Science.gov

Sample records for oriented molecular assemblies

  1. Orientational Order of Molecular Assemblies on Inorganic Crystals

    NASA Astrophysics Data System (ADS)

    Chun, Jaehun; Saville, Dudley; Li, Je-Luen; Schniepp, Hannes; Car, Roberto; Aksay, Ilhan

    2006-03-01

    Surfactant micelles form oriented arrays on crystalline substrates such as HOPG (Highly Ordered Pyrolytic Graphite) although registration is unexpected since the template unit cell is small compared to the size of a rod-like micelle. In addition, with atomic force microscopy, we show that orientational ordering is a dynamic, multi-molecule process. Interaction energy calculations based on molecular simulations reveal that orientational energy differences on a molecular scale are too small to explain matters. However, treating the cooperative processes as a balance between van der Waals torque on a large, rod-like micellar assembly and Brownian motion shows that orientation is favored. Our study provides a physical insight on regulation of self-assembly structures at small length scale.

  2. Self-assembly and separation of nematic colloids through photo-patterned molecular orientation

    NASA Astrophysics Data System (ADS)

    Peng, Chenhui; Guo, Yubing; Conklin, Christopher; Viñals, Jorge; Shiyanovskii, Sergij; Wei, Qi-Huo; Lavrentovich, Oleg; Oleg D. Lavrentovich Team; Jorge Viñals Collaboration

    Design and control of particles self-assembly is an important theme in colloidal science. Dispersions of colloids in a nematic liquid crystal (LC) show a diversity of self-assembled structures guided by long-range interactions. Here we describe a versatile approach to control colloidal structures through surface-patterned molecular orientation and dynamic processes of LC-enabled electrokinetics (LCEK). In presence of the electric field, the surface-imprinted pattern of molecular orientation triggers LCEK flows which transport the colloidal aggregates to specified locations. The aggregation is directed by the director gradients. Colloids that differ in surface anchoring or shape are guided into different areas of the cell, thus being sorted. The dynamic approach to control colloidal systems through LCEK in cells with patterned director field opens the opportunities in the microfluidic and lab on a chip applications. This work was supported by NSF grants DMR-1507637 , DMS-1434185 and CMMI-1436565.

  3. Orientational nanoparticle assemblies and biosensors.

    PubMed

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

    2016-05-15

    Assemblies of nanoparticles (NPs) have regional correlated properties with new features compared to individual NPs or random aggregates. The orientational NP assembly contributes greatly to the collective interaction of individual NPs with geometrical dependence. Therefore, orientational NPs assembly techniques have emerged as promising tools for controlling inorganic NPs spatial structures with enhanced interesting properties. The research fields of orientational NP assembly have developed rapidly with characteristics related to the different methods used, including chemical, physical and biological techniques. The current and potential applications, important challenges remain to be investigated. An overview of recent developments in orientational NPs assemblies, the multiple strategies, biosensors and challenges will be discussed in this review. PMID:26708241

  4. PM-IRRAS Determination of Molecular Orientation of Phosphonic Acid Self-Assembled Monolayers on Indium Zinc Oxide.

    PubMed

    Sang, Lingzi; Mudalige, Anoma; Sigdel, Ajaya K; Giordano, Anthony J; Marder, Seth R; Berry, Joseph J; Pemberton, Jeanne E

    2015-05-26

    Self-assembled monolayers (SAMs) of phosphonic acids (PAs) on transparent conductive oxide (TCO) surfaces can facilitate improvement in TCO/organic semiconductor interface properties. When ordered PA SAMs are formed on oxide substrates, interface dipole and electronic structure are affected by the functional group properties, orientation, and binding modes of the modifiers. Choosing octylphosphonic acid (OPA), F13-octylphosphonic acid (F13OPA), pentafluorophenyl phosphonic acid (F5PPA), benzyl phosphonic acid (BnPA), and pentafluorobenzyl phosphonic acid (F5BnPA) as a representative group of modifiers, we report polarization modulation-infrared reflection-absorption spectroscopy (PM-IRRAS) of binding and molecular orientation on indium-doped zinc oxide (IZO) substrates. Considerable variability in molecular orientation and binding type is observed with changes in PA functional group. OPA exhibits partially disordered alkyl chains but on average the chain axis is tilted ∼57° from the surface normal. F13OPA tilts 26° with mostly tridentate binding. The F5PPA ring is tilted 23° from the surface normal with a mixture of bidentate and tridentate binding; the BnPA ring tilts 31° from normal with a mixture of bidentate and tridentate binding, and the F5BnPA ring tilts 58° from normal with a majority of bidentate with some tridenate binding. These trends are consistent with what has been observed previously for the effects of fluorination on orientation of phosphonic acid modifiers. These results from PM-IRRAS are correlated with recent results on similar systems from near-edge X-ray absorption fine structure (NEXAFS) and density functional theory (DFT) calculations. Overall, these results indicate that both surface binding geometry and intermolecular interactions play important roles in dictating the orientation of PA modifiers on TCO surfaces. This work also establishes PM-IRRAS as a routine method for SAM orientation determination on complex oxide substrates

  5. Fragment oriented molecular shapes.

    PubMed

    Hain, Ethan; Camacho, Carlos J; Koes, David Ryan

    2016-05-01

    Molecular shape is an important concept in drug design and virtual screening. Shape similarity typically uses either alignment methods, which dynamically optimize molecular poses with respect to the query molecular shape, or feature vector methods, which are computationally less demanding but less accurate. The computational cost of alignment can be reduced by pre-aligning shapes, as is done with the Volumetric-Aligned Molecular Shapes (VAMS) method. Here, we introduce and evaluate fragment oriented molecular shapes (FOMS), where shapes are aligned based on molecular fragments. FOMS enables the use of shape constraints, a novel method for precisely specifying molecular shape queries that provides the ability to perform partial shape matching and supports search algorithms that function on an interactive time scale. When evaluated using the challenging Maximum Unbiased Validation dataset, shape constraints were able to extract significantly enriched subsets of compounds for the majority of targets, and FOMS matched or exceeded the performance of both VAMS and an optimizing alignment method of shape similarity search. PMID:27085751

  6. Conformation-dependent Molecular Orientation Deduced from First-principles Modeling of Oligo(ethylene glycol)-terminated and Amide Group Containing Alkanethiolates Self-assembled on Gold

    NASA Astrophysics Data System (ADS)

    Malysheva, L.; Onipko, A.; Valiokas, R.; Liedberg, B.

    2005-09-01

    We report orientation angles for the alkyl chain, amide group, and oligo(ethylene glycol) (OEG) portion within self-assembled monolayers (SAMs) of OEG-terminated and amide containing alkanethiolates which, depending on the OEG length and substrate temperature, display unique conformations — all-trans or helical. Optimized geometries of the molecular constituents, characteristic vibration frequencies and transition dipole moments are obtained by using DFT methods with gradient corrections. These ab initio data are subsequently used to simulate infrared reflection-absorption (RA) spectra associated with different conformations and orientations. The obtained results have generated a deeper knowledge of the internal SAM structure, which is crucial for understanding phase and folding characteristics, interaction with water and ultimately the protein repellent properties of OEG-containing SAMs.

  7. Study of the Packing Density and Molecular Orientation of Bimolecular Self-Assembled Monolayers of Aromatic and Aliphatic Organosilanes on Silica

    SciTech Connect

    Smith,M.; Efimenko, K.; Fischer, D.; Lappi, S.; Kilpatrick, P.; Genzer, J.

    2007-01-01

    Bimolecular self-assembled monolayers (SAMs) of aromatic and aliphatic chlorosilanes were self-assembled onto silica, and their characteristics were established by contact angle measurement, near-edge X-ray absorption fine structure spectroscopy, and Fourier transform infrared spectroscopy. Three aromatic constituents (phenyltrichlorosilane, benzyltrichlorosilane, and phenethyltrichlorosilane) were studied in combination with four aliphatic coadsorbates (butyltrichlorosilane, butyldimethylchlorosilane, octadecyltrichlorosilane, and octadecyldimethylchlorosilane). Our results demonstrate that whereas SAMs made of trichlorinated organosilanes are densely packed, SAMs prepared from monochlorinated species are less dense and poorly ordered. In mixed systems, trichlorinated aromatics and trichlorinated aliphatics formed SAMs with highly tunable compositions; their surfaces were compositionally homogeneous with no large-scale domain separation. The homogeneous nature of the resulting SAM was a consequence of the formation of in-plane siloxane linkages among neighboring molecules. In contrast, when mixing monochlorinated aliphatics with trichlorinated aromatics, molecular segregation occurred. Although the two shortest aromatic species did not display significant changes in orientation upon mixing with aliphatics, the aromatic species with the longest polymethylene spacer, phenethyltrichlorosilane, displayed markedly different orientation behavior in mixtures of short- and long-chain aliphatics.

  8. Cooperative synchronized assemblies enhance orientation discrimination

    PubMed Central

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

    2004-01-01

    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. PMID:15096595

  9. Cobalt(II) metal-organic framework micro-nanoparticles: Molecular self-assembly from layers to micropores showing the conjunctive orientation of carboxyl groups

    NASA Astrophysics Data System (ADS)

    Ye, Jing; Li, Xiaoqi; Xu, Zhen-liang; Xu, Haitao

    2015-08-01

    Cobalt metal-organic framework (MOF) materials CoL(1,4-chdc)·mH2O (1,4-chdc = 1,4-cyclohexanedicarboxylic acid, L1 = 1,2-di(4-pyridyl)ethylene, and m = 0 for 1Co; L2 = 1,4-bis(4-pyridyl)-2,3-diaza-1,3-butadiene and m = 2 for 2Co) were assembled in a MeOH-H2O solvent system. They crystallized in a monoclinic system with space group P2(1)/c, Z = 4, a = 9.479(4) Å, b = 13.704(6) Å, c = 14.455(6) Å, and β = 99.424(6)° for 1Co, and a = 14.349(11) Å, b = 12.088(9) Å, c = 26.62(2) Å, and β = 97.255(11)° for 2Co. It was shown that N-ligand can regulate and control the conjunctive orientation of carboxyl groups in these MOFs; thus, the MOFs exhibited structures that ranged from layers to micropores. Furthermore, the micro-nanoparticles of 1Co and 2Co were investigated for new potential applications of micro-nano MOFs.

  10. Visualization Software for Molecular Assemblies

    PubMed Central

    Goddard, Thomas D; Ferrin, Thomas E

    2007-01-01

    Summary Software for viewing three-dimensional models and maps of viruses, ribosomes, filaments and other molecular assemblies is advancing on many fronts. New developments include molecular representations that offer better control over level of detail, lighting that improves the perception of depth, and two-dimensional projections that simplify data interpretation. Programmable graphics processors offer quality, speed and visual effects not previously possible, while 3D printers, haptic interaction devices, and auto-stereo displays show promise in more naturally engaging our senses. Visualization methods are developed by diverse groups of researchers with differing goals: experimental biologists, database developers, computer scientists, and package developers. We survey recent developments and problems faced by the developer community in bringing innovative visualization methods into widespread use. PMID:17728125

  11. Efficient molecular mechanics simulations of the folding, orientation, and assembly of peptides in lipid bilayers using an implicit atomic solvation model

    PubMed Central

    Bordner, Andrew J.; Zorman, Barry; Abagyan, Ruben

    2014-01-01

    Membrane proteins comprise a significant fraction of the proteomes of sequenced organisms and are the targets of approximately half of marketed drugs. However, in spite of their prevalence and biomedical importance, relatively few experimental structures are available due to technical challenges. Computational simulations can potentially address this deficit by providing structural models of membrane proteins. Solvation within the spatially heterogeneous membrane/solvent environment provides a major component of the energetics driving protein folding and association within the membrane. We have developed an implicit solvation model for membranes that is both computationally efficient and accurate enough to enable molecular mechanics predictions for the folding and association of peptides within the membrane. We derived the new atomic solvation model parameters using an unbiased fitting procedure to experimental data and have applied it to diverse problems in order to test its accuracy and to gain insight into membrane protein folding. First, we predicted the positions and orientations of peptides and complexes within the lipid bilayer and compared the simulation results with solid-state NMR structures. Next, we performed folding simulations for a series of host-guest peptides with varying propensities to form alpha helices in a hydrophobic environment and compared the structures with experimental measurements. We were also able to successfully predict the structures of amphipathic peptides as well as the structures for dimeric complexes of short hexapeptides that have experimentally characterized propensities to form beta sheets within the membrane. Finally, we compared calculated relative transfer energies with data from experiments measuring the effects of mutations on the free energies of translocon-mediated insertion of proteins into lipid bilayers and of combined folding and membrane insertion of a beta barrel protein. PMID:21904908

  12. Rigorous theory of molecular orientational nonlinear optics

    SciTech Connect

    Kwak, Chong Hoon 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 molecular 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.

  13. Rigorous theory of molecular orientational nonlinear optics

    NASA Astrophysics Data System (ADS)

    Kwak, Chong Hoon; Kim, Gun Yeup

    2015-01-01

    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 molecular 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.

  14. Oriented assembly of polyhedral plasmonic nanoparticle clusters

    PubMed Central

    Henzie, Joel; Andrews, Sean C.; Ling, Xing Yi; Li, Zhiyong; Yang, Peidong

    2013-01-01

    Shaped colloids can be used as nanoscale building blocks for the construction of composite, functional materials that are completely assembled from the bottom up. Assemblies of noble metal nanostructures have unique optical properties that depend on key structural features requiring precise control of both position and connectivity spanning nanometer to micrometer length scales. Identifying and optimizing structures that strongly couple to light is important for understanding the behavior of surface plasmons in small nanoparticle clusters, and can result in highly sensitive chemical and biochemical sensors using surface-enhanced Raman spectroscopy (SERS). We use experiment and simulation to examine the local surface plasmon resonances of different arrangements of Ag polyhedral clusters. High-resolution transmission electron microscopy shows that monodisperse, atomically smooth Ag polyhedra can self-assemble into uniform interparticle gaps that result in reproducible SERS enhancement factors from assembly to assembly. We introduce a large-scale, gravity-driven assembly method that can generate arbitrary nanoparticle clusters based on the size and shape of a patterned template. These templates enable the systematic examination of different cluster arrangements and provide a means of constructing scalable and reliable SERS sensors. PMID:23569275

  15. Photoswitchable gel assembly based on molecular recognition.

    PubMed

    Yamaguchi, Hiroyasu; Kobayashi, Yuichiro; Kobayashi, Ryosuke; Takashima, Yoshinori; Hashidzume, Akihito; Harada, Akira

    2012-01-01

    The formation of effective and precise linkages in bottom-up or top-down processes is important for the development of self-assembled materials. Self-assembly through molecular recognition events is a powerful tool for producing functionalized materials. Photoresponsive molecular recognition systems can permit the creation of photoregulated self-assembled macroscopic objects. Here we demonstrate that macroscopic gel assembly can be highly regulated through photoisomerization of an azobenzene moiety that interacts differently with two host molecules. A photoregulated gel assembly system is developed using polyacrylamide-based hydrogels functionalized with azobenzene (guest) or cyclodextrin (host) moieties. Reversible adhesion and dissociation of the host gel from the guest gel may be controlled by photoirradiation. The differential affinities of α-cyclodextrin or β-cyclodextrin for the trans-azobenzene and cis-azobenzene are employed in the construction of a photoswitchable gel assembly system. PMID:22215078

  16. Photoswitchable gel assembly based on molecular recognition

    PubMed Central

    Yamaguchi, Hiroyasu; Kobayashi, Yuichiro; Kobayashi, Ryosuke; Takashima, Yoshinori; Hashidzume, Akihito; Harada, Akira

    2012-01-01

    The formation of effective and precise linkages in bottom-up or top-down processes is important for the development of self-assembled materials. Self-assembly through molecular recognition events is a powerful tool for producing functionalized materials. Photoresponsive molecular recognition systems can permit the creation of photoregulated self-assembled macroscopic objects. Here we demonstrate that macroscopic gel assembly can be highly regulated through photoisomerization of an azobenzene moiety that interacts differently with two host molecules. A photoregulated gel assembly system is developed using polyacrylamide-based hydrogels functionalized with azobenzene (guest) or cyclodextrin (host) moieties. Reversible adhesion and dissociation of the host gel from the guest gel may be controlled by photoirradiation. The differential affinities of α-cyclodextrin or β-cyclodextrin for the trans-azobenzene and cis-azobenzene are employed in the construction of a photoswitchable gel assembly system. PMID:22215078

  17. Fundamentals and application of ordered molecular assemblies to affinity biosensing.

    PubMed

    Matharu, Zimple; Bandodkar, Amay Jairaj; Gupta, Vinay; Malhotra, Bansi Dhar

    2012-02-01

    Organization of biomolecules in two/three dimensional assemblies has recently aroused much interest in nanobiotechnology. In this context, the development of techniques for controlling spatial arrangement and orientation of the desired molecules to generate highly-ordered nanostructures in the form of a mono/multi layer is considered highly significant. The studies of monolayer films to date have focused on three distinct methods of preparation: (i) the Langmuir-Blodgett (LB) technique, involving the transfer of a monolayer assembled at the gas-liquid interface; (ii) self-assembly at the liquid-solid interface, based on spontaneous adsorption of desired molecules from a solution directly onto a solid surface; and (iii) Layer-by-layer (LBL) self-assembly at a liquid-solid interface, based on inter-layer electrostatic attractions for fabrication of multilayers. A variety of monolayers have been utilized to fabricate biomolecular electronic devices including biosensors. The composition of a monolayer based matrix has been found to influence the activity(ies) of biomolecule(s). We present comprehensive and critical analysis of ordered molecular assemblies formed by LB and self-assembly with potential applications to affinity biosensing. This critical review on fundamentals and application of ordered molecular assemblies to affinity biosensing is likely to benefit researchers working in this as well as related fields of research (401 references). PMID:22105315

  18. Computing by molecular self-assembly

    PubMed Central

    Jonoska, Nataša; Seeman, Nadrian C.

