systems allow researchers to study the structure and function of membrane proteins in a matrix that approximates their natural environment and to integrate these proteins in ex-vivo devices such as electronic biosensors, thin-film protein arrays, or bio-fuel cells. Since most membrane proteins have vectorial functions, both functional studies and applications require effective control over protein orientation within a lipid bilayer. In our work, we have explored the role of the bilayer surface charge in determining transmembrane protein orientation and functionality during formation of proteoliposomes. We reconstituted a model vectorial ion pump, proteorhodopsin, in liposomes of opposite charges and varying charge densities and determined the resultant protein orientation. Antibody-binding assay and proteolysis of proteoliposomes showed physical evidence of preferential orientation, and functional assays verified vectorial nature of ion transport in this system. Our results indicate that the manipulation of lipid composition can indeed control orientation of an asymmetrically charged membrane protein, proteorhodopsin, in liposomes. One-dimensional inorganic nanostructures, which have critical dimensions comparable to the sizes of biological molecules, form an excellent materials platform for building such integrated structures. Researchers already use silicon nanowire-based field effect transistors functionalized with molecular recognition sites in a diverse array of biosensors. In our group, we have been developing a platform for integration of membrane protein functionality and electronic devices using a 1-D phospholipid bilayer device architecture. In these devices, the membrane proteins reside within the lipid bilayer that covers a nanowire channel of a field-effect transistor. This lipid bilayer performs several functions: it shields the nanowire from the solution species; it serves as a native-like environment for membrane proteins and preserves their functionality, integrity, and even vectorality. In this work, we show that a 1-D bilayer device incorporating a rhodopsin proton pump allows us to couple light-driven proton transport to a bioelectronic circuit. We also report that we were able to adapt another distinctive feature of biological signal processing---their widespread use of modifiers, co-factors, and mediator molecules---to regulate and fine-tune the operational characteristics of the bioelectronic device. In our example, we use co-assembly of protein channels and ionophores in the 1-D bilayer to modify the device output levels and response time.

Thermally stable solids based on endohedrally doped ZnS clusters.

PubMed

Matxain, Jon M; Piris, Mario; Lopez, Xabier; Ugalde, Jesus M

2009-01-01

The existence of inorganic, hollow, fullerene-like ZnS clusters has been theoretically predicted and then recently confirmed experimentally. These clusters were observed to trap alkali metals and halogens because the ionization energies (IE) of alkali metals are very similar to the electron affinities (EA) of halogens. This opens the possibility of forming molecular solids composed of these fullerene building blocks because the energy released due to the difference between the IE and EA would be very small. Herein we have focused on assembling bare Zn(12)S(12) and endohedral X@Zn(12)S(12)-Y@Zn(12)S(12) dimers (X = Na, K; Y = Cl, Br) by considering the square-faces-square orientation of every two adjacent clusters, which leads to a fcc cubic crystal structure in the solid. The structures were fully optimized in all cases, and their thermal stability was confirmed by ab initio thermal molecular dynamics calculations. The optimum lattice parameter of the solids was found to be around 13.8 A, which corresponds to distances of about 2.5 A between monomers, which is typical of covalent Zn-S bonds. The resulting solids are nanoporous materials similar to B(12)N(12). Due to their nanoporous structure, these zeolite-shaped solids could be used in heterogeneous catalysis and as storage materials and molecular sieves.

Self-assembly: Misfits unite

NASA Astrophysics Data System (ADS)

Grason, Gregory M.

2017-12-01

The spontaneous assembly of particulate or molecular 'building blocks' into larger architectures underlies structure formation in many biological and synthetic materials. Shape frustration of ill-fitting blocks holds a surprising key to more regular assemblies.

Alignment between Protostellar Outflows and Filamentary Structure

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

Stephens, Ian W.; Dunham, Michael M.; Myers, Philip C.

2017-09-01

We present new Submillimeter Array (SMA) observations of CO(2–1) outflows toward young, embedded protostars in the Perseus molecular cloud as part of the Mass Assembly of Stellar Systems and their Evolution with the SMA (MASSES) survey. For 57 Perseus protostars, we characterize the orientation of the outflow angles and compare them with the orientation of the local filaments as derived from Herschel observations. We find that the relative angles between outflows and filaments are inconsistent with purely parallel or purely perpendicular distributions. Instead, the observed distribution of outflow-filament angles are more consistent with either randomly aligned angles or a mixmore » of projected parallel and perpendicular angles. A mix of parallel and perpendicular angles requires perpendicular alignment to be more common by a factor of ∼3. Our results show that the observed distributions probably hold regardless of the protostar’s multiplicity, age, or the host core’s opacity. These observations indicate that the angular momentum axis of a protostar may be independent of the large-scale structure. We discuss the significance of independent protostellar rotation axes in the general picture of filament-based star formation.« less

Spectroscopic and Structural Studies of a Surface Active Porphyrin in Solution and in Langmuir-Blodgett Films.

PubMed

Ponce, Concepcion P; Araghi, Hessamaddin Younesi; Joshi, Neeraj K; Steer, Ronald P; Paige, Matthew F

2015-12-22

Controlling aggregation of the dual sensitizer-emitter (S-E) zinc tetraphenylporphyrin (ZnTPP) is an important consideration in solid state noncoherent photon upconversion (NCPU) applications. The Langmuir-Blodgett (LB) technique is a facile means of preparing ordered assemblies in thin films to study distance-dependent energy transfer processes in S-E systems and was used in this report to control the aggregation of a functionalized ZnTPP on solid substrates. This was achieved by synthetic addition of a short polar tail to one of the pendant phenyl rings in ZnTPP in order to make it surface active. The surface active ZnTPP derivative formed rigid films at the air-water interface and exhibited mean molecular areas consistent with approximately vertically oriented molecules under appropriate film compression. A red shift in the UV-vis spectra as well as unquenched fluorescence emission of the LB films indicated formation of well-ordered aggregates. However, NCPU, present in the solution phase, was not observed in the LB films, suggesting that NCPU from ZnTPP as a dual S-E required not just a controlled aggregation but a specific orientation of the molecules with respect to each other.

Micelle-assisted fabrication of necklace-shaped assembly of inorganic fullerene-like molybdenum disulfide nanospheres

NASA Astrophysics Data System (ADS)

Xiong, Yujie; Xie, Yi; Li, Zhengquan; Li, Xiaoxu; Zhang, Rong

2003-11-01

The fabrication of necklace-shaped assembly of inorganic fullerene-like molybdenum disulfide nanospheres via a micelle-assisted route is reported, in which necklace-shaped assembly of amorphous MoS 3 nanospheres is driven by the aggregation transformation of surfactants at low temperatures and then is transformed to the assembly of target fullerene-like MoS 2 by annealing. This nanostructure is a type of oriented assembly of inorganic fullerene-like structures, which is confirmed by the transmission electron microscopy and high-resolution transmission electron microscopy analysis. The optical absorption property is investigated to show their inorganic fullerene-like structure and uniform shape.

From Fullerene-Polymer to All-Polymer Solar Cells: The Importance of Molecular Packing, Orientation, and Morphology Control.

PubMed

Kang, Hyunbum; Lee, Wonho; Oh, Jiho; Kim, Taesu; Lee, Changyeon; Kim, Bumjoon J

2016-11-15

All-polymer solar cells (all-PSCs), consisting of conjugated polymers as both electron donor (P D ) and acceptor (P A ), have recently attracted great attention. Remarkable progress has been achieved during the past few years, with power conversion efficiencies (PCEs) now approaching 8%. In this Account, we first discuss the major advantages of all-PSCs over fullerene-polymer solar cells (fullerene-PSCs): (i) high light absorption and chemical tunability of P A , which affords simultaneous enhancement of both the short-circuit current density (J SC ) and the open-circuit voltage (V OC ), and (ii) superior long-term stability (in particular, thermal and mechanical stability) of all-PSCs due to entangled long P A chains. In the second part of this Account, we discuss the device operation mechanism of all-PSCs and recognize the major challenges that need to be addressed in optimizing the performance of all-PSCs. The major difference between all-PSCs and fullerene-PSCs originates from the molecular structures and interactions, i.e., the electron transport ability in all-PSCs is significantly affected by the packing geometry of two-dimensional P A chains relative to the electrodes (e.g., face-on or edge-on orientation), whereas spherically shaped fullerene acceptors can facilitate isotropic electron transport properties in fullerene-PSCs. Moreover, the crystalline packing structures of P D and P A at the P D -P A interface greatly affect their free charge carrier generation efficiencies. The design of P A polymers (e.g., main backbone, side chain, and molecular weight) should therefore take account of optimizing three major aspects in all-PSCs: (1) the electron transport ability of P A , (2) the molecular packing structure and orientation of P A , and (3) the blend morphology. First, control of the backbone and side-chain structures, as well as the molecular weight, is critical for generating strong intermolecular assembly of P A and its network, thus enabling high electron transport ability of P A comparable to that of fullerenes. Second, the molecular orientation of anisotropically structured P A should be favorably controlled in order to achieve efficient charge transport as well as charge transfer at the P D -P A interface. For instance, face-to-face stacking between P D and P A at the interface is desired for efficient free charge carrier generation because misoriented chains often cause an additional energy barrier for overcoming the binding energy of the charge transfer state. Third, large-scale phase separation often occurs in all-PSCs because of the significantly reduced entropic contribution by two macromolecular chains of P D and P A that energetically disfavors mixing. In this Account, we review the recent progress toward overcoming each recognized challenge and intend to provide guidelines for the future design of P A . We believe that by optimization of the parameters discussed above the PCE values of all-PSCs will surpass the 10% level in the near future and that all-PSCs are promising candidates for the successful realization of flexible and portable power generators.

Unusual large-pitch banding in poly(L-lactic acid): Effects of composition and geometry confinement

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

Woo, Eamor M.; Lugito, Graecia; Hsieh, Ya-Ting

2014-02-24

Lamellar patterns and orientations in blends of two crystalline polymers: poly(ethylene oxide) (PEO) and low-molecular-weight poly(L-lactic acid) (PLLA) were investigated using polarizing light optical microscopy (POM), and atomic and scanning electron microscopy (AFM, SEM). Specific etching off of PEO was used to reveal the complex earlier-grown PLLA lamellae patterns with various PEO content in blends. Banding of extremely long pitch (50 μm) in crystallized PLLA spherulites was induced by two kinetic factors: geometry confinement by top cover and introduction of diluent such as PEO. The mechanisms and correlation among the lamellar assembly, ring bands, and cracks are exemplified. Lamellar patternsmore » and ring-band types in blends were found to vary with respect to not only blend compositions, but also confinement of top-cover.« less

Integration of planar cell polarity and ECM signaling in elongation of the vertebrate body plan.

PubMed

Skoglund, Paul; Keller, Ray

2010-10-01

The shaping of the vertebrate embryonic body plan depends heavily on the narrowing and lengthening (convergence and extension) of embryonic tissues by cell intercalation, a process by which cells actively crawl between one another along the axis of convergence to produce a narrower, longer array. We discuss recent evidence that the vertebrate non-canonical Wnt/Planar Cell Polarity (PCP) pathway, known to directly function in polarizing the movements of intercalating cells, is also involved in the localized assembly of extracellular matrix (ECM). These cell-ECM interactions, in turn, are necessary for expression of the oriented, polarized cell intercalation. The mechanism of PCP/ECM interactions, their molecular signaling, and their mechanical consequences for morphogenesis are discussed with the goal of identifying important unsolved issues. Copyright © 2010 Elsevier Ltd. All rights reserved.

Programming Enzyme-Initiated Autonomous DNAzyme Nanodevices in Living Cells.

PubMed

Chen, Feng; Bai, Min; Cao, Ke; Zhao, Yue; Cao, Xiaowen; Wei, Jing; Wu, Na; Li, Jiang; Wang, Lihua; Fan, Chunhai; Zhao, Yongxi

2017-12-26

Molecular nanodevices are computational assemblers that switch defined states upon external stimulation. However, interfacing artificial nanodevices with natural molecular machineries in living cells remains a great challenge. Here, we delineate a generic method for programming assembly of enzyme-initiated DNAzyme nanodevices (DzNanos). Two programs including split assembly of two partzymes and toehold exchange displacement assembly of one intact DNAzyme initiated by telomerase are computed. The intact one obtains higher assembly yield and catalytic performance ascribed to proper conformation folding and active misplaced assembly. By employing MnO 2 nanosheets as both DNA carriers and source of Mn 2+ as DNAzyme cofactor, we find that this DzNano is well assembled via a series of conformational states in living cells and operates autonomously with sustained cleavage activity. Other enzymes can also induce corresponding DzNano assembly with defined programming modules. These DzNanos not only can monitor enzyme catalysis in situ but also will enable the implementation of cellular stages, behaviors, and pathways for basic science, diagnostic, and therapeutic applications as genetic circuits.

Molecular details of the yeast frataxin-Isu1 interaction during mitochondrial Fe-S cluster assembly

PubMed Central

Cook, Jeremy D.; Kondapalli, Kalyan C.; Rawat, Swati; Childs, William C.; Murugesan, Yogapriya; Dancis, Andrew; Stemmler, Timothy L.

2010-01-01

Frataxin, a conserved nuclear encoded mitochondrial protein, plays a direct role in iron-sulfur cluster biosynthesis within the ISC assembly pathway. Humans with frataxin deficiency have Friedreich’s ataxia, a neurodegenerative disorder characterized by mitochondrial iron overload and disruption in Fe-S cluster synthesis. Biochemical and genetic studies have shown frataxin interacts with the iron-sulfur cluster assembly scaffold protein (in yeast, there are two: Isu1 and Isu2), indicating frataxin plays a direct role in cluster assembly, possibly by serving as an iron chaperone n the assembly pathway. Here we provide molecular details of how yeast frataxin (Yfh1) interacts with Isu1 as a structural module to better understand the multiprotein complex assembly that completes Fe-S cluster assembly; this complex also includes the cysteine desulfurase (Nfs1 in yeast) and the accessory protein (Isd11), together in the mitochondria. Thermodynamic binding parameters for protein partner and iron binding were measured for the yeast orthologs using isothermal titration calorimetry (ITC). Nuclear magnetic resonance spectroscopy was used to provide the molecular details to understand how Yfh1 interacts with Isu1. X-ray absorption studies were used to electronically and structurally characterize how iron is transferred to Isu1 and then incorporated into a Fe-S cluster. These results were combined with previously published data to generate a structural model for how the Fe-S cluster protein assembly complex can come together to accomplish Fe-S cluster assembly. PMID:20815377

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

Uzun, Suzan; Ilavsky, Jan; Padua, Graciela Wild

Zein, a protein of corn, has an amphiphilic molecule capable of self-assembly into distinctly different structures. In this work, ultra-small-angle X-ray scattering (USAXS) was applied to investigate the formation of self-assembled zein structures in binary solvent systems of ethanol and water. Our study included observing structural changes due to aging. Three hierarchical structures were identified in zein-solvent systems, molecular zein 2D films, believed to be formed by zein rods assembled first into one-dimensional fibers and then into two-dimensional films, and 3D spherical aggregates. Aging did not change the size or shape of primary units, but promoted their self-assembly into intermediatemore » 2D structures and shaped 3D structures into well19 defined spheres. We found that the rheological parameters, consistency index (K) and behavior index (n), storage and loss moduli (G’ and G”) were also measured. K and n, changed markedly with aging, from nearly Newtonian low consistency fresh samples to highly viscous pseudoplastic aged samples. G’ and G” increased with aging for all samples reflecting increased interactions among zein self-assembled structures. Furthermore, viscoelastic parameters indicated that zein dispersions formed gels upon aging. It was observed that USAX reported on molecular scale self-assembly processes, while rheological measurements reported on the macroscale interaction between self-assembled particles. Raman spectra suggested that α-helix to β-sheet transformations prompted zein self-assembly, which influenced the size and morphology of molecular assemblies and ultimately the rheological properties of zein dispersions.« less

Molecular Details of the Yeast Frataxin-Isu1 Interaction during Mitochondrial Fe-S Cluster Assembly

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

Cook, J.; Kondapalli, K; Rawat, S

2010-01-01

Frataxin, a conserved nuclear-encoded mitochondrial protein, plays a direct role in iron-sulfur cluster biosynthesis within the ISC assembly pathway. Humans with frataxin deficiency have Friedreich's ataxia, a neurodegenerative disorder characterized by mitochondrial iron overload and disruption in Fe-S cluster synthesis. Biochemical and genetic studies have shown frataxin interacts with the iron-sulfur cluster assembly scaffold protein (in yeast, there are two, Isu1 and Isu2), indicating frataxin plays a direct role in cluster assembly, possibly by serving as an iron chaperone in the assembly pathway. Here we provide molecular details of how yeast frataxin (Yfh1) interacts with Isu1 as a structural modulemore » to improve our understanding of the multiprotein complex assembly that completes Fe-S cluster assembly; this complex also includes the cysteine desulfurase (Nfs1 in yeast) and the accessory protein (Isd11), together in the mitochondria. Thermodynamic binding parameters for protein partner and iron binding were measured for the yeast orthologs using isothermal titration calorimetry. Nuclear magnetic resonance spectroscopy was used to provide the molecular details to understand how Yfh1 interacts with Isu1. X-ray absorption studies were used to electronically and structurally characterize how iron is transferred to Isu1 and then incorporated into an Fe-S cluster. These results were combined with previously published data to generate a structural model for how the Fe-S cluster protein assembly complex can come together to accomplish Fe-S cluster assembly.« less

Molecular details of the yeast frataxin-Isu1 interaction during mitochondrial Fe-S cluster assembly.

PubMed

Cook, Jeremy D; Kondapalli, Kalyan C; Rawat, Swati; Childs, William C; Murugesan, Yogapriya; Dancis, Andrew; Stemmler, Timothy L

2010-10-12

Frataxin, a conserved nuclear-encoded mitochondrial protein, plays a direct role in iron-sulfur cluster biosynthesis within the ISC assembly pathway. Humans with frataxin deficiency have Friedreich's ataxia, a neurodegenerative disorder characterized by mitochondrial iron overload and disruption in Fe-S cluster synthesis. Biochemical and genetic studies have shown frataxin interacts with the iron-sulfur cluster assembly scaffold protein (in yeast, there are two, Isu1 and Isu2), indicating frataxin plays a direct role in cluster assembly, possibly by serving as an iron chaperone in the assembly pathway. Here we provide molecular details of how yeast frataxin (Yfh1) interacts with Isu1 as a structural module to improve our understanding of the multiprotein complex assembly that completes Fe-S cluster assembly; this complex also includes the cysteine desulfurase (Nfs1 in yeast) and the accessory protein (Isd11), together in the mitochondria. Thermodynamic binding parameters for protein partner and iron binding were measured for the yeast orthologs using isothermal titration calorimetry. Nuclear magnetic resonance spectroscopy was used to provide the molecular details to understand how Yfh1 interacts with Isu1. X-ray absorption studies were used to electronically and structurally characterize how iron is transferred to Isu1 and then incorporated into an Fe-S cluster. These results were combined with previously published data to generate a structural model for how the Fe-S cluster protein assembly complex can come together to accomplish Fe-S cluster assembly.

A molecular chaperone for mitochondrial complex I assembly is mutated in a progressive encephalopathy

PubMed Central

Ogilvie, Isla; Kennaway, Nancy G.; Shoubridge, Eric A.

2005-01-01

NADH:ubiquinone oxidoreductase (complex I) deficiency is a common cause of mitochondrial oxidative phosphorylation disease. It is associated with a wide range of clinical phenotypes in infants, including Leigh syndrome, cardiomyopathy, and encephalomyopathy. In at least half of patients, enzyme deficiency results from a failure to assemble the holoenzyme complex; however, the molecular chaperones required for assembly of the mammalian enzyme remain unknown. Using whole genome subtraction of yeasts with and without a complex I to generate candidate assembly factors, we identified a paralogue (B17.2L) of the B17.2 structural subunit. We found a null mutation in B17.2L in a patient with a progressive encephalopathy and showed that the associated complex I assembly defect could be completely rescued by retroviral expression of B17.2L in patient fibroblasts. An anti-B17.2L antibody did not associate with the holoenzyme complex but specifically recognized an 830-kDa subassembly in several patients with complex I assembly defects and coimmunoprecipitated a subset of complex I structural subunits from normal human heart mitochondria. These results demonstrate that B17.2L is a bona fide molecular chaperone that is essential for the assembly of complex I and for the normal function of the nervous system. PMID:16200211

Encapsulation of [F4(H2O)10](4-) in a dimeric assembly of an unidirectional arene based hexapodal amide receptor.

PubMed

Arunachalam, M; Ghosh, Pradyut

2011-06-14

An unidirectional orientation of all six arms of an arene based hexapodal amide receptor shows dimeric capsular assembly templated by a [F(4)(H(2)O)(10)](4-) cluster. This journal is © The Royal Society of Chemistry 2011

Inventorying national forest resources...for planning-programing-budgeting system

Treesearch

Miles R. Hill; Elliot L. Amidon

1968-01-01

New systems for analyzing resource management problems, such as Planning-Programing-Budgeting, will require automated procedures to collect and assemble resource inventory data. A computer - oriented system called Map Information Assembly and Display System developed for this purpose was tested on a National Forest in California. It provided information on eight forest...

A Module for Hospital Central Processing Technicians on Decontamination, Assembly and Wrapping Concepts of GYN Hysterectomy Instruments.

ERIC Educational Resources Information Center

Wojcik, Roseann B.; Moseley, James L.

This learning module can be used as an orientation guide, inservice tool, or resource guide for hospital central processing department technicians and instructors. It contains information sheets, worksheets, worksheet answers, a posttest, and posttest answers on correct procedures for decontaminating, assembling, and wrapping the medical…

The space station assembly phase: System design trade-offs for the flight telerobotic servicer

NASA Technical Reports Server (NTRS)

Smith, Jeffrey H.; Gyamfi, Max; Volkmer, Kent; Zimmerman, Wayne

1988-01-01

The effects of a recent study aimed at identifying key issues and trade-offs associated with using a Flight Telerobotic Servicer (FTS) to aid in Space Station assembly-phase tasks is described. The use of automation and robotic (A and R) technologies for large space systems often involves a substitution of automation capabilities for human EVA or IVA activities. A methodology is presented that incorporates assessment of candidate assembly-phase tasks, telerobotic performance capabilities, development costs, and effects of operational constaints. Changes in the region of cost-effectiveness are examined under a variety of system design assumptions. A discussion of issues is presented with focus on three roles the FTS might serve: as a research-oriented test bed to learn more about space usage of telerobotics; as a research based test bed having an experimental demonstration orientation with limited assembly and servicing applications; or as an operational system to augment EVA and to aid construction of the Space Station and to reduce the program (schedule) risk by increasing the flexibility of mission operations.

Structural insights of a self-assembling 9-residue peptide from the C-terminal tail of the SARS corona virus E-protein in DPC and SDS micelles: A combined high and low resolution spectroscopic study.

PubMed

Ghosh, Anirban; Bhattacharyya, Dipita; Bhunia, Anirban

2018-02-01

In recent years, several studies based on the interaction of self-assembling short peptides derived from viroporins with model membranes, have improved our understanding of the molecular mechanism of corona virus (CoV) infection under physiological conditions. In this study, we have characterized the mechanism of membrane interaction of a short, 9-residue peptide TK9 (T 55 VYVYSRVK 63 ) that had been derived from the carboxyl terminal of the Severe Acute Respiratory Syndrome (SARS) corona virus (SARS CoV) envelope (E) protein. The peptide has been studied for its physical changes in the presence of both zwitterionic DPC and negatively charged SDS model membrane micelles, respectively, with the help of a battery of biophysical techniques including two-dimensional solution state NMR spectroscopy. Interestingly, in both micellar environments, TK9 adopted an alpha helical conformation; however, the helical propensities were much higher in the case of DPC compared to those of SDS micelle, suggesting that TK9 has more specificity towards eukaryotic cell membrane than the bacterial cell membrane. The orientation of the peptide TK9 also varies in the different micellar environments. The peptide's affinity was further manifested by its pronounced membrane disruption ability towards the mammalian compared to the bacterial membrane mimic. Collectively, the in-depth structural information on the interaction of TK9 with different membrane environments explains the host specificity and membrane orientation owing to subsequent membrane disruption implicated in the viral pathogenesis. Copyright © 2017 Elsevier B.V. All rights reserved.

Characterization of zein assemblies by ultra-small-angle X-ray scattering

DOE PAGES

Uzun, Suzan; Ilavsky, Jan; Padua, Graciela Wild

2017-03-23

Zein, a protein of corn, has an amphiphilic molecule capable of self-assembly into distinctly different structures. In this work, ultra-small-angle X-ray scattering (USAXS) was applied to investigate the formation of self-assembled zein structures in binary solvent systems of ethanol and water. Our study included observing structural changes due to aging. Three hierarchical structures were identified in zein-solvent systems, molecular zein 2D films, believed to be formed by zein rods assembled first into one-dimensional fibers and then into two-dimensional films, and 3D spherical aggregates. Aging did not change the size or shape of primary units, but promoted their self-assembly into intermediatemore » 2D structures and shaped 3D structures into well19 defined spheres. We found that the rheological parameters, consistency index (K) and behavior index (n), storage and loss moduli (G’ and G”) were also measured. K and n, changed markedly with aging, from nearly Newtonian low consistency fresh samples to highly viscous pseudoplastic aged samples. G’ and G” increased with aging for all samples reflecting increased interactions among zein self-assembled structures. Furthermore, viscoelastic parameters indicated that zein dispersions formed gels upon aging. It was observed that USAX reported on molecular scale self-assembly processes, while rheological measurements reported on the macroscale interaction between self-assembled particles. Raman spectra suggested that α-helix to β-sheet transformations prompted zein self-assembly, which influenced the size and morphology of molecular assemblies and ultimately the rheological properties of zein dispersions.« less

Probing amyloid protein aggregation with optical superresolution methods: from the test tube to models of disease

PubMed Central

Kaminski, Clemens F.; Kaminski Schierle, Gabriele S.

2016-01-01

Abstract. The misfolding and self-assembly of intrinsically disordered proteins into insoluble amyloid structures are central to many neurodegenerative diseases such as Alzheimer’s and Parkinson’s diseases. Optical imaging of this self-assembly process in vitro and in cells is revolutionizing our understanding of the molecular mechanisms behind these devastating conditions. In contrast to conventional biophysical methods, optical imaging and, in particular, optical superresolution imaging, permits the dynamic investigation of the molecular self-assembly process in vitro and in cells, at molecular-level resolution. In this article, current state-of-the-art imaging methods are reviewed and discussed in the context of research into neurodegeneration. PMID:27413767

Electrostatically Tuned Self-Assembly of Branched Amphiphilic Peptides

DOE PAGES

Ting, Christina L.; Frischknecht, Amalie L.; Stevens, Mark J.; ...

2014-06-19

Electrostatics plays an important role in the self-assembly of amphiphilic peptides. To develop a molecular understanding of the role of the electrostatic interactions, we develop a coarse-grained model peptide and apply self-consistent field theory to investigate the peptide assembly into a variety of aggregate nanostructures. We find that the presence and distribution of charged groups on the hydrophilic branches of the peptide can modify the molecular configuration from extended to collapsed. This change in molecular configuration influences the packing into spherical micelles, cylindrical micelles (nanofibers), or planar bilayers. The effects of charge distribution therefore has important implications for the designmore » and utility of functional materials based on peptides.« less

The One-Pot Directed Assembly of Cylinder-Forming Block Copolymer on Adjacent Chemical Patterns for Bimodal Patterning.

PubMed

Chang, Tzu-Hsuan; Xiong, Shisheng; Liu, Chi-Chun; Liu, Dong; Nealey, Paul F; Ma, Zhenqiang

2017-09-01

The direct self-assembly of cylinder-forming poly(styrene-block-methyl-methacrylate) (PS-b-PMMA) block copolymer is successfully assembled into two orientations, according to the underlying guiding pattern in different areas. Lying-down and perpendicular cylinders are formed, respectively, depending on the design of chemical pattern: sparse line/space pattern or hexagonal dot array. The first chemical pattern composed of prepatterned cross-linked polystyrene (XPS) line/space structure has a period (L S ) equal to twice the intercylinder period of the block copolymer (L 0 ). The PS-b-PMMA thin film on the prepared chemical template after thermal annealing forms a lying-down cylinder morphology when the width of the PS strips is less than the width of PS block in the PS-b-PMMA block copolymer. The morphology is only applicable at the discrete thickness of the PS-b-PMMA film. In addition to forming the lying-down cylinders directly on the XPS guiding pattern, the cylinder-forming block copolymer can also be assembled in a perpendicular way on the second guiding pattern (the hexagonal dot array). The block copolymer films are registered into two orientations in a single directed self-assembly process. The features of the assembled patterns are successfully transferred down to the silicon oxide substrate. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Self-assembly patterning of organic molecules on a surface

DOEpatents

Pan, Minghu; Fuentes-Cabrera, Miguel; Maksymovych, Petro; Sumpter, Bobby G.; Li, Qing

2017-04-04

The embodiments disclosed herein include all-electron control over a chemical attachment and the subsequent self-assembly of an organic molecule into a well-ordered three-dimensional monolayer on a metal surface. The ordering or assembly of the organic molecule may be through electron excitation. Hot-electron and hot-hole excitation enables tethering of the organic molecule to a metal substrate, such as an alkyne group to a gold surface. All-electron reactions may allow a direct control over the size and shape of the self-assembly, defect structures and the reverse process of molecular disassembly from single molecular level to mesoscopic scale.

Engineering solid-state materials. Strategies for modeling and packing control of molecular assemblies into 3-D networks

NASA Astrophysics Data System (ADS)

Videnova-Adrabinska, V.; Etter, M. C.; Ward, M. D.

1993-04-01

The crystal structure and properties of a number of urea cocrystals are studied with regard to symmetry of the hydrogen-bonded molecular assemblies. The logical consequences of hydrogen bonding interactions are followed step-by-step. The problems of aggregate formation, nucleation, and crystal growth are also elucidated. Endeavor is made to envisage the 2-D and 3-D hydrogen bond network in a manageable way by exploiting graph set short hand. Strategies of how to control the symmetry of molecular packing are still to be elaborated. In our strategy, the programmed self-assembly has been based on the principle of molecular recognition of self- and hetero-complementary functional groups. However, the main focus for pre-organizational control has been put on the two-fold axis estimator of the urea molecule.

Porous organic cages

NASA Astrophysics Data System (ADS)

Tozawa, Tomokazu; Jones, James T. A.; Swamy, Shashikala I.; Jiang, Shan; Adams, Dave J.; Shakespeare, Stephen; Clowes, Rob; Bradshaw, Darren; Hasell, Tom; Chong, Samantha Y.; Tang, Chiu; Thompson, Stephen; Parker, Julia; Trewin, Abbie; Bacsa, John; Slawin, Alexandra M. Z.; Steiner, Alexander; Cooper, Andrew I.

2009-12-01

Porous materials are important in a wide range of applications including molecular separations and catalysis. We demonstrate that covalently bonded organic cages can assemble into crystalline microporous materials. The porosity is prefabricated and intrinsic to the molecular cage structure, as opposed to being formed by non-covalent self-assembly of non-porous sub-units. The three-dimensional connectivity between the cage windows is controlled by varying the chemical functionality such that either non-porous or permanently porous assemblies can be produced. Surface areas and gas uptakes for the latter exceed comparable molecular solids. One of the cages can be converted by recrystallization to produce either porous or non-porous polymorphs with apparent Brunauer-Emmett-Teller surface areas of 550 and 23m2g-1, respectively. These results suggest design principles for responsive porous organic solids and for the modular construction of extended materials from prefabricated molecular pores.

De novo Assembly and Analysis of the Chilean Pencil Catfish Trichomycterus areolatus Transcriptome

PubMed Central

Schulze, Thomas T.; Ali, Jonathan M.; Bartlett, Maggie L.; McFarland, Madalyn M.; Clement, Emalie J.; Won, Harim I.; Sanford, Austin G.; Monzingo, Elyssa B.; Martens, Matthew C.; Hemsley, Ryan M.; Kumar, Sidharta; Gouin, Nicolas; Kolok, Alan S.; Davis, Paul H.

2016-01-01

Trichomycterus areolatus is an endemic species of pencil catfish that inhabits the riffles and rapids of many freshwater ecosystems of Chile. Despite its unique adaptation to Chile's high gradient watersheds and therefore potential application in the investigation of ecosystem integrity and environmental contamination, relatively little is known regarding the molecular biology of this environmental sentinel. Here, we detail the assembly of the Trichomycterus areolatus transcriptome, a molecular resource for the study of this organism and its molecular response to the environment. RNA-Seq reads were obtained by next-generation sequencing with an Illumina® platform and processed using PRINSEQ. The transcriptome assembly was performed using TRINITY assembler. Transcriptome validation was performed by functional characterization with KOG, KEGG, and GO analyses. Additionally, differential expression analysis highlights sex-specific expression patterns, and a list of endocrine and oxidative stress related transcripts are included. PMID:27672404

Self-assembled microstructures of confined rod-coil diblock copolymers by self-consistent field theory.

PubMed

Yang, Guang; Tang, Ping; Yang, Yuliang; Wang, Qiang

2010-11-25

We employ the self-consistent field theory (SCFT) incorporating Maier-Saupe orientational interactions between rods to investigate the self-assembly of rod-coil diblock copolymers (RC DBC) in bulk and especially confined into two flat surfaces in 2D space. A unit vector defined on a spherical surface for describing the orientation of rigid blocks in 3D Euclidean space is discretized with an icosahedron triangular mesh to numerically integrate over rod orientation, which is confirmed to have numerical accuracy and stability higher than that of the normal Gaussian quadrature. For the hockey puck-shaped phases in bulk, geometrical confinement, i.e., the film thickness, plays an important role in the self-assembled structures' transitions for the neutral walls. However, for the lamellar phase (monolayer smectic-C) in bulk, the perpendicular lamellae are always stable, less dependent on the film thicknesses because they can relax to the bulk spacing with less-paid coil-stretching in thin films. In particular, a very thin rod layer near the surfaces is formed even in a very thin film. When the walls prefer rods, parallel lamellae are obtained, strongly dependent on the competition between the degree of the surface fields and film geometrical confinement, and the effect of surface field on lamellar structure as a function of film thickness is investigated. Our simulation results provide a guide to understanding the self-assembly of the rod-coil films with desirable application prospects in the fabrication of organic light emitting devices.

Different interface orientations of pentacene and PTCDA induce different degrees of disorder

PubMed Central

2012-01-01

Organic polymers or crystals are commonly used in manufacturing of today‘s electronically functional devices (OLEDs, organic solar cells, etc). Understanding their morphology in general and at the interface in particular is of paramount importance. Proper knowledge of molecular orientation at interfaces is essential for predicting optoelectronic properties such as exciton diffusion length, charge carrier mobility, and molecular quadrupole moments. Two promising candidates are pentacene and 3,4:9,10-perylenetetracarboxylic dianhydride (PTCDA). Different orientations of pentacene on PTCDA have been investigated using an atomistic molecular dynamics approach. Here, we show that the degree of disorder at the interface depends largely on the crystal orientation and that more ordered interfaces generally suffer from large vacancy formation. PMID:22583772

Assembling new technologies at the interface of materials science and biology

NASA Astrophysics Data System (ADS)

Stendahl, John C.

Molecular self-assembly can be used to construct advanced materials by taking cues from nature and harnessing noncovalent interactions. This bottom-up approach affords molecular level precision that can cultivate pathways to improved materials function. The graduate research presented in this thesis integrates molecular self-assembly with traditional concepts in chemistry and materials science, with the ultimate goal of developing innovative solutions in technology and medicine. In the field of polymer engineering, self-assembly was used to create supramolecular nanoribbons that, when incorporated into polystyrene, modify its microstructure and significantly enhance its toughness and ductility. In medicine, self-assembly was used to create ordered, chemically functional materials to improve interactions with cells and other constituents of the biological environment. One system that was investigated is based on a triblock molecule in which cholesterol is connected to a lysine dendron by a flexible oligo-(L-lactic acid) spacer. These molecules self-assemble into polar surface coatings on fibrous poly(L-lactic acid) scaffolds that improve the scaffold's wettability and increase its retention of cells during seeding. Another self-assembling system that was investigated for biomedical applications is a family of molecules referred to as peptide amphiphiles (PA's). PA's consist of hydrophobic alkyl tails connected to short, hydrophilic peptides that incorporate biological signaling epitopes. These molecules spontaneously assemble into networks of well-defined nanofibers in aqueous environments, with the signaling epitopes presented in high density on the nanofiber exteriors. Nanofiber assembly is triggered by charge screening on the peptides and is able to produce self-supporting gels in concentrations of less than 1.0 wt.-%. The assembly process and mechanical properties of PA gels was investigated in detail with vibrational spectroscopy and oscillatory rheology. PA nanofibers were used in conjunction with fibrous poly(L-lactic acid] fabrics to create chemically functional scaffolds to facilitate islet cell transplantation. In transplant studies in diabetic mice, the use of scaffolds for islet delivery was shown to significantly improve transplant outcomes over free islet injections. Together, these studies illustrate that molecular self-assembly can be used to create functional materials for a variety of applications. These materials utilize noncovalent interactions to produce supramolecular structures that have important impacts on properties.

Pressure-induced orientational glass phase in molecular para-hydrogen.

PubMed

Schelkacheva, T I; Tareyeva, E E; Chtchelkatchev, N M

2009-02-01

We propose a theoretical description of a possible orientational glass transition in solid molecular para-hydrogen and ortho-deuterium under pressure supposing that they are mixtures of J=0 and J=2 states of molecules. The theory uses the basic concepts and methods of standard spin-glass theory. We expect our orientational glass to correspond to the II' phase of the high-pressure hydrogen phase diagram.

Through-Thickness Vertically Ordered Lamellar Block Copolymer Thin Films on Unmodified Quartz with Cold Zone Annealing [Thru-Thickness Vertically Ordered Lamellar Block Copolymer Thin Films on Unmodified Quartz with Cold Zone Annealing

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

Basutkar, Monali N.; Samant, Saumil; Strzalka, Joseph

Here, template-free directed self-assembly of ultrathin (~10’s nm) lamellar block copolymer (l-BCP) films of high-interfacial area into vertically oriented nanodomains holds much technological relevance for fabrication of next-generation devices from nanoelectronics to nanomembranes due to domain interconnectivity and high interfacial area. We report for the first time, the formation of full thru-thickness vertically oriented lamellar domains in 100 nm thin polystyrene- block-poly(methyl methacrylate) (PS- b-PMMA) films on quartz substrate, achieved without any PMMA-block wetting layer formation, quartz surface modification (templating chemical, topographical) or system modifications (added surfactant, top-layer coat). Vertical ordering of l-BCPs results from the coupling between a molecularmore » and a macroscopic phenomenon. A molecular relaxation induced vertical l-BCP ordering occurs under a transient macroscopic vertical strain field, imposed by a high film thermal expansion rate under sharp thermal gradient cold zone annealing (CZA-S). The parametric window for vertical ordering is quantified via a coupling constant, C (= v∇ T), whose range is established in terms of a thermal gradient (∇ T) above a threshold value, and an optimal dynamic sample sweep rate ( v ~ d/τ), where τ is the l-BCP’s longest molecular relaxation time and d is the T g,heat- T g,cool distance. Real-time CZA-S morphology evolution of vertically oriented l-BCP tracked along ∇ T using in-situ Grazing Incidence Small Angle X-ray Scattering exhibited an initial formation phase of vertical lamellae, a polygrain structure formation stage, and a grain coarsening phase to fully vertically ordered l-BCP morphology development. CZA-S is a roll-to-roll manufacturing method, rendering this template-free thru-thickness vertical ordering of l-BCP films highly attractive and industrially relevant.« less

Through-Thickness Vertically Ordered Lamellar Block Copolymer Thin Films on Unmodified Quartz with Cold Zone Annealing [Thru-Thickness Vertically Ordered Lamellar Block Copolymer Thin Films on Unmodified Quartz with Cold Zone Annealing

DOE PAGES

Basutkar, Monali N.; Samant, Saumil; Strzalka, Joseph; ...

2017-11-14

Here, template-free directed self-assembly of ultrathin (~10’s nm) lamellar block copolymer (l-BCP) films of high-interfacial area into vertically oriented nanodomains holds much technological relevance for fabrication of next-generation devices from nanoelectronics to nanomembranes due to domain interconnectivity and high interfacial area. We report for the first time, the formation of full thru-thickness vertically oriented lamellar domains in 100 nm thin polystyrene- block-poly(methyl methacrylate) (PS- b-PMMA) films on quartz substrate, achieved without any PMMA-block wetting layer formation, quartz surface modification (templating chemical, topographical) or system modifications (added surfactant, top-layer coat). Vertical ordering of l-BCPs results from the coupling between a molecularmore » and a macroscopic phenomenon. A molecular relaxation induced vertical l-BCP ordering occurs under a transient macroscopic vertical strain field, imposed by a high film thermal expansion rate under sharp thermal gradient cold zone annealing (CZA-S). The parametric window for vertical ordering is quantified via a coupling constant, C (= v∇ T), whose range is established in terms of a thermal gradient (∇ T) above a threshold value, and an optimal dynamic sample sweep rate ( v ~ d/τ), where τ is the l-BCP’s longest molecular relaxation time and d is the T g,heat- T g,cool distance. Real-time CZA-S morphology evolution of vertically oriented l-BCP tracked along ∇ T using in-situ Grazing Incidence Small Angle X-ray Scattering exhibited an initial formation phase of vertical lamellae, a polygrain structure formation stage, and a grain coarsening phase to fully vertically ordered l-BCP morphology development. CZA-S is a roll-to-roll manufacturing method, rendering this template-free thru-thickness vertical ordering of l-BCP films highly attractive and industrially relevant.« less

Chemical Interactions and Their Role in the Microphase Separation of Block Copolymer Thin Films

PubMed Central

Farrell, Richard A.; Fitzgerald, Thomas G.; Borah, Dipu; Holmes, Justin D.; Morris, Michael A.

2009-01-01

The thermodynamics of self-assembling systems are discussed in terms of the chemical interactions and the intermolecular forces between species. It is clear that there are both theoretical and practical limitations on the dimensions and the structural regularity of these systems. These considerations are made with reference to the microphase separation that occurs in block copolymer (BCP) systems. BCP systems self-assemble via a thermodynamic driven process where chemical dis-affinity between the blocks driving them part is balanced by a restorative force deriving from the chemical bond between the blocks. These systems are attracting much interest because of their possible role in nanoelectronic fabrication. This form of self-assembly can obtain highly regular nanopatterns in certain circumstances where the orientation and alignment of chemically distinct blocks can be guided through molecular interactions between the polymer and the surrounding interfaces. However, for this to be possible, great care must be taken to properly engineer the interactions between the surfaces and the polymer blocks. The optimum methods of structure directing are chemical pre-patterning (defining regions on the substrate of different chemistry) and graphoepitaxy (topographical alignment) but both centre on generating alignment through favourable chemical interactions. As in all self-assembling systems, the problems of defect formation must be considered and the origin of defects in these systems is explored. It is argued that in these nanostructures equilibrium defects are relatively few and largely originate from kinetic effects arising during film growth. Many defects also arise from the confinement of the systems when they are ‘directed’ by topography. The potential applications of these materials in electronics are discussed. PMID:19865513

Assembling oppositely charged lock and key responsive colloids: A mesoscale analog of adaptive chemistry

PubMed Central

Mihut, Adriana M.; Stenqvist, Björn; Lund, Mikael; Schurtenberger, Peter; Crassous, Jérôme J.