    2012-01-01

    The paper reviews two computing models by DNA self-assembly whose proof of principal have recently been experimentally confirmed. The first model incorporates DNA nano-devices and triple crossover DNA molecules to algorithmically arrange non-DNA species. This is achieved by simulating a finite-state automaton with output where golden nanoparticles are assembled to read-out the result. In the second model, a complex DNA molecule representing a graph emerges as a solution of a computational problem. This supports the idea that in molecular self-assembly computing, it may be necessary to develop the notion of shape processing besides the classical approach through symbol processing. PMID:23919130

  19. Molecular Motors and Synaptic Assembly

    PubMed Central

    Cai, Qian; Sheng, Zu-Hang

    2016-01-01

    Proper synaptic function requires the seamless integration of the transport, assembly, and regulation of synaptic components and structures. Inasmuch as the synapse is often distant from the neuronal cell body, newly synthesized synaptic proteins, the precursors of synaptic vesicles, active zone compartments, channels and receptors, and mitochondria, must be transported along lengthy neuronal processes to participate in synaptogenesis. Neuronal transport is mediated by motor proteins that associate with their cargoes via adaptors (or receptors) and that travel along the cytoskeleton network within the neuronal processes. Thus, the identity of membranous protein cargoes and the specificity of motor-cargo interactions are critical for correctly targeting cargoes and properly assembling synapses in developing neurons and in remodeling synapses of mature neurons in response to neuronal activity. In this article, the authors review recent progress in characterizing microtubule- and actin-based motor proteins that are involved in delivering synaptic components and discuss potential mechanisms underlying the formation of motor- receptor-cargo complexes that contribute to synaptogenesis and activity-induced synaptic plasticity. PMID:19218232

  20. Chemical designs of functional photoactive molecular assemblies.

    PubMed

    Yan, Qifan; Luo, Zhouyang; Cai, Kang; Ma, Yuguo; Zhao, Dahui

    2014-06-21

    Molecular assemblies with well-defined structures capable of photo-induced electron transfer and charge transport or photochemical reactions are reviewed. Hierarchical supramolecular architectures, which assemble the modular units into specific spatial arrangements and facilitate them to work cooperatively, are vital for the achievement of photo-functions in these systems. The chemical design of molecular building blocks and noncovalent interactions exploited to realize supramolecular organizations are particularly discussed. Reviewing and recapitulating the chemical evolution traces of these accomplished systems will hopefully delineate certain fundamental design principles and guidelines useful for developing more advanced functions in the future. PMID:24492680

  1. Adaptive soft molecular self-assemblies.

    PubMed

    Wang, Andong; Shi, Wenyue; Huang, Jianbin; Yan, Yun

    2016-01-14

    Adaptive molecular self-assemblies provide possibility of constructing smart and functional materials in a non-covalent bottom-up manner. Exploiting the intrinsic properties of responsiveness of non-covalent interactions, a great number of fancy self-assemblies have been achieved. In this review, we try to highlight the recent advances in this field. The following contents are focused: (1) environmental adaptiveness, including smart self-assemblies adaptive to pH, temperature, pressure, and moisture; (2) special chemical adaptiveness, including nanostructures adaptive to important chemicals, such as enzymes, CO2, metal ions, redox agents, explosives, biomolecules; (3) field adaptiveness, including self-assembled materials that are capable of adapting to external fields such as magnetic field, electric field, light irradiation, and shear forces. PMID:26509717

  2. Direct Assembly of Large Arrays of Oriented Conducting Polymer Nanowires

    SciTech Connect

    Liang, Liang; Liu, Jun; Windisch, Charles F.; Exarhos, Gregory J.; Lin, Yuehe

    2002-10-04

    Although oriented carbon nanotubes, oriented nanowires of metals, semiconductors and oxides have attracted wide attention, there have been few reports on oriented polymer nanostructures such as nanowires. In this paper we report the assembly of large arrays of oriented nanowires through controlled nucleation and growth during a stepwise electrochemical deposition process in which a large number of nuclei were first deposited on the substrate using a large current density. After the initial nucleation, the current density was reduced step by step to grow the oriented nanowires from the nucleation sites created in the first step. A very different morphology was also demonstrated by first depositing a monolayer of close-packed colloidal spheres using a similar step-wise deposition process. As a result, the polymer nanofibers grew from the spheres in a radial fashion and formed the continuous three-dimensional network of nanofibers in the film. The principles of control nucleation and growth in electrochemical deposition investigated in this paper should be applicable to other electrical conducting and electrochemical active materials, including metals and conducting oxides. We also hope the oriented electroactive polymer nanostructure will open the door for new applications, such as miniaturized biosensors.

  3. 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. PMID:17761249

  4. Designed self-assembly of molecular necklaces.

    PubMed

    Park, Ki-Min; Kim, Soo-Young; Heo, Jungseok; Whang, Dongmok; Sakamoto, Shigeru; Yamaguchi, Kentaro; Kim, Kimoon

    2002-03-13

    This paper reports an efficient strategy to synthesize molecular necklaces, in which a number of small rings are threaded onto a large ring, utilizing the principles of self-assembly and coordination chemistry. Our strategy involves (1) threading a molecular "bead" with a short "string" to make a pseudorotaxane and then (2) linking the pseudorotaxanes with a metal complex with two cis labile ligands acting as an "angle connector" to form a cyclic product (molecular necklace). A 4- or 3-pyridylmethyl group is attached to each end of 1,4-diaminobutane or 1,5-diaminopentane to produce the short "strings" (C4N4(2+), C4N3(2+), C5N4(2+), and C5N3(2+)), which then react with a cucurbituril (CB) "bead" to form stable pseudorotaxanes (PR44(2+), PR43(2+), PR54(2+), and PR53(2+), respectively). The reaction of the pseudorotaxanes with Pt(en)(NO(3))(2) (en = ethylenediamine) produces a molecular necklace [4]MN, in which three molecular "beads" are threaded on a triangular framework, and/or a molecular necklace [5]MN, in which four molecular "beads" are threaded on a square framework. Under refluxing conditions, the reaction with PR44(2+) or PR54(2+) yields exclusively [4]MN (MN44T or MN54T, respectively), whereas that with PR43(2+) or PR53(2+) produces exclusively [5]MN (MN43S or MN53S, respectively). The products have been characterized by various methods including X-ray crystallography. At lower temperatures, on the other hand, the reaction with PR44(2+) or PR54(2+) affords both [4]MN and [5]MN. The supermolecules reported here are the first series of molecular necklaces obtained as thermodynamic products. The overall structures of the molecular necklaces are strongly influenced by the structures of pseudorotaxane building blocks, which is discussed in detail on the basis of the X-ray crystal structures. The temperature dependence of the product distribution observed in this self-assembly process is also discussed. PMID:11878967

  5. Free-volume hole relaxation in molecularly oriented glassy polymers

    NASA Astrophysics Data System (ADS)

    Xia, Zhiyong; Trexler, Morgana; Wu, Fei; Jean, Yan-Ching; Van Horn, J. David

    2014-02-01

    The free-volume hole relaxation in polycarbonate and poly(methyl methacrylate) with different levels of molecular orientation was studied by positron annihilation lifetime spectroscopy at variable pressures. The molecular orientation was achieved through a simple shear process performed at different temperatures and extrusion rates. It has been demonstrated that the β relaxation is largely responsible for the free-volume hole anisotropy after simple shear orientation. Upon the removal of mechanical force, the deformation of the free volume is mostly reversible at temperatures much lower than the glass transition. No strong correlation between macroscopic deformation and the free-volume hole deformation was found regardless of molecular orientation.

  6. Free-volume hole relaxation in molecularly oriented glassy polymers.

    PubMed

    Xia, Zhiyong; Trexler, Morgana; Wu, Fei; Jean, Yan-Ching; Van Horn, J David

    2014-02-01

    The free-volume hole relaxation in polycarbonate and poly(methyl methacrylate) with different levels of molecular orientation was studied by positron annihilation lifetime spectroscopy at variable pressures. The molecular orientation was achieved through a simple shear process performed at different temperatures and extrusion rates. It has been demonstrated that the β relaxation is largely responsible for the free-volume hole anisotropy after simple shear orientation. Upon the removal of mechanical force, the deformation of the free volume is mostly reversible at temperatures much lower than the glass transition. No strong correlation between macroscopic deformation and the free-volume hole deformation was found regardless of molecular orientation. PMID:25353498

  7. Self-Assembly and Orientation of Hydrogen-Bonded Oligothiophene Polymorphs at Liquid-Membrane-Liquid Interfaces

    SciTech Connect

    Tevis, Ian D; Palmer, Liam C; Herman, David J; Murray, Ian P; Stone, David A; Stupp, Samuel I

    2012-03-15

    One of the challenges in organic systems with semiconducting function is the achievement of molecular orientation over large scales. We report here on the use of self-assembly kinetics to control long-range orientation of a quarterthiophene derivative designed to combine intermolecular π-π stacking and hydrogen bonding among amide groups. Assembly of these molecules in the solution phase is prevented by the hydrogen-bond-accepting solvent tetrahydrofuran, whereas formation of H-aggregates is facilitated in toluene. Rapid evaporation of solvent in a solution of the quarterthiophene in a 2:1:1 mixture of 1,4-dioxane/tetrahydrofuran/toluene leads to self-assembly of kinetically trapped mats of bundled fibers. In great contrast, slow drying in a toluene atmosphere leads to the homogeneous nucleation and growth of ordered structures shaped as rhombohedra or hexagonal prisms depending on concentration. Furthermore, exceedingly slow delivery of toluene from a high molecular weight polymer solution into the system through a porous aluminum oxide membrane results in the growth of highly oriented hexagonal prisms perpendicular to the interface. The amide groups of the compound likely adsorb onto the polar aluminum oxide surface and direct the self-assembly pathway toward heterogeneous nucleation and growth to form hexagonal prisms. We propose that the oriented prismatic polymorph results from the synergy of surface interactions rooted in hydrogen bonding on the solid membrane and the slow kinetics of self-assembly. These observations demonstrate how self-assembly conditions can be used to guide the supramolecular energy landscape to generate vastly different structures. These fundamental principles allowed us to grow oriented prismatic assemblies on transparent indium-doped tin oxide electrodes, which are of interest in organic electronics.

  8. Cellulose microfibril assembly and orientation in higher plant cells

    SciTech Connect

    Mueller, S.C.; Maclachlan, G.A.; Brown, R.M. Jr.

    1983-01-01

    Freeze-fractured plasma membranes of seedlings of Zea mays L., Burpee's Snowcross, and Pisum sativum L., variety Alsaka, contain terminal complex structures and the impressions of microfibrils from the newest cell wall layer.Terminal complex subunits are on the exoplasmic fracture (EF) face, and rosette subunits are on the protoplasmic fracture (PF) face of the membrane. The association of terminal complexes and rosettes with microfibril tips and their association with newly deposited groups of microfibrils is indirect evidence for their role in microfibril assembly. Microtubules may be responsible for certain orientations of microfibrils, particularly the formation of bands of microfibrils in newly deposited wall layers. However, microfibril orienting mechanisms are more complex, involving factors still present during colchicine treatment. Since UDP-glucose is thought to be a precursor of cellulose microfibrils in higher plant cells, EM radioautography was used to determine the site of incorporation of glucose. However, under the conditions used, glucose was only incorporated from UDP-glucose at the surface of cut or damaged pea stem cells, i.e., in vitro. Thus, incorporation of glucose from UDP-glucose was not useful for probing the patterns of cellulose microfibril synthesis in vivo. 18 references, 8 figures.

  9. Orientational order and translational dynamics of magnetic particle assemblies in liquid crystals.

    PubMed

    Peroukidis, Stavros D; Klapp, Sabine H L

    2016-08-10

    Implementing extensive molecular dynamics simulations we explore the organization of magnetic particle assemblies (clusters) in a uniaxial liquid crystalline matrix comprised of rodlike particles. The magnetic particles are modelled as soft dipolar spheres with diameter significantly smaller than the width of the rods. Depending on the dipolar strength coupling the magnetic particles arrange into head-to-tail configurations forming various types of clusters including rings (closed loops) and chains. In turn, the liquid crystalline matrix induces long range orientational ordering to these structures and promotes their diffusion along the director of the phase. Different translational dynamics are exhibited as the liquid crystalline matrix transforms either from isotropic to nematic or from nematic to smectic state. This is caused due to different collective motion of the magnetic particles into various clusters in the anisotropic environments. Our results offer a physical insight for understanding both the structure and dynamics of magnetic particle assemblies in liquid crystalline matrices. PMID:27460190

  10. Photonic properties of organic molecular assemblies

    NASA Astrophysics Data System (ADS)

    Huggins, Kevin Edward

    1997-12-01

    This work attempts to characterize various photonic properties of spontaneously created organic molecular objects. A novel diacetylene monomer was synthesized and found to polymerize forming two-dimensional supramolecular assemblies. The two-dimensional structure self assembles when UV light generates polydiacetylene comb polymers. The material forms blue solid thin films which have been characterized by x-ray diffraction, infrared spectroscopy and Raman scattering. The photopolymerization rate of the monomer was followed by Raman scattering and was shown to be of second order. A reaction rate threshold was observed between 300 and 400mW of incident 647.1nm laser radiation where the reaction rate increased substantially. The material generates high third order nonlinear optical signals and have remarkable photochemical stability to 1064nm radiation from a Q-switched Nd:YAG laser. Upon heating to 62oC, the material turns bright red reversibly while maintaining its two-dimensional structure, characterized by differential scanning calorimetry. Heating to 180oC results in an irreversible color change to bright orange characterized by UV-Vis-NIR spectrophotometry. Variable temperature sum frequency generation experiments show that the third harmonic generation signals retain much of their original intensity through the thermochromic transitions. A system of novel rodcoil materials self assembles into mushroom-shaped supramolecular objects. These nanophase separated aggregates form oblique-plane superlattices exhibiting long-range order. The superlattice is composed of isolated crystallized rod domains surrounded by amorphous coil which form from simple solvent casting techniques. Second harmonic generation was used to confirm the polar head-to-tail stacking of the aggregates and to determine the average physical tilt of (5/pm 5)o of the aggregates relative to the film plane. A novel chiral oligomer synthesized in our group gave rise to interesting phase behavior

  11. Effect of molecular orientation on the elastic constants of polypropylene.

    SciTech Connect

    Kumar, S. R.; Renusch, D. P.; Grimsditch, M.; Materials Science Division; Amoco Polymers Research & Development

    2000-03-07

    The Brillouin spectroscopic measurements of elastic properties of polypropylene films fabricated by different processing techniques are described. We find that the elastic symmetry and the associated elastic constants are dependent on the molecular orientation brought about by the processing conditions used to produce the films. We have shown that Brillouin scattering techniques can successfully be used to track the molecular orientation induced by uniaxial stretching. We find a direct correspondence between the Brillouin measurements and optical birefringence measurements, illustrating that molecular orientation plays a dominant role in determining the mechanical anisotropy in these materials.

  12. On-chip molecular electronic plasmon sources based on self-assembled monolayer tunnel junctions

    NASA Astrophysics Data System (ADS)

    Du, Wei; Wang, Tao; Chu, Hong-Son; Wu, Lin; Liu, Rongrong; Sun, Song; Phua, Wee Kee; Wang, Lejia; Tomczak, Nikodem; Nijhuis, Christian A.

    2016-04-01

    Molecular electronic control over plasmons offers a promising route for on-chip integrated molecular plasmonic devices for information processing and computing. To move beyond the currently available technologies and to miniaturize plasmonic devices, molecular electronic plasmon sources are required. Here, we report on-chip molecular electronic plasmon sources consisting of tunnel junctions based on self-assembled monolayers sandwiched between two metallic electrodes that excite localized plasmons, and surface plasmon polaritons, with tunnelling electrons. The plasmons originate from single, diffraction-limited spots within the junctions, follow power-law distributed photon statistics, and have well-defined polarization orientations. The structure of the self-assembled monolayer and the applied bias influence the observed polarization. We also show molecular electronic control of the plasmon intensity by changing the chemical structure of the molecules and by bias-selective excitation of plasmons using molecular diodes.

  13. Molecular assembly of botulinum neurotoxin progenitor complexes.

    PubMed

    Benefield, Desirée A; Dessain, Scott K; Shine, Nancy; Ohi, Melanie D; Lacy, D Borden

    2013-04-01

    Botulinum neurotoxin (BoNT) is produced by Clostridium botulinum and associates with nontoxic neurotoxin-associated proteins to form high-molecular weight progenitor complexes (PCs). The PCs are required for the oral toxicity of BoNT in the context of food-borne botulism and are thought to protect BoNT from destruction in the gastrointestinal tract and aid in absorption from the gut lumen. The PC can differ in size and protein content depending on the C. botulinum strain. The oral toxicity of the BoNT PC increases as the size of the PC increases, but the molecular architecture of these large complexes and how they contribute to BoNT toxicity have not been elucidated. We have generated 2D images of PCs from strains producing BoNT serotypes A1, B, and E using negative stain electron microscopy and single-particle averaging. The BoNT/A1 and BoNT/B PCs were observed as ovoid-shaped bodies with three appendages, whereas the BoNT/E PC was observed as an ovoid body. Both the BoNT/A1 and BoNT/B PCs showed significant flexibility, and the BoNT/B PC was documented as a heterogeneous population of assembly/disassembly intermediates. We have also determined 3D structures for each serotype using the random conical tilt approach. Crystal structures of the individual proteins were placed into the BoNT/A1 and BoNT/B PC electron density maps to generate unique detailed models of the BoNT PCs. The structures highlight an effective platform that can be engineered for the development of mucosal vaccines and the intestinal absorption of oral biologics. PMID:23509303

  14. Molecular engineering and characterization of self-assembled biorecognition surfaces

    NASA Astrophysics Data System (ADS)

    Pan, Sheng

    The development of molecular engineering techniques for the fabrication of biomaterial surfaces is of importance in the field of biomaterials. It offers opportunities for better understanding of biological processes on material surfaces and rational design of contemporary biomaterials. Our work in this area aims to develop novel engineering strategies to design biorecognition surfaces via self-assembly and surface derivatization. Fundamental issues regarding self-assembled monolayer (SAM) structure, formation kinetics, and chemical derivatization were investigated systematically using electron spectroscopy for chemical analysis (ESCA), time-of-flight secondary ion mass spectrometry (TOF-SIMS), infrared reflection absorption spectroscopy (IRAS), atomic force microscopy (AFM), and contact angle measurements. Novel engineering concepts based on multifunctionality and statistical pattern matching were introduced and applied to develop biomimetic surfaces. Our study illustrated that molecules underwent structural transition and orientation development during self-assembly formation, from a disordered, low-density, more liquid-like structure to a highly ordered, closed-packed crystalline-like structure. Surface properties, such as wettability and the reactivity of outermost functional groups can be related to film structure, packing density, as well as molecular orientation. Given the order and organization of SAMs, the accessibility and reactivity of the outermost functional groups, reaction kinetics, stoichiometry, and SAMs stability were studied systematically by surface derivatization of trifluoroacetic anhydride (TFAA). The TFAA derivatization reactions exhibited rapid kinetics on the hydroxyl-terminated SAMs. The data from complementary surface analytical techniques consistently indicated a nearly complete surface reaction. Biomimetic surfaces were made by random immobilization of amino acid of arginine (R), glycine (G), and aspartic acid (D) on well-defined SAMs

  15. Molecular assembly at bare semiconductor surfaces

    NASA Astrophysics Data System (ADS)

    McGuiness, Christine L.