2017-01-01

We have seen a considerable effort in colloid sciences to copy Nature’s successful strategies to fabricate complex functional structures through self-assembly. This includes attempts to design colloidal building blocks and their intermolecular interactions, such as creating the colloidal analogs of directional molecular interactions, molecular recognition, host-guest systems, and specific binding. We show that we can use oppositely charged thermoresponsive particles with complementary shapes, such as spherical and bowl-shaped particles, to implement an externally controllable lock-and-key self-assembly mechanism. The use of tunable electrostatic interactions combined with the temperature-dependent size and shape and van der Waals interactions of these building blocks provides an exquisite control over the selectivity and specificity of the interactions and self-assembly process. The dynamic nature of the mechanism allows for reversibly cycling through various structures that range from weakly structured dense liquids to well-defined molecule-shaped clusters with different configurations through variations in temperature and ionic strength. We link this complex and dynamic self-assembly behavior to the relevant molecular interactions, such as screened Coulomb and van der Waals forces and the geometrical complementarity of the two building blocks, and discuss our findings in the context of the concepts of adaptive chemistry recently introduced to molecular systems. PMID:28929133

End Groups of Functionalized Siloxane Oligomers Direct Block-Copolymeric or Liquid-Crystalline Self-Assembly Behavior

PubMed Central

2016-01-01

Monodisperse oligodimethylsiloxanes end-functionalized with the hydrogen-bonding ureidopyrimidinone (UPy) motif undergo phase separation between their aromatic end groups and dimethylsiloxane midblocks to form ordered nanostructures with domain spacings of <5 nm. The self-assembly behavior of these well-defined oligomers resembles that of high degree of polymerization (N)–high block interaction parameter (χ) linear diblock copolymers despite their small size. Specifically, the phase morphology varies from lamellar to hexagonal to body-centered cubic with increasing asymmetry in molecular volume fraction. Mixing molecules with different molecular weights to give dispersity >1.13 results in disorder, showing importance of molecular monodispersity for ultrasmall ordered phase separation. In contrast, oligodimethylsiloxanes end-functionalized with an O-benzylated UPy derivative self-assemble into lamellar nanostructures regardless of volume fraction because of the strong preference of the end groups to aggregate in a planar geometry. Thus, these molecules display more classically liquid-crystalline self-assembly behavior where the lamellar bilayer thickness is determined by the siloxane midblock. Here the lamellar nanostructure is tolerant to molecular polydispersity. We show the importance of end groups in high χ–low N block molecules, where block-copolymer-like self-assembly in our UPy-functionalized oligodimethylsiloxanes relies upon the dominance of phase separation effects over directional end group aggregation. PMID:27054381

Halogen-Adatom Mediated Phase Transition of Two-Dimensional Molecular Self-Assembly on a Metal Surface.

PubMed

Niu, Tianchao; Wu, Jinge; Ling, Faling; Jin, Shuo; Lu, Guanghong; Zhou, Miao

2018-01-09

Construction of tunable and robust two-dimensional (2D) molecular arrays with desirable lattices and functionalities over a macroscopic scale relies on spontaneous and reversible noncovalent interactions between suitable molecules as building blocks. Halogen bonding, with active tunability of direction, strength, and length, is ideal for tailoring supramolecular structures. Herein, by combining low-temperature scanning tunneling microscopy and systematic first-principles calculations, we demonstrate novel halogen bonding involving single halogen atoms and phase engineering in 2D molecular self-assembly. On the Au(111) surface, we observed catalyzed dehalogenation of hexabromobenzene (HBB) molecules, during which negatively charged bromine adatoms (Br δ- ) were generated and participated in assembly via unique C-Br δ+ ···Br δ- interaction, drastically different from HBB assembly on a chemically inert graphene substrate. We successfully mapped out different phases of the assembled superstructure, including densely packed hexagonal, tetragonal, dimer chain, and expanded hexagonal lattices at room temperature, 60 °C, 90 °C, and 110 °C, respectively, and the critical role of Br δ- in regulating lattice characteristics was highlighted. Our results show promise for manipulating the interplay between noncovalent interactions and catalytic reactions for future development of molecular nanoelectronics and 2D crystal engineering.

Amyloid Oligomers and Protofibrils, but Not Filaments, Self-Replicate from Native Lysozyme

PubMed Central

2015-01-01

Self-assembly of amyloid fibrils is the molecular mechanism best known for its connection with debilitating human disorders such as Alzheimer’s disease but is also associated with various functional cellular responses. There is increasing evidence that amyloid formation proceeds along two distinct assembly pathways involving either globular oligomers and protofibrils or rigid monomeric filaments. Oligomers, in particular, have been implicated as the dominant molecular species responsible for pathogenesis. Yet the molecular mechanisms regulating their self-assembly have remained elusive. Here we show that oligomers/protofibrils and monomeric filaments, formed along distinct assembly pathways, display critical differences in their ability to template amyloid growth at physiological vs denaturing temperatures. At physiological temperatures, amyloid filaments remained stable but could not seed growth of native monomers. In contrast, oligomers and protofibrils not only remained intact but were capable of self-replication using native monomers as the substrate. Kinetic data further suggested that this prion-like growth mode of oligomers/protofibrils involved two distinct activities operating orthogonal from each other: autocatalytic self-replication of oligomers from native monomers and nucleated polymerization of oligomers into protofibrils. The environmental changes to stability and templating competence of these different amyloid species in different environments are likely to be important for understanding the molecular mechanisms underlying both pathogenic and functional amyloid self-assembly. PMID:24884889

Amyloid oligomers and protofibrils, but not filaments, self-replicate from native lysozyme.

PubMed

Mulaj, Mentor; Foley, Joseph; Muschol, Martin

2014-06-25

Self-assembly of amyloid fibrils is the molecular mechanism best known for its connection with debilitating human disorders such as Alzheimer's disease but is also associated with various functional cellular responses. There is increasing evidence that amyloid formation proceeds along two distinct assembly pathways involving either globular oligomers and protofibrils or rigid monomeric filaments. Oligomers, in particular, have been implicated as the dominant molecular species responsible for pathogenesis. Yet the molecular mechanisms regulating their self-assembly have remained elusive. Here we show that oligomers/protofibrils and monomeric filaments, formed along distinct assembly pathways, display critical differences in their ability to template amyloid growth at physiological vs denaturing temperatures. At physiological temperatures, amyloid filaments remained stable but could not seed growth of native monomers. In contrast, oligomers and protofibrils not only remained intact but were capable of self-replication using native monomers as the substrate. Kinetic data further suggested that this prion-like growth mode of oligomers/protofibrils involved two distinct activities operating orthogonal from each other: autocatalytic self-replication of oligomers from native monomers and nucleated polymerization of oligomers into protofibrils. The environmental changes to stability and templating competence of these different amyloid species in different environments are likely to be important for understanding the molecular mechanisms underlying both pathogenic and functional amyloid self-assembly.

Molecular assemblies as protective barriers and adhesion promotion interlayer

DOEpatents

King, David E.; Czanderna, Alvin W.; Kennedy, Cheryl E.

1996-01-01

A protective diffusion barrier having adhesive qualifies for metalized surfaces is provided by a passivating agent having the formula HS--(CH.sub.2).sub.11 --COOH Which forms a very dense, transparent organized molecular assembly or layer that is impervious to water, alkali, and other impurities and corrosive substances that typically attack metal surfaces.

Molecular Motions in Functional Self-Assembled Nanostructures

PubMed Central

Dhotel, Alexandre; Chen, Ziguang; Delbreilh, Laurent; Youssef, Boulos; Saiter, Jean-Marc; Tan, Li

2013-01-01

The construction of “smart” materials able to perform specific functions at the molecular scale through the application of various stimuli is highly attractive but still challenging. The most recent applications indicate that the outstanding flexibility of self-assembled architectures can be employed as a powerful tool for the development of innovative molecular devices, functional surfaces and smart nanomaterials. Structural flexibility of these materials is known to be conferred by weak intermolecular forces involved in self-assembly strategies. However, some fundamental mechanisms responsible for conformational lability remain unexplored. Furthermore, the role played by stronger bonds, such as coordination, ionic and covalent bonding, is sometimes neglected while they can be employed readily to produce mechanically robust but also chemically reversible structures. In this review, recent applications of structural flexibility and molecular motions in self-assembled nanostructures are discussed. Special focus is given to advanced materials exhibiting significant performance changes after an external stimulus is applied, such as light exposure, pH variation, heat treatment or electromagnetic field. The crucial role played by strong intra- and weak intermolecular interactions on structural lability and responsiveness is highlighted. PMID:23348927

Digital Material Assembly by Passive Means and Modular Isotropic Lattice Extruder System

NASA Technical Reports Server (NTRS)

Gershenfeld, Neil (Inventor); Carney, Matthew Eli (Inventor); Jenett, Benjamin (Inventor)

2017-01-01

A set of machines and related systems build structures by the additive assembly of discrete parts. These digital material assemblies constrain the constituent parts to a discrete set of possible positions and orientations. In doing so, the structures exhibit many of the properties inherent in digital communication such as error correction, fault tolerance and allow the assembly of precise structures with comparatively imprecise tools. Assembly of discrete cellular lattices by a Modular Isotropic Lattice Extruder System (MILES) is implemented by pulling strings of lattice elements through a forming die that enforces geometry constraints that lock the elements into a rigid structure that can then be pushed against and extruded out of the die as an assembled, loadbearing structure.

Automated assembly in space

NASA Technical Reports Server (NTRS)

Srivastava, Sandanand; Dwivedi, Suren N.; Soon, Toh Teck; Bandi, Reddy; Banerjee, Soumen; Hughes, Cecilia

1989-01-01

The installation of robots and their use of assembly in space will create an exciting and promising future for the U.S. Space Program. The concept of assembly in space is very complicated and error prone and it is not possible unless the various parts and modules are suitably designed for automation. Certain guidelines are developed for part designing and for an easy precision assembly. Major design problems associated with automated assembly are considered and solutions to resolve these problems are evaluated in the guidelines format. Methods for gripping and methods for part feeding are developed with regard to the absence of gravity in space. The guidelines for part orientation, adjustments, compliances and various assembly construction are discussed. Design modifications of various fasteners and fastening methods are also investigated.

Investigating Factors that Generate and Maintain Variation in Migratory Orientation: A Primer for Recent and Future Work.

PubMed

Delmore, Kira E; Liedvogel, Miriam

2016-01-01

The amazing accuracy of migratory orientation performance across the animal kingdom is facilitated by the use of magnetic and celestial compass systems that provide individuals with both directional and positional information. Quantitative genetics analyses in several animal systems suggests that migratory orientation has a strong genetic component. Nevertheless, the exact identity of genes controlling orientation remains largely unknown, making it difficult to obtain an accurate understanding of this fascinating behavior on the molecular level. Here, we provide an overview of molecular genetic techniques employed thus far, highlight the pros and cons of various approaches, generalize results from species-specific studies whenever possible, and evaluate how far the field has come since early quantitative genetics studies. We emphasize the importance of examining different levels of molecular control, and outline how future studies can take advantage of high-resolution tracking and sequencing techniques to characterize the genomic architecture of migratory orientation.

Molecular self-assembly approaches for supramolecular electronic and organic electronic devices

NASA Astrophysics Data System (ADS)

Yip, Hin-Lap

Molecular self-assembly represents an efficient bottom-up strategy to generate structurally well-defined aggregates of semiconducting pi-conjugated materials. The capability of tuning the chemical structures, intermolecular interactions and nanostructures through molecular engineering and novel materials processing renders it possible to tailor a large number of unprecedented properties such as charge transport, energy transfer and light harvesting. This approach does not only benefit traditional electronic devices based on bulk materials, but also generate a new research area so called "supramolecular electronics" in which electronic devices are built up with individual supramolecular nanostructures with size in the sub-hundred nanometers range. My work combined molecular self-assembly together with several novel materials processing techniques to control the nucleation and growth of organic semiconducting nanostructures from different type of pi-conjugated materials. By tailoring the interactions between the molecules using hydrogen bonds and pi-pi stacking, semiconducting nanoplatelets and nanowires with tunable sizes can be fabricated in solution. These supramolecular nanostructures were further patterned and aligned on solid substrates through printing and chemical templating methods. The capability to control the different hierarchies of organization on surface provides an important platform to study their structural-induced electronic properties. In addition to using molecular self-assembly to create different organic nanostructures, functional self-assembled monolayer (SAM) formed by spontaneous chemisorption on surfaces was used to tune the interfacial property in organic solar cells. Devices showed dramatically improved performance when appropriate SAMs were applied to optimize the contact property for efficiency charge collection.

A molecular modeling based method to predict elution behavior and binding patches of proteins in multimodal chromatography.

PubMed

Banerjee, Suvrajit; Parimal, Siddharth; Cramer, Steven M

2017-08-18

Multimodal (MM) chromatography provides a powerful means to enhance the selectivity of protein separations by taking advantage of multiple weak interactions that include electrostatic, hydrophobic and van der Waals interactions. In order to increase our understanding of such phenomena, a computationally efficient approach was developed that combines short molecular dynamics simulations and continuum solvent based coarse-grained free energy calculations in order to study the binding of proteins to Self Assembled Monolayers (SAM) presenting MM ligands. Using this method, the free energies of protein-MM SAM binding over a range of incident orientations of the protein can be determined. The resulting free energies were then examined to identify the more "strongly bound" orientations of different proteins with two multimodal surfaces. The overall free energy of protein-MM surface binding was then determined and correlated to retention factors from isocratic chromatography. This correlation, combined with analytical expressions from the literature, was then employed to predict protein gradient elution salt concentrations as well as selectivity reversals with different MM resin systems. Patches on protein surfaces that interacted strongly with MM surfaces were also identified by determining the frequency of heavy atom contacts with the atoms of the MM SAMs. A comparison of these patches to Electrostatic Potential and hydrophobicity maps indicated that while all of these patches contained significant positive charge, only the highest frequency sites also possessed hydrophobicity. The ability to identify key binding patches on proteins may have significant impact on process development for the separation of bioproduct related impurities. Copyright © 2017 Elsevier B.V. All rights reserved.

Higher-order structures assembly of gold nanorods caused by captopril in high ionic strength solutions.

PubMed

Shen, Sufen; Zhao, Huawen; Huang, Chengzhi; Wu, Liping

2010-02-01

The ability to construct self-assembled architectures is essential for the exploration of nanoparticle-structured properties. It is one of good strategies by employing molecule-modificated nanoparticles to prepare new materials with particular properties. Herein, we found that captopril (Cap), a biocompatible medicament, could adjust and control the formation of self-assembled gold nanorods (Au-NRs) in high ionic strength solutions. The assembly is in higher-order structures containing both end-to-end and side-by-side orientations. Furthermore, these structures of Au-NRs could be served as plasmonic waveguide in future biological nanodevices.

Molecular Origin of the Self-Assembly of Lanreotide into Nanotubes: A Mutational Approach☆

PubMed Central

Valéry, Céline; Pouget, Emilie; Pandit, Anjali; Verbavatz, Jean-Marc; Bordes, Luc; Boisdé, Isabelle; Cherif-Cheikh, Roland; Artzner, Franck; Paternostre, Maité

2008-01-01

Lanreotide, a synthetic, therapeutic octapeptide analog of somatostatin, self-assembles in water into perfectly hollow and monodisperse (24-nm wide) nanotubes. Lanreotide is a cyclic octapeptide that contains three aromatic residues. The molecular packing of the peptide in the walls of a nanotube has recently been characterized, indicating four hierarchical levels of organization. This is a fascinating example of spontaneous self-organization, very similar to the formation of the gas vesicle walls of Halobacterium halobium. However, this unique peptide self-assembly raises important questions about its molecular origin. We adopted a directed mutation approach to determine the molecular parameters driving the formation of such a remarkable peptide architecture. We have modified the conformation by opening the cycle and by changing the conformation of a Lys residue, and we have also mutated the aromatic side chains of the peptide. We show that three parameters are essential for the formation of lanreotide nanotubes: i), the specificity of two of the three aromatic side chains, ii), the spatial arrangement of the hydrophilic and hydrophobic residues, and iii), the aromatic side chain in the β-turn of the molecule. When these molecular characteristics are modified, either the peptides lose their self-assembling capability or they form less-ordered architectures, such as amyloid fibers and curved lamellae. Thus we have determined key elements of the molecular origins of lanreotide nanotube formation. PMID:17993497

Mesoscale Simulation and Machine Learning of Asphaltene Aggregation Phase Behavior and Molecular Assembly Landscapes.

PubMed

Wang, Jiang; Gayatri, Mohit A; Ferguson, Andrew L

2017-05-11

Asphaltenes constitute the heaviest fraction of the aromatic group in crude oil. Aggregation and precipitation of asphaltenes during petroleum processing costs the petroleum industry billions of dollars each year due to downtime and production inefficiencies. Asphaltene aggregation proceeds via a hierarchical self-assembly process that is well-described by the Yen-Mullins model. Nevertheless, the microscopic details of the emergent cluster morphologies and their relative stability under different processing conditions remain poorly understood. We perform coarse-grained molecular dynamics simulations of a prototypical asphaltene molecule to establish a phase diagram mapping the self-assembled morphologies as a function of temperature, pressure, and n-heptane:toluene solvent ratio informing how to control asphaltene aggregation by regulating external processing conditions. We then combine our simulations with graph matching and nonlinear manifold learning to determine low-dimensional free energy surfaces governing asphaltene self-assembly. In doing so, we introduce a variant of diffusion maps designed to handle data sets with large local density variations, and report the first application of many-body diffusion maps to molecular self-assembly to recover a pseudo-1D free energy landscape. Increasing pressure only weakly affects the landscape, serving only to destabilize the largest aggregates. Increasing temperature and toluene solvent fraction stabilizes small cluster sizes and loose bonding arrangements. Although the underlying molecular mechanisms differ, the strikingly similar effect of these variables on the free energy landscape suggests that toluene acts upon asphaltene self-assembly as an effective temperature.

Design, Synthesis, and Self-Assembly of Well-Defined Hybrid Materials Including Polymer Amphiphiles and Giant Tetrahedra Molecules Based on Poss Nanoparticles

NASA Astrophysics Data System (ADS)

Huang, Mingjun

"Bottom-up" techniques-based self-assembly are always attracting people's interests since this technology provides relatively low economic cost and fast route to construct organized structures at different scales. Considering unprecedented benefits from polymer materials, self-assemblies utilizing polymer building blocks have been extensively studied to achieve diverse hierarchical structures and various attractive properties. However, precise controls of chemical primary structures and compositions and exact constructions of hierarchal ordered structures in synthetic polymers are far from being fully appreciated. In this dissertation, a novel approach has been utilized to construct diverse well-defined nano-building blocks, giant molecules, via conjugating different, and functionalized molecular nanoparticles (MNPs) which are shape- and volume-persistent nano-objects with precise molecular structure and specific symmetry. The representative examples of the three basic categories of giant molecules, "giant polyhedra", "giant surfactants", and "giant shape amphiphiles" were discussed in details. First, a class of precisely defined, nanosized giant tetrahedra was constructed by placing different polyhedral oligomeric silsesquioxane (POSS) molecular nanoparticles at the vertices of a rigid tetrahedral framework. Designed symmetry breaking of these giant tetrahedra introduces accurate positional interactions and results in diverse selectively assembled, highly ordered supramolecular lattices including a Frank-Kasper (FK) A15 phase. The FK and quasicrystal phases are originally identified in metal alloys and only sporadically observed in soft matters. It remains unclear how to correlate their stability with the chemical composition and molecular topology in the self-assembling systems. We then for this purpose designed and studied the self-assembly phase transition sequences of four series of hybrid giant surfactants based on hydrophilic POSS cages tethered with one to four polystyrene (PS) tails. With increasing the number of tails, molecular topological variations not only affect phase boundaries in terms of the PS volume fraction, but also open a window to stabilize supramolecular FK and quasicrystal phases in the spherical phase region, demonstrating the critical role of molecular topology in dictating the formation of unconventional supramolecular lattices of "soft" spherical motifs. The FK A15 phase was even surprisingly observed in the giant shape amphiphile molecule, triphenylene-6BPOSS, which has a disk-like flat triphenylene core connected with six hydrophobic POSS cages by sides. Without conical molecular shape, triphenylene-6BPOSS self-assembled and stabilized into supramolecular sphere via pi-pi interactions through a completely different mechanism with precious two cases. These studies indicate that "bottom-up" self-assemble based on well-defined giant molecules approach can be rather powerful to fabricate usually complicated hierarchical structures and open up a wide field of supramolecular self-assembly with unexpected structure and properties.

Molecular alignment and orientation with a hybrid Raman scattering technique

NASA Astrophysics Data System (ADS)

Bustard, Philip J.; Lausten, R.; Sussman, Benjamin J.

2012-11-01

We demonstrate a scheme for the preparation of molecular alignment and angular momentum orientation using a hybrid combination of two limits of Raman scattering. First a weak, impulsive pump pulse initializes the system via the nonresonant dynamic Stark effect. Then, having overcome the influence of the vacuum fluctuations, an amplification pulse selectively enhances the initial coherences by transient stimulated Raman scattering, generating alignment and angular momentum orientation of molecular hydrogen. The amplitude and phase of the resulting coherent dynamics are experimentally probed, indicating an amplification factor of 4.5. An analytic theory is developed to model the dynamics.

Tunable molecular orientation and elevated thermal stability of vapor-deposited organic semiconductors

DOE PAGES

Dalal, Shakeel S.; Walters, Diane M.; Lyubimov, Ivan; ...