    The formation of well-organized monolayers with highly reproducible structures by solution self assembly of octadecanethiol (ODT) on GaAs (001) and (011) surfaces at ambient temperature through rigorous control of assembly conditions is demonstrated. Using TOF-SIMs and HRXPS measurements, it is shown that ODT molecules form a direct S-GaAs attachment with little to no substrate oxidation and exhibit an overall thermal stability up to ˜100°C, lower than the same monolayers on Au{111} surfaces. Detailed characterization using a combination of ellipsometry, liquid drop contact angles, atomic force microscopy, near edge x-ray absorption fine structure, infrared spectroscopy and x-ray photoemission spectroscopy probes reveal a structure with conformationally ordered alkyl chains tilted 14 +/-1° from the surface normal with a 43 +/-5° twist, a highly oleophobic and hydrophobic ambient surface. On GaAs (111A) surfaces, the ODT monolayers also form a direct S-GaAs attachment with little to no substrate oxidation but the final monolayer structure is more disordered, with the alkyl chains tilted 25 +/-5° from surface normal with a 45 +/-5° twist, resulting in a less oleophobic and hydrophobic ambient surface. Further, in contrast to previously reported results with Na2S9H2O treatments, Raman scattering measurements reveal that the ODT monolayers do not significantly modify the near-surface electronic structure of GaAs. Analysis of the tilt angle and film thickness data in conjunction with grazing incidence x-ray diffraction measurements show that the monolayers form structures with a significant mismatch of the average adsorbate molecule spacings with the spacings of intrinsic GaAs crystal lattices. For the square surface lattices of GaAs (001) and (011), ODT monolayers are observed to form pseudo-hcp structures. On the hcp surface lattice of GaAs (111A) however, the monolayers form a true hcp structure. This suggests that formation of the monolayers is driven

  16. Mechanoresponsive Luminescent Molecular Assemblies: An Emerging Class of Materials.

    PubMed

    Sagara, Yoshimitsu; Yamane, Shogo; Mitani, Masato; Weder, Christoph; Kato, Takashi

    2016-02-01

    The possibility to change the molecular assembled structures of organic and organometallic materials through mechanical stimulation is emerging as a general and powerful concept for the design of functional materials. In particular, the photophysical properties such as photoluminescence color, quantum yield, and emission lifetime of organic and organometallic fluorophores can significantly depend on the molecular packing, enabling the development of molecular materials with mechanoresponsive luminescence characteristics. Indeed, an increasing number of studies have shown in recent years that mechanical force can be utilized to change the molecular arrangement, and thereby the optical response, of luminescent molecular assemblies of π-conjugated organic or organometallic molecules. Here, the development of such mechanoresponsive luminescent (MRL) molecular assemblies consisting of organic or organometallic molecules is reviewed and emerging trends in this research field are summarized. After a brief introduction of mechanoresponsive luminescence observed in molecular assemblies, the concept of "luminescent molecular domino" is introduced, before molecular materials that show turn-on/off of photoluminescence in response to mechanical stimulation are reviewed. Mechanically stimulated multicolor changes and water-soluble MRL materials are also highlighted and approaches that combine the concept of MRL molecular assemblies with other materials types are presented in the last part of this progress report. PMID:26461848

  17. An autonomous molecular assembler for programmable chemical synthesis

    NASA Astrophysics Data System (ADS)

    Meng, Wenjing; Muscat, Richard A.; McKee, Mireya L.; Milnes, Phillip J.; El-Sagheer, Afaf H.; Bath, Jonathan; Davis, Benjamin G.; Brown, Tom; O'Reilly, Rachel K.; Turberfield, Andrew J.

    2016-06-01

    Molecular machines that assemble polymers in a programmed sequence are fundamental to life. They are also an achievable goal of nanotechnology. Here, we report synthetic molecular machinery made from DNA that controls and records the formation of covalent bonds. We show that an autonomous cascade of DNA hybridization reactions can create oligomers, from building blocks linked by olefin or peptide bonds, with a sequence defined by a reconfigurable molecular program. The system can also be programmed to achieve combinatorial assembly. The sequence of assembly reactions and thus the structure of each oligomer synthesized is recorded in a DNA molecule, which enables this information to be recovered by PCR amplification followed by DNA sequencing.

  18. Control of liquid crystal molecular orientation using ultrasound vibration

    NASA Astrophysics Data System (ADS)

    Taniguchi, Satoki; Koyama, Daisuke; Shimizu, Yuki; Emoto, Akira; Nakamura, Kentaro; Matsukawa, Mami

    2016-03-01

    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 distribution 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.

  19. Molecular self-assembly on two-dimensional atomic crystals: insights from molecular dynamics simulations.

    PubMed

    Zhao, Yinghe; Wu, Qisheng; Chen, Qian; Wang, Jinlan

    2015-11-19

    van der Waals (vdW) epitaxy of ultrathin organic films on two-dimensional (2D) atomic crystals has become a sovereign area because of their unique advantages in organic electronic devices. However, the dynamic mechanism of the self-assembly remains elusive. Here, we visualize the nanoscale self-assembly of organic molecules on graphene and boron nitride monolayer from a disordered state to a 2D lattice via molecular dynamics simulation for the first time. It is revealed that the assembly toward 2D ordered structures is essentially the minimization of the molecule-molecule interaction, that is, the vdW interaction in nonpolar systems and the vdW and Coulomb interactions in polar systems that are the decisive factors for the formation of the 2D ordering. The role of the substrate is mainly governing the array orientation of the adsorbates. The mechanisms unveiled here are generally applicable to a broad class of organic thin films via vdW epitaxy. PMID:26523464

  20. Orientational anisotropy in simulated vapor-deposited molecular glasses

    SciTech Connect

    Lyubimov, Ivan; Antony, Lucas; Walters, Diane M.; Ediger, M. D.; Rodney, David; Pablo, Juan J. de

    2015-09-07

    Enhanced kinetic stability of vapor-deposited glasses has been established for a variety of glass organic formers. Several recent reports indicate that vapor-deposited glasses can be orientationally anisotropic. In this work, we present results of extensive molecular simulations that mimic a number of features of the experimental vapor deposition process. The simulations are performed on a generic coarse-grained model and an all-atom representation of N,N′-bis(3-methylphenyl)-N,N′-diphenylbenzidine (TPD), a small organic molecule whose vapor-deposited glasses exhibit considerable orientational anisotropy. The coarse-grained model adopted here is found to reproduce several key aspects reported in experiments. In particular, the molecular orientation of vapor-deposited glasses is observed to depend on substrate temperature during deposition. For a fixed deposition rate, the molecular orientation in the glasses changes from isotropic, at the glass transition temperature, T{sub g}, to slightly normal to the substrate at temperatures just below T{sub g}. Well below T{sub g}, molecular orientation becomes predominantly parallel to the substrate. The all-atom model is used to confirm some of the equilibrium structural features of TPD interfaces that arise above the glass transition temperature. We discuss a mechanism based on distinct orientations observed at equilibrium near the surface of the film, which get trapped within the film during the non-equilibrium process of vapor deposition.

  1. Magnetotactic molecular architectures from self-assembly of β-peptide foldamers

    PubMed Central

    Kwon, Sunbum; Kim, Beom Jin; Lim, Hyung-Kyu; Kang, Kyungtae; Yoo, Sung Hyun; Gong, Jintaek; Yoon, Eunyoung; Lee, Juno; Choi, Insung S.; Kim, Hyungjun; Lee, Hee-Seung

    2015-01-01

    The design of stimuli-responsive self-assembled molecular systems capable of undergoing mechanical work is one of the most important challenges in synthetic chemistry and materials science. Here we report that foldectures, that is, self-assembled molecular architectures of β-peptide foldamers, uniformly align with respect to an applied static magnetic field, and also show instantaneous orientational motion in a dynamic magnetic field. This response is explained by the amplified anisotropy of the diamagnetic susceptibilities as a result of the well-ordered molecular packing of the foldectures. In addition, the motions of foldectures at the microscale can be translated into magnetotactic behaviour at the macroscopic scale in a way reminiscent to that of magnetosomes in magnetotactic bacteria. This study will provide significant inspiration for designing the next generation of biocompatible peptide-based molecular machines with applications in biological systems. PMID:26510658

  2. Magnetotactic molecular architectures from self-assembly of β-peptide foldamers

    NASA Astrophysics Data System (ADS)

    Kwon, Sunbum; Kim, Beom Jin; Lim, Hyung-Kyu; Kang, Kyungtae; Yoo, Sung Hyun; Gong, Jintaek; Yoon, Eunyoung; Lee, Juno; Choi, Insung S.; Kim, Hyungjun; Lee, Hee-Seung

    2015-10-01

    The design of stimuli-responsive self-assembled molecular systems capable of undergoing mechanical work is one of the most important challenges in synthetic chemistry and materials science. Here we report that foldectures, that is, self-assembled molecular architectures of β-peptide foldamers, uniformly align with respect to an applied static magnetic field, and also show instantaneous orientational motion in a dynamic magnetic field. This response is explained by the amplified anisotropy of the diamagnetic susceptibilities as a result of the well-ordered molecular packing of the foldectures. In addition, the motions of foldectures at the microscale can be translated into magnetotactic behaviour at the macroscopic scale in a way reminiscent to that of magnetosomes in magnetotactic bacteria. This study will provide significant inspiration for designing the next generation of biocompatible peptide-based molecular machines with applications in biological systems.

  3. Photocatalytic water oxidation by molecular assemblies based on cobalt catalysts.

    PubMed

    Zhou, Xu; Li, Fei; Li, Hua; Zhang, Biaobiao; Yu, Fengshou; Sun, Licheng

    2014-09-01

    Chromophore-catalyst molecular assemblies towards visible light-driven water oxidation were synthesized by covalent integration of a light-harvesting complex [Ru(bpy)3](2+) (bpy=2,2'-bipyridine) and a Co4O4 cubane water oxidation catalyst. The two components were assembled either in linear or macrocyclic configurations. In the presence of the sacrificial reagent, the Ru-Co metallocycle exhibits remarkable photocatalytic activity for oxygen evolution, which is one order of magnitude higher than that of a multicomponent system and exceeds that of a linear assembly by a factor of five, offering access to highly active photocatalyst through molecular design. PMID:25111070

  4. Numerical optimization of laser fields to control molecular orientation

    SciTech Connect

    Ben Haj-Yedder, A.; Auger, A.; Dion, C.M.; Cances, E.; Le Bris, C.; Keller, A.; Atabek, O.

    2002-12-01

    A thorough numerical illustration of an optimal control scenario dealing with the laser-induced orientation of a diatomic molecule (LiF) is presented. Special emphasis is laid on the definition of the various targets dealing with different orientation characteristics, identified in terms of maximum efficiency (i.e., molecular axis direction closest to the direction of the laser polarization vector), maximum duration (i.e., the time interval during which this orientation is maintained), or of a compromise between efficiency and duration. Excellent postpulse orientation is achieved by sudden, intense pulses. Thermal effects are also studied with an extension of the control scenarios to Boltzmann averaged orientation dynamics at T=5 K.

  5. Laser-field-free three-dimensional molecular orientation

    NASA Astrophysics Data System (ADS)

    Takei, Daisuke; Mun, Je Hoi; Minemoto, Shinichirou; Sakai, Hirofumi

    2016-07-01

    Laser-field-free three-dimensional orientation, corresponding to the complete control of spatial directions of asymmetric top molecules, is achieved with combined weak electrostatic and elliptically polarized laser fields with an 8-ns turnon and a 150-fs turnoff, which is shaped by a plasma shutter. Rotationally cold 3,4-dibromothiophene molecules are used as a sample, and their lower-lying rotational states are selected by a molecular deflector to increase the degrees of orientation. After the rapid turnoff of the pump pulse, higher degrees of orientation are maintained for 5-10 ps, which is long enough for various applications including electronic stereodynamics in molecules with femtosecond pulses.

  6. Molecular Orientation of Liquid Crystals on Topographic Nanopatterns.

    PubMed

    Ryu, Seong Ho; Yoon, Dong Ki

    2016-07-13

    Controlling the orientation of building blocks in soft matter on the substrate has been a big challenge in material sciences. We have controlled the molecular orientation of liquid crystal (LC) materials on the porous anodic aluminum oxide (AAO) film having hexagonal pore arrays on the top surface. In our method, anchoring conditions can be varied by changing the pore size (Dp) and the porosity (P). As a proof-of-concept, the orientation of smectic A (SmA) structure at different anchoring conditions was successfully controlled in a sandwich cell consisting of AAO and a glass substrate, which has not been successfully controlled by conventional methods. PMID:27322013

  7. Self-assembly of supramolecular chiral insulated molecular wire.

    PubMed

    Li, Chun; Numata, Munenori; Bae, Ah-Hyun; Sakurai, Kazuo; Shinkai, Seiji

    2005-04-01

    Supramolecular chiral insulated molecular wire was constructed by self-assembly of a neutral one-dimensional schizophyllan host and a water-soluble polythiophene guest. The work presented here will not only open a door to a new application of polysaccharides but also provide an important clue to prepare stable supramolecular insulated molecular wires with one-handed helical structure. PMID:15796500

  8. 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.

  9. Electric Field Assisted Assembly of Perpendicular Oriented NanorodSuperlattices

    SciTech Connect

    Ryan, Kevin M.; Mastroianni, Alex; Stancil, Kimani A.; Liu,Haitao; Alivisatos, Paul A.

    2006-04-10

    We observe the assembly of CdS nanorod superlattices by thecombination of a DC electric field and solvent evaporation. In eachelectric field (1 V/um) assisted assembly, CdS nanorods (5 x 30 nm)suspended initially in toluene were observed to align perpendicularly tothe substrate. Azimuthal alignment along the nanorod crystal faces andthe presence of stacking faults indicate that both 2D and 3D assemblieswere formed by a process of controlled super crystal growth.

  10. Harnessing Surface Dislocation Networks for Molecular Self-Assembly

    NASA Astrophysics Data System (ADS)

    Pohl, Karsten

    2009-03-01

    The controlled fabrication of functional wafer-based nano-arrays is one of the ultimate quests in current nanotechnologies. Well-ordered misfit dislocation networks of ultrathin metal films are viable candidates for the growth of two- dimensional ordered cluster arrays in the nanometer regime. Such bottom-up processes can be very complex, involving collective effects from a large number of atoms. Unraveling the fundamental forces that drive these self-assembly processes requires detailed experimental information at the atomic level of large ensembles of hundreds to thousands of atoms. The combination of variable temperature measurements from our home-built STM correlated with 2D Frenkel-Kontorova models based on first-principle interaction parameters is used to explain how uniform arrays can form with the strain in the thin film as the driving force responsible for the surface self-assembly process. This process is generally applicable to assemble many molecular species thus opening avenues towards complex self-assembled structures based on a lock-and-key type approach. Moreover, when increasing the molecular coverage and/or decreasing the strain in the thin film the intermolecular interactions will eventually dominate the elastic effects and dictate the self-assembly process via molecular structure and functionality. We will show that controlling this delicate balance leads to a richness of structures, ranging from disperse ordered arrays of molecular clusters to patterned self-assembled monolayers (SAMs) of functionalized fullerenes and methanethiol.

  11. Structural investigations of oriented membrane assemblies by FTIR-ATR spectroscopy

    NASA Astrophysics Data System (ADS)

    Fringeli, Urs Peter; Goette, Jeannette; Reiter, Gerald; Siam, Monira; Baurecht, Dieter

    1998-06-01

    In situ attenuated total reflection (ATR) Fourier transform (FT) spectroscopy is presented as an adequate tool for studying molecular structure and function of biomembranes. In this article emphasis was directed to the production of suitable model bilayer membranes for optimum mimicking of natural biomembranes, and to special FTIR ATR techniques to achieve enhanced selectivity as well as time resolved information on complex membrane assemblies. In this context, the preparation of supported bilayers according to the LB/vesicle method is presented and the use of such model membranes to build more complex assemblies, e.g. with creatine kinase, a surface bound enzyme, and alkaline phosphatase, a membrane anchored enzyme. A comprehensive summary of equations used for quantitative ATR spectroscopy is given and applied to determine the surface concentration and orientation of membrane bound molecules. The use of supported bilayers for drug membrane interaction studies is demonstrated by the local anesthetic dibucaine. Besides of structural information's, such studies result also thermodynamic date, such as adsorption isotherm and partition coefficient. A special ATR set-up for more precise background compensation is presented enabling the conversion of a single beam spectrometer into a pseudo double beam spectrometer. This optical component may be placed in the sample compartment of the spectrometer, and is referred to as single-beam-sample-reference (SBSR) attachment. Finally, a short theoretical introduction into time resolved modulation spectroscopy is given. Temperature modulated excitation of reversible conformational changes in the polypeptide poly-L-lysine and the enzyme RNase are shown as examples.

  12. Molecular orientation of rhodamine dyes on surfaces of layered silicates.

    PubMed

    Bujdák, Juraj; Iyi, Nobuo

    2005-03-17

    Films of the layered silicates fluorohectorite (FH) and saponite (Sap) with various rhodamine dyes were prepared. The dyes with acidic as well as large hydrophobic groups in their molecule were not adsorbed on the surface of FH, which was interpreted in terms of high charge density on the surface of this silicate. All adsorbed dyes formed similar forms, such as isolated cations and H-type molecular aggregates, which were characterized by different spectral properties. Polarized ultraviolet-visible (UV-vis) spectroscopy was used for the characterization of the molecular orientation of dye chromophores on the silicate surface. The isolated dye cations and species, which absorbed light at the low energy part of the spectra, were only slightly tilted with respect to the plane of the silicate surface. The cations forming H-aggregates and absorbing light at low wavelengths were oriented in a nearly perpendicular fashion. The nearly perpendicular orientation was observed as a strong increase of dichroic ratio with film tilting. The orientation of the cations in H-aggregates depends partially on the structure of the dye molecule, namely, on the type of amino group (primary, secondary, or tertiary) in the dye molecule. The type of amino groups probably plays a role in the suitable orientation of dye cations for effective electrostatic interaction between the cations and the negatively charged siloxane surface. X-ray powder diffraction could not distinguish dye phases of dye monomers and molecular aggregates. PMID:16851539

  13. 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.

  14. 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. PMID:26358333

  15. Engineering and Assembly of Protein Modules into Functional Molecular Systems.

    PubMed

    Hirschi, Stephan; Stauffer, Mirko; Harder, Daniel; Müller, Daniel J; Meier, Wolfgang; Fotiadis, Dimitrios

    2016-01-01

    Synthetic biology approaches range from the introduction of unique features into organisms to the assembly of isolated biomacromolecules or synthetic building blocks into artificial biological systems with biomimetic or completely novel functionalities. Simple molecular systems can be based on containers on the nanoscale that are equipped with tailored functional modules for various applications in healthcare, industry or biological and medical research. The concept, or vision, of assembling native or engineered proteins and/or synthetic components as functional modules into molecular systems is discussed. The main focus is laid on the engineering of energizing modules generating chemical energy, transport modules using this energy to translocate molecules between compartments of a molecular system, and catalytic modules (bio-)chemically processing the molecules. Further key aspects of this discourse are possible approaches for the assembly of simple nanofactories and their applications in biotechnology and medical health. PMID:27363367

  16. An autonomous molecular assembler for programmable chemical synthesis.

    PubMed

    Meng, Wenjing; Muscat, Richard A; McKee, Mireya L; Milnes, Phillip J; El-Sagheer, Afaf H; Bath, Jonathan; Davis, Benjamin G; Brown, Tom; O'Reilly, Rachel K; Turberfield, Andrew J

    2016-06-01

    Molecular machines that assemble polymers in a programmed sequence are fundamental to life. They are also an achievable goal of nanotechnology. Here, we report synthetic molecular machinery made from DNA that controls and records the formation of covalent bonds. We show that an autonomous cascade of DNA hybridization reactions can create oligomers, from building blocks linked by olefin or peptide bonds, with a sequence defined by a reconfigurable molecular program. The system can also be programmed to achieve combinatorial assembly. The sequence of assembly reactions and thus the structure of each oligomer synthesized is recorded in a DNA molecule, which enables this information to be recovered by PCR amplification followed by DNA sequencing. PMID:27219697

  17. Easy creation of polymeric systems for molecular dynamics with Assemble!

    NASA Astrophysics Data System (ADS)

    Degiacomi, Matteo T.; Erastova, Valentina; Wilson, Mark R.

    2016-05-01

    We present Assemble!, a program greatly simplifying the preparation of molecular dynamics simulations of polymeric systems. The program is controlled either via command line or an intuitive Graphical User Interface, and runs on all major operating systems. Assemble! allows the creation of a desired system of polymer chains from constituent monomers, packs the chains into a box according to the required concentration and returns all the files needed for simulation with Gromacs. We illustrate the capabilities of Assemble! by demonstrating the easy preparation of a 300 monomers-long polyisoprene in hexane, and a heterogeneous mixture of polybutadiene.

  18. The art and science of self-assembling molecular machines

    NASA Astrophysics Data System (ADS)

    Gómez-López, Marcos; Preece, Jon A.; Fraser Stoddart, J.

    1996-09-01

    In this review, we show how noncovalent bonding interactions between 0957-4484/7/3/004/img1-electron rich aromatic ring systems (e.g. hydroquinone) and the 0957-4484/7/3/004/img1-electron deficient tetracationic cyclophane, cyclobis(paraquat-p-phenylene) can be used to self-assemble novel molecular architectures which are not only interesting to us, because of their fascinating topologies, but also because they have the potential to be developed into molecular structures with switchable properties on the nanometre scale. The high efficiency observed in the self-assembly of a [2]catenane, and its dynamic properties in solution, represent the first step in the design and self-assembly of other molecular assemblies better suited for the study of molecular switching processes. Therefore, a series of [2]rotaxanes, mechanically-interlocked molecular compounds, consisting of a linear 0957-4484/7/3/004/img1-electron rich dumbbell-shaped component and the 0957-4484/7/3/004/img1-electron deficient tetracationic cyclophane as the cyclic component, have been self-assembled and evaluated. All of the so-called molecular shuttles show translational isomerism and one of them, comprising benzidine and biphenol recognition sites as the non-degenerate 0957-4484/7/3/004/img1-electron rich sites, shows molecular switching properties when it is perturbed by external stimuli, such as electrons and protons. The versatility of our approach to nanoscale molecular switches is proven by the description of a series of molecular assemblies and supramolecular arrays, consisting of 0957-4484/7/3/004/img1-electron rich and 0957-4484/7/3/004/img1-electron deficient components, which display molecular switching properties when they are influenced by external stimuli that are photochemical, electrochemical and/or chemical in nature. However, the molecular switching phenomena take place in the solution state. Therefore, finally we describe how simple molecular structures can be ordered on to a solid

  19. Role of molecular orientational anisotropy in the chiral resolution of enantiomers in adsorbed overlayers.

    PubMed

    Szabelski, Paweł; Woszczyk, Aleksandra

    2012-07-31

    Separation of chiral molecules using achiral inputs is an interesting alternative to traditional techniques based on the chiral recognition mechanism. In this article we propose a lattice gas Monte Carlo model of two-dimensional chiral segregation induced by breaking of molecular orientational symmetry. Simulations were performed on a square lattice for rigid chain molecules composed of four and five identical segments. Mirror-image flat chain conformations resulting in different enantiomeric pairs were considered for each probe molecule. The enantiomers were assumed to interact via short-ranged segment-segment interaction potential limited to nearest neighbors on the lattice. We considered two qualitatively different situations in which (1) the molecules were allowed to rotate on the surface and adopt any of the four planar orientations and (2) the rotation was blocked, so that only one planar orientation was possible. The results obtained for the racemic overlayers showed clearly that the orientational symmetry breaking can induce spontaneous segregation of the enantiomers into large enantiopure domains. However, this effect was observed only for molecules with sufficiently long linear fragment. In the case of kinked bulky molecules a mixed assembly was formed, demonstrating the role of molecular shape in the orientationally biased segregation of enantiomers in adsorbed films. The insights from this study can be useful in developing strategies for 2D chiral separations in which external directional fields are used. PMID:22747234

  20. A novel orientation and position measuring system for large & medium scale precision assembly

    NASA Astrophysics Data System (ADS)

    Li, Yuhe; Qiu, Yongrong; Chen, Yanxiang; Guan, Kaisen

    2014-11-01

    In the field of precision assembly of large & medium scale, the orientation and position measurement system is quite demanding. In this paper a novel measuring system, consisting of four motorized stages, a laser rangefinder, an autocollimator and a camera is proposed to assist precision assembly. Through the design of coaxial optical system, the autocollimator is integrated with a laser rangefinder into a collimation rangefinder, which is used for measuring orientation and position synchronously. The laser spot is adopted to guide autocollimation over a large space and assist the camera in finding collimated measurand. The mathematical models and practical calibration methods for measurement are elaborated. The preliminary experimental results agree with the methods currently being used for orientation and position measurement. The measuring method provides an alternative choice for the metrology in precision assembly.

  1. Task oriented nonlinear control laws for telerobotic assembly operations

    NASA Technical Reports Server (NTRS)

    Walker, R. A.; Ward, L. S.; Elia, C. F.

    1987-01-01

    The goal of this research is to achieve very intelligent telerobotic controllers which are capable of receiving high-level commands from the human operator and implementing them in an adaptive manner in the object/task/manipulator workspace. Initiatives by the authors at Integrated Systems, Inc. to identify and develop the key technologies necessary to create such a flexible, highly programmable, telerobotic controller are presented. The focus of the discussion is on the modeling of insertion tasks in three dimensions and nonlinear implicit force feedback control laws which incorporate tool/workspace constraints. Preliminary experiments with dual arm beam assembly in 2-D are presented.

  2. Assembly of oriented zeolite monolayers and thin films on polymeric surfaces via hydrogen bonding.

    PubMed

    Zhou, Ming; Liu, Xiufeng; Zhang, Baoquan; Zhu, Huiming

    2008-10-21

    The b-oriented monolayers of microsized silicalite-1 crystals have been manually assembled on glass plate supported poly(ethylene oxide) (PEO), poly(vinyl alcohol) (PVA), chitosan, and poly(methyl methacrylate) (PMMA) thin films via hydrogen bonding with much enhanced binding strength and satisfactory degrees of coverage and close packing. The exerted pressure and rubbing time in the manual assembly do not affect the binding strength of the silicalite-1 monolayer on the glass plate supported polymeric film. This manual assembly has been further applied to fabricate zeolite monolayers on commercially available Plexiglas surfaces and b-oriented multilayered films of silicalite-1 crystals on glass plates. The assembly method established in this study provides a feasible way to produce zeolite monolayers on polymer-modified solid substrates and Plexiglas and to fabricate zeolite-polymer composite membranes by means of the layer-by-layer technique. PMID:18785711

  3. 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.

  4. 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.

  5. Mechanically induced luminescence changes in molecular assemblies.

    PubMed

    Sagara, Yoshimitsu; Kato, Takashi

    2009-11-01

    Altering the shape and properties of a material through external factors such as heat, light, pressure, pH, electric or magnetic fields, or the introduction of a guest molecule, is an attractive prospect. In this Perspective, piezochromic luminescent materials - which change the colour of their luminescence in response to mechanical stimuli - are described. Such piezochromism has been observed for a few molecular materials that contain luminescent cores in liquid-crystalline and crystalline solid states, as well as for polymeric materials doped with dyes. These changes in photoluminescent colour can be activated by various types of mechanical pressure such as shearing, grinding or elongation, which can trigger different mechanisms of producing the colour. Such stimuli-responsive materials have potential for various applications, including sensors, memory and displays. PMID:21378953

  6. Ligand Pose and Orientational Sampling in Molecular Docking

    PubMed Central

    Coleman, Ryan G.; Carchia, Michael; Sterling, Teague; Irwin, John J.; Shoichet, Brian K.

    2013-01-01

    Molecular docking remains an important tool for structure-based screening to find new ligands and chemical probes. As docking ambitions grow to include new scoring function terms, and to address ever more targets, the reliability and extendability of the orientation sampling, and the throughput of the method, become pressing. Here we explore sampling techniques that eliminate stochastic behavior in DOCK3.6, allowing us to optimize the method for regularly variable sampling of orientations. This also enabled a focused effort to optimize the code for efficiency, with a three-fold increase in the speed of the program. This, in turn, facilitated extensive testing of the method on the 102 targets, 22,805 ligands and 1,411,214 decoys of the Directory of Useful Decoys - Enhanced (DUD-E) benchmarking set, at multiple levels of sampling. Encouragingly, we observe that as sampling increases from 50 to 500 to 2000 to 5000 to 20000 molecular orientations in the binding site (and so from about 1×1010 to 4×1010 to 1×1011 to 2×1011 to 5×1011 mean atoms scored per target, since multiple conformations are sampled per orientation), the enrichment of ligands over decoys monotonically increases for most DUD-E targets. Meanwhile, including internal electrostatics in the evaluation ligand conformational energies, and restricting aromatic hydroxyls to low energy rotamers, further improved enrichment values. Several of the strategies used here to improve the efficiency of the code are broadly applicable in the field. PMID:24098414

  7. Chloroaluminum phthalocyanine thin films: chemical reaction and molecular orientation.

    PubMed

    Latteyer, Florian; Peisert, Heiko; Uihlein, Johannes; Basova, Tamara; Nagel, Peter; Merz, Michael; Schuppler, Stefan; Chassé, Thomas

    2013-05-01

    The chemical transformation of the polar chloroaluminum phthalocyanine, AlClPc, to μ-(oxo)bis(phthalocyaninato)aluminum(III), (PcAl)2O, in thin films on indium tin oxide is studied and its influence on the molecular orientation is discussed. The studies were conducted using complementary spectroscopic techniques: Raman spectroscopy, X-ray photoelectron spectroscopy, and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy. In addition, density functional theory calculations were performed in order to identify specific vibrations and to monitor the product formation. The thin films of AlClPc were annealed in controlled environmental conditions to obtain (PcAl)2O. It is shown that the chemical transformation in the thin films can proceed only in the presence of water. The influence of the reaction and the annealing on the molecular orientation was studied with Raman spectroscopy and NEXAFS spectroscopy in total electron yield and partial electron yield modes. The comparison of the results obtained from these techniques allows the determination of the molecular orientation of the film as a function of the probing depth. PMID:23494276

  8. Colloid-guided assembly of oriented 3D neuronal networks

    PubMed Central

    Pautot, Sophie; Wyart, Claire; Isacoff, Ehud Y

    2009-01-01

    A central challenge in neuroscience is to understand the formation and function of three-dimensional (3D) neuronal networks. In vitro studies have been mainly limited to measurements of small numbers of neurons connected in two dimensions. Here we demonstrate the use of colloids as moveable supports for neuronal growth, maturation, transfection and manipulation, where the colloids serve as guides for the assembly of controlled 3D, millimeter-sized neuronal networks. Process growth can be guided into layered connectivity with a density similar to what is found in vivo. The colloidal superstructures are optically transparent, enabling remote stimulation and recording of neuronal activity using layer-specific expression of light-activated channels and indicator dyes. The modular approach toward in vitro circuit construction provides a stepping stone for applications ranging from basic neuroscience to neuron-based screening of targeted drugs. PMID:18641658

  9. Molecular mechanism of bacterial type 1 and P pili assembly.

    PubMed

    Busch, Andreas; Phan, Gilles; Waksman, Gabriel

    2015-03-01

    The formation of adhesive surface structures called pili or fimbriae ('bacterial hair') is an important contributor towards bacterial pathogenicity and persistence. To fight often chronic or recurrent bacterial infections such as urinary tract infections, it is necessary to understand the molecular mechanism of the nanomachines assembling such pili. Here, we focus on the so far best-known pilus assembly machinery: the chaperone-usher pathway producing the type 1 and P pili, and highlight the most recently acquired structural knowledge. First, we describe the subunits' structure and the molecular role of the periplasmic chaperone. Second, we focus on the outer-membrane usher structure and the catalytic mechanism of usher-mediated pilus biogenesis. Finally, we describe how the detailed understanding of the chaperone-usher pathway at a molecular level has paved the way for the design of a new generation of bacterial inhibitors called 'pilicides'. PMID:25624519

  10. 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.