2015-03-23

Physical vapor deposition is commonly used to prepare organic glasses that serve as the active layers in light-emitting diodes, photovoltaics, and other devices. Recent work has shown that orienting the molecules in such organic semiconductors can significantly enhance device performance. In this paper, we apply a high-throughput characterization scheme to investigate the effect of the substrate temperature (T substrate) on glasses of three organic molecules used as semiconductors. The optical and material properties are evaluated with spectroscopic ellipsometry. We find that molecular orientation in these glasses is continuously tunable and controlled by T substrate/T g, where T g is themore » glass transition temperature. All three molecules can produce highly anisotropic glasses; the dependence of molecular orientation upon substrate temperature is remarkably similar and nearly independent of molecular length. All three compounds form “stable glasses” with high density and thermal stability, and have properties similar to stable glasses prepared from model glass formers. Simulations reproduce the experimental trends and explain molecular orientation in the deposited glasses in terms of the surface properties of the equilibrium liquid. Finally, by showing that organic semiconductors form stable glasses, these results provide an avenue for systematic performance optimization of active layers in organic electronics.« less

Quantitative self-assembly prediction yields targeted nanomedicines

NASA Astrophysics Data System (ADS)

Shamay, Yosi; Shah, Janki; Işık, Mehtap; Mizrachi, Aviram; Leibold, Josef; Tschaharganeh, Darjus F.; Roxbury, Daniel; Budhathoki-Uprety, Januka; Nawaly, Karla; Sugarman, James L.; Baut, Emily; Neiman, Michelle R.; Dacek, Megan; Ganesh, Kripa S.; Johnson, Darren C.; Sridharan, Ramya; Chu, Karen L.; Rajasekhar, Vinagolu K.; Lowe, Scott W.; Chodera, John D.; Heller, Daniel A.

2018-02-01

Development of targeted nanoparticle drug carriers often requires complex synthetic schemes involving both supramolecular self-assembly and chemical modification. These processes are generally difficult to predict, execute, and control. We describe herein a targeted drug delivery system that is accurately and quantitatively predicted to self-assemble into nanoparticles based on the molecular structures of precursor molecules, which are the drugs themselves. The drugs assemble with the aid of sulfated indocyanines into particles with ultrahigh drug loadings of up to 90%. We devised quantitative structure-nanoparticle assembly prediction (QSNAP) models to identify and validate electrotopological molecular descriptors as highly predictive indicators of nano-assembly and nanoparticle size. The resulting nanoparticles selectively targeted kinase inhibitors to caveolin-1-expressing human colon cancer and autochthonous liver cancer models to yield striking therapeutic effects while avoiding pERK inhibition in healthy skin. This finding enables the computational design of nanomedicines based on quantitative models for drug payload selection.

Lattice-free prediction of three-dimensional structure of programmed DNA assemblies

PubMed Central

Pan, Keyao; Kim, Do-Nyun; Zhang, Fei; Adendorff, Matthew R.; Yan, Hao; Bathe, Mark

2014-01-01

DNA can be programmed to self-assemble into high molecular weight 3D assemblies with precise nanometer-scale structural features. Although numerous sequence design strategies exist to realize these assemblies in solution, there is currently no computational framework to predict their 3D structures on the basis of programmed underlying multi-way junction topologies constrained by DNA duplexes. Here, we introduce such an approach and apply it to assemblies designed using the canonical immobile four-way junction. The procedure is used to predict the 3D structure of high molecular weight planar and spherical ring-like origami objects, a tile-based sheet-like ribbon, and a 3D crystalline tensegrity motif, in quantitative agreement with experiments. Our framework provides a new approach to predict programmed nucleic acid 3D structure on the basis of prescribed secondary structure motifs, with possible application to the design of such assemblies for use in biomolecular and materials science. PMID:25470497

Directed Assembly of Molecules on Graphene/Ru(0001)

NASA Astrophysics Data System (ADS)

Zhang, L. Z.; Zhang, H. G.; Sun, J. T.; Pan, Y.; Liu, Q.; Mao, J. H.; Zhou, H. T.; Low, T.; Guo, H. M.; Du, S. X.; Gao, H.-J.

2012-02-01

Recently, the graphene monolayers have been seen to adopt a superstructure - moir'e pattern - on Ru(0001). By using low temperature scanning tunneling spectroscopy, we identified the laterally localized electronic states on this system. The individual states are separated by 3 nm and comprise regions of about 90 carbon atoms. This constitutes a highly regular quantum dot-array with molecular precision. It is evidenced by quantum well resonances with energies that relate to the corrugation of the graphene layer. By using scanning tunneling microscopy/spectroscopy, we demonstrate the selective adsorption and formation of ordered molecular arrays of FePc and pentacene molecules on the graphene/Ru(0001) templates. With in-depth investigations of the molecular adsorption and assembly processes we reveal the existence lateral electric dipoles in the epitaxial graphene monolayers and the capability of the dipoles in directing and driving the molecular adsorption and assembly. When increasing the molecular coverage, we observed the formation of regular Kagome lattices that duplicate the lattice of the moir'e pattern of monolayer graphene.

Self-assembled molecular magnets on patterned silicon substrates: bridging bio-molecules with nanoelectronics.

PubMed

Chang, Chia-Ching; Sun, Kien Wen; Lee, Shang-Fan; Kan, Lou-Sing

2007-04-01

The paper reports the methods of preparing molecular magnets and patterning of the molecules on a semiconductor surface. A highly magnetically aligned metallothionein containing Mn and Cd (Mn,Cd-MT-2) is first synthesized, and the molecules are then placed into nanopores prepared on silicon (001) surfaces using electron beam lithography and reactive ion-etching techniques. We have observed the self-assemble growth of the MT molecules on the patterned Si surface such that the MT molecules have grown into rod or ring type three-dimensional nanostructures, depending on the patterned nanostructures on the surface. We also provide scanning electron microscopy, atomic force microscopy, and magnetic force microscope studies of the molecular nanostructures. This engineered molecule shows molecular magnetization and is biocompatible with conventional semiconductors. These features make Mn,Cd-MT-2 a good candidate for biological applications and sensing sources of new nanodevices. Using molecular self-assembly and topographical patterning of the semiconductor substrate, we can close the gap between bio-molecules and nanoelectronics built into the semiconductor chip.

Homochiral Evolution in Self-Assembled Chiral Polymers and Block Copolymers.

PubMed

Wen, Tao; Wang, Hsiao-Fang; Li, Ming-Chia; Ho, Rong-Ming

2017-04-18

The significance of chirality transfer is not only involved in biological systems, such as the origin of homochiral structures in life but also in man-made chemicals and materials. How the chiral bias transfers from molecular level (molecular chirality) to helical chain (conformational chirality) and then to helical superstructure or phase (hierarchical chirality) from self-assembly is vital for the chemical and biological processes in nature, such as communication, replication, and enzyme catalysis. In this Account, we summarize the methodologies for the examination of homochiral evolution at different length scales based on our recent studies with respect to the self-assembly of chiral polymers and chiral block copolymers (BCPs*). A helical (H*) phase to distinguish its P622 symmetry from that of normal hexagonally packed cylinder phase was discovered in the self-assembly of BCPs* due to the chirality effect on BCP self-assembly. Enantiomeric polylactide-containing BCPs*, polystyrene-b-poly(l-lactide) (PS-PLLA) and polystyrene-b-poly(d-lactide) (PS-PDLA), were synthesized for the examination of homochiral evolution. The optical activity (molecular chirality) of constituted chiral repeating unit in the chiral polylactide is detected by electronic circular dichroism (ECD) whereas the conformational chirality of helical polylactide chain can be explicitly determined by vibrational circular dichroism (VCD). The H* phases of the self-assembled polylactide-containing BCPs* can be directly visualized by 3D transmission electron microscopy (3D TEM) technique at which the handedness (hierarchical chirality) of the helical nanostructure is thus determined. The results from the ECD, VCD, and 3D TEM for the investigated chirality at different length scales suggest the homochiral evolution in the self-assembly of the BCPs*. For chiral polylactides, twisted lamellae in crystalline banded spherulite can be formed by dense packing scheme and effective interactions upon helical chains from self-assembly. The handedness of the twisted lamella can be determined by using rotation experiment of polarized light microscopy (PLM). Similar to the self-assembly of BCPs*, the examined results suggest the homochiral evolution in the crystallized chiral polylactides. The results presented in this Account demonstrate the notable progress in the spectral and morphological determination for the examination of molecular, conformational, and hierarchical chirality in self-assembled twisted superstructures of chiral polymers and helical phases of block copolymers and suggest the attainability of homochiral evolution in the self-assembly of chiral homopolymers and BCPs*. The suggested methodologies for the understanding of the mechanisms of the chirality transfer at different length scales provide the approaches to give Supporting Information for disclosing the mysteries of the homochiral evolution from molecular level.

Cellular automata with object-oriented features for parallel molecular network modeling.

PubMed

Zhu, Hao; Wu, Yinghui; Huang, Sui; Sun, Yan; Dhar, Pawan

2005-06-01

Cellular automata are an important modeling paradigm for studying the dynamics of large, parallel systems composed of multiple, interacting components. However, to model biological systems, cellular automata need to be extended beyond the large-scale parallelism and intensive communication in order to capture two fundamental properties characteristic of complex biological systems: hierarchy and heterogeneity. This paper proposes extensions to a cellular automata language, Cellang, to meet this purpose. The extended language, with object-oriented features, can be used to describe the structure and activity of parallel molecular networks within cells. Capabilities of this new programming language include object structure to define molecular programs within a cell, floating-point data type and mathematical functions to perform quantitative computation, message passing capability to describe molecular interactions, as well as new operators, statements, and built-in functions. We discuss relevant programming issues of these features, including the object-oriented description of molecular interactions with molecule encapsulation, message passing, and the description of heterogeneity and anisotropy at the cell and molecule levels. By enabling the integration of modeling at the molecular level with system behavior at cell, tissue, organ, or even organism levels, the program will help improve our understanding of how complex and dynamic biological activities are generated and controlled by parallel functioning of molecular networks. Index Terms-Cellular automata, modeling, molecular network, object-oriented.

Low molecular weight oligomers of amyloid peptides display β-barrel conformations: A replica exchange molecular dynamics study in explicit solvent

NASA Astrophysics Data System (ADS)

De Simone, Alfonso; Derreumaux, Philippe

2010-04-01

The self-assembly of proteins and peptides into amyloid fibrils is connected to over 40 pathological conditions including neurodegenerative diseases and systemic amyloidosis. Diffusible, low molecular weight protein and peptide oligomers that form in the early steps of aggregation appear to be the harmful cytotoxic species in the molecular etiology of these diseases. So far, the structural characterization of these oligomers has remained elusive owing to their transient and dynamic features. We here address, by means of full atomistic replica exchange molecular dynamics simulations, the energy landscape of heptamers of the amyloidogenic peptide NHVTLSQ from the beta-2 microglobulin protein. The simulations totaling 5 μs show that low molecular weight oligomers in explicit solvent consist of β-barrels in equilibrium with amorphous states and fibril-like assemblies. The results, also accounting for the influence of the pH on the conformational properties, provide a strong evidence of the formation of transient β-barrel assemblies in the early aggregation steps of amyloid-forming systems. Our findings are discussed in terms of oligomers cytotoxicity.

Growing And Assembling Cells Into Tissues

NASA Technical Reports Server (NTRS)

Wolf, David A.; Schwarz, Ray P.; Lewis, Marian L.; Cross, John H.; Huls, M. Helen

1990-01-01

Laboratory process for growth and assembly of mammalian cells into tissue-like masses demonstrated with hamster and rat cells. New process better able to provide culture environment with reduced fluid shear stress, freedom for three-dimensional spatial orientation of particles suspended in culture medium, and localization of particles of different or similar sedimentation properties in similar spatial region.

In Situ Electrochemical Synthesis of Oriented and Defect-Free AEL Molecular-Sieve Films Using Ionic Liquids.

PubMed

Yu, Tongwen; Chu, Wenling; Cai, Rui; Liu, Yanchun; Yang, Weishen

2015-10-26

Simply preparing oriented and defect-free molecular-sieve films have been a long-standing challenge both in academia and industry. Most of the early works focus on the careful and multiple controls of the seeds layer or synthesis conditions. Herein, we report a one-step in situ electrochemical ionothermal method that combines a controllable electric field with ionic liquids. We demonstrate that an in-plane oriented and defect-free AEL (one molecular-sieve framework type) molecular-sieve film was obtained using an Al electrode as the Al source. The excellent corrosion-resistant performance of the film makes this technology promising in multiple applications, such as anti-corrosion coatings. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Discovery of genes related to insecticide resistance in Bactrocera dorsalis by functional genomic analysis of a de novo assembled transcriptome.

PubMed

Hsu, Ju-Chun; Chien, Ting-Ying; Hu, Chia-Cheng; Chen, Mei-Ju May; Wu, Wen-Jer; Feng, Hai-Tung; Haymer, David S; Chen, Chien-Yu

2012-01-01

Insecticide resistance has recently become a critical concern for control of many insect pest species. Genome sequencing and global quantization of gene expression through analysis of the transcriptome can provide useful information relevant to this challenging problem. The oriental fruit fly, Bactrocera dorsalis, is one of the world's most destructive agricultural pests, and recently it has been used as a target for studies of genetic mechanisms related to insecticide resistance. However, prior to this study, the molecular data available for this species was largely limited to genes identified through homology. To provide a broader pool of gene sequences of potential interest with regard to insecticide resistance, this study uses whole transcriptome analysis developed through de novo assembly of short reads generated by next-generation sequencing (NGS). The transcriptome of B. dorsalis was initially constructed using Illumina's Solexa sequencing technology. Qualified reads were assembled into contigs and potential splicing variants (isotigs). A total of 29,067 isotigs have putative homologues in the non-redundant (nr) protein database from NCBI, and 11,073 of these correspond to distinct D. melanogaster proteins in the RefSeq database. Approximately 5,546 isotigs contain coding sequences that are at least 80% complete and appear to represent B. dorsalis genes. We observed a strong correlation between the completeness of the assembled sequences and the expression intensity of the transcripts. The assembled sequences were also used to identify large numbers of genes potentially belonging to families related to insecticide resistance. A total of 90 P450-, 42 GST-and 37 COE-related genes, representing three major enzyme families involved in insecticide metabolism and resistance, were identified. In addition, 36 isotigs were discovered to contain target site sequences related to four classes of resistance genes. Identified sequence motifs were also analyzed to characterize putative polypeptide translational products and associate them with specific genes and protein functions.

In silico modeling of the cryptic E2∼ubiquitin-binding site of E6-associated protein (E6AP)/UBE3A reveals the mechanism of polyubiquitin chain assembly.

PubMed

Ronchi, Virginia P; Kim, Elizabeth D; Summa, Christopher M; Klein, Jennifer M; Haas, Arthur L

2017-11-03

To understand the mechanism for assembly of Lys 48 -linked polyubiquitin degradation signals, we previously demonstrated that the E6AP/UBE3A ligase harbors two functionally distinct E2∼ubiquitin-binding sites: a high-affinity Site 1 required for E6AP Cys 820 ∼ubiquitin thioester formation and a canonical Site 2 responsible for subsequent chain elongation. Ordered binding to Sites 1 and 2 is here revealed by observation of UbcH7∼ubiquitin-dependent substrate inhibition of chain formation at micromolar concentrations. To understand substrate inhibition, we exploited the PatchDock algorithm to model in silico UbcH7∼ubiquitin bound to Site 1, validated by chain assembly kinetics of selected point mutants. The predicted structure buries an extensive solvent-excluded surface bringing the UbcH7∼ubiquitin thioester bond within 6 Å of the Cys 820 nucleophile. Modeling onto the active E6AP trimer suggests that substrate inhibition arises from steric hindrance between Sites 1 and 2 of adjacent subunits. Confirmation that Sites 1 and 2 function in trans was demonstrated by examining the effect of E6APC820A on wild-type activity and single-turnover pulse-chase kinetics. A cyclic proximal indexation model proposes that Sites 1 and 2 function in tandem to assemble thioester-linked polyubiquitin chains from the proximal end attached to Cys 820 before stochastic en bloc transfer to the target protein. Non-reducing SDS-PAGE confirms assembly of the predicted Cys 820 -linked 125 I-polyubiquitin thioester intermediate. Other studies suggest that Glu 550 serves as a general base to generate the Cys 820 thiolate within the low dielectric binding interface and Arg 506 functions to orient Glu 550 and to stabilize the incipient anionic transition state during thioester exchange. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Hierarchical Co-Assembly Enhanced Direct Ink Writing.

PubMed

Li, Longyu; Zhang, Pengfei; Zhang, Zhiyun; Lin, Qianming; Wu, Yuyang; Cheng, Alexander; Lin, Yunxiao; Thompson, Christina M; Smaldone, Ronald A; Ke, Chenfeng

2018-04-23

Integrating intelligent molecular systems into 3D printing materials and transforming their molecular functions to the macroscale with controlled superstructures will unleash great potential for the development of smart materials. Compared to macromolecular 3D printing materials, self-assembled small-molecule-based 3D printing materials are very rare owing to the difficulties of facilitating 3D printability as well as preserving their molecular functions macroscopically. Herein, we report a general approach for the integration of functional small molecules into 3D printing materials for direct ink writing through the introduction of a supramolecular template. A variety of inorganic and organic small-molecule-based inks were 3D-printed, and their superstructures were refined by post-printing hierarchical co-assembly. Through spatial and temporal control of individual molecular events from the nano- to the macroscale, fine-tuned macroscale features were successfully installed in the monoliths. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Molecular assemblies as protective barriers and adhesion promotion interlayer

DOEpatents

King, D.E.; Czanderna, A.W.; Kennedy, C.E.

1996-01-30

A protective diffusion barrier having adhesive qualities for metalized surfaces is provided by a passivating agent having the formula HS--(CH{sub 2}){sub 11}--COOH which forms a very dense, transparent organized molecular assembly or layer that is impervious to water, alkali, and other impurities and corrosive substances that typically attack metal surfaces. 8 figs.

A universal molecular translator for non-nucleic acid targets that enables dynamic DNA assemblies and logic operations.

PubMed

Tang, Wei; Hu, Shichao; Wang, Huaming; Zhao, Yan; Li, Na; Liu, Feng

2014-11-28

A universal molecular translator based on the target-triggered DNA strand displacement was developed, which was able to convert various kinds of non-nucleic acid targets into a unique output DNA. This translation strategy was successfully applied in directing dynamic DNA assemblies and in realizing three-input logic gate operations.

High-Throughput Sequencing to Reveal Genes Involved in Reproduction and Development in Bactrocera dorsalis (Diptera: Tephritidae)

PubMed Central

Zheng, Weiwei; Peng, Tao; He, Wei; Zhang, Hongyu

2012-01-01

Background Tephritid fruit flies in the genus Bactrocera are of major economic significance in agriculture causing considerable loss to the fruit and vegetable industry. Currently, there is no ideal control program. Molecular means is an effective method for pest control at present, but genomic or transcriptomic data for members of this genus remains limited. To facilitate molecular research into reproduction and development mechanisms, and finally effective control on these pests, an extensive transcriptome for the oriental fruit fly Bactrocera dorsalis was produced using the Roche 454-FLX platform. Results We obtained over 350 million bases of cDNA derived from the whole body of B. dorsalis at different developmental stages. In a single run, 747,206 sequencing reads with a mean read length of 382 bp were obtained. These reads were assembled into 28,782 contigs and 169,966 singletons. The mean contig size was 750 bp and many nearly full-length transcripts were assembled. Additionally, we identified a great number of genes that are involved in reproduction and development as well as genes that represent nearly all major conserved metazoan signal transduction pathways, such as insulin signal transduction. Furthermore, transcriptome changes during development were analyzed. A total of 2,977 differentially expressed genes (DEGs) were detected between larvae and pupae libraries, while there were 1,621 DEGs between adults and larvae, and 2,002 between adults and pupae. These DEGs were functionally annotated with KEGG pathway annotation and 9 genes were validated by qRT-PCR. Conclusion Our data represent the extensive sequence resources available for B. dorsalis and provide for the first time access to the genetic architecture of reproduction and development as well as major signal transduction pathways in the Tephritid fruit fly pests, allowing us to elucidate the molecular mechanisms underlying courtship, ovipositing, development and detailed analyses of the signal transduction pathways. PMID:22570719

Emerging Applications of Polymersomes in Delivery: from Molecular Dynamics to Shrinkage of Tumors

PubMed Central

Discher, Dennis E.; Ortiz, Vanessa; Srinivas, Goundla; Klein, Michael L.; Kim, Younghoon; Christian, David; Cai, Shenshen; Photos, Peter; Ahmed, Fariyal

2014-01-01

Polymersomes are self-assembled shells of amphiphilic block copolymers that are currently being developed by many groups for fundamental insights into the nature of self-assembled states as well as for a variety of potential applications. While recent reviews have highlighted distinctive properties – particularly stability – that are strongly influenced by both copolymer type and polymer molecular weight, here we first review some of the more recent developments in computational molecular dynamics (MD) schemes that lend insight into assembly. We then review polymersome loading, in vivo stealthiness, degradation-based disassembly for controlled release, and even tumor-shrinkage in vivo. Comparisons of polymersomes with viral capsids are shown to encompass and inspire many aspects of current designs. PMID:24692840

Swell Gels to Dumbbell Micelles: Construction of Materials and Nanostructure with Self-assembly

NASA Astrophysics Data System (ADS)

Pochan, Darrin

2007-03-01

Bionanotechnology, the emerging field of using biomolecular and biotechnological tools for nanostructure or nanotecnology development, provides exceptional opportunity in the design of new materials. Self-assembly of molecules is an attractive materials construction strategy due to its simplicity in application. By considering peptidic or charged synthetic polymer 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 interactions; in addition to more traditional self-assembling molecular attributes such as amphiphilicty, to define hierarchical material structure and consequent properties. Several molecular systems will be discussed. Synthetic block copolymers with charged corona blocks can be assembled in dilute solution containing multivalent organic counterions to produce micelle structures such as toroids. These ring-like micelles are similar to the toroidal bundling of charged semiflexible biopolymers like DNA in the presence of multivalent counterions. Micelle structure can be tuned between toroids, cylinders, and disks simply by using different concentrations or molecular volumes of organic counterion. In addition, these charged blocks can consist of amino acids as monomers producing block copolypeptides. In addition to the above attributes, block copolypeptides provide the control of block secondary structure to further control self-assembly. Design strategies based on small (less than 24 amino acids) beta-hairpin peptides will be discussed. Self-assembly of the peptides is predicated on an intramolecular folding event caused by desired solution properties. Importantly, the intramolecular folding event impart a molecular-level mechanism for environmental responsiveness at the material level (e.g. infinite change in viscosity of a solution to a gel with changes in pH, ionic strength, temperature).