  11. Liquid crystalline collagen: a self-assembled morphology for the orientation of mammalian cells.

    PubMed

    Kirkwood, John E; Fuller, Gerald G

    2009-03-01

    We report the creation of collagen films having a cholesteric banding structure with an orientation that can be systematically controlled. The action of hydrodynamic flow and rapid desiccation was used to influence the orientation of collagen fibrils, producing a film with a twisted plywood architecture. Adult human fibroblasts cultured on these substrates orient in the direction of the flow deposition, and filopodia are extended onto individual bands. Atomic force microscopy reveals the assembly of 30 nm collagen fibrils into the uniform cholesteric collagen films with a periodic surface relief. The generation of collagen with a reticular, "basket-weave" morphology when using lower concentrations is also discussed. PMID:19437784

  12. Faunus: An object oriented framework for molecular simulation

    PubMed Central

    Lund, Mikael; Trulsson, Martin; Persson, Björn

    2008-01-01

    Background We present a C++ class library for Monte Carlo simulation of molecular systems, including proteins in solution. The design is generic and highly modular, enabling multiple developers to easily implement additional features. The statistical mechanical methods are documented by extensive use of code comments that – subsequently – are collected to automatically build a web-based manual. Results We show how an object oriented design can be used to create an intuitively appealing coding framework for molecular simulation. This is exemplified in a minimalistic C++ program that can calculate protein protonation states. We further discuss performance issues related to high level coding abstraction. Conclusion C++ and the Standard Template Library (STL) provide a high-performance platform for generic molecular modeling. Automatic generation of code documentation from inline comments has proven particularly useful in that no separate manual needs to be maintained. PMID:18241331

  13. Molecular orientation of tropoelastin is determined by surface hydrophobicity.

    PubMed

    Le Brun, Anton P; Chow, John; Bax, Daniel V; Nelson, Andrew; Weiss, Anthony S; James, Michael

    2012-02-13

    Tropoelastin is the precursor of the extracellular protein elastin and is utilized in tissue engineering and implant technology by adapting the interface presented by surface-bound tropoelastin. The preferred orientation of the surface bound protein is relevant to biointerface interactions, as the C-terminus of tropoelastin is known to be a binding target for cells. Using recombinant human tropoelastin we monitored the binding of tropoelastin on hydrophilic silica and on silica made hydrophobic by depositing a self-assembled monolayer of octadecyl trichlorosilane. The layered organization of deposited tropoelastin was probed using neutron and X-ray reflectometry under aqueous and dried conditions. In a wet environment, tropoelastin retained a solution-like structure when adsorbed on silica but adopted a brush-like structure when on hydrophobized silica. The orientation of the surface-bound tropoelastin was investigated using cell binding assays and it was found that the C-terminus of tropoelastin faced the bulk solvent when bound to the hydrophobic surface, but a mixture of orientations was adopted when tropoelastin was bound to the hydrophilic surface. Drying the tropoelastin-coated surfaces irreversibly altered these protein structures for both hydrophilic and hydrophobic surfaces. PMID:22176209

  14. 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

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

    NASA Astrophysics Data System (ADS)

    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

  16. Design and Fabrication of Molecular Assemblies of Conductive Polymers

    NASA Astrophysics Data System (ADS)

    Cheung, Josephine Ho-Wah

    Two new methods of fabricating multilayer Langmuir -Blodgett (LB) thin films of electrically conductive polyaniline and a novel method of constructing molecular assemblies of polyaniline via the spontaneous adsorption (SA) technique were developed. Quantitative transmission/reflection Fourier transform infrared spectroscopy, polarized ultraviolet -visible spectroscopy and X-ray diffraction techniques were used to examine the structure and composition of multilayer thin films. In the structural study of LB films fabricated from 3-octadecyl pyrrole (3-ODP), 3-octadecanoyl pyrrole (3-ODOP) and polypyrrole/3-ODOP (PPY/3-ODOP), the level of order and orientation were found to be affected by the intermolecular and intramolecular interactions between molecules. For the manipulation of polyaniline using the LB technique, stable and easily transferrable LB monolayers were formed at the air-water interface by mixing polyaniline in its emeraldine-base form (PANb) with two processing aids. Films fabricated from the PANb/StA mixture were found to be phase separated with domains of polyaniline and stearic acid while those from the PANb/PI blend were found to be miscible. Both polyaniline LB films were rendered conductive by doping with 1 M HCl or HCl vapor. Multilayer polyaniline films were also constructed via a SA process. The multilayer buildup of doped polyaniline and sulfonated polystyrene (PANi/SPS) is facilitated by the electrostatic attraction between the delocalized positive -charged defects along the PANi backbone and the negative charges present in the ionizable pendant sulfonic acid groups of the SPS. Uniform multilayer thin films with thicknesses between 20 A and 100 A were constructed on different surfaces with complex topologies. Conductivities in the level of 0.1-1 S/cm were achieved by doping the multilayer PANi/SPS films with 1 M HCl. This level of conductivity was achieved by films with as few as 4 layers of PANi/SPS, that is, films with thicknesses of about

  17. Photon-Regulated DNA-Enzymatic Nanostructures by Molecular Assembly

    PubMed Central

    You, Mingxu; Wang, Ruo-Wen; Zhang, Xiaobing; Chen, Yan; Wang, Kelong; Peng, Lu; Tan, Weihong

    2011-01-01

    Future smart nanostructures will have to rely on molecular assembly for unique or advanced desired functions. For example, the evolved ribosome in nature is one example of functional self-assembly of nucleic acids and proteins employed in nature to perform specific tasks. Artificial self-assembled nanodevices have also been developed to mimic key biofunctions, and various nucleic acid- and protein-based functional nanoassemblies have been reported. However, functionally regulating these nanostructures is still a major challenge. Here we report a general approach to fine-tune the catalytic function of DNA-enzymatic nanosized assemblies by taking advantage of the trans-cis isomerization of azobenzene molecules. To the best of our knowledge, this is the first study to precisely modulate the structures and functions of an enzymatic assembly based on light-induced DNA scaffold switching. Via photocontrolled DNA conformational switching, the proximity of multiple enzyme catalytic centers can be adjusted, as well as the catalytic efficiency of cofactor-mediated DNAzymes. We expect that this approach will lead to the advancement of DNA-enzymatic functional nanostructures in future biomedical and analytical applications. PMID:22098552

  18. 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

  19. Shape-controlled orientation and assembly of colloids with sharp edges in nematic liquid crystals.

    PubMed

    Beller, Daniel A; Gharbi, Mohamed A; Liu, Iris B

    2015-02-14

    The assembly of colloids in nematic liquid crystals via topological defects has been extensively studied for spherical particles, and investigations of other colloid shapes have revealed a wide array of new assembly behaviors. We show, using Landau-de Gennes numerical modeling, that nematic defect configurations and colloidal assembly can be strongly influenced by fine details of colloid shape, in particular the presence of sharp edges. For cylinder, microbullet, and cube colloid geometries, we obtain the particles' equilibrium alignment directions and effective pair interaction potentials as a function of simple shape parameters. We find that defects pin at sharp edges, and that the colloid consequently orients at an oblique angle relative to the far-field nematic director that depends on the colloid's shape. This shape-dependent alignment, which we confirm in experimental measurements, raises the possibility of selecting self-assembly outcomes for colloids in liquid crystals by tuning particle geometry. PMID:25523158

  20. Edge-to-Edge Oriented Self-Assembly of ReS2 Nanoflakes.

    PubMed

    Zhang, Qin; Wang, Wenjie; Kong, Xin; Mendes, Rafael G; Fang, Liwen; Xue, Yinghui; Xiao, Yao; Rümmeli, Mark H; Chen, Shengli; Fu, Lei

    2016-09-01

    The self-assembly of two-dimensional (2D) nanomaterials, an emerging research area, still remains largely unexplored. The strong interlayer attraction between 2D nanosheets leads to face-to-face stacking rather than edge-to-edge coupling. We demonstrate, for the first time, how one can induce and control an edge-to-edge self-assembly process for 2D nanomaterials. The extremely weak van der Waals coupling and strong anisotropy of ReS2 allow us to realize an oriented self-assembly (OSA) process. The aspect ratio of the resulting ReS2 nanoscrolls can be well controlled. In addition, we perform simulations to further explain and confirm the OSA process, demonstrating its great potential to be expanded as a general edge-to-edge self-assembly process suitable for other 2D nanomaterials. PMID:27547983

  1. Mechanical Characterization of Molecular Assemblies at Oil/Water Interfaces

    NASA Astrophysics Data System (ADS)

    Yuan, Wa

    The self-assembly of charged molecules in liquid phases and their ability to form functional layers at immiscible interfaces are areas of great interest. However, the implementation of these assemblies is often limited by a lack of understanding of the detailed assembly mechanisms. In order to enhance the performance of interfacial assemblies it is essential to be able to characterize the physical and mechanical properties of assembled layers, as well as develop model systems that will allow us to examine the factors that govern their interaction with the surrounding environment. The key purpose of this thesis is to develop an understanding of some of the important factors influencing interfacial assemblies at immiscible liquid interfaces. The first portion of the work involves mechanical characterization of interfacial layers formed by large amphiphilic molecules. The study of block and gradient copolymers, reveals the effect of copolymer sequence distribution on the ability of these molecules to form interfacial assemblies. Specifically, the unique network structure formed by gradient copolymers at oil/water interfaces enables us to create a robust membrane at the interface by ionic crosslinking. The second part of this thesis explores smaller molecule assemblies at liquid interfaces, including commonly used commercial surfactant (span 80) and nano particles (graphene oxide). Both studies demonstrate an interesting correlation between molecular structure and overall properties of the assembled layers. Factors such as interfacial density, particle sizes and pH can greatly influence the structure of the assembled layers, resulting in interesting phenomena such as spontaneous emulsification, wrinkling and layer collapse. The bulk of the oil/water interface study was performed using axisymmetric drop shape analysis (DSA), which successfully quantifies the mechanical tension in the interfacial layer. This analysis was further extended by a development of a double

  2. Complex molecular assemblies at hand via interactive simulations.

    PubMed

    Delalande, Olivier; Férey, Nicolas; Grasseau, Gilles; Baaden, Marc

    2009-11-30

    Studying complex molecular assemblies interactively is becoming an increasingly appealing approach to molecular modeling. Here we focus on interactive molecular dynamics (IMD) as a textbook example for interactive simulation methods. Such simulations can be useful in exploring and generating hypotheses about the structural and mechanical aspects of biomolecular interactions. For the first time, we carry out low-resolution coarse-grain IMD simulations. Such simplified modeling methods currently appear to be more suitable for interactive experiments and represent a well-balanced compromise between an important gain in computational speed versus a moderate loss in modeling accuracy compared to higher resolution all-atom simulations. This is particularly useful for initial exploration and hypothesis development for rare molecular interaction events. We evaluate which applications are currently feasible using molecular assemblies from 1900 to over 300,000 particles. Three biochemical systems are discussed: the guanylate kinase (GK) enzyme, the outer membrane protease T and the soluble N-ethylmaleimide-sensitive factor attachment protein receptors complex involved in membrane fusion. We induce large conformational changes, carry out interactive docking experiments, probe lipid-protein interactions and are able to sense the mechanical properties of a molecular model. Furthermore, such interactive simulations facilitate exploration of modeling parameters for method improvement. For the purpose of these simulations, we have developed a freely available software library called MDDriver. It uses the IMD protocol from NAMD and facilitates the implementation and application of interactive simulations. With MDDriver it becomes very easy to render any particle-based molecular simulation engine interactive. Here we use its implementation in the Gromacs software as an example. PMID:19353597

  3. Molecular Microbial Analyses of the Mars Exploration Rovers Assembly Facility

    NASA Technical Reports Server (NTRS)

    Venkateswaran, Kasthuri; LaDuc, Myron T.; Newcombe, David; Kempf, Michael J.; Koke, John. A.; Smoot, James C.; Smoot, Laura M.; Stahl, David A.

    2004-01-01

    During space exploration, the control of terrestrial microbes associated with robotic space vehicles intended to land on extraterrestrial solar system bodies is necessary to prevent forward contamination and maintain scientific integrity during the search for life. Microorganisms associated with the spacecraft assembly environment can be a source of contamination for the spacecraft. In this study, we have monitored the microbial burden of air samples of the Mars Exploration Rovers' assembly facility at the Kennedy Space Center utilizing complementary diagnostic tools. To estimate the microbial burden and identify potential contaminants in the assembly facility, several microbiological techniques were used including culturing, cloning and sequencing of 16S rRNA genes, DNA microarray analysis, and ATP assays to assess viable microorganisms. Culturing severely underestimated types and amounts of contamination since many of the microbes implicated by molecular analyses were not cultivable. In addition to the cultivation of Agrobacterium, Burkholderia and Bacillus species, the cloning approach retrieved 16s rDNA sequences of oligotrophs, symbionts, and y-proteobacteria members. DNA microarray analysis based on rational probe design and dissociation curves complemented existing molecular techniques and produced a highly parallel, high resolution analysis of contaminating microbial populations. For instance, strong hybridization signals to probes targeting the Bacillus species indicated that members of this species were present in the assembly area samples; however, differences in dissociation curves between perfect-match and air sample sequences showed that these samples harbored nucleotide polymorphisms. Vegetative cells of several isolates were resistant when subjected to treatments of UVC (254 nm) and vapor H202 (4 mg/L). This study further validates the significance of non-cultivable microbes in association with spacecraft assembly facilities, as our analyses have

  4. Enhanced Rates of Photoinduced Molecular Orientation in a Series of Molecular Glassy Thin Films.

    PubMed

    Snell, Kristen E; Hou, Renjie; Ishow, Eléna; Lagugné-Labarthet, François

    2015-07-01

    Photoinduced orientation in a series of molecular glasses made of small push-pull azo derivatives is dynamically investigated for the first time. Birefringence measurements at 632.8 nm are conducted with a temporal resolution of 100 ms to probe the fast rate of the azo orientation induced under polarized light and its temporal stability over several consecutive cycles. To better evaluate the influence of the azo chemical substituents and their electronic properties on the orientation of the whole molecule, a series of push-pull azo derivatives involving a triphenylaminoazo core substituted with distinct electron-withdrawing moieties is studied. All resulting thin films are probed using polarization modulation infrared spectroscopy that yields dynamical linear dichroism measurements during a cycle of orientation followed by relaxation. We show here in particular that the orientation rates of small molecule-based azo materials are systematically increased up to 7-fold compared to those of a reference polymer counterpart. For specific compounds, the percentage of remnant orientation is also higher, which makes these materials of great interest and promising alternatives to azobenzene-containing polymers for a variety of applications requiring a fast response and absolute control over the molecular weight. PMID:26072966

  5. Response of liquid scintillator assemblies as a function of angular orientation

    NASA Astrophysics Data System (ADS)

    Naeem, S. F.; Scarpelli, M.; Miller, E.; Clarke, S. D.; Pozzi, S. A.

    2014-06-01

    Liquid scintillator detector assemblies contain an inert nitrogen expansion volume to allow for expansion of the liquid with changing temperature. Measurements and Geant4 Monte Carlo simulations are performed to study the dependence of pulse height distribution shapes as a function of detector angle for two liquid scintillators assemblies filled with 97% organic-liquid cocktail and a 3% expansion volume. A 12.7-cm diameter by 12.7-cm long and a 7.6-cm diameter by 9.1-cm long EJ-309 liquid scintillator assemblies are investigated using a 137Cs gamma-ray source. Aside from the differences in dimensions, the detector assemblies also differed in the design of the active detector volume: there is no light guide in the 12.7-cm-diameter detector assembly, whereas the 7.6-cm-diameter detector contains a BK7 light guide between the scintillation liquid and optical coupling to the photomultiplier tube. Results for the 12.7-cm-diameter detector show a decrease in the position of the Compton edge ranges from 4% to 40% at detector orientations where the expansion volume exists between scintillating medium and the photomultiplier tube. Results for the 7.6-cm-diameter detector show that the position of the Compton edge is relatively unaffected at all detector orientations due to the presence of light guide.

  6. Molecular mobility in self-assembled dendritic chromophore glasses.

    PubMed

    Knorr, Daniel B; Zhou, Xing-Hua; Shi, Zhengwei; Luo, Jingdong; Jang, Sei-Hum; Jen, Alex K-Y; Overney, René M

    2009-10-29

    Increasing complexity in bottom-up molecular designs of amorphous structures with multiple relaxation modes demands an integrated and cognitive design approach, where chemical synthesis is guided by both analytical tools and theoretical simulations. In particular, this is apparent for novel organic second-order nonlinear optical materials of self-assembling molecular glasses involving dendritic arene stabilization moieties (phenyl, naphthyl, and anthryl) with electro-optical activities above 300 pm/V. In this study, nanoscale thermo-mechanical analyses yield direct insight into the molecular enthalpic and entropic relaxation modes. Arene-perfluoroarene interactions for coarse self-assembly are found to impose three phase relaxation regimes, with intermediate regimes of 8-15 degrees C in width and apparent activation energies between 40 and 60 kcal/mol to be the most effective for poling. Energetic analyses based on intrinsic friction microscopy (IFA) identify increasing temporal stability with increasing arene size for the low-temperature regime. Electric field poling efficiency is found to be inversely proportional to entropic cooperative contributions that can make up 80% of the overall apparent relaxation energy for the high-temperature regime. The origin for the activation energies below the incipient glass transition temperature, based on complementary molecular dynamic simulations, is tied primarily to noncovalent interactions between chromophore (dipole), dendritic (quadrupole) moieties, and combinations thereof. PMID:19780549

  7. Molecular Self-Assembly Driven by London Dispersion Forces

    SciTech Connect

    Li, Guo; Cooper, Valentino R; Cho, Jun-Hyung; Du, Shixuan; Gao, Hongjun; Zhang, Zhenyu

    2011-01-01

    The nature and strength of intermolecular interactions are crucial to a variety of kinetic and dynamic processes at surfaces. Whereas strong chemisorption bonds are known to facilitate molecular binding, the importance of the weaker yet ubiquitous van der Waals (vdW) interactions remains elusive in most cases. Here we use first-principles calculations combined with kinetic Monte Carlo simulations to unambiguously demonstrate the vital role that vdW interactions play in molecular self-assembly, using styrene nanowire growth on silicon as a prototypical example. We find that, only when the London dispersion forces are included, accounting for the attractive parts of vdW interactions, can the effective intermolecular interaction be reversed from being repulsive to attractive. Such attractive interactions, in turn, ensure the preferred growth of long wires under physically realistic conditions as observed experimentally. We further propose a cooperative scheme, invoking the application of an electric field and the selective creation of Si dangling bonds, to drastically improve the ordered arrangement of the molecular structures. The present study represents a significant step forward in the fundamental understanding and precise control of molecular self-assembly guided by London dispersion forces.

  8. Molecular-level assemblies on metal oxide surfaces

    SciTech Connect

    Schoonover, J.R.; Bignozzi, C.; Meyer, T.

    1996-07-01

    This is the final report of a one-year, Laboratory-Directed Research and Development project at the Los Alamos National Laboratory (LANL). The objective of this project was to explore molecular-level assemblies based on polypyridyl transition metal complexes attached to metal oxide surfaces to provide the basis for applications such as energy conversion and electricity generation, photoremediation of hazardous waste, chemical sensors, and optical storage and photorefractive devices for communications and optical computing. We have elucidated the fundamental factors that determine the photochemistry and photophysics of a series of these photoactive inorganic complexes in solution and on metal oxide substrates by exploiting our unique transient laser capabilities. This data is being utilized to design and fabricate molecular-level photonic devices. The rich chemistry of transition metal polypyridyl complexes can be utilized to prepare molecular assemblies having well-defined redox or excited-state properties that can be finely tuned to produce desired materials properties. We plan to explore other novel applications such as photorefractive switches and optical sensors using this molecular engineering approach.