Elucidating energy and electron transfer dynamics within molecular assemblies for solar energy conversion

NASA Astrophysics Data System (ADS)

Morseth, Zachary Aaron

The use of sunlight to make chemical fuels (i.e. solar fuels) is an attractive approach in the quest to develop sustainable energy sources. Using nature as a guide, assemblies for artificial photosynthesis will need to perform multiple functions. They will need to be able to harvest light across a broad region of the solar spectrum, transport excited-state energy to charge-separation sites, and then transport and store redox equivalents for use in the catalytic reactions that produce chemical fuels. This multifunctional behavior will require the assimilation of multiple components into a single macromolecular system. A wide variety of different architectures including porphyrin arrays, peptides, dendrimers, and polymers have been explored, with each design posing unique challenges. Polymer assemblies are attractive due to their relative ease of production and facile synthetic modification. However, their disordered nature gives rise to stochastic dynamics not present in more ordered assemblies. The rational design of assemblies requires a detailed understanding of the energy and electron transfer events that follow light absorption, which can occur on timescales ranging from femtoseconds to hundreds of microseconds, necessitating the use of sophisticated techniques. We have used a combination of time-resolved absorption and emission spectroscopies with observation times that span nine orders of magnitude to follow the excited-state evolution within single-site and polymer-based molecular assemblies. We complement experimental observations with electronic structure calculations, molecular dynamics simulations, and kinetic modeling to develop a microscopic view of these dynamics. This thesis provides an overview of work on single-site molecular assemblies and polymers decorated with pendant chromophores, both in solution and on surfaces. This work was made possible through extensive collaboration with Dr. Kirk Schanze's and Dr. John Reynolds' research groups who synthesized the samples for study.

Topography and transport properties of oligo(phenylene ethynylene) molecular wires studied by scanning tunneling microscopy

NASA Technical Reports Server (NTRS)

Dholakia, Geetha R.; Fan, Wendy; Koehne, Jessica; Han, Jie; Meyyappan, M.

2003-01-01

Conjugated phenylene(ethynylene) molecular wires are of interest as potential candidates for molecular electronic devices. Scanning tunneling microscopic study of the topography and current-voltage (I-V) characteristics of self-assembled monolayers of two types of molecular wires are presented here. The study shows that the topography and I-Vs, for small scan voltages, of the two wires are quite similar and that the electronic and structural changes introduced by the substitution of an electronegative N atom in the central phenyl ring of these wires does not significantly alter the self-assembly or the transport properties.

Stacking Orientation Mediation of Pentacene and Derivatives for High Open-Circuit Voltage Organic Solar Cells.

PubMed

Chou, Chi-Ta; Lin, Chien-Hung; Tai, Yian; Liu, Chin-Hsin J; Chen, Li-Chyong; Chen, Kuei-Hsien

2012-05-03

In this Letter, we investigated the effect of the molecular stacking orientation on the open circuit voltage (VOC) of pentacene-based organic solar cells. Two functionalized pentacenes, namely, 6,13-diphenyl-pentacene (DP-penta) and 6,13-dibiphenyl-4-yl-pentacene (DB-penta), were utilized. Different molecular stacking orientations of the pentacene derivatives from the pristine pentacene were identified by angle-dependent near-edge X-ray absorption fine structure measurements. It is concluded that pentacene molecules stand up on the substrate surface, while both functionalized pentacenes lie down. A significant increase of the VOC from 0.28 to 0.83 V can be achieved upon the utilization of functionalized pentacene, owing to the modulation of molecular stacking orientation, which induced a vacuum-level shift.

Self-assembly of crystalline nanotubes from monodisperse amphiphilic diblock copolypeptoid tiles

DOE PAGES

Sun, Jing; Jiang, Xi; Lund, Reidar; ...

2016-03-28

The folding and assembly of sequence-defined polymers into precisely ordered nanostructures promises a class of well-defined biomimetic architectures with specific function. Amphiphilic diblock copolymers are known to self-assemble in water to form a variety of nanostructured morphologies including spheres, disks, cylinders, and vesicles. In all of these cases, the predominant driving force for assembly is the formation of a hydrophobic core that excludes water, whereas the hydrophilic blocks are solvated and extend into the aqueous phase. However, such polymer systems typically have broad molar mass distributions and lack the purity and sequence-defined structure often associated with biologically derived polymers. Here,more » we demonstrate that purified, monodisperse amphiphilic diblock copolypeptoids, with chemically distinct domains that are congruent in size and shape, can behave like molecular tile units that spontaneously assemble into hollow, crystalline nanotubes in water. The nanotubes consist of stacked, porous crystalline rings, and are held together primarily by side-chain van der Waals interactions. The peptoid nanotubes form without a central hydrophobic core, chirality, a hydrogen bond network, and electrostatic or π-π interactions. These results demonstrate the remarkable structure-directing influence of n-alkane and ethyleneoxy side chains in polymer self-assembly. More broadly, this work suggests that flexible, low-molecular-weight sequence-defined polymers can serve as molecular tile units that can assemble into precision supramolecular architectures.« less

Hierarchical Self-Organization of Perylene Bisimides into Supramolecular Spheres and Periodic Arrays Thereof.

PubMed

Sahoo, Dipankar; Peterca, Mihai; Aqad, Emad; Partridge, Benjamin E; Heiney, Paul A; Graf, Robert; Spiess, Hans W; Zeng, Xiangbing; Percec, Virgil

2016-11-09

Perylene bisimide derivatives (PBIs) are known to form only columnar or lamellar assemblies. There is no known example of a PBI self-assembling into a supramolecular sphere. Therefore, periodic and quasiperiodic arrays generated from spherical assemblies produced from PBIs are also not known. Here, a PBI functionalized at its imide groups with a second generation self-assembling dendron is reported to self-assemble into supramolecular spheres. These spheres self-organize in a body-centered cubic (BCC) periodic array, rarely encountered for self-assembling dendrons but often encountered in block copolymers. These supramolecular spheres also assemble into a columnar hexagonal array in which the supramolecular columns are unexpectedly and unprecedentedly made from spheres. At lower temperature, two additional columnar hexagonal phases consisting of symmetric and asymmetric tetrameric crowns of PBI are observed. Structural and retrostructural analysis via X-ray diffraction (XRD), molecular modeling, molecular simulation, and solid state NMR suggests that inversion of the symmetric tetrameric crowns at high temperature mediates their transformation into supramolecular spheres. The tetrameric crowns of PBIs are able to form an isotropic sphere in the cubic phase due to rapid molecular motion at high temperature, unobservable by XRD but demonstrated by solid state NMR studies. This mechanism of hierarchical self-organization of PBI into supramolecular spheres is most probably general and can be applied to other related planar molecules to generate new functions.

Self-assembly of crystalline nanotubes from monodisperse amphiphilic diblock copolypeptoid tiles

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

Sun, Jing; Jiang, Xi; Lund, Reidar

The folding and assembly of sequence-defined polymers into precisely ordered nanostructures promises a class of well-defined biomimetic architectures with specific function. Amphiphilic diblock copolymers are known to self-assemble in water to form a variety of nanostructured morphologies including spheres, disks, cylinders, and vesicles. In all of these cases, the predominant driving force for assembly is the formation of a hydrophobic core that excludes water, whereas the hydrophilic blocks are solvated and extend into the aqueous phase. However, such polymer systems typically have broad molar mass distributions and lack the purity and sequence-defined structure often associated with biologically derived polymers. Here,more » we demonstrate that purified, monodisperse amphiphilic diblock copolypeptoids, with chemically distinct domains that are congruent in size and shape, can behave like molecular tile units that spontaneously assemble into hollow, crystalline nanotubes in water. The nanotubes consist of stacked, porous crystalline rings, and are held together primarily by side-chain van der Waals interactions. The peptoid nanotubes form without a central hydrophobic core, chirality, a hydrogen bond network, and electrostatic or π-π interactions. These results demonstrate the remarkable structure-directing influence of n-alkane and ethyleneoxy side chains in polymer self-assembly. More broadly, this work suggests that flexible, low-molecular-weight sequence-defined polymers can serve as molecular tile units that can assemble into precision supramolecular architectures.« less

Breakthrough and future: nanoscale controls of compositions, morphologies, and mesochannel orientations toward advanced mesoporous materials.

PubMed

Yamauchi, Yusuke; Suzuki, Norihiro; Radhakrishnan, Logudurai; Wang, Liang

2009-01-01

Currently, ordered mesoporous materials prepared through the self-assembly of surfactants have attracted growing interests owing to their special properties, including uniform mesopores and a high specific surface area. Here we focus on fine controls of compositions, morphologies, mesochannel orientations which are important factors for design of mesoporous materials with new functionalities. This Review describes our recent progress toward advanced mesoporous materials. Mesoporous materials now include a variety of inorganic-based materials, for example, transition-metal oxides, carbons, inorganic-organic hybrid materials, polymers, and even metals. Mesoporous metals with metallic frameworks can be produced by using surfactant-based synthesis with electrochemical methods. Owing to their metallic frameworks, mesoporous metals with high electroconductivity and high surface areas hold promise for a wide range of potential applications, such as electronic devices, magnetic recording media, and metal catalysts. Fabrication of mesoporous materials with controllable morphologies is also one of the main subjects in this rapidly developing research field. Mesoporous materials in the form of films, spheres, fibers, and tubes have been obtained by various synthetic processes such as evaporation-mediated direct templating (EDIT), spray-dried techniques, and collaboration with hard-templates such as porous anodic alumina and polymer membranes. Furthermore, we have developed several approaches for orientation controls of 1D mesochannels. The macroscopic-scale controls of mesochannels are important for innovative applications such as molecular-scale devices and electrodes with enhanced diffusions of guest species. Copyright 2009 The Japan Chemical Journal Forum and Wiley Periodicals, Inc.

Effect of molecular shape on rotation under severe confinement

DOE PAGES

Dhiman, Indu; Bhowmik, Debsindhu; Shrestha, Utsab R.; ...

2018-01-31

Orientational structure and dynamics of molecules is known to be affected by confinement in space comparable in size to the molecule itself. ZSM-5 with porous channels of ≈0.55 nm is such a porous medium, which offers a strict spatial confinement on low molecular weight hydrocarbons. An important factor that determines these properties is the shape of the confined molecules. In this work, we employed molecular dynamics simulation to study the orientational structure and dynamics of four molecules that differ in shape but have similar kinetic diameters and moments of inertia, confined in ZSM-5. The effect of molecular shape on themore » orientational structure and dynamics of propane, acetonitrile, acetaldehyde and acetone in ZSM-5 is studied by means of probing the differences in the orientational distribution of molecules in the ZSM-5 channels, and extracting time scales of the decay of correlation functions related to rotational motion. Orientational correlation functions of all the four molecules exhibit two regimes of rotational motion. While the short time regime represents free rotation of the molecules before they collide with the pore walls, the long time orientational jumps driven by inter-channel migrations give rise to a very slow varying second regime. Of the molecules studied, orientational structure and dynamics of propane is found to be least affected by confinement under ZSM-5, whereas charge and shape asymmetry of other molecules makes their interchannel migration-driven rotation slow. The time scales involved in the rotational motion for the molecules studied are compared with similar studies reported in literature. Lastly, this study reveals the important role that molecular shape plays in the behavior of confined molecules.« less

Effect of molecular shape on rotation under severe confinement

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

Dhiman, Indu; Bhowmik, Debsindhu; Shrestha, Utsab R.

Orientational structure and dynamics of molecules is known to be affected by confinement in space comparable in size to the molecule itself. ZSM-5 with porous channels of ≈0.55 nm is such a porous medium, which offers a strict spatial confinement on low molecular weight hydrocarbons. An important factor that determines these properties is the shape of the confined molecules. In this work, we employed molecular dynamics simulation to study the orientational structure and dynamics of four molecules that differ in shape but have similar kinetic diameters and moments of inertia, confined in ZSM-5. The effect of molecular shape on themore » orientational structure and dynamics of propane, acetonitrile, acetaldehyde and acetone in ZSM-5 is studied by means of probing the differences in the orientational distribution of molecules in the ZSM-5 channels, and extracting time scales of the decay of correlation functions related to rotational motion. Orientational correlation functions of all the four molecules exhibit two regimes of rotational motion. While the short time regime represents free rotation of the molecules before they collide with the pore walls, the long time orientational jumps driven by inter-channel migrations give rise to a very slow varying second regime. Of the molecules studied, orientational structure and dynamics of propane is found to be least affected by confinement under ZSM-5, whereas charge and shape asymmetry of other molecules makes their interchannel migration-driven rotation slow. The time scales involved in the rotational motion for the molecules studied are compared with similar studies reported in literature. Lastly, this study reveals the important role that molecular shape plays in the behavior of confined molecules.« less

The assembly of cellulose microfibrils in Valonia macrophysa Kütz.

PubMed

Itoh, T; Brown, R M

1984-03-01

The assembly of cellulose microfibrils was investigated in artificially induced protoplasts of the alga, Valonia macrophysa (Siphonocladales). Primary-wall microfibrills, formed within 72 h of protoplast induction, are randomly oriented. Secondary-wall lamellae, which are produced within 96 h after protoplast induction, have more than three orientations of highly ordered microfibrils. The innermost, recently deposited micofibrils are not parallel with the cortical microtubules, thus indicating a more indirect role of microtubules in the orientation of microfibrils. Fine filamentous structures with a periodicity of 5.0-5.5 nm and the dimensions of actin were observed adjacent to the plasma membrane. Linear cellulose-terminal synthesizing complexes (TCs) consisting of three rows, each with 30-40 particles, were observed not only on the E fracture (EF) but also on P fracture (PF) faces of the plasma membrane. The TC appears to span both faces of the bimolecular leaflet. The average length of the TC is 350 nm, and the number of TCs per unit area during primary-wall synthesis is 1 per μm(2). Neither paired TCs nor granule bands characteristic of Oocystis were observed. Changes in TC structure and distribution during the conversion from primary- to secondary-wall formation have been described. Cellulose microfibril assembly in Valonia is discussed in relation to the process among other eukaryotic systems.

Orientational control of block copolymer microdomains by sub-tesla magnetic fields

NASA Astrophysics Data System (ADS)

Gopinadhan, Manesh; Choo, Youngwoo; Feng, Xunda; Kawabata, Kohsuke; di, Xiaojun; Osuji, Chinedum

Magnetic fields offer a versatile approach to controlling the orientation of block copolymer (BCP) microdomains during self-assembly. To date however, such control has required the imposition of large magnetic fields (>3T), necessitating the use of complex magnet systems - either superconducting or very large conventional resistive magnets. Here we demonstrate the ability to direct BCP self-assembly using considerably smaller fields (<1T) which are accessible using simple rare-earth permanent magnets. The low field alignment is enabled by the presence of small quantities of mesogenic species that are blended into, and co-assemble with the liquid crystalline (LC) mesophase of the side-chain LC BCP under study. In situ SAXS experiments reveal a pronounced dependence of the critical alignment field strength on the stoichiometry of the blend, and the ability to generate aligned microdomains with orientational distribution coefficients exceeding 0.95 at sub-1 T fields for appropriate stoichiometries. The alignment response overall can be rationalized in terms of increased mobility and grain size due to the presence of the mesogenic additive. We use a permanent magnet to fabricate films with aligned nanopores, and the utility of this approach to generate complex BCP microdomain patterns in thin films by local field screening are highlighted. NSF DMR-1410568 and DMR-0847534.

Molecular orientation distributions during injection molding of liquid crystalline polymers: Ex situ investigation of partially filled moldings

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

Fang, Jun; Burghardt, Wesley R.; Bubeck, Robert A.

The development of molecular orientation in thermotropic liquid crystalline polymers (TLCPs) during injection molding has been investigated using two-dimensional wide-angle X-ray scattering coordinated with numerical computations employing the Larson-Doi polydomain model. Orientation distributions were measured in 'short shot' moldings to characterize structural evolution prior to completion of mold filling, in both thin and thick rectangular plaques. Distinct orientation patterns are observed near the filling front. In particular, strong extension at the melt front results in nearly transverse molecular alignment. Far away from the flow front shear competes with extension to produce complex spatial distributions of orientation. The relative influence ofmore » shear is stronger in the thin plaque, producing orientation along the filling direction. Exploiting an analogy between the Larson-Doi model and a fiber orientation model, we test the ability of process simulation tools to predict TLCP orientation distributions during molding. Substantial discrepancies between model predictions and experimental measurements are found near the flow front in partially filled short shots, attributed to the limits of the Hele-Shaw approximation used in the computations. Much of the flow front effect is however 'washed out' by subsequent shear flow as mold filling progresses, leading to improved agreement between experiment and corresponding numerical predictions.« less

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

Javaid, Saqib; National Centre of Physics, Islamabad 45320; Javed Akhtar, M., E-mail: javedakhtar6@gmail.com

Recently, experimental results have shown that photovoltaic properties of Fullerene (C60)/Phthalocyanine based devices improve considerably as molecular orientation is changed from edge-on to face-on. In this work, we have studied the impact of molecular orientation on C60/ZnPc interfacial properties, particularly focusing on experimentally observed face-on and edge-on configuration, using density functional theory based simulations. The results show that the interfacial electronic properties are strongly anisotropic: direction of charge transfer and interface dipole fluctuates as molecular orientation is switched. As a result of orientation dependant interface dipole, difference between acceptor LUMO and donor HOMO increases as the orientation is changed frommore » edge-on to face-on, suggesting a consequent increase in open circuit voltage (V{sub OC}). Moreover, adsorption and electronic properties indicate that the interfacial interactions are much stronger in the face-on configuration which should further facilitate the charge-separation process. These findings elucidate the energy level alignment at C60/ZnPc interface and help to identify interface dipole as the origin of the orientation dependence of V{sub OC}.« less

Weak competing interactions control assembly of strongly bonded TCNQ ionic acceptor molecules on silver surfaces

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

Park, Changwon; Rojas, Geoffrey A.; Jeon, Seokmin

2014-09-19

The energy scales of interactions that control molecular adsorption and assembly on surfaces can vary by several orders of magnitude, yet the importance of each contributing interaction is not apparent a priori. Tetracyanoquinodimethane (TCNQ) is an archetypal electron acceptor molecule and it is a key component of organic metals. On metal surfaces, this molecule also acts as an electron acceptor, producing negatively charged adsorbates. It is therefore rather intriguing to observe attractive molecular interactions in this system that were reported previously for copper and silver surfaces. In this paper, our experiments compared TCNQ adsorption on noble metal surfaces of Ag(100)more » and Ag(111). In both cases we found net attractive interactions down to the lowest coverage. However, the morphology of the assemblies was strikingly different, with two-dimensional islands on Ag(100) and one-dimensional chains on Ag(111) surfaces. This observation suggests that the registry effect governed by the molecular interaction with the underlying lattice potential is critical in determining the dimensionality of the molecular assembly. Using first-principles density functional calculations with a van der Waals correction scheme, we revealed that the strengths of major interactions (i.e., lattice potential corrugation, intermolecular attraction, and charge-transfer-induced repulsion) are all similar in energy. The van der Waals interactions, in particular, almost double the strength of attractive interactions, making the intermolecular potential comparable in strength to the diffusion potential and promoting self-assembly. However, it is the anisotropy of local intermolecular interactions that is primarily responsible for the difference in the topology of the molecular islands on Ag(100) and Ag(111) surfaces. Finally, we anticipate that the intermolecular potential will become more attractive and dominant over the diffusion potential with increasing molecular size, providing new design strategies for the structure and charge transfer within molecular layers.« less

Orientation of Space Station Freedom electrical power system in environmental effects assessment

NASA Technical Reports Server (NTRS)

Lu, Cheng-Yi

1990-01-01

The orientation effects of six Space Station Freedom Electrical Power System (EPS) components are evaluated for three environmental interactions: aerodynamic drag, atomic oxygen erosion, and orbital debris impact. Designers can directly apply these orientation factors to estimate the magnitude of the examined environment and the environmental effects for the EPS component of interest. The six EPS components are the solar array, photovoltaic module radiator, integrated equipment assembly, solar dynamic concentrator, solar dynamic radiator, and beta gimbal.

Programmable assembly of nanoarchitectures using genetically engineered viruses.

PubMed

Huang, Yu; Chiang, Chung-Yi; Lee, Soo Kwan; Gao, Yan; Hu, Evelyn L; De Yoreo, James; Belcher, Angela M

2005-07-01

Biological systems possess inherent molecular recognition and self-assembly capabilities and are attractive templates for constructing complex material structures with molecular precision. Here we report the assembly of various nanoachitectures including nanoparticle arrays, hetero-nanoparticle architectures, and nanowires utilizing highly engineered M13 bacteriophage as templates. The genome of M13 phage can be rationally engineered to produce viral particles with distinct substrate-specific peptides expressed on the filamentous capsid and the ends, providing a generic template for programmable assembly of complex nanostructures. Phage clones with gold-binding motifs on the capsid and streptavidin-binding motifs at one end are created and used to assemble Au and CdSe nanocrytals into ordered one-dimensional arrays and more complex geometries. Initial studies show such nanoparticle arrays can further function as templates to nucleate highly conductive nanowires that are important for addressing/interconnecting individual nanostructures.

Method and apparatus for assembling solid oxide fuel cells

DOEpatents

Szreders, Bernard E.; Campanella, Nicholas

1989-01-01

A plurality of jet air tubes are supported and maintained in a spaced matrix array by a positioning/insertion assembly for insertion in respective tubes of a solid oxide fuel cell (SOFC) in the assembly of an SOFC module. The positioning/insertion assembly includes a plurality of generally planar, elongated, linear vanes which are pivotally mounted at each end thereof to a support frame. The vanes, which each include a plurality of spaced slots along the facing edges thereof, may be pivotally displaced from a generally vertical orientation, wherein each jet air tube is positioned within and engaged by the aligned slots of a plurality of paired upper and lower vanes to facilitate their insertion in respective aligned SOFC tubes arranged in a matrix array, to an inclined orientation, wherein the jet air tubes may be removed from the positioning/insertion assembly after being inserted in the SOFC tubes. A rectangular compression assembly of adjustable size is adapted to receive and squeeze a matrix of SOFC tubes so as to compress the inter-tube nickel felt conductive pads which provide series/parallel electrical connection between adjacent SOFCs, with a series of increasingly larger retainer frames used to maintain larger matrices of SOFC tubes in position. Expansion of the SOFC module housing at the high operating temperatures of the SOFC is accommodated by conductive, flexible, resilient expansion, connector bars which provide support and electrical coupling at the top and bottom of the SOFC module housing.

Self-Assembly of Natural and Synthetic Drug Amphiphiles into Discrete Supramolecular Nanostructures

PubMed Central

Lock, Lye Lin; LaComb, Michelle; Schwarz, Kelly; Cheetham, Andrew G.; Lin, Yi-an; Zhang, Pengcheng

2014-01-01

Molecular assembly provides an effective approach to construct discrete supramolecular nanostructures of various sizes and shapes in a simple manner. One important technological application of the resulting nanostructures is their potential use as anticancer drug carriers to facilitate targeted delivery to tumour sites and consequently to improve clinical outcomes. In this carrier-assisted delivery strategy, anticancer drugs have been almost exclusively considered as the cargo to be carried and delivered, and their potential as molecular building blocks has been largely ignored. In this discussion, we report the use of anticancer drugs as molecular building units to create discrete supramolecular nanostructures that contain a high and quantitative drug loading and also have the potential for self-delivery. We first show the direct assembly of two amphiphilic drug molecules (methotrexate and folic acid) into discrete nanostructures. Our results reveal that folic acid exhibits rich self-assembly behaviours via Hoogsteen hydrogen bonding in various solvent conditions, whereas methotrexate was unable to assemble into any well-defined nanostructures under the same conditions, despite its similar chemical structures. Considering the low water solubility of most anticancer drugs, hydrophilic segments must be conjugated to the drug in order to bestow the necessary amphiphilicity. We have demonstrated this for camptothecin through the attachment of β-sheet-forming peptides with overall hydrophilicity. We found that the intermolecular interactions among camptothecin segments and those among β-sheet peptides act together to define the formation of stable one-dimensional nanostructures in dilute solutions, giving rise to nanotubes or nanofibers depending upon the processing conditions used. These results lead us to believe that self-assembly of drugs into discrete nanostructures not only offers an innovative way to craft self-delivering anticancer drugs, but also extends the paradigm of using molecular assembly as a toolbox to achieve functional nanostructures, to a new area which is specifically focused on the direct assembly of functional molecules (e.g. drugs, or imaging agents) into nanostructures of their own. PMID:24611283

PAMAM-Based Dendrimers with Different Alkyl Chains Self-Assemble on Silica Surfaces: Controllable Layer Structure and Molecular Aggregation.

PubMed

Zhang, Minghui; Yang, Hui; Wang, Shujuan; Zhang, Wei; Hou, Qingfeng; Guo, Donghong; Liu, Fanghui; Chen, Ting; Wu, Xu; Wang, Jinben

2018-06-20

Amphiphilic poly(amidoamine) (PAMAM) dendrimers are a well-known dendritic family due to their remarkable ability to self-assemble on solid surface. However, the relationship between molecular conformation (or adsorption kinetics) of a self-assembled layer and molecular amphiphilicity of such kind of dendrimer is still lacking, which limits the development of modulating self-assembling structures and surface functionality. With this in mind, we synthesized a series of amphiphilic PAMAM-based dendrimers, denoted as G 1 C n , with different alkyl chains ( n = 8, 12, and 16), and investigated the molecular aggregation on silica surfaces by means of quartz crystal microbalance with dissipation, atomic force microscopy, and contact angle. After rinsing, remaining adsorption amounts of G 1 C 12 were higher than those of G 1 C 8 at high concentrations, suggesting that G 1 C 12 adlayers were more stable due to the stronger intermolecular hydrophobic interactions, whereas it preferred to adopt the intramolecular hydrophobic interactions for G 1 C 16 , with low adsorption amounts and unstable adlayers. Bilayer-like structures were inferred in G 1 C 8 and G 1 C 12 adlayers with loose conformation, whereas monolayer structures were likely to exist in the sparse adsorption film of G 1 C 16 . Our results provided more detailed understanding of the effect of molecular structure on the self-assembled structures of amphiphilic dendrimers on solid surfaces, shedding light on the controlled microstructure and wettability of functional surface by modulating the length of hydrophobic chains of dendrimers and a potential application of dendrimer-substrate combinations.

Multivalent display of proteins on viral nanoparticles using molecular recognition and chemical ligation strategies

PubMed Central

Venter, P. Arno; Dirksen, Anouk; Thomas, Diane; Manchester, Marianne; Dawson, Philip E.; Schneemann, Anette

2011-01-01

Multivalent display of heterologous proteins on viral nanoparticles forms a basis for numerous applications in nanotechnology, including vaccine development, targeted therapeutic delivery and tissue-specific bio-imaging. In many instances, precise placement of proteins is required for optimal functioning of the supramolecular assemblies, but orientation- and site-specific coupling of proteins to viral scaffolds remains a significant technical challenge. We have developed two strategies that allow for controlled attachment of a variety of proteins on viral particles using covalent and noncovalent principles. In one strategy, an interaction between domain 4 of anthrax protective antigen and its receptor was used to display multiple copies of a target protein on virus-like particles. In the other, expressed protein ligation and aniline-catalyzed oximation was used to covalently display a model protein. The latter strategy, in particular, yielded nanoparticles that induced potent immune responses to the coupled protein, suggesting potential applications in vaccine development. PMID:21545187

Microscopic Simulations of Charge Transport in Disordered Organic Semiconductors

PubMed Central

2011-01-01

Charge carrier dynamics in an organic semiconductor can often be described in terms of charge hopping between localized states. The hopping rates depend on electronic coupling elements, reorganization energies, and driving forces, which vary as a function of position and orientation of the molecules. The exact evaluation of these contributions in a molecular assembly is computationally prohibitive. Various, often semiempirical, approximations are employed instead. In this work, we review some of these approaches and introduce a software toolkit which implements them. The purpose of the toolkit is to simplify the workflow for charge transport simulations, provide a uniform error control for the methods and a flexible platform for their development, and eventually allow in silico prescreening of organic semiconductors for specific applications. All implemented methods are illustrated by studying charge transport in amorphous films of tris-(8-hydroxyquinoline)aluminum, a common organic semiconductor. PMID:22076120

Controlling bottom-up rapid growth of single crystalline gallium nitride nanowires on silicon.

PubMed

Wu, Ko-Li; Chou, Yi; Su, Chang-Chou; Yang, Chih-Chaing; Lee, Wei-I; Chou, Yi-Chia

2017-12-20

We report single crystalline gallium nitride nanowire growth from Ni and Ni-Au catalysts on silicon using hydride vapor phase epitaxy. The growth takes place rapidly; efficiency in time is higher than the conventional nanowire growth in metal-organic chemical vapor deposition and thin film growth in molecular beam epitaxy. The effects of V/III ratio and carrier gas flow on growth are discussed regarding surface polarity and sticking coefficient of molecules. The nanowires of gallium nitride exhibit excellent crystallinity with smooth and straight morphology and uniform orientation. The growth mechanism follows self-assembly from both catalysts, where Au acts as a protection from etching during growth enabling the growth of ultra-long nanowires. The photoluminescence of such nanowires are adjustable by tuning the growth parameters to achieve blue emission. The practical range of parameters for mass production of such high crystal quality and uniformity of nanowires is suggested.

Single-protein detection in crowded molecular environments in cryo-EM images

PubMed Central

Rickgauer, J Peter; Grigorieff, Nikolaus; Denk, Winfried

2017-01-01

We present an approach to study macromolecular assemblies by detecting component proteins’ characteristic high-resolution projection patterns, calculated from their known 3D structures, in single electron cryo-micrographs. Our method detects single apoferritin molecules in vitreous ice with high specificity and determines their orientation and location precisely. Simulations show that high spatial-frequency information and—in the presence of protein background—a whitening filter are essential for optimal detection, in particular for images taken far from focus. Experimentally, we could detect small viral RNA polymerase molecules, distributed randomly among binding locations, inside rotavirus particles. Based on the currently attainable image quality, we estimate a threshold for detection that is 150 kDa in ice and 300 kDa in 100 nm thick samples of dense biological material. DOI: http://dx.doi.org/10.7554/eLife.25648.001 PMID:28467302

Molecular association via halogen bonding and other weak interactions in the crystal structures of 11-bromo-12-oxo-5β-cholan derivatives

NASA Astrophysics Data System (ADS)

Salunke, Deepak B.; Hazra, Braja G.; Gonnade, Rajesh G.; Pore, Vandana S.; Bhadbhade, Mohan M.

2008-12-01

Methyl 3α,7α-diacetoxy-12-oxo-5β-cholan-24-oate 2, methyl 11α-bromo-3α,7α-diacetoxy-12-oxo-5β-cholan-24-oate 3, methyl 11β-bromo-3α,7α-diacetoxy-12-oxo-5β-cholan-24-oate 4 and methyl 11,11-dibromo-3α,7α-diacetoxy-12-oxo-5β-cholan-24-oate 5 were synthesized. The crystal structures of these molecules were resolved to study the effect of bulky bromine atom in the steroid skeleton of cholic acid with different stereo-chemical orientations at C-11 on the two-dimensional arrangement of molecules and solid-state properties. All the molecules associate only via weak intermolecular interactions in their crystal structures, notable one being the Halogen Bonded assembly (C-Br…O) in 5.

Expeditious diastereoselective synthesis of elaborated ketones via remote Csp3-H functionalization

NASA Astrophysics Data System (ADS)

Shu, Wei; Lorente, Adriana; Gómez-Bengoa, Enrique; Nevado, Cristina

2017-01-01

The quest for selective C-H functionalization reactions, able to provide new strategic opportunities for the rapid assembly of molecular complexity, represents a major focus of the chemical community. Examples of non-directed, remote Csp3-H activation to forge complex carbon frameworks remain scarce due to the kinetic stability and thus intrinsic challenge associated to the chemo-, regio- and stereoselective functionalization of aliphatic C-H bonds. Here we describe a radical-mediated, directing-group-free regioselective 1,5-hydrogen transfer of unactivated Csp3-H bonds followed by a second Csp2-H functionalization to produce, with exquisite stereoselectivity, a variety of elaborated fused ketones. This study demonstrates that aliphatic acids can be strategically harnessed as 1,2-diradical synthons and that secondary aliphatic C-H bonds can be engaged in stereoselective C-C bond-forming reactions, highlighting the potential of this protocol for target-oriented natural product and pharmaceutical synthesis.

Energy level alignment and molecular conformation at rubrene/Ag interfaces: Impact of contact contaminations on the interfaces

NASA Astrophysics Data System (ADS)

Sinha, Sumona; Wang, C.-H.; Mukherjee, M.

2017-07-01

This paper addresses the impact of electrode contaminations on the interfacial energy level alignment, the molecular conformation, orientation and surface morphology deposited organic film at organic semiconductor/noble metal interfaces by varying of film thickness from sub-monolayer to multilayer, which currently draws significant attention with regard to its application in organic electronics. The UHV clean Ag and unclean Ag were employed as substrate whereas rubrene was used as an organic semiconducting material. The photoelectron spectroscopy (XPS and UPS) was engaged to investigate the evolution of interfacial energetics; polarization dependent near edge x-ray absorption fine structure spectroscopy (NEXAFS) was employed to understand the molecular conformation as well as orientation whereas atomic force microscopy (AFM) was used to investigate the surface morphologies of the films. The adventitious contamination layer was acted as a spacer layer between clean Ag substrate surface and rubrene molecular layer. As a consequence, hole injection barrier height, interface dipole as well as molecular-conformation, molecular-orientation and surface morphology of rubrene thin films were found to depend on the cleanliness of Ag substrate. The results have important inferences about the understanding of the impact of substrate contamination on the energy level alignment, the molecular conformation as well as orientation and surface morphology of deposited rubrene thin film at rubrene/Ag interfaces and are beneficial for the improvement of the device performance.

A computer-oriented system for assembling and displaying land management information

Treesearch

Elliot L. Amidon

1964-01-01

Maps contain information basic to land management planning. By transforming conventional map symbols into numbers which are punched into cards, the land manager can have a computer assemble and display information required for a specific job. He can let a computer select information from several maps, combine it with such nonmap data as treatment cost or benefit per...

Radiation hybrid maps of D-genome of Aegilops tauschii and their application in sequence assembly of large and complex plant genomes

USDA-ARS?s Scientific Manuscript database

The large and complex genome of bread wheat (Triticum aestivum L., ~17 Gb) requires high-resolution genome maps saturated with ordered markers to assist in anchoring and orienting BAC contigs/ sequence scaffolds for whole genome sequence assembly. Radiation hybrid (RH) mapping has proven to be an e...

Infrared vibrational nanocrystallography and nanoimaging

PubMed Central

Muller, Eric A.; Pollard, Benjamin; Bechtel, Hans A.; van Blerkom, Peter; Raschke, Markus B.

2016-01-01

Molecular solids and polymers can form low-symmetry crystal structures that exhibit anisotropic electron and ion mobility in engineered devices or biological systems. The distribution of molecular orientation and disorder then controls the macroscopic material response, yet it is difficult to image with conventional techniques on the nanoscale. We demonstrated a new form of optical nanocrystallography that combines scattering-type scanning near-field optical microscopy with both optical antenna and tip-selective infrared vibrational spectroscopy. From the symmetry-selective probing of molecular bond orientation with nanometer spatial resolution, we determined crystalline phases and orientation in aggregates and films of the organic electronic material perylenetetracarboxylic dianhydride. Mapping disorder within and between individual nanoscale domains, the correlative hybrid imaging of nanoscale heterogeneity provides insight into defect formation and propagation during growth in functional molecular solids. PMID:27730212

Probing molecular orientations in thin films by x-ray photoelectron spectroscopy

NASA Astrophysics Data System (ADS)

Li, Y.; Li, P.; Lu, Z.-H.

2018-03-01

A great number of functional organic molecules in active thin-film layers of optoelectronic devices have highly asymmetric structures, such as plate-like, rod-like, etc. This makes molecular orientation an important aspect in thin-films as it can significantly affect both the optical and electrical performance of optoelectronic devices. With a combination of in-situ ultra violet photoelectron spectroscopy (UPS) and x-ray photoelectron spectroscopy (XPS) investigations for organic molecules having a broad range of structural properties, we discovered a rigid connection of core levels and frontier highest occupied molecular orbital levels at organic interfaces. This finding opens up opportunities of using X-ray photoemission spectroscopy as an alternative tool to UPS for providing an easy and unambiguous data interpretation in probing molecular orientations.

Driven assembly with multiaxial fields: Creating a soft mode in assemblies of anisometric induced dipoles

DOE PAGES

Martin, James E.; Swol, Frank Van

2015-07-10

We show that multiaxial fields can induce time-averaged, noncentrosymmetric interactions between particles having polarization anisotropy, yet the multiaxial field itself does not exert either a force or a torque on an isolated particle. These induced interactions lead to particle assemblies whose energy is strongly dependent on both the translational and orientational degrees of freedom of the system. The situation is similar to a collection of permanent dipoles, but the symmetry of the time-averaged interaction is quite distinct, and the scale of the system energy can be dynamically controlled by the magnitude of the applied multiaxial field. In our paper, themore » case of polarizable rods is considered in detail, and it is suggested that collections of rods embedded in spheres can be used to create a material with a dynamically tunable magnetic permeability or dielectric permittivity. We report on Monte Carlo simulations performed to investigate the behavior of assemblies of both multiaxial-field induced dipoles and permanent dipoles arranged onto two-dimensional lattices. Lastly, the ground state of the induced dipoles is an orientational soft mode of aligned dipoles, whereas that of the permanent dipoles is a vortex state.« less

Key aromatic/hydrophobic amino acids controlling a cross-amyloid peptide interaction versus amyloid self-assembly.

PubMed

Bakou, Maria; Hille, Kathleen; Kracklauer, Michael; Spanopoulou, Anna; Frost, Christina V; Malideli, Eleni; Yan, Li-Mei; Caporale, Andrea; Zacharias, Martin; Kapurniotu, Aphrodite

2017-09-01

The interaction of the intrinsically disordered polypeptide islet amyloid polypeptide (IAPP), which is associated with type 2 diabetes (T2D), with the Alzheimer's disease amyloid-β (Aβ) peptide modulates their self-assembly into amyloid fibrils and may link the pathogeneses of these two cell-degenerative diseases. However, the molecular determinants of this interaction remain elusive. Using a systematic alanine scan approach, fluorescence spectroscopy, and other biophysical methods, including heterocomplex pulldown assays, far-UV CD spectroscopy, the thioflavin T binding assay, transmission EM, and molecular dynamics simulations, here we identified single aromatic/hydrophobic residues within the amyloid core IAPP region as hot spots or key residues of its cross-interaction with Aβ40(42) peptide. Importantly, we also find that none of these residues in isolation plays a key role in IAPP self-assembly, whereas simultaneous substitution of four aromatic/hydrophobic residues with Ala dramatically impairs both IAPP self-assembly and hetero-assembly with Aβ40(42). Furthermore, our experiments yielded several novel IAPP analogs, whose sequences are highly similar to that of IAPP but have distinct amyloid self- or cross-interaction potentials. The identified similarities and major differences controlling IAPP cross-peptide interaction with Aβ40(42) versus its amyloid self-assembly offer a molecular basis for understanding the underlying mechanisms. We propose that these insights will aid in designing intervention strategies and novel IAPP analogs for the management of type 2 diabetes, Alzheimer's disease, or other diseases related to IAPP dysfunction or cross-amyloid interactions. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Design and construction of a first-generation high-throughput integrated molecular biology platform for production of optimized synthetic genes and improved industrial strains

USDA-ARS?s Scientific Manuscript database

The molecular biological techniques for plasmid-based assembly and cloning of synthetic assembled gene open reading frames are essential for elucidating the function of the proteins encoded by the genes. These techniques involve the production of full-length cDNA libraries as a source of plasmid-bas...

Nanoscale Electronics from a Molecular Perspective

DTIC Science & Technology

2012-01-19

Cyclohexanethiolate Self-Assembled Monolayers with Local Barrier Height Imaging, Journal of Physical Chemistry C, (07 2011): 0. doi: 2012/01/05 20:34:27...accepted for publication in the Journal of Physical Chemistry-C regarding the adsorption, ordering, and local work function measurements for...cyclohexanethiol on Au(111): Unveiling Molecular Adsorption Geometry in Cyclohexanethiolate Self-Assembled Monolayers with Local Barrier Height Imaging

Self-assembly of Spherical Macroions in Solution: A Coarse-grained Molecular Dynamics Study

NASA Astrophysics Data System (ADS)

Liu, Zhuonan; Liu, Tianbo; Tsige, Mesfin

2015-03-01

Macroions (such as polyoxometalates) in solution can form a stable hollow spherical super-molecular structure called blackberry when they have moderate surface charge density and size (1-10 nm). Depending on the surface charge density of macroions, the size of the blackberry can be from 20 to more than 100 nm. Other macroions such as dendrimers can also self-assemble into similar super-molecular structure in solution. Existing theories such as Debye-Hückel and DLVO theories cannot explain this phenomenon and we are not aware of any other theory that can explain this. Previous studies using all-atom Molecular Dynamics simulations have shown identical macroions forming oligomers mediated by counterions. Due to the limitations in all-atom simulation and available computational capabilities, these studies handled only small systems with simple macroions, leading to less conclusive but still relevant results on the self-assembly behavior. To overcome these limitations, in this work large-scale coarse-grained modeling of macroions in solution is used. In order to understand the origin of the attractive force that is responsible for the self-assembly of macroions, different types of macroions in different solution conditions are studied. This work was supported by NSF Grant DMR0847580.

A slippery molecular assembly allows water as a self-erasable security marker

PubMed Central

Thirumalai, Rajasekaran; Mukhopadhyay, Rahul Dev; Praveen, Vakayil K.; Ajayaghosh, Ayyappanpillai

2015-01-01

Protection of currency and valuable documents from counterfeit continues to be a challenge. While there are many embedded security features available for document safety, they are not immune to forgery. Fluorescence is a sensitive property, which responds to external stimuli such as solvent polarity, temperature or mechanical stress, however practical use in security applications is hampered due to several reasons. Therefore, a simple and specific stimuli responsive security feature that is difficult to duplicate is of great demand. Herein we report the design of a fluorescent molecular assembly on which water behaves as a self-erasable security marker for checking the authenticity of documents at point of care. The underlying principle involves the disciplined self-assembly of a tailor-made fluorescent molecule, which initially form a weak blue fluorescence (λem = 425 nm, Φf = 0.13) and changes to cyan emission (λem = 488 nm,Φf = 0.18) in contact with water due to a reversible molecular slipping motion. This simple chemical tool, based on the principles of molecular self-assembly and fluorescence modulation, allows creation of security labels and optically masked barcodes for multiple documents authentication. PMID:25940779

Self-Assembly and Drug Release Capacities of Organogels via Some Amide Compounds with Aromatic Substituent Headgroups

PubMed Central

Zhang, Lexin; Jiao, Tifeng; Ma, Kai; Xing, Ruirui; Liu, Yamei; Xiao, Yong; Zhou, Jingxin; Zhang, Qingrui; Peng, Qiuming

2016-01-01

In this work, some amide compounds with different aromatic substituent headgroups were synthesized and their gelation self-assembly behaviors in 22 solvents were characterized as new gelators. The obtained results indicated that the size of aromatic substituent headgroups in molecular skeletons in gelators showed crucial effect in the gel formation and self-assembly behavior of all compounds in the solvents used. Larger aromatic headgroups in molecular structures in the synthesized gelator molecules are helpful to form various gel nanostructures. Morphological investigations showed that the gelator molecules can self-assembly and stack into various organized aggregates with solvent change, such as wrinkle, belt, rod, and lamella-like structures. Spectral characterizations suggested that there existed various weak interactions including π-π stacking, hydrogen bonding, and hydrophobic forces due to aromatic substituent headgroups and alkyl substituent chains in molecular structures. In addition, the drug release capacities experiments demonstrated that the drug release rate in present obtained gels can be tuned by adjusting the concentrations of dye. The present work would open up enormous insight to design and investigate new kind of soft materials with designed molecular structures and tunable drug release performance. PMID:28773663

A slippery molecular assembly allows water as a self-erasable security marker.