  9. A Molecular Switch for the Orientation of Epithelial Cell Polarization

    PubMed Central

    Bryant, David M.; Roignot, Julie; Datta, Anirban; Overeem, Arend W.; Kim, Minji; Yu, Wei; Peng, Xiao; Eastburn, Dennis J.; Ewald, Andrew J.; Werb, Zena; Mostov, Keith E.

    2014-01-01

    SUMMARY The formation of epithelial tissues containing lumens requires not only the apical-basolateral polarization of cells, but also the coordinated orientation of this polarity such that the apical surfaces of neighboring cells all point toward the central lumen. Defects in extracellular matrix (ECM) signaling lead to inverted polarity so that the apical surfaces face the surrounding ECM. We report a molecular switch mechanism controlling polarity orientation. ECM signals through a β1-integrin/FAK/p190RhoGAP complex to down-regulate a RhoA/ROCK/Ezrin pathway at the ECM interface. PKCβII phosphorylates the apical identity-promoting Podocalyxin/NHERF1/Ezrin complex, removing Podocalyxin from the ECM-abutting cell surface and initiating its transcytosis to an apical membrane initiation site for lumen formation. Inhibition of this switch mechanism results in the retention of Podocalyxin at the ECM interface and the development instead of collective front-rear polarization and motility. Thus, ECM-derived signals control the morphogenesis of epithelial tissues by controlling the collective orientation of epithelial polarization. PMID:25307480

  10. Molecular Self-Assembly into One-Dimensional Nanostructures

    PubMed Central

    PALMER, LIAM C.; STUPP, SAMUEL I.

    2008-01-01

    CONSPECTUS Self-assembly of small molecules into one-dimensional nanostructures offers many potential applications in electronically and biologically active materials. The recent advances discussed in this Account demonstrate how researchers can use the fundamental principles of supramolecular chemistry to craft the size, shape, and internal structure of nanoscale objects. In each system described here, we used atomic force microscopy (AFM) and transmission electron microscopy (TEM) to study the assembly morphology. Circular dichroism, nuclear magnetic resonance, infrared, and optical spectroscopy provided additional information about the self-assembly behavior in solution at the molecular level. Dendron rod–coil molecules self-assemble into flat or helical ribbons. They can incorporate electronically conductive groups and can be mineralized with inorganic semiconductors. To understand the relative importance of each segment in forming the supramolecular structure, we synthetically modified the dendron, rod, and coil portions. The self-assembly depended on the generation number of the dendron, the number of hydrogen-bonding functions, and the length of the rod and coil segments. We formed chiral helices using a dendron–rod–coil molecule prepared from an enantiomerically enriched coil. Because helical nanostructures are important targets for use in biomaterials, nonlinear optics, and stereoselective catalysis, researchers would like to precisely control their shape and size. Tripeptide-containing peptide lipid molecules assemble into straight or twisted nanofibers in organic solvents. As seen by AFM, the sterics of bulky end groups can tune the helical pitch of these peptide lipid nanofibers in organic solvents. Furthermore, we demonstrated the potential for pitch control using trans-to-cis photoisomerization of a terminal azobenzene group. Other molecules called peptide amphiphiles (PAs) are known to assemble in water into cylindrical nanostructures that

  11. Molecular simulations of assembly of functionalized spherical nanoparticles

    NASA Astrophysics Data System (ADS)

    Seifpour, Arezou

    Precise assembly of nanoparticles is crucial for creating spatially engineered materials that can be used for photonics, photovoltaic, and metamaterials applications. One way to control nanoparticle assembly is by functionalizing the nanoparticle with ligands, such as polymers, DNA, and proteins, that can manipulate the interactions between the nanoparticles in the medium the particles are placed in. This thesis research aims to design ligands to provide a new route to the programmable assembly of nanoparticles. We first investigate using Monte Carlo simulation the effect of copolymer ligands on nanoparticle assembly. We first study a single nanoparticle grafted with many copolymer chains to understand how monomer sequence (e.g. alternating ABAB, or diblock AxBx) and chemistry of the copolymers affect the grafted chain conformation at various particle diameters, grafting densities, copolymer chain lengths, and monomer-monomer interactions in an implicit small molecule solvent. We find that the size of the grafted chain varies non-monotonically with increasing blockiness of the monomer sequence for a small particle diameter. From this first study, we selected the two sequences with the most different chain conformations---alternating and diblock---and studied the effect of the sequence and a range of monomer chemistries of the copolymer on the characteristics of assembly of multiple copolymer-functionalized nanoparticles. We find that the alternating sequence produces nanoclusters that are relatively isotropic, whereas diblock sequence tends to form anisotropic structures that are smaller and more compact when the block closer to the surface is attractive and larger loosely held together clusters when the outer block is attractive. Next, we conduct molecular dynamics simulations to study the effect of DNA ligands on nanoparticle assembly. Specifically we investigate the effect of grafted DNA strand composition (e.g. G/C content, placement and sequence) and

  12. Role of redox centre in charge transport investigated by novel self-assembled conjugated polymer molecular junctions

    NASA Astrophysics Data System (ADS)

    Wang, Zongrui; Dong, Huanli; Li, Tao; Hviid, Rune; Zou, Ye; Wei, Zhongming; Fu, Xiaolong; Wang, Erjing; Zhen, Yonggang; Nørgaard, Kasper; Laursen, Bo W.; Hu, Wenping

    2015-06-01

    Molecular electronics describes a field that seeks to implement electronic components made of molecular building blocks. To date, few studies have used conjugated polymers in molecular junctions despite the fact that they potentially transport charge more efficiently than the extensively investigated small-molecular systems. Here we report a novel type of molecular tunnelling junction exploring the use of conjugated polymers, which are self-assembled into ultrathin films in a distinguishable `planar' manner from the traditional vertically oriented small-molecule monolayers. Electrical measurements on the junctions reveal molecular-specific characteristics of the polymeric molecules in comparison with less conjugated small molecules. More significantly, we decorate redox-active functionality into polymeric backbones, demonstrating a key role of redox centre in the modulation of charge transport behaviour via energy level engineering and external stimuli, and implying the potential of employing tailor-made polymeric components as alternatives to small molecules for future molecular-scale electronics.

  13. Molecular assembly for high-performance bivalent nucleic acid inhibitor.

    PubMed

    Kim, Youngmi; Cao, Zehui; Tan, Weihong

    2008-04-15

    It is theorized that multivalent interaction can result in better affinity and selectivity than monovalent interaction in the design of high-performance ligands. Accordingly, biomolecular engineers are increasingly taking advantage of multivalent interactions to fabricate novel molecular assemblies, resulting in new functions for ligands or enhanced performance of existing ligands. Substantial efforts have been expended in using small molecules or epitopes of antibodies for designing multifunctional or better-performing ligands. However, few attempts to use nucleic acid aptamers as functional domains have been reported. In this study, we explore the design of bivalent nucleic acid ligands by using thrombin and its aptamers as the model by which to evaluate its functions. By assembling two thrombin-binding aptamers with optimized design parameters, this assembly has resulted in the successful development of a nucleic acid-based high-performance bivalent protein inhibitor. Our experimentation proved (i) that the simultaneous binding of two aptamers after linkage achieved 16.6-fold better inhibition efficiency than binding of the monovalent ligand and (ii) that such an improvement originated from changes in the kinetics of the binding interactions, with a k(off) rate approximately 1/50 as fast. In addition, the newly generated aptamer assembly is an excellent anticoagulant reagent when tested with different samples. Because this optimized ligand design offers a simple and noninvasive means of accomplishing higher performance from known functional aptamers, it holds promise as a potent antithrombin agent in the treatment of various diseases related to abnormal thrombin activities. PMID:18398007

  14. Molecular pathways for defect annihilation in directed self-assembly.

    PubMed

    Hur, Su-Mi; Thapar, Vikram; Ramírez-Hernández, Abelardo; Khaira, Gurdaman; Segal-Peretz, Tamar; Rincon-Delgadillo, Paulina A; Li, Weihua; Müller, Marcus; Nealey, Paul F; de Pablo, Juan J

    2015-11-17

    Over the last few years, the directed self-assembly of block copolymers by surface patterns has transitioned from academic curiosity to viable contender for commercial fabrication of next-generation nanocircuits by lithography. Recently, it has become apparent that kinetics, and not only thermodynamics, plays a key role for the ability of a polymeric material to self-assemble into a perfect, defect-free ordered state. Perfection, in this context, implies not more than one defect, with characteristic dimensions on the order of 5 nm, over a sample area as large as 100 cm(2). In this work, we identify the key pathways and the corresponding free energy barriers for eliminating defects, and we demonstrate that an extraordinarily large thermodynamic driving force is not necessarily sufficient for their removal. By adopting a concerted computational and experimental approach, we explain the molecular origins of these barriers and how they depend on material characteristics, and we propose strategies designed to overcome them. The validity of our conclusions for industrially relevant patterning processes is established by relying on instruments and assembly lines that are only available at state-of-the-art fabrication facilities, and, through this confluence of fundamental and applied research, we are able to discern the evolution of morphology at the smallest relevant length scales-a handful of nanometers-and present a view of defect annihilation in directed self-assembly at an unprecedented level of detail. PMID:26515095

  15. Molecular pathways for defect annihilation in directed self-assembly

    PubMed Central

    Hur, Su-Mi; Thapar, Vikram; Ramírez-Hernández, Abelardo; Khaira, Gurdaman; Segal-Peretz, Tamar; Rincon-Delgadillo, Paulina A.; Li, Weihua; Müller, Marcus; Nealey, Paul F.; de Pablo, Juan J.

    2015-01-01

    Over the last few years, the directed self-assembly of block copolymers by surface patterns has transitioned from academic curiosity to viable contender for commercial fabrication of next-generation nanocircuits by lithography. Recently, it has become apparent that kinetics, and not only thermodynamics, plays a key role for the ability of a polymeric material to self-assemble into a perfect, defect-free ordered state. Perfection, in this context, implies not more than one defect, with characteristic dimensions on the order of 5 nm, over a sample area as large as 100 cm2. In this work, we identify the key pathways and the corresponding free energy barriers for eliminating defects, and we demonstrate that an extraordinarily large thermodynamic driving force is not necessarily sufficient for their removal. By adopting a concerted computational and experimental approach, we explain the molecular origins of these barriers and how they depend on material characteristics, and we propose strategies designed to overcome them. The validity of our conclusions for industrially relevant patterning processes is established by relying on instruments and assembly lines that are only available at state-of-the-art fabrication facilities, and, through this confluence of fundamental and applied research, we are able to discern the evolution of morphology at the smallest relevant length scales—a handful of nanometers—and present a view of defect annihilation in directed self-assembly at an unprecedented level of detail. PMID:26515095

  16. Molecular pathways for defect annihilation in directed self-assembly.

    SciTech Connect

    Hur, Su-Mi; Thapar, Vikram; Ramirez-Hernandez, Abelardo; Khaira, Gurdaman S.; Segal-Peretz, Tamar; Rincon-Delgadillo, Paulina A.; Li, Weihua; Muller, Marcus; Nealey, Paul F.; de Pablo, Juan J.

    2015-11-17

    Over the last few years, the directed self-assembly of block copolymers by surface patterns has transitioned from academic curiosity to viable contender for commercial fabrication of next-generation nanocircuits by lithography. Recently, it has become apparent that kinetics, and not only thermodynamics, plays a key role for the ability of a polymeric material to self-assemble into a perfect, defect-free ordered state. Perfection, in this context, implies not more than one defect, with characteristic dimensions on the order of 5 nm, over a sample area as large as 100 cm2. In this work, we identify the key pathways and the corresponding free-energy barriers for eliminating defects, and we demonstrate that an extraordinarily large thermodynamic driving force is not necessarily sufficient for their removal. By adopting a concerted computational and experimental approach, we explain the molecular origins of these barriers, how they depend on material characteristics, and we propose strategies designed to over-come them. The validity of our conclusions for industrially-relevant patterning processes is established by relying on instruments and assembly lines that are only available at state-of-the-art fabrication facilities and, through this confluence of fundamental and applied research, we are able to discern the evolution of morphology at the smallest relevant length scales - a handful of nanometers -, and present a view of defect annihilation in directed self-assembly at an unprecedented level of detail.

  17. Molecular gated transistors: Role of self-assembled monolayers

    NASA Astrophysics Data System (ADS)

    Shaya, O.; Halpern, E.; Khamaisi, B.; Shaked, M.; Usherenko, Y.; Shalev, G.; Doron, A.; Levy, I.; Rosenwaks, Y.

    2010-07-01

    In order to understand the biosensing mechanism of field-effect based biosensors and optimize their performance, the effect of each of its molecular building block must be understood. In this work the gating effect of self-assembled linker molecules on field-effect transistor was studied in detail. We have combined Kelvin probe force microscopy, current-voltage measurements, capacitance-voltage measurements, equivalent circuit modeling and device simulations in order to trace the mechanism of silicon-on-insulator biological field-effect transistors. The measurements were conducted on the widely used linker molecules (3-aminopropyl)-trimethoxysilane (APTMS) and 11-aminoundecyl-triethoxysilane (AUTES), which were self-assembled on ozone activated silicon oxide surface covering the transistor channel. In a dry environment, the work function of the modified silicon oxide decreased by more than 1.5 eV, and the transistor threshold voltage increased by about 30 V following the self-assembly. A detailed analysis indicates that these changes are due to negative induced charges on the top dielectric layer, and an effective dipole due to the polar monolayer. However, the self-assembly did not change the silicon flat-band voltage when in contact with an electrolyte. This is attributed to electrostatic screening by the electrolyte.

  18. Molecular pathways for defect annihilation in directed self-assembly.

    DOE PAGESBeta

    Hur, Su-Mi; Thapar, Vikram; Ramirez-Hernandez, Abelardo; Khaira, Gurdaman S.; Segal-Peretz, Tamar; Rincon-Delgadillo, Paulina A.; Li, Weihua; Muller, Marcus; Nealey, Paul F.; de Pablo, Juan J.

    2015-11-17

    Over the last few years, the directed self-assembly of block copolymers by surface patterns has transitioned from academic curiosity to viable contender for commercial fabrication of next-generation nanocircuits by lithography. Recently, it has become apparent that kinetics, and not only thermodynamics, plays a key role for the ability of a polymeric material to self-assemble into a perfect, defect-free ordered state. Perfection, in this context, implies not more than one defect, with characteristic dimensions on the order of 5 nm, over a sample area as large as 100 cm2. In this work, we identify the key pathways and the corresponding free-energymore » barriers for eliminating defects, and we demonstrate that an extraordinarily large thermodynamic driving force is not necessarily sufficient for their removal. By adopting a concerted computational and experimental approach, we explain the molecular origins of these barriers, how they depend on material characteristics, and we propose strategies designed to over-come them. The validity of our conclusions for industrially-relevant patterning processes is established by relying on instruments and assembly lines that are only available at state-of-the-art fabrication facilities and, through this confluence of fundamental and applied research, we are able to discern the evolution of morphology at the smallest relevant length scales - a handful of nanometers -, and present a view of defect annihilation in directed self-assembly at an unprecedented level of detail.« less

  19. Stable doping of carbon nanotubes via molecular self assembly

    SciTech Connect

    Lee, B.; Chen, Y.; Podzorov, V.; Cook, A.; Zakhidov, A.

    2014-10-14

    We report a novel method for stable doping of carbon nanotubes (CNT) based on methods of molecular self assembly. A conformal growth of a self-assembled monolayer of fluoroalkyl trichloro-silane (FTS) at CNT surfaces results in a strong increase of the sheet conductivity of CNT electrodes by 60–300%, depending on the CNT chirality and composition. The charge carrier mobility of undoped partially aligned CNT films was independently estimated in a field-effect transistor geometry (~100 cm²V⁻¹s⁻¹). The hole density induced by the FTS monolayer in CNT sheets is estimated to be ~1.8 ×10¹⁴cm⁻². We also show that FTS doping of CNT anodes greatly improves the performance of organic solar cells. This large and stable doping effect, easily achieved in large-area samples, makes this approach very attractive for applications of CNTs in transparent and flexible electronics.

  20. Molecular assembly and organic film growth on complex intermetallic surfaces

    NASA Astrophysics Data System (ADS)

    Al-Mahboob, Abdullah; Sharma, Hem Raj; Sadowski, Jerzy T.; Ledieu, Julian; Fournée, Vincent; McGrath, Ronan

    We extensively studied the role of molecular symmetry and symmetry/structures of wide ranges of substrate-surfaces from non-periodic to periodic to quasi-crystalline in nucleation, growth and phase transition in films made of organic molecular materials. Recently, most interest in quasicrystals is due to the generalization of aperiodic ordering to several classes of systems. Compared to periodic materials, these provide a closer approximation to an isotropic first Brillouin zone, which is of great importance to the design of new functional materials. Here, we present results obtained from our ongoing study of interface mediated molecular assembly extended on complex intermetallic surfaces with specific examples of C60 and Zn-phthalocyanine on quasicrystalline and approximant surfaces. We employed in-situ real-time low-energy electron microscopy (LEEM) for investigation of the processes in assembly and film growth and post-growth STM study and DFT calculations to understand structural details and growth mechanism. Research were carried out in part at the Center for Functional Nanomaterials, Brookhaven National Lab, USA; partly at Institut Jean Lamour, Université de Lorraine, France; and partly at the Surface Science Research Centre, University of Liverpool, UK.

  1. Orientational disorder: A key to understand polarity of molecular crystals

    NASA Astrophysics Data System (ADS)

    Hulliger, J.; Brahimi, K.; Burgener, M.; Dulcevscaia, G.

    2014-12-01

    Polarity of molecular crystals is understood here as a result of 180° orientational disorder of asymmetrical building blocks. Symmetry arguments based on (i) a single rotational degree of freedom, (ii) the finite size of crystals and (iii) interactions in between asymmetrical molecules lead to the conclusion that such crystals should express a bi-polar (∞/∞m) average state of zero polarity. This basic property of molecular crystals is exemplified by forming solid solutions of 4-iodo-4‧-nitro-biphenyl (INBP) and symmetrical bi-phenyls (BP: A-π-A, D-π-D; A: acceptor; D: donor). Monte Carlo simulations based on a layer-by-layer growth model predict a reversal of the bi-polar state of pure INBP by forming a solid solution of (INBP)1-x(D-π-D)x. In the case of the addition of A-π-A reversal as found for pure INBP is promoted, i.e. needs less growth steps (layers) to be accomplished. Real crystals representing solid solutions were grown from 2-butanon solutions using symmetrical BPs. Scanning pyroelectric microscopy confirmed the qualitative behavior seen in Monte Carlo simulations. These findings represent an experimentum crucis supporting the general validity of the theory of stochastic polarity formation applied to single component or solid solution molecular crystals.

  2. 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.

  3. Nanostructure and molecular mechanics of spider dragline silk protein assemblies

    PubMed Central

    Keten, Sinan; Buehler, Markus J.

    2010-01-01

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

  4. Molecularly Oriented Polymeric Thin Films for Space Applications

    NASA Technical Reports Server (NTRS)

    Fay, Catharine C.; Stoakley, Diane M.; St.Clair, Anne K.

    1997-01-01

    The increased commitment from NASA and private industry to the exploration of outer space and the use of orbital instrumentation to monitor the earth has focused attention on organic polymeric materials for a variety of applications in space. Some polymeric materials have exhibited short-term (3-5 yr) space environmental durability; however, future spacecraft are being designed with lifetimes projected to be 10-30 years. This gives rise to concern that material property change brought about during operation may result in unpredicted spacecraft performance. Because of their inherent toughness and flexibility, low density, thermal stability, radiation resistance and mechanical strength, aromatic polyimides have excellent potential use as advanced materials on large space structures. Also, there exists a need for high temperature (200-300 C) stable, flexible polymeric films that have high optical transparency in the 300-600nm range of the electromagnetic spectrum. Polymers suitable for these space applications were fabricated and characterized. Additionally, these polymers were molecularly oriented to further enhance their dimensional stability, stiffness, elongation and strength. Both unoriented and oriented polymeric thin films were also cryogenically treated to temperatures below -184 C to show their stability in cold environments and determine any changes in material properties.

  5. Controllable Orientation of Ester-Group-Induced Intermolecular Halogen Bonding in a 2D Self-Assembly.

    PubMed

    Zha, Bao; Dong, Meiqiu; Miao, Xinrui; Miao, Kai; Hu, Yi; Wu, Yican; Xu, Li; Deng, Wenli

    2016-08-18

    Halogen bonding with high specificity and directionality in the geometry has proven to be an important type of noncovalent interaction to fabricate and control 2D molecular architectures on surfaces. Herein, we first report how the orientation of the ester substituent for thienophenanthrene derivatives (5,10-DBTD and 5,10-DITD) affects positive charge distribution of halogens by density functional theory, thus determining the formation of an intermolecular halogen bond and different self-assembled patterns by scanning tunneling microscopy. The system presented here mainly includes heterohalogen X···O═C and X···S halogen bonds, H···Br and H···O hydrogen bonds, and I···I interaction, where the directionality and strength of such weak bonds determine the molecular arrangement by varying the halogen substituent. This study provides a detailed understanding of the role of ester orientation, concentration, and solvent effects on the formation of halogen bonds and proves relevant for identification of multiple halogen bonding in supramolecular chemistry. PMID:27482936

  6. Dipolar Self-Assembling in Mixtures of Propylene Carbonate and Dimethyl Sulfoxide as Revealed by the Orientational Entropy.

    PubMed

    Płowaś, Iwona; Świergiel, Jolanta; Jadżyn, Jan

    2016-08-18

    This article presents the results of static dielectric studies performed on mixtures of two strongly polar liquids important from a technological point of view: propylene carbonate (PC) and dimethyl sulfoxide (DMSO). The dielectric data were analyzed in terms of the molar orientational entropy increment induced by the probing electric field. It was found that the two polar liquids in the neat state reveal quite different molecular organization in terms of dipole-dipole self-assembling: PC exhibits a dipolar coupling of the head-to-tail type, whereas in DMSO one observes extreme restriction of dipolar association in any form. In PC + DMSO mixtures, the disintegration of the dipolar ensembles of PC molecules takes place and the progress of that process is strictly proportional to the concentration of DMSO. The static permittivity of mixtures of such differently self-organized liquids exhibits a positive deviation from the additive rule and the deviation develops symmetrically within the concentration scale. PMID:27458791

  7. Molecular self assembly on optical fiber-based fluorescence sensor

    NASA Astrophysics Data System (ADS)

    Ayyagari, Madhu S. R.; Gao, Harry H.; Bihari, Bipin; Chittibabu, Kethinni G.; Kumar, Jayant; Marx, Kenneth A.; Kaplan, David L.; Tripathy, Sukant K.

    1994-03-01

    We discuss the molecular self-assembly on optical fibers in which a novel method for protein attachment to the sensing tip of the fiber is used. Our objective is to assemble a conjugated polythiophene copolymer as an attachment vehicle. Subsequent attachment of the photodynamic phycobiliprotein serves as the fluorescence probe element. Following our earlier experiments from Langmuir-Blodgett deposition of these polymeric materials as thin films on glass substrates, we extended the technique to optical fibers. First, the bare fiber surface is silanized with a C18 silane compound. The copolymer (3-undecylthiophene-co-3- methanolthiophene, biotinylated at the methanol moiety) assembly on the fiber is carried out presumable through van der Waals interactions between the hydrophobic fiber surface and the undecyl alkyl chains on the polymer backbone. A conjugated Str-PE (streptavidin covalently attached to phycoerythrin) complex is then attached to the copolymer via the conventional biotin-streptavidin interaction. The conjugated polymer not only supports the protein but, in principle, may help to transduce the signal generated by phycoerythrin to the fiber. Our results from fluorescence intensity measurements proved the efficacy of this system. An improved methodology is also sought to more strongly attach the conjugated copolymer to the fiber surface, and a covalent scheme is developed to polymerize and biotinylate polythiophene in situ on the fiber surface.

  8. 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

  9. Molecular mechanics methods for individual carbon nanotubes and nanotube assemblies

    NASA Astrophysics Data System (ADS)

    Eberhardt, Oliver; Wallmersperger, Thomas

    2015-04-01

    Since many years, carbon nanotubes (CNTs) have been considered for a wide range of applications due to their outstanding mechanical properties. CNTs are tubular structures, showing a graphene like hexagonal lattice. Our interest in the calculation of the mechanical properties is motivated by several applications which demand the knowledge of the material behavior. One application in which the knowledge of the material behavior is vital is the CNT based fiber. Due to the excellent stiffness and strength of the individual CNTs, these fibers are expected to be a promising successor for state of the art carbon fibers. However, the mechanical properties of the fibers fall back behind the properties of individual CNTs. It is assumed that this gap in the properties is a result of the van-der-Waals interactions of the individual CNTs within the fiber. In order to understand the mechanical behavior of the fibers we apply a molecular mechanics approach. The mechanical properties of the individual CNTs are investigated by using a modified structural molecular mechanics approach. This is done by calculating the properties of a truss-beam element framework representing the CNT with the help of a chemical force field. Furthermore, we also investigate the interactions of CNTs arranged in basic CNT assemblies, mimicking the ones in a simple CNT fiber. We consider the van-der-Waals interactions in the structure and calculate the potential surface of the CNT assemblies.

  10. Orientational dynamics of colloidal ribbons self-assembled from microscopic magnetic ellipsoids.

    PubMed

    Martinez-Pedrero, Fernando; Cebers, Andrejs; Tierno, Pietro

    2016-04-20

    We combine experiments and theory to investigate the orientational dynamics of dipolar ellipsoids, which self-assemble into elongated ribbon-like structures due to the presence of a permanent magnetic moment, perpendicular to the long axis in each particle. Monodisperse hematite ellipsoids are synthesized via the sol-gel technique and arrange into ribbons in the presence of static or time-dependent magnetic fields. We find that under an oscillating field, the ribbons reorient perpendicular to the field direction, in contrast with the behaviour observed under a static field. This observation is explained theoretically by treating a chain of interacting ellipsoids as a single particle with orientational and demagnetizing field energy. The model allows us to describe the orientational behaviour of the chain and captures well its dynamics at different strengths of the actuating field. The understanding of the complex dynamics and assembly of anisotropic magnetic colloids is a necessary step for controlling the structure formation, which has direct applications in different fluid-based microscale technologies. PMID:26936015

  11. 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.

  12. De Novo Transcriptome Assembly of Pummelo and Molecular Marker Development

    PubMed Central

    Liang, Mei; Yang, Xiaoming; Li, Hang; Su, Shiying; Yi, Hualin; Chai, Lijun; Deng, Xiuxin

    2015-01-01

    Pummelo (Citrus grandis) is an important fruit crop worldwide because of its nutritional value. To accelerate the pummelo breeding program, it is essential to obtain extensive genetic information and develop relative molecular markers. Here, we obtained a 12-Gb transcriptome dataset of pummelo through a mixture of RNA from seven tissues using Illumina pair-end sequencing, assembled into 57,212 unigenes with an average length of 1010 bp. The annotation and classification results showed that a total of 39,584 unigenes had similar hits to the known proteins of four public databases, and 31,501 were classified into 55 Gene Ontology (GO) functional sub-categories. The search for putative molecular markers among 57,212 unigenes identified 10,276 simple sequence repeats (SSRs) and 64,720 single nucleotide polymorphisms (SNPs). High-quality primers of 1174 SSR loci were designed, of which 88.16% were localized to nine chromosomes of sweet orange. Of 100 SSR primers that were randomly selected for testing, 87 successfully amplified clear banding patterns. Of these primers, 29 with a mean PIC (polymorphic information content) value of 0.52 were effectively applied for phylogenetic analysis. Of the 20 SNP primers, 14 primers, including 54 potential SNPs, yielded target amplifications, and 46 loci were verified via Sanger sequencing. This new dataset will be a valuable resource for molecular biology studies of pummelo and provides reliable information regarding SNP and SSR marker development, thus expediting the breeding program of pummelo. PMID:25799271

  13. Smart dust: self-assembling, self-orienting photonic crystals of porous Si.

    PubMed

    Link, Jamie R; Sailor, Michael J

    2003-09-16

    Micrometer-sized one-dimensional photonic crystals of porous Si that spontaneously assemble, orient, and sense their local environment are prepared. The photonic crystals are generated by electrochemically etching two discrete porous multilayered dielectric mirrors into Si, one on top of the other. The first mirror is chemically modified by hydrosilylation with dodecene before the etching of the second mirror, which is prepared with an optical reflectivity spectrum that is distinct from the first. The entire film is removed from the substrate, and the second mirror is then selectively modified by mild thermal oxidation. The films are subsequently fractured into small particles by sonication. The chemically asymmetric particles spontaneously align at an organic liquid-water interface, with the hydrophobic side oriented toward the organic phase and the hydrophilic side toward the water. Sensing is accomplished when liquid at the interface infuses into the porous mirrors, inducing predictable shifts in the optical spectra of both mirrors. PMID:12947036

  14. 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.

  15. A self-assembling lanthanide molecular nanoparticle for optical imaging†

    PubMed Central

    Brown, Katherine A.; Yang, Xiaoping; Schipper, Desmond; Hall, Justin W.; DePue, Lauren J.; Gnanam, Annie J.; Arambula, Jonathan F.; Jones, Jessica N.; Swaminathan, Jagannath; Dieye, Yakhya; Vadivelu, Jamuna; Chandler, Don J.; Marcotte, Edward M.; Sessler, Jonathan L.; Ehrlich, Lauren I. R.; Jones, Richard A.

    2015-01-01

    Chromophores that incorporate f-block elements have considerable potential for use in bioimaging applications because of their advantageous photophysical properties compared to organic dye, which are currently widely used. We are developing new classes of lanthanide-based self-assembling molecular nanoparticles as reporters for imaging and as multi-functional nanoprobes or nanosensors for use with biological samples. One class of these materials, which we call lanthanide “nano-drums”, are homogeneous 4d–4f clusters approximately 25 to 30 Å in diameter. These are capable of emitting from the visible to near-infrared wavelengths. Here, we present the synthesis, crystal structure, photophysical properties and comparative cytotoxicity data for a 32 metal Eu-Cd nano-drum [Eu8Cd24L12(OAc)48] (1). We also explored the imaging capabilities of this nano-drum using epifluorescence, TIRF, and two-photon microscopy platforms. PMID:25512085

  16. Advantages of Catalysis in Self-Assembled Molecular Capsules.

    PubMed

    Catti, Lorenzo; Zhang, Qi; Tiefenbacher, Konrad

    2016-06-27

    Control over the local chemical environment of a molecule can be achieved by encapsulation in supramolecular host systems. In supramolecular catalysis, this control is used to gain advantages over classical homogeneous catalysis in bulk solution. Two of the main advantages concern influencing reactions in terms of substrate and product selectivity. Due to size and/or shape recognition, substrate selective conversion can be realized. Additionally, noncovalent interactions with the host environment facilitate alternative reaction pathways and can yield unusual products. This Concept article discusses and highlights literature examples utilizing self-assembled molecular capsules to achieve catalytic transformations displaying a high degree of substrate and/or product selectivity. Furthermore, the advantage of supramolecular hosts in multicatalyst tandem reactions is covered. PMID:27150251

  17. Self-assembled molecular corrals on a semiconductor surface

    NASA Astrophysics Data System (ADS)

    Dobrin, S.; Harikumar, K. R.; Jones, R. V.; Li, N.; McNab, I. R.; Polanyi, J. C.; Sloan, P. A.; Waqar, Z.; Yang, J.(S. Y.); Ayissi, S.; Hofer, W. A.

    2006-03-01

    Nano-corrals for capturing surface electrons are of interest in molecular electronics. Here we show that haloalkane molecules, e.g., 1-chlorododecane, physisorbed on Si(1 1 1)-(7 × 7) self-assemble to form dimers stable to 100 °C which corral silicon adatoms. Corral size is shown to be governed by the haloalkane chain-length. Spectroscopic and theoretical evidence shows that the haloalkane dimer induces electron transfer to the corralled adatom, shifting its energy levels by ˜1 eV. Isolation of a labile pre-cursor points to a model for corral formation which combines mobility with immobility; monomers diffusing in a mobile vertical state meet and convert to the immobile horizontal dimers constituting the corrals.

  18. Structural Assembly of Molecular Complexes Based on Residual Dipolar Couplings

    PubMed Central

    Berlin, Konstantin; O’Leary, Dianne P.; Fushman, David

    2010-01-01

    We present and evaluate a rigid-body molecular docking method, called PATIDOCK, that relies solely on the three-dimensional structure of the individual components and the experimentally derived residual dipolar couplings (RDC) for the complex. We show that, given an accurate ab initio predictor of the alignment tensor from a protein structure, it is possible to accurately assemble a protein-protein complex by utilizing the RDC’s sensitivity to molecular shape to guide the docking. The proposed docking method is robust against experimental errors in the RDCs and computationally efficient. We analyze the accuracy and efficiency of this method using experimental or synthetic RDC data for several proteins, as well as synthetic data for a large variety of protein-protein complexes. We also test our method on two protein systems for which the structure of the complex and steric-alignment data are available (Lys48-linked diubiquitin and a complex of ubiquitin and a ubiquitin-associated domain) and analyze the effect of flexible unstructured tails on the outcome of docking. The results demonstrate that it is fundamentally possible to assemble a protein-protein complex based solely on experimental RDC data and the prediction of the alignment tensor from three-dimensional structures. Thus, despite the purely angular nature of residual dipolar couplings, they can be converted into intermolecular distance/translational constraints. Additionally we show a method for combining RDCs with other experimental data, such as ambiguous constraints from interface mapping, to further improve structure characterization of the protein complexes. PMID:20550109

  19. Topological defects in liquid crystals as templates for molecular self-assembly

    NASA Astrophysics Data System (ADS)

    Wang, Xiaoguang; Miller, Daniel S.; Bukusoglu, Emre; de Pablo, Juan J.; Abbott, Nicholas L.

    2016-01-01

    Topological defects in liquid crystals (LCs) have been widely used to organize colloidal dispersions and template polymerization, leading to a range of assemblies, elastomers and gels. However, little is understood about molecular-level assembly processes within defects. Here, we report 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, we observed signatures of molecular self-assembly of amphiphilic molecules in topological defects, including cooperativity, reversibility and controlled growth. We also show that nanoscopic o-rings synthesized from Saturn-ring disclinations and other molecular assemblies templated by defects can be preserved by using photocrosslinkable amphiphiles. Our results reveal that, in analogy to other classes of macromolecular templates such as polymer-surfactant complexes, topological defects in LCs are a versatile class of three-dimensional, dynamic and reconfigurable templates that can direct processes of molecular self-assembly.

  20. Self-Assembly of Graphene Single Crystals with Uniform Size and Orientation: The First 2D Super-Ordered Structure.

    PubMed

    Zeng, Mengqi; Wang, Lingxiang; Liu, Jinxin; Zhang, Tao; Xue, Haifeng; Xiao, Yao; Qin, Zhihui; Fu, Lei

    2016-06-29

    The challenges facing the rapid developments of highly integrated electronics, photonics, and microelectromechanical systems suggest that effective fabrication technologies are urgently needed to produce ordered structures using components with high performance potential. Inspired by the spontaneous organization of molecular units into ordered structures by noncovalent interactions, we succeed for the first time in synthesizing a two-dimensional superordered structure (2DSOS). As demonstrated by graphene, the 2DSOS was prepared via self-assembly of high-quality graphene single crystals under mutual electrostatic force between the adjacent crystals assisted by airflow-induced hydrodynamic forces at the liquid metal surface. The as-obtained 2DSOS exhibits tunable periodicity in the crystal space and outstanding uniformity in size and orientation. Moreover, the intrinsic property of each building block is preserved. With simplicity, scalability, and continuously adjustable feature size, the presented approach may open new territory for the precise assembly of 2D atomic crystals and facilitate its application in structurally derived integrated systems. PMID:27313075

  1. SHG microscopy excited by polarization controlled beam for three-dimensional molecular orientation measurement

    NASA Astrophysics Data System (ADS)

    Yoshiki, K.; Hashimoto, M.; Araki, T.

    2006-08-01

    We have developed a second-harmonic-generation (SGH) microscope to observe the three-dimensional molecular orientation with three-dimensional high spatial resolution using a polarization mode converter. The mode converter consists of a parallel-aligned nematic-liquid-crystal spatial-light-modulator (PAL-SLM) and quarter-waveplates, and converts a incident linearly polarized beam to orthogonal linearly polarized beams or radially polarized beam. We combined the mode converter with SHG microscope to obtain the local information of the three-dimensional molecular orientation. We demonstrated the detection of three-dimensional molecular orientation of collagen fiber in human Achilles' tendon. For high precision three-dimensional molecular orientation measurement, we propose a technique to calibrate the dependence of SHG detection efficiencies on molecular orientation using a liposome.

  2. Applications of molecular self-assembly in tissue engineering

    NASA Astrophysics Data System (ADS)

    Harrington, Daniel Anton

    This thesis studied the application of three self-assembling molecular systems, as potential biomaterials for tissue engineering applications. Cholesteryl-(L-lactic acid)n molecules form thermotropic liquid crystals, which could be coated onto the inner and outer pores of biodegradable PLLA scaffolds, while retaining the lamellar order of the neat material. Primary bovine chondrocytes were cultured on these structures, demonstrating improved attachment and extended retention of phenotype on the C-LA-coated scaffolds. No difference in fibronectin adsorption to C-LA and PLLA surfaces was observed, suggesting a strong role for cholesterol in influencing cell phenotype. A family of peptide-amphiphiles, bearing the "RGD" adhesion sequence from fibronectin, was also assessed in the contexts of cartilage and bladder repair. These molecules self-assemble into one-dimensional fibers, with diameters of 6--8 nm, and lengths of 500 nm or greater. Chondrocytes were seeded and cultured on covalently-crosslinked PA gels and embedded within calcium-triggered PA gels. Cells became dormant over time, but remained viable, suggesting an inappropriate display of the adhesion sequence to cells. A family of "branched" PA molecules with lysine dendron headgroups was designed, in an effort to increase the spatial separation between molecules in the assembled state, and to theoretically improve epitope accessibility. These molecules coated reliably onto PGA fiber scaffolds, and dramatically increased the attachment of human bladder smooth muscle cells, possibly through better epitope display or electrostatic attraction. They also formed strong gels with several negatively-charged biologically-relevant macromolecules. In a third system, amphiphilic segmented dendrimers based on phenylene vinylene and L-lysine entered cells through an endocytic pathway with no discernible toxic effect on cell proliferation or morphology. These amphiphiles formed complex aggregates in aqueous solution, likely

  3. Estimation of the mutual orientation and intermolecular interaction of C12Ex from molecular dynamics simulations.

    PubMed

    Velinova, Maria; Tsoneva, Yana; Ivanova, Anela; Tadjer, Alia

    2012-04-26

    Nonionic surfactants, such as poly(ethylene glycol) alkyl ethers (abbreviated as CyEx) show a rich phase behavior in aqueous solution, i.e., they form micellar, lamellar, cubic, and so forth phases depending on experimental parameters such as the hydrophobic and hydrophilic chain lengths, temperature, or concentration. The aim of the present study is to determine the nature of the preaggregates, which are inferred to exist before the actual self-assembly process in aqueous solution, and to assess the aptitude to their formation. The target molecules are C12E3, C12E4 and C12E5, surfactants of moderate water solubility. Coarse-grained and all-atom molecular dynamics simulations (NPT/293 K) of two molecules of each species with explicit water in periodic boundary conditions are carried out to estimate the mutual orientation and the interaction between the surfactants in their dimers. The force fields are MARTINI and Amber99, the latter with self-derived parameters for the ether groups. The change in the orientation and distance between the molecules in the dimers are discussed based on different structural parameters. In addition, the interaction between the surfactants is evaluated from quantum chemistry calculations in terms of binding energy for the average structures from the cluster analysis. The solvent-solute interaction is quantified by the mean number of hydrogen bonds formed between them. On the basis of combined analysis, a series of different structures for subsequent study of the possible self-assembly patterns of C12E3, C12E4, and C12E5 is outlined. PMID:22448734

  4. Directed self-assembly of mesoscopic electronic components into sparse arrays with controlled orientation using diamagnetic levitation

    NASA Astrophysics Data System (ADS)

    Tkachenko, Anton; Lu, James J.-Q.

    2015-07-01

    This paper presents a directed self-assembly (DSA) approach for assembling small electronic components, such as semiconductor dies, into sparse 2D arrays using diamagnetic levitation. The dies attached to a diamagnetic layer can be levitated at a room temperature over a stage made of magnets arranged in a checkerboard pattern. By selecting a proper die design, levitation height, and vibration pattern of the magnetic stage we assemble the dies into a regular 2D array with a specific lateral and vertical orientation of the dies. The assembled dies are transferred to a receiving substrate using capillary force.

  5. Structural investigations of surfaces and orientation-specific phenomena in nanocrystals and their assemblies

    NASA Astrophysics Data System (ADS)

    Aruguete, Deborah Michiko

    Studies of colloidal nanocrystals and their assemblies are presented. Two of these studies concern the atomic-level structural characterization of the surfaces, interfaces, and interiors present in II-VI semiconductor nanorods. The third study investigates the crystallographic arrangement of cobalt nanocrystals in self-assembled aggregates. Crystallographically-aligned assemblies of colloidal CdSe nanorods are examined with linearly-polarized Se-EXAFS spectroscopy, which probes bonding along different directions in the nanorod. This orientation-specific probe is used, because it is expected that the presence of specific surfaces in a nanorod might cause bond relaxations specific to different crystallographic directions. Se-Se distances are found to be contracted along the long axis of the nanorod, while Cd-Se distances display no angular dependence, which is different from the bulk. Ab-initio density functional theory calculations upon CdSe nanowires indicate that relaxations on the rod surfaces cause these changes. ZnS/CdS-CdSe core-shell nanorods are studied with Se, Zn, Cd, and S X-ray absorption spectroscopy (XAS). It is hypothesized that there are two major factors influencing the core and shell structures of the nanorods: the large surface area-to-volume ratio, and epitaxial strain. The presence of the surface may induce bond rearrangements or relaxations to minimize surface energy, epitaxial strain might cause the core and shell lattices to contract or expand to minimize strain energy. A marked contraction of Zn-S bonds is observed in the core-shell nanorods, indicating that surface relaxations may dominate the structure of the nanorod (strain might otherwise drive the Zn-S lattice to accommodate the larger US or CdSe lattices via bond expansion). EXAFS and X-ray diffraction (XRD) indicate that Cd-Se bond relaxations might be anisotropic, an expected phenomenon for a rod-shaped nanocrystal. Ordered self-assembled aggregates of cobalt nanocrystals are

  6. Structural Investigations of Surfaces and Orientation-SpecificPhenomena in Nanocrystals and Their Assemblies

    SciTech Connect

    Aruguete, Deborah Michiko

    2006-06-17

    Studies of colloidal nanocrystals and their assemblies are presented. Two of these studies concern the atomic-level structural characterization of the surfaces, interfaces, and interiors present in II-VI semiconductor nanorods. The third study investigates the crystallographic arrangement of cobalt nanocrystals in self-assembled aggregates. Crystallographically-aligned assemblies of colloidal CdSe nanorods are examined with linearly-polarized Se-EXAFS spectroscopy, which probes bonding along different directions in the nanorod. This orientation-specific probe is used, because it is expected that the presence of specific surfaces in a nanorod might cause bond relaxations specific to different crystallographic directions. Se-Se distances are found to be contracted along the long axis of the nanorod, while Cd-Se distances display no angular dependence, which is different from the bulk. Ab-initio density functional theory calculations upon CdSe nanowires indicate that relaxations on the rod surfaces cause these changes. ZnS/CdS-CdSe core-shell nanorods are studied with Se, Zn, Cd, and S X-ray absorption spectroscopy (XAS). It is hypothesized that there are two major factors influencing the core and shell structures of the nanorods: the large surface area-to-volume ratio, and epitaxial strain. The presence of the surface may induce bond rearrangements or relaxations to minimize surface energy; epitaxial strain might cause the core and shell lattices to contract or expand to minimize strain energy. A marked contraction of Zn-S bonds is observed in the core-shell nanorods, indicating that surface relaxations may dominate the structure of the nanorod (strain might otherwise drive the Zn-S lattice to accommodate the larger CdS or CdSe lattices via bond expansion). EXAFS and X-ray diffraction (XRD) indicate that Cd-Se bond relaxations might be anisotropic, an expected phenomenon for a rod-shaped nanocrystal. Ordered self-assembled aggregates of cobalt nanocrystals are

  7. Molecular relaxations, molecular orientation, and the friction characteristics of polyimide films. [wear characteristics of polymeric lubricant

    NASA Technical Reports Server (NTRS)

    Fusaro, R. L.

    1975-01-01

    The friction characteristics of polyimide films bonded to metallic substrates were studied from 25 to 500 C. These results were interpreted in terms of molecular orientation and thermomechanical data obtained by torsional braid analysis (TBA). A large friction transition was found to occur at 40 + or - 10 C in a dry argon atmosphere (10 ppm H2O). It was postulated that the mechanical stresses of sliding transform or reorder the molecules on the surface into a configuration conducive to easy shear, such as an extended chain. The molecular relaxation which occurs in this temperature region appears to give the molecules the necessary freedom for this reordering process to occur. The effects of velocity, reversibility, and thermal prehistory on the friction properties of polyimide were also studied.

  8. Self-assembly of multilevel branched rutile-type TiO2 structures via oriented lateral and twin attachment

    NASA Astrophysics Data System (ADS)

    Jordan, Vanja; Javornik, Uroš; Plavec, Janez; Podgornik, Aleš; Rečnik, Aleksander

    2016-04-01

    Recent breakthrough of novel hierarchic materials, orchestrated through oriented attachment of crystal subunits, opened questions on what is the mechanism of their self-assembly. Using rutile-type TiO2, synthesized by hydrothermal reaction of Ti(IV)-butoxide in highly acidic aqueous medium, we uncovered the key processes controlling this nonclassical crystallization process. Formation of complex branched mesocrystals of rutile is accomplished by oriented assembly of precipitated fibers along the two low-energy planes, i.e. {110} and {101}, resulting in lateral attachment and twinning. Phase analysis of amorphous material enclosed in pockets between imperfectly assembled rutile fibers clearly shows harmonic ordering resembling that of the adjacent rutile structure. To our understanding this may be the first experimental evidence indicating the presence of electromagnetic force-fields that convey critical structural information through which oriented attachment of nanocrystals is made possible.

  9. Self-assembly of multilevel branched rutile-type TiO2 structures via oriented lateral and twin attachment

    PubMed Central

    Jordan, Vanja; Javornik, Uroš; Plavec, Janez; Podgornik, Aleš; Rečnik, Aleksander

    2016-01-01

    Recent breakthrough of novel hierarchic materials, orchestrated through oriented attachment of crystal subunits, opened questions on what is the mechanism of their self-assembly. Using rutile-type TiO2, synthesized by hydrothermal reaction of Ti(IV)-butoxide in highly acidic aqueous medium, we uncovered the key processes controlling this nonclassical crystallization process. Formation of complex branched mesocrystals of rutile is accomplished by oriented assembly of precipitated fibers along the two low-energy planes, i.e. {110} and {101}, resulting in lateral attachment and twinning. Phase analysis of amorphous material enclosed in pockets between imperfectly assembled rutile fibers clearly shows harmonic ordering resembling that of the adjacent rutile structure. To our understanding this may be the first experimental evidence indicating the presence of electromagnetic force-fields that convey critical structural information through which oriented attachment of nanocrystals is made possible. PMID:27063110

  10. Molecular self-assembly for biological investigations and nanoscale lithography

    NASA Astrophysics Data System (ADS)

    Cheunkar, Sarawut

    Small, diffusible molecules when recognized by their binding partners, such as proteins and antibodies, trigger enzymatic activity, cell communication, and immune response. Progress in analytical methods enabling detection, characterization, and visualization of biological dynamics at the molecular level will advance our exploration of complex biological systems. In this dissertation, analytical platforms were fabricated to capture membrane-associated receptors, which are essential proteins in cell signaling pathways. The neurotransmitter serotonin and its biological precursor were immobilized on gold substrates coated with self-assembled monolayers (SAMs) of oligo(ethylene glycol)alkanethiols and their reactive derivatives. The SAM-coated substrates present the biologically selective affinity of immobilized molecules to target native membrane-associated receptors. These substrates were also tested for biospecificity using antibodies. In addition, small-molecule-functionalized platforms, expressing neurotransmitter pharmacophores, were employed to examine kinetic interactions between G-protein-coupled receptors and their associated neurotransmitters. The binding interactions were monitored using a quartz crystal microbalance equipped with liquid-flow injection. The interaction kinetics of G-protein-coupled serotonin 1A receptor and 5-hydroxytyptophan-functionalized surfaces were studied in a real-time, label-free environment. Key binding parameters, such as equilibrium dissociation constants, binding rate constants, and dissociative half-life, were extracted. These parameters are critical for understanding and comparing biomolecular interactions in modern biomedical research. By integrating self-assembly, surface functionalization, and nanofabrication, small-molecule microarrays were created for high-throughput screening. A hybrid soft-lithography, called microcontact insertion printing, was used to pattern small molecules at the dilute scales necessary for highly

  11. Molecular Architecture of  Yeast Chromatin Assembly Factor 1.

    PubMed

    Kim, Daegeun; Setiaputra, Dheva; Jung, Taeyang; Chung, Jaehee; Leitner, Alexander; Yoon, Jungmin; Aebersold, Ruedi; Hebert, Hans; Yip, Calvin K; Song, Ji-Joon

    2016-01-01

    Chromatin Assembly Complex 1 (CAF-1) is a major histone chaperone involved in deposition of histone H3 and H4 into nucleosome. CAF-1 is composed of three subunits; p150, p60 and p48 for human and Cac1, Cac2 and Cac3 for yeast. Despite of its central role in chromatin formation, structural features of the full CAF-1 in complex with histones and other chaperones have not been well characterized. Here, we dissect molecular architecture of yeast CAF-1 (yCAF-1) by cross-linking mass spectrometry (XL-MS) and negative stain single-particle electron microscopy (EM). Our work revealed that Cac1, the largest subunit of yCAF-1, might serve as a major histone binding platform linking Cac2 and Cac3. In addition, EM analysis showed that yCAF-1 adopts a bilobal shape and Cac1 connecting Cac2 and Cac3 to generate a platform for binding histones. This study provides the first structural glimpse of the full CAF-1 complex and a structural framework to understand histone chaperoning processes. PMID:27221973

  12. Gold nanoparticles assembled with dithiocarbamate-anchored molecular wires.

    PubMed

    Reeler, Nini E A; Lerstrup, Knud A; Somerville, Walter; Speder, Jozsef; Petersen, Søren V; Laursen, Bo W; Arenz, Matthias; Qiu, Xiaohui; Vosch, Tom; Nørgaard, Kasper

    2015-01-01

    A protocol for the bottom-up self-assembly of nanogaps is developed through molecular linking of gold nanoparticles (AuNPs). Two π-conjugated oligo(phenylene ethynylene) molecules (OPE) with dithiocarbamate anchoring groups are used as ligands for the AuNPs. OPE-4S with a dithiocarbamate in each end of the molecule and a reference molecule OPE-2S with only a single dithiocarbamate end group. The linking mechanism of OPE-4S is investigated by using a combination of TEM, UV-Vis absorption and surface enhanced Raman spectroscopy (SERS) as well as studying the effect of varying the OPE-4S to AuNP concentration ratio. UV-Vis absorption confirms the formation of AuNP aggregates by the appearance of an extended plasmon band (EPB) for which the red shift and intensity depend on the OPE-4S:AuNP ratio. SERS confirms the presence of OPE-4S and shows a gradual increase of the signal intensity with increasing OPE-4S:AuNP ratios up to a ratio of about 4000, after which the SERS intensity does not increase significantly. For OPE-2S, no linking is observed below full coverage of the AuNPs indicating that the observed aggregate formation at high OPE-2S:AuNP ratios, above full AuNP coverage, is most likely of a physical nature (van der Waals forces or π-π interactions). PMID:26471461

  13. Gold nanoparticles assembled with dithiocarbamate-anchored molecular wires

    PubMed Central

    Reeler, Nini E. A.; Lerstrup, Knud A.; Somerville, Walter; Speder, Jozsef; Petersen, Søren V.; Laursen, Bo W.; Arenz, Matthias; Qiu, Xiaohui; Vosch, Tom; Nørgaard, Kasper

    2015-01-01

    A protocol for the bottom-up self-assembly of nanogaps is developed through molecular linking of gold nanoparticles (AuNPs). Two π-conjugated oligo(phenylene ethynylene) molecules (OPE) with dithiocarbamate anchoring groups are used as ligands for the AuNPs. OPE-4S with a dithiocarbamate in each end of the molecule and a reference molecule OPE-2S with only a single dithiocarbamate end group. The linking mechanism of OPE-4S is investigated by using a combination of TEM, UV-Vis absorption and surface enhanced Raman spectroscopy (SERS) as well as studying the effect of varying the OPE-4S to AuNP concentration ratio. UV-Vis absorption confirms the formation of AuNP aggregates by the appearance of an extended plasmon band (EPB) for which the red shift and intensity depend on the OPE-4S:AuNP ratio