PubMed

Thirumalai, Rajasekaran; Mukhopadhyay, Rahul Dev; Praveen, Vakayil K; Ajayaghosh, Ayyappanpillai

2015-05-05

Protection of currency and valuable documents from counterfeit continues to be a challenge. While there are many embedded security features available for document safety, they are not immune to forgery. Fluorescence is a sensitive property, which responds to external stimuli such as solvent polarity, temperature or mechanical stress, however practical use in security applications is hampered due to several reasons. Therefore, a simple and specific stimuli responsive security feature that is difficult to duplicate is of great demand. Herein we report the design of a fluorescent molecular assembly on which water behaves as a self-erasable security marker for checking the authenticity of documents at point of care. The underlying principle involves the disciplined self-assembly of a tailor-made fluorescent molecule, which initially form a weak blue fluorescence (λem = 425 nm, Φf = 0.13) and changes to cyan emission (λem = 488 nm,Φf = 0.18) in contact with water due to a reversible molecular slipping motion. This simple chemical tool, based on the principles of molecular self-assembly and fluorescence modulation, allows creation of security labels and optically masked barcodes for multiple documents authentication.

Shock compression and flash-heating of molecular adsorbates on the picosecond time scale

NASA Astrophysics Data System (ADS)

Berg, Christopher Michael

An ultrafast nonlinear coherent laser spectroscopy termed broadband multiplex vibrational sum-frequency generation (SFG) with nonresonant suppression was employed to monitor vibrational transitions of molecular adsorbates on metallic substrates during laser-driven shock compression and flash-heating. Adsorbates were in the form of well-ordered self-assembled monolayers (SAMs) and included molecular explosive simulants, such as nitroaromatics, and long chain-length alkanethiols. Based on reflectance measurements of the metallic substrates, femtosecond flash-heating pulses were capable of producing large-amplitude temperature jumps with DeltaT = 500 K. Laser-driven shock compression of SAMs produced pressures up to 2 GPa, where 1 GPa ≈ 1 x 104 atm. Shock pressures were estimated via comparison with frequency shifts observed in the monolayer vibrational transitions during hydrostatic pressure measurements in a SiC anvil cell. Molecular dynamics during flash-heating and shock loading were probed with vibrational SFG spectroscopy with picosecond temporal resolution and sub-nanometer spatial resolution. Flash-heating studies of 4-nitrobenzenethiolate (NBT) on Au provided insight into effects from hot-electron excitation of the molecular adsorbates at early pump-probe delay times. At longer delay times, effects from the excitation of SAM lattice modes and lower-energy NBT vibrations were shown. In addition, flash-heating studies of alkanethiolates demonstrated chain disordering behaviors as well as interface thermal conductances across the Au-SAM junction, which was of specific interest within the context of molecular electronics. Shock compression studies of molecular explosive simulants, such as 4-nitrobenzoate (NBA), demonstrated the proficiency of this technique to observe shock-induced molecular dynamics, in this case orientational dynamics, on the picosecond time scale. Results validated the utilization of these refined shock loading techniques to probe the shock initiation or first bond-breaking reactions in molecular explosives such as delta-HMX: a necessary study for the development of safer and more effective energetic materials.

Crystallography and Molecular Arrangement of Polymorphic Monolayer J-Aggregates of a Cyanine Dye: Multiangle Polarized Light Fluorescence Optical Microscopy Study.

PubMed

Prokhorov, Valery V; Pozin, Sergey I; Perelygina, Olga M; Mal'tsev, Eugene I

2018-04-24

The molecular orientation in monolayer J-aggregates of 3,3-di(γ-sulfopropyl)-5,5-dichlorotiamonomethinecyanine dye has been precisely estimated using improved linear polarization measurements in the fluorescence microscope in which a multiangle set of polarization data is obtained using sample rotation. The estimated molecular orientation supplemented with the previously established crystallographic constraints based on the analysis of the well-developed two-dimensional J-aggregate shapes unambiguously indicate the staircase type of molecular arrangement for striplike J-aggregates with the staircases oriented along strips. The molecular transition dipoles are inclined at an angle of ∼25° to the strip direction, whereas the characteristic strip vertex angle ∼45° is formed by the [100] and [1-10] directions of the monoclinic unit cell. Measurements of the geometry of partially unwound tubes and their polarization properties support the model of tube formation by close-packed helical winding of flexible monolayer strips. In the tubes, the long molecular axes are oriented at a small angle in the range of 5-15° to the normal to the tube axis providing low bending energy. At a nanoscale, high-resolution atomic force microscopy imaging of J-aggregate monolayers reveals a complex quasi-one-dimensional organization.

Structural determinants of APOBEC3B non-catalytic domain for molecular assembly and catalytic regulation

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

Xiao, Xiao; Yang, Hanjing; Arutiunian, Vagan

The catalytic activity of human cytidine deaminase APOBEC3B (A3B) has been correlated with kataegic mutational patterns within multiple cancer types. The molecular basis of how the N-terminal non-catalytic CD1 regulates the catalytic activity and consequently, biological function of A3B remains relatively unknown. Here, we report the crystal structure of a soluble human A3B-CD1 variant and delineate several structural elements of CD1 involved in molecular assembly, nucleic acid interactions and catalytic regulation of A3B. We show that (i) A3B expressed in human cells exists in hypoactive high-molecular-weight (HMW) complexes, which can be activated without apparent dissociation into low-molecular-weight (LMW) species aftermore » RNase A treatment. (ii) Multiple surface hydrophobic residues of CD1 mediate the HMW complex assembly and affect the catalytic activity, including one tryptophan residue W127 that likely acts through regulating nucleic acid binding. (iii) One of the highly positively charged surfaces on CD1 is involved in RNA-dependent attenuation of A3B catalysis. (iv) Surface hydrophobic residues of CD1 are involved in heterogeneous nuclear ribonucleoproteins (hnRNPs) binding to A3B. The structural and biochemical insights described here suggest that unique structural features on CD1 regulate the molecular assembly and catalytic activity of A3B through distinct mechanisms.« less

Optimized assembly and covalent coupling of single-molecule DNA origami nanoarrays.

PubMed

Gopinath, Ashwin; Rothemund, Paul W K

2014-12-23

Artificial DNA nanostructures, such as DNA origami, have great potential as templates for the bottom-up fabrication of both biological and nonbiological nanodevices at a resolution unachievable by conventional top-down approaches. However, because origami are synthesized in solution, origami-templated devices cannot easily be studied or integrated into larger on-chip architectures. Electrostatic self-assembly of origami onto lithographically defined binding sites on Si/SiO2 substrates has been achieved, but conditions for optimal assembly have not been characterized, and the method requires high Mg2+ concentrations at which most devices aggregate. We present a quantitative study of parameters affecting origami placement, reproducibly achieving single-origami binding at 94±4% of sites, with 90% of these origami having an orientation within ±10° of their target orientation. Further, we introduce two techniques for converting electrostatic DNA-surface bonds to covalent bonds, allowing origami arrays to be used under a wide variety of Mg2+-free solution conditions.

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

Influence of Molecular Orientation on Charge-Transfer Processes at Phthalocyanine/Metal Oxide Interfaces and Relationship to Organic Photovoltaic Performance

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

Lin, Hsiao-Chu; MacDonald, Gordon A.; Shi, Yanrong

2015-05-04

The effect of the molecular orientation distribution of the first monolayer of donor molecules at the hole-harvesting contact in an organic photovoltaic (OPV) on device efficiency was investigated. Two zinc phthalocyanine (ZnPc) phosphonic acids (PA) deposited on indium tin oxide (ITO) electrodes are compared: ZnPc(PA)4 contains PA linkers in all four quadrants, and ZnPcPA contains a PA linker in one quadrant. ZnPcPA monolayers exhibited a broad distribution of molecular orientations whereas ZnPc(PA)4 adsorption produced a monolayer with a narrower orientation distribution with the molecular plane more parallel to the ITO surface. We used potential-modulated attenuated total reflectance spectroelectrochemistry (PM-ATR) tomore » characterize the charge-transfer kinetics of these films and show that the highest rate constants correspond to ZnPc subpopulations that are oriented more parallel to the ITO surface plane. For ZnPc(PA)4, rate constants exceeded 104 s–1 and are among the highest ever reported for a surface-confined redox couple, which is attributable to both its orientation and the small ZnPc–electrode separation distance. The performance of OPVs with ITO hole-harvesting contacts modified with ZnPc(PA)4 was comparable to that achieved with highly activated bare ITO contacts, whereas for ZnPcPA-modified contacts, the OPV performance was similar to that observed with (hole-blocking) alkyl-PA modifiers. These results demonstrate the synergism between molecular structure, energetics, and dynamics at interfaces in OPVs.« less

Self-assembled nanostructures of optically active phthalocyanine derivatives. Effect of central metal ion on the morphology, dimension, and handedness.

PubMed

Sun, Ranran; Wang, Liang; Tian, Jing; Zhang, Xiaomei; Jiang, Jianzhuang

2012-11-21

Four optically active {(2,3,9,10,16,17,23,24-octa[(S)-2-methylbutoxy]} phthalocyanine derivatives with different central metal ions, namely (S)-H2Pc(β-OC5H11)8 (1), (S)-ZnPc(β-OC5H11)8 (2), (S)-CuPc(β-OC5H11)8 (3), and (S)-NiPc(β-OC5H11)8 (4) have been synthesized and their self-assembly behaviors systematically investigated by electronic absorption and circular dichroism (CD) spectroscopy, scanning electron microscopy (SEM), transmission electron microscopy (TEM), X-ray diffraction (XRD) techniques, and X-ray photoelectron spectroscopy (XPS). Metal free phthalocyanine together with its zinc and copper congeners self-assembles into right-handed helical arrangements in a stack of phthalocyanine chromophores according to the CD spectroscopic result, while the nickel complex does so into the left-handed helical arrangements. These helical arrangements, acting as elemental primary structures, further pack in a hierarchical fashion into either highly ordered right-handed fibrous nanostructures with average 300 μm length, 4.8 μm width, and 4.4 μm helical pitch for 1 and 300 μm length, 2.4 μm width, and 1.8 μm helical pitch for 2 but left-handed fibrous nanostructures with average 4 μm length, 0.48 μm width, and 0.12 μm helical pitch for 3 and 300 μm length, 2 μm width, and 1.2 μm helical pitch for 4, clearly revealing the effect of central metal ion on the distance and relative orientation of neighboring phthalocyanine chromophores and in turn the supramolecular chirality, morphology, dimension, and handedness of the self-assembled nanostructures. The present result not only represents a unique phenomenon in the self-assembly of phthalocyanine compounds but more importantly denotes the transcription and amplification of molecular chirality to supramolecular helicity with different helical bias during the self-assembly processes without changing the chiral handles attached to the phthalocyanine chromophore.

Atomistic Monte Carlo Simulation of Lipid Membranes

PubMed Central

Wüstner, Daniel; Sklenar, Heinz

2014-01-01

Biological membranes are complex assemblies of many different molecules of which analysis demands a variety of experimental and computational approaches. In this article, we explain challenges and advantages of atomistic Monte Carlo (MC) simulation of lipid membranes. We provide an introduction into the various move sets that are implemented in current MC methods for efficient conformational sampling of lipids and other molecules. In the second part, we demonstrate for a concrete example, how an atomistic local-move set can be implemented for MC simulations of phospholipid monomers and bilayer patches. We use our recently devised chain breakage/closure (CBC) local move set in the bond-/torsion angle space with the constant-bond-length approximation (CBLA) for the phospholipid dipalmitoylphosphatidylcholine (DPPC). We demonstrate rapid conformational equilibration for a single DPPC molecule, as assessed by calculation of molecular energies and entropies. We also show transition from a crystalline-like to a fluid DPPC bilayer by the CBC local-move MC method, as indicated by the electron density profile, head group orientation, area per lipid, and whole-lipid displacements. We discuss the potential of local-move MC methods in combination with molecular dynamics simulations, for example, for studying multi-component lipid membranes containing cholesterol. PMID:24469314

Fabrication and Characterization of a Novel Nanodendrite-based Electrochemical Sensor for the Detection of Disease Biomarkers

NASA Astrophysics Data System (ADS)

Connolly, Timothy; Archibald, Michelle M.; Nesbitt, Nathan T.; Rossi, Matthew; Glover, Jennifer A.; Burns, Michael J.; Naughton, Michael J.; Chiles, Thomas C.

2014-03-01

Technologies to detect early stage cancer would provide significant benefit to cancer disease patients. Clinical measurement of biomarkers offers the promise of a noninvasive and cost effective screening for early stage detection. We are currently developing a novel 3-dimensional nanopillar dendrite biosensor array for the detection of human cancer biomarkers (e . g . CA-125 for early-stage ovarian cancer) in serum and other fluids. Here, we describe a nanoscale 3D architecture that can afford molecular detection at room temperature. We report our efforts on the development of an all-electronic, ambient temperature, rapid-response dendritic biosensor fabricated by directed electrochemical nanowire assembly (DENA) that achieves molecular-scale sensitivity for protein biomarker based detection. Each sensor is a vertically-oriented nanodendritic array where an electrochemical signal is detected from the oxidation of the redox end-product of an enzyme-linked immunosorbent assay (ELISA). Our results demonstrate the feasibility of using the present nanodendritic array structure as a sensitive device to detect a range of proteins of interest, including disease biomarkers. Supported by NIH (National Cancer Institute and the National Institute of Allergy and Infectious Diseases).

Transcriptome analysis of molecular mechanisms responsible for light-stress response in Mythimna separata (Walker)

PubMed Central

Duan, Yun; Gong, ZhongJun; Wu, RenHai; Miao, Jin; Jiang, YueLi; Li, Tong; Wu, XiaoBo; Wu, YuQing

2017-01-01

Light is an important environmental signal for most insects. The Oriental Armyworm, Mythimna separata, is a serious pest of cereal crops worldwide, and is highly sensitive to light signals during its developmental and reproductive stages. However, molecular biological studies of its response to light stress are scarce, and related genomic information is not available. In this study, we sequenced and de novo assembled the transcriptomes of M. separata exposed to four different light conditions: dark, white light (WL), UV light (UVL) and yellow light (YL). A total of 46,327 unigenes with an average size of 571 base pairs (bp) were obtained, among which 24,344 (52.55%) matched to public databases. The numbers of genes differentially expressed between dark vs WL, dark vs UVL, dark vs YL, and UVL vs YL were 12,012, 12,950, 14,855, and 13,504, respectively. These results suggest that light exposure altered gene expression patterns in M. separata. Putative genes involved in phototransduction-fly, phototransduction, circadian rhythm-fly, olfactory transduction, and taste transduction were identified. This study thus identified a series of candidate genes and pathways potentially related to light stress in M. separata. PMID:28345615

Theoretical investigation of interaction between the set of ligands and α7 nicotinic acetylcholine receptor

NASA Astrophysics Data System (ADS)

Glukhova, O. E.; Prytkova, T. R.; Shmygin, D. S.

2016-03-01

Nicotinic acetylcholine receptors (nAChRs) are neuron receptor proteins that provide a transmission of nerve impulse through the synapses. They are composed of a pentametric assembly of five homologous subunits (5 α7 subunits for α7nAChR, for example), oriented around the central pore. These receptors might be found in the chemical synapses of central and peripheral nervous system, and also in the neuromuscular synapses. Transmembrane domain of the one of such receptors constitutes ion channel. The conductive properties of ion channel strongly depend on the receptor conformation changes in the response of binding with some molecule, f.e. acetylcholine. Investigation of interaction between ligands and acetylcholine receptor is important for drug design. In this work we investigate theoretically the interaction between the set of different ligands (such as vanillin, thymoquinone, etc.) and the nicotinic acetylcholine receptor (primarily with subunit of the α7nAChR) by different methods and packages (AutodockVina, GROMACS, KVAZAR, HARLEM, VMD). We calculate interaction energy between different ligands in the subunit using molecular dynamics. On the base of obtained calculation results and using molecular docking we found an optimal location of different ligands in the subunit.

Drug Partitioning in Micellar Media and Its Implications in Rational Drug Design: Insights with Streptomycin.

PubMed

Judy, Eva; Pagariya, Darshna; Kishore, Nand

2018-03-20

Oral bioavailability of a drug molecule requires its effective delivery to the target site. In general, majority of synthetically developed molecular entities have high hydrophobic nature as well as low bioavailability, therefore the need for suitable delivery vehicles arises. Self-assembled structures such as micelles, niosomes, and liposomes have been used as effective delivery vehicles and studied extensively. However, the information available in literature is mostly qualitative in nature. We have quantitatively investigated the partitioning of antibiotic drug streptomycin into cationic, nonionic, and a mixture of cationic and nonionic surfactant micelles and its interaction with the transport protein serum albumin upon subsequent delivery. A combination of calorimetry and spectroscopy has been used to obtain the thermodynamic signatures associated with partitioning and interaction with the protein and the resulting conformational changes in the latter. The results have been correlated with other class of drugs of different nature to understand the role of molecular features in the partitioning process. These studies are oriented toward understanding the physical chemistry of partitioning of a variety of drug molecules into suitable delivery vehicles and hence establishing structure-property-energetics relationships. Such studies provide general guidelines toward a broader goal of rational drug design.

Peptides for functionalization of InP semiconductors.

PubMed

Estephan, Elias; Saab, Marie-belle; Larroque, Christian; Martin, Marta; Olsson, Fredrik; Lourdudoss, Sebastian; Gergely, Csilla

2009-09-15

The challenge is to achieve high specificity in molecular sensing by proper functionalization of micro/nano-structured semiconductors by peptides that reveal specific recognition for these structures. Here we report on surface modification of the InP semiconductors by adhesion peptides produced by the phage display technique. An M13 bacteriophage library has been used to screen 10(10) different peptides against the InP(001) and the InP(111) surfaces to finally isolate specific peptides for each orientation of the InP. MALDI-TOF/TOF mass spectrometry has been employed to study real affinity of the peptide towards the InP surfaces. The peptides serve for controlled placement of biotin onto InP to bind then streptavidin. Our Atomic Force Microscopy study revealed a total surface coverage of molecules when the InP surface was functionalized by its specific biotinylated peptide (YAIKGPSHFRPS). Finally, fluorescence microscopy has been employed to demonstrate the preferential attachment of the peptide onto a micro-patterned InP surface. Use of substrate specific peptides could present an alternative solution for the problems encountered in the actually existing sensing methods and molecular self-assembly due to the unwanted unspecific interactions.

Hydrogen-bonded side chain liquid crystalline block copolymer: Molecular design, synthesis, characterization and applications

NASA Astrophysics Data System (ADS)

Chao, Chi-Yang

Block copolymers can self-assemble into highly regular, microphase-separated morphologies with dimensions at nanometer length scales. Potential applications such as optical wavelength photonic crystals, templates for nanolithographic patterning, or nanochannels for biomacromolecular separation take advantage of the well-ordered, controlled size microdomains of block copolymers. Side-chain liquid crystalline block copolymers (SCLCBCPs) are drawing increasing attention since the incorporation of liquid crystallinity turns their well-organized microstructures into dynamic functional materials. As a special type of block copolymer, hydrogen-bonded SCLCBCPs are unique, compositionally tunable materials with multiple dynamic functionalities that can readily respond to thermal, electrical and mechanical fields. Hydrogen-bonded SCLCBCPs were synthesized and assembled from host poly(styrene- b-acrylic acid) diblock copolymers with narrow molecular weight distributions as proton donors and guest imidazole functionalized mesogenic moieties as proton acceptors. In these studies non-covalent hydrogen bonding is employed to connect mesogenic side groups to a block copolymer backbone, both for its dynamic character as well as for facile materials preparation. The homogeneity and configuration of the hydrogen-bonded complexes were determined by both the molecular architecture of imidazolyl side groups and the process conditions. A one-dimensional photonic crystal composed of high molecular weight hydrogen-bonded SCLCBCP, with temperature dependent optical wavelength stop bands was successfully produced. The microstructures of hydrogen-bonded complexes could be rapidly aligned in an AC electric field at temperatures below the order-disorder transition but above their glass transitions. Remarkable dipolar properties of the mesogenic groups and thermal dissociation of hydrogen bonds are key elements to fast orientation switching. Studies of a wide range of mesogen and polymer combinations were carried out to investigate the interplay between morphology, mesophase behavior and blend composition (molar ratios of proton acceptors to proton donors). A critical composition for mesophase formation was identified and the characteristics of the H-bonded complexes below the critical blend ratios were very different than those above. Hydrogen bonding was also used to direct microphase separation of miscible poly(hydroxystyrene-b-methyl methacrylate) diblock copolymer by adopting imidazolyl additives able to hydrogen bond with poly(hydroxystyrene). The miscibility between PHS and PMMA segments was diminished significantly by introducing small quantities of H-binding additives. The critical blend ratio for microphase separation was determined more by the molecular structure of the additives than the number of hydrogen bonds formed between PHS and additives.

Construction of Reference Chromosome-Scale Pseudomolecules for Potato: Integrating the Potato Genome with Genetic and Physical Maps

PubMed Central

Sharma, Sanjeev Kumar; Bolser, Daniel; de Boer, Jan; Sønderkær, Mads; Amoros, Walter; Carboni, Martin Federico; D’Ambrosio, Juan Martín; de la Cruz, German; Di Genova, Alex; Douches, David S.; Eguiluz, Maria; Guo, Xiao; Guzman, Frank; Hackett, Christine A.; Hamilton, John P.; Li, Guangcun; Li, Ying; Lozano, Roberto; Maass, Alejandro; Marshall, David; Martinez, Diana; McLean, Karen; Mejía, Nilo; Milne, Linda; Munive, Susan; Nagy, Istvan; Ponce, Olga; Ramirez, Manuel; Simon, Reinhard; Thomson, Susan J.; Torres, Yerisf; Waugh, Robbie; Zhang, Zhonghua; Huang, Sanwen; Visser, Richard G. F.; Bachem, Christian W. B.; Sagredo, Boris; Feingold, Sergio E.; Orjeda, Gisella; Veilleux, Richard E.; Bonierbale, Merideth; Jacobs, Jeanne M. E.; Milbourne, Dan; Martin, David Michael Alan; Bryan, Glenn J.

2013-01-01

The genome of potato, a major global food crop, was recently sequenced. The work presented here details the integration of the potato reference genome (DM) with a new sequence-tagged site marker−based linkage map and other physical and genetic maps of potato and the closely related species tomato. Primary anchoring of the DM genome assembly was accomplished by the use of a diploid segregating population, which was genotyped with several types of molecular genetic markers to construct a new ~936 cM linkage map comprising 2469 marker loci. In silico anchoring approaches used genetic and physical maps from the diploid potato genotype RH89-039-16 (RH) and tomato. This combined approach has allowed 951 superscaffolds to be ordered into pseudomolecules corresponding to the 12 potato chromosomes. These pseudomolecules represent 674 Mb (~93%) of the 723 Mb genome assembly and 37,482 (~96%) of the 39,031 predicted genes. The superscaffold order and orientation within the pseudomolecules are closely collinear with independently constructed high density linkage maps. Comparisons between marker distribution and physical location reveal regions of greater and lesser recombination, as well as regions exhibiting significant segregation distortion. The work presented here has led to a greatly improved ordering of the potato reference genome superscaffolds into chromosomal “pseudomolecules”. PMID:24062527

Platelet factor 4 (CXCL4) seals blood clots by altering the structure of fibrin.

PubMed

Amelot, Aymeric A; Tagzirt, Madjid; Ducouret, Guylaine; Kuen, René Lai; Le Bonniec, Bernard F

2007-01-05

Platelet factor-4 (PF4/CXCL4) is an orphan chemokine released in large quantities in the vicinity of growing blood clots. Coagulation of plasma supplemented with a matching amount of PF4 results in a translucent jelly-like clot. Saturating amounts of PF4 reduce the porosity of the fibrin network 4.4-fold and decrease the values of the elastic and loss moduli by 31- and 59-fold, respectively. PF4 alters neither the cleavage of fibrinogen by thrombin nor the cross-linking of protofibrils by activated factor XIII but binds to fibrin and dramatically transforms the structure of the ensuing network. Scanning electron microscopy showed that PF4 gives rise to a previously unreported pattern of polymerization where fibrin assembles to form a sealed network. The subunits constituting PF4 form a tetrahedron having at its corners a RPRH motif that mimics (in reverse orientation) the Gly-His-Arg-Pro-amide peptides that co-crystallize with fibrin. Molecular modeling showed that PF4 could be docked to fibrin with remarkable complementarities and absence of steric clashes, allowing the assembly of irregular polymers. Consistent with this hypothesis, as little as 50 microm the QVRPRHIT peptide derived from PF4 affects the polymerization of fibrin.

Effect of Interfacial Molecular Orientation on Power Conversion Efficiency of Perovskite Solar Cells.

PubMed

Xiao, Minyu; Joglekar, Suneel; Zhang, Xiaoxian; Jasensky, Joshua; Ma, Jialiu; Cui, Qingyu; Guo, L Jay; Chen, Zhan

2017-03-08

A wide variety of charge carrier dynamics, such as transport, separation, and extraction, occur at the interfaces of planar heterojunction solar cells. Such factors can affect the overall device performance. Therefore, understanding the buried interfacial molecular structure in various devices and the correlation between interfacial structure and function has become increasingly important. Current characterization techniques for thin films such as X-ray diffraction, cross section scanning electronmicroscopy, and UV-visible absorption spectroscopy are unable to provide the needed molecular structural information at buried interfaces. In this study, by controlling the structure of the hole transport layer (HTL) in a perovskite solar cell and applying a surface/interface-sensitive nonlinear vibrational spectroscopic technique (sum frequency generation vibrational spectroscopy (SFG)), we successfully probed the molecular structure at the buried interface and correlated its structural characteristics to solar cell performance. Here, an edge-on (normal to the interface) polythiophene (PT) interfacial molecular orientation at the buried perovskite (photoactive layer)/PT (HTL) interface showed more than two times the power conversion efficiency (PCE) of a lying down (tangential) PT interfacial orientation. The difference in interfacial molecular structure was achieved by altering the alkyl side chain length of the PT derivatives, where PT with a shorter alkyl side chain showed an edge-on interfacial orientation with a higher PCE than that of PT with a longer alkyl side chain. With similar band gap alignment and bulk structure within the PT layer, it is believed that the interfacial molecular structural variation (i.e., the orientation difference) of the various PT derivatives is the underlying cause of the difference in perovskite solar cell PCE.

Molecular Engineering of Self-assembled Nanoreactors

DTIC Science & Technology

2014-08-15

substrate diffusion. We demonstrated spatial control of the GOx/HRP cascade organized by DNA origami structures. As shown in Figure 13, the...quantify the level of protein assembly on the DNA origami tiles - assembled enzymes exhibited higher surface landscapes than the underlying origami ... origami tiles with assembled Gox/HRP pairs with inter-enzyme distances ranging from 10 nm to 65 nm. GOx/HRP co-assembly yields were determined from AFM

Dynamics of self-assembled cytosine nucleobases on graphene

NASA Astrophysics Data System (ADS)

Saikia, Nabanita; Johnson, Floyd; Waters, Kevin; Pandey, Ravindra

2018-05-01

Molecular self-assembly of cytosine (C n ) bases on graphene was investigated using molecular dynamics methods. For free-standing C n bases, simulation conditions (gas versus aqueous) determine the nature of self-assembly; the bases prefer to aggregate in the gas phase and are stabilized by intermolecular H-bonds, while in the aqueous phase, the water molecules disrupt base-base interactions, which facilitate the formation of π-stacked domains. The substrate-induced effects, on the other hand, find the polarity and donor-acceptor sites of the bases to govern the assembly process. For example, in the gas phase, the assembly of C n bases on graphene displays short-range ordered linear arrays stabilized by the intermolecular H-bonds. In the aqueous phase, however, there are two distinct configurations for the C n bases assembly on graphene. For the first case corresponding to low surface coverage, the bases are dispersed on graphene and are isolated. The second configuration archetype is disordered linear arrays assembled with medium and high surface coverage. The simulation results establish the role of H-bonding, vdW π-stacking, and the influence of graphene surface towards the self-assembly. The ability to regulate the assembly into well-defined patterns can aid in the design of self-assembled nanostructures for the next-generation DNA based biosensors and nanoelectronic devices.

Effect of substrates on the molecular orientation of silicon phthalocyanine dichloride thin films

NASA Astrophysics Data System (ADS)

Deng, Juzhi; Baba, Yuji; Sekiguchi, Tetsuhiro; Hirao, Norie; Honda, Mitsunori

2007-05-01

Molecular orientations of silicon phthalocyanine dichloride (SiPcCl2) thin films deposited on three different substrates have been measured by near-edge x-ray absorption fine structure (NEXAFS) spectroscopy using linearly polarized synchrotron radiation. The substrates investigated were highly oriented pyrolitic graphite (HOPG), polycrystalline gold and indium tin oxide (ITO). For thin films of about five monolayers, the polarization dependences of the Si K-edge NEXAFS spectra showed that the molecular planes of SiPcCl2 on three substrates were nearly parallel to the surface. Quantitative analyses of the polarization dependences revealed that the tilted angle on HOPG was only 2°, which is interpreted by the perfect flatness of the HOPG surface. On the other hand, the tilted angle on ITO was 26°. Atomic force microscopy (AFM) observation of the ITO surface showed that the periodicity of the horizontal roughness is of the order of a few nanometres, which is larger than the molecular size of SiPcCl2. It is concluded that the morphology of the top surface layer of the substrate affects the molecular orientation of SiPcCl2 molecules not only for mono-layered adsorbates but also for multi-layered thin films.

Angular displacement measuring device

NASA Technical Reports Server (NTRS)

Seegmiller, H. Lee B. (Inventor)

1992-01-01

A system for measuring the angular displacement of a point of interest on a structure, such as aircraft model within a wind tunnel, includes a source of polarized light located at the point of interest. A remote detector arrangement detects the orientation of the plane of the polarized light received from the source and compares this orientation with the initial orientation to determine the amount or rate of angular displacement of the point of interest. The detector arrangement comprises a rotating polarizing filter and a dual filter and light detector unit. The latter unit comprises an inner aligned filter and photodetector assembly which is disposed relative to the periphery of the polarizer so as to receive polarized light passing the polarizing filter and an outer aligned filter and photodetector assembly which receives the polarized light directly, i.e., without passing through the polarizing filter. The purpose of the unit is to compensate for the effects of dust, fog and the like. A polarization preserving optical fiber conducts polarized light from a remote laser source to the point of interest.

Acentric 2-D ensembles of D-br-A electron-transfer chromophores via vectorial orientation within amphiphilic n-helix bundle peptides for photovoltaic device applications.

PubMed

Koo, Jaseung; Park, Jaehong; Tronin, Andrey; Zhang, Ruili; Krishnan, Venkata; Strzalka, Joseph; Kuzmenko, Ivan; Fry, H Christopher; Therien, Michael J; Blasie, J Kent

2012-02-14

We show that simply designed amphiphilic 4-helix bundle peptides can be utilized to vectorially orient a linearly extended donor-bridge-acceptor (D-br-A) electron transfer (ET) chromophore within its core. The bundle's interior is shown to provide a unique solvation environment for the D-br-A assembly not accessible in conventional solvents and thereby control the magnitudes of both light-induced ET and thermal charge recombination rate constants. The amphiphilicity of the bundle's exterior was employed to vectorially orient the peptide-chromophore complex at a liquid-gas interface, and its ends were tailored for subsequent covalent attachment to an inorganic surface, via a "directed assembly" approach. Structural data, combined with evaluation of the excited state dynamics exhibited by these peptide-chromophore complexes, demonstrate that densely packed, acentrically ordered 2-D monolayer ensembles of such complexes at high in-plane chromophore densities approaching 1/200 Å(2) offer unique potential as active layers in binary heterojunction photovoltaic devices.

Developments in Molecular Recognition and Sensing at Interfaces

PubMed Central

Ariga, Katsuhiko; Hill, Jonathan P.; Endo, Hiroshi

2007-01-01

In biological systems, molecular recognition events occur mostly within interfacial environments such as at membrane surfaces, enzyme reaction sites, or at the interior of the DNA double helix. Investigation of molecular recognition at model interfaces provides great insights into biological phenomena. Molecular recognition at interfaces not only has relevance to biological systems but is also important for modern applications such as high sensitivity sensors. Selective binding of guest molecules in solution to host molecules located at solid surfaces is crucial for electronic or photonic detection of analyte substances. In response to these demands, molecular recognition at interfaces has been investigated extensively during the past two decades using Langmuir monolayers, self-assembled monolayers, and lipid assemblies as recognition media. In this review, advances of molecular recognition at interfaces are briefly summarized.

Molecular subtypes of Alzheimer's disease.

PubMed

Di Fede, Giuseppe; Catania, Marcella; Maderna, Emanuela; Ghidoni, Roberta; Benussi, Luisa; Tonoli, Elisa; Giaccone, Giorgio; Moda, Fabio; Paterlini, Anna; Campagnani, Ilaria; Sorrentino, Stefano; Colombo, Laura; Kubis, Adriana; Bistaffa, Edoardo; Ghetti, Bernardino; Tagliavini, Fabrizio

2018-02-19

Protein misfolding and aggregation is a central feature of several neurodegenerative disorders including Alzheimer's disease (AD), in which assemblies of amyloid β (Aβ) peptides accumulate in the brain in the form of parenchymal and/or vascular amyloid. A widely accepted concept is that AD is characterized by distinct clinical and neuropathological phenotypes. Recent studies revealed that Aβ assemblies might have structural differences among AD brains and that such pleomorphic assemblies can correlate with distinct disease phenotypes. We found that in both sporadic and inherited forms of AD, amyloid aggregates differ in the biochemical composition of Aβ species. These differences affect the physicochemical properties of Aβ assemblies including aggregation kinetics, resistance to degradation by proteases and seeding ability. Aβ-amyloidosis can be induced and propagated in animal models by inoculation of brain extracts containing aggregated Aβ. We found that brain homogenates from AD patients with different molecular profiles of Aβ are able to induce distinct patterns of Aβ-amyloidosis when injected into mice. Overall these data suggest that the assembly of mixtures of Aβ peptides into different Aβ seeds leads to the formation of distinct subtypes of amyloid having distinctive physicochemical and biological properties which result in the generation of distinct AD molecular subgroups.

Giant surfactants of poly(ethylene oxide)- b-polystyrene-(molecular nanoparticle): nanoparticle-driven self-assembly with sub-10-nm nanostructures in thin films

NASA Astrophysics Data System (ADS)

Hsu, Chih-Hao; Lin, Zhiwei; Dong, Xue-Hui; Hsieh, I.-Fan; Cheng, Stephen Z. D.

2014-03-01

Giant surfactants are built upon precisely attaching shape- and volume-persistent molecular nanoparticles (MNP) to polymeric flexible tails. The unique class of self-assembling materials, giant surfactants, has been demonstrated to form self-assembled ordered nanostructures, and their self-assembly behaviors are remarkably sensitive to primary chemical structures. In this work, two sets of giant surfactants with functionalized MNP attached to diblock copolymer tails were studied in thin films. Carboxylic acid-functionalized [60]fullerene (AC60) tethered with PEO- b-PS (PEO-PS-AC60) represents an ABA' (hydrophilic-hydrophobic-hydrophilic) giant surfactant, and fluoro-functionalized polyhedral oligomeric silsesquioxane (FPOSS) tethered with PEO- b-PS (PEO-PS-FPOSS) represents an ABC (hydrophilic-hydrophobic-omniphobic) one. The dissimilar chemical natures of the MNPs result in different arrangement of MNPs in self-assembled structures, the dispersion of AC60 in PEO domain and the single domain of FPOSS. Moreover, the chemically bonded MNPs could induce the originally disordered small molecular PEO- b-PS to form ordered cylindrical and lamellar structure, as evidenced by TEM and GISAXS, leading to sub-10-nm nanostructures of copolymer in the thin film state.

Biomimetic Hierarchical Assembly of Helical Supraparticles from Chiral Nanoparticles

DOE PAGES

Zhou, Yunlong; Marson, Ryan L.; van Anders, Greg; ...

2016-02-22

Chiroptical materials found in butterflies, beetles, stomatopod crustaceans, and other creatures are attributed to biocomposites with helical motifs and multiscale hierarchical organization. These structurally sophisticated materials self-assemble from primitive nanoscale building blocks, a process that is simpler and more energy efficient than many top-down methods currently used to produce similarly sized three-dimensional materials. In this paper, we report that molecular-scale chirality of a CdTe nanoparticle surface can be translated to nanoscale helical assemblies, leading to chiroptical activity in the visible electromagnetic range. Chiral CdTe nanoparticles coated with cysteine self-organize around Te cores to produce helical supraparticles. D-/L-Form of the aminomore » acid determines the dominant left/right helicity of the supraparticles. Coarse-grained molecular dynamics simulations with a helical pair-potential confirm the assembly mechanism and the origin of its enantioselectivity, providing a framework for engineering three-dimensional chiral materials by self-assembly. Finally, the helical supraparticles further self-organize into lamellar crystals with liquid crystalline order, demonstrating the possibility of hierarchical organization and with multiple structural motifs and length scales determined by molecular-scale asymmetry of nanoparticle interactions.« less

Role of Bassoon and Piccolo in Assembly and Molecular Organization of the Active Zone

PubMed Central

Gundelfinger, Eckart D.; Reissner, Carsten; Garner, Craig C.

2016-01-01

Bassoon and Piccolo are two very large scaffolding proteins of the cytomatrix assembled at the active zone (CAZ) where neurotransmitter is released. They share regions of high sequence similarity distributed along their entire length and seem to share both overlapping and distinct functions in organizing the CAZ. Here, we survey our present knowledge on protein-protein interactions and recent progress in understanding of molecular functions of these two giant proteins. These include roles in the assembly of active zones (AZ), the localization of voltage-gated Ca2+ channels (VGCCs) in the vicinity of release sites, synaptic vesicle (SV) priming and in the case of Piccolo, a role in the dynamic assembly of the actin cytoskeleton. Piccolo and Bassoon are also important for the maintenance of presynaptic structure and function, as well as for the assembly of CAZ specializations such as synaptic ribbons. Recent findings suggest that they are also involved in the regulation activity-dependent communication between presynaptic boutons and the neuronal nucleus. Together these observations suggest that Bassoon and Piccolo use their modular structure to organize super-molecular complexes essential for various aspects of presynaptic function. PMID:26793095

Self-Assembling Multi-Component Nanofibers for Strong Bioinspired Underwater Adhesives

PubMed Central

Zhong, Chao; Gurry, Thomas; Cheng, Allen A; Downey, Jordan; Deng, Zhengtao; Stultz, Collin M.; Lu, Timothy K

2014-01-01

Many natural underwater adhesives harness hierarchically assembled amyloid nanostructures to achieve strong and robust interfacial adhesion under dynamic and turbulent environments. Despite recent advances, our understanding of the molecular design, self-assembly, and structure-function relationship of those natural amyloid fibers remains limited. Thus, designing biomimetic amyloid-based adhesives remains challenging. Here, we report strong and multi-functional underwater adhesives obtained from fusing mussel foot proteins (Mfps) of Mytilus galloprovincialis with CsgA proteins, the major subunit of Escherichia coli amyloid curli fibers. These hybrid molecular materials hierarchically self-assemble into higher-order structures, in which, according to molecular dynamics simulations, disordered adhesive Mfp domains are exposed on the exterior of amyloid cores formed by CsgA. Our fibers have an underwater adhesion energy approaching 20.9 mJ/m2, which is 1.5 times greater than the maximum of bio-inspired and bio-derived protein-based underwater adhesives reported thus far. Moreover, they outperform Mfps or curli fibers taken on their own at all pHs and exhibit better tolerance to auto-oxidation than Mfps at pH ≥7.0. This work establishes a platform for engineering multi-component self-assembling materials inspired by nature. PMID:25240674

Molecular bacterial community analysis of clean rooms where spacecraft are assembled.

PubMed

Moissl, Christine; Osman, Shariff; La Duc, Myron T; Dekas, Anne; Brodie, Eoin; DeSantis, Todd; Desantis, Tadd; Venkateswaran, Kasthuri

2007-09-01

Molecular bacterial community composition was characterized from three geographically distinct spacecraft-associated clean rooms to determine whether such populations are influenced by the surrounding environment or the maintenance of the clean rooms. Samples were collected from facilities at the Jet Propulsion Laboratory (JPL), Kennedy Space Flight Center (KSC), and Johnson Space Center (JSC). Nine clone libraries representing different surfaces within the spacecraft facilities and three libraries from the surrounding air were created. Despite the highly desiccated, nutrient-bare conditions within these clean rooms, a broad diversity of bacteria was detected, covering all the main bacterial phyla. Furthermore, the bacterial communities were significantly different from each other, revealing only a small subset of microorganisms common to all locations (e.g. Sphingomonas, Staphylococcus). Samples from JSC assembly room surfaces showed the greatest diversity of bacteria, particularly within the Alpha- and Gammaproteobacteria and Actinobacteria. The bacterial community structure of KSC assembly surfaces revealed a high presence of proteobacterial groups, whereas the surface samples collected from the JPL assembly facility showed a predominance of Firmicutes. Our study presents the first extended molecular survey and comparison of NASA spacecraft assembly facilities, and provides new insights into the bacterial diversity of clean room environments .

Orientation and size dependence of the elastic properties of zinc oxide nanobelts

NASA Astrophysics Data System (ADS)

Kulkarni, A. J.; Zhou, M.; Ke, F. J.

2005-12-01

Molecular dynamics simulations are performed to characterize the response of zinc oxide (ZnO) nanobelts to tensile loading. The ultimate tensile strength (UTS) and Young's modulus are obtained as functions of size and growth orientation. Nanobelts in three growth orientations are generated by assembling the unit wurtzite cell along the [0001], [01\\bar {1} 0] , and [2\\bar {1} \\bar {1}0] crystalline axes. Following the geometric construction, dynamic relaxation is carried out to yield free-standing nanobelts at 300 K. Two distinct configurations are observed in the [0001] and [01\\bar {1} 0] orientations. When the lateral dimensions are above 10 Å, nanobelts with rectangular cross-sections are seen. Below this critical size, tubular structures involving two concentric shells similar to double-walled carbon nanotubes are obtained. Quasi-static deformations of belts with [2\\bar {1} \\bar {1} 0] and [01\\bar {1} 0] orientations consist of three stages, including initial elastic stretching, wurtzite-ZnO to graphitic-ZnO structural transformation, and cleavage fracture. On the other hand, [0001] belts do not undergo any structural transformation and fail through cleavage along (0001) planes. Calculations show that the UTS and Young's modulus of the belts are size dependent and are higher than the corresponding values for bulk ZnO. Specifically, as the lateral dimensions increase from 10 to 40 Å, decreases between 38-76% and 24-63% are observed for the UTS and Young's modulus, respectively. This effect is attributed to the size-dependent compressive stress induced by tensile surface stress in the nanobelts. [01\\bar {1} 0] and [2\\bar {1} \\bar {1} 0] nanobelts with multi-walled tubular structures are seen to have higher values of elastic moduli (~340 GPa) and UTS (~36 GPa) compared to their wurtzite counterparts, echoing a similar trend in multi-walled carbon nanotubes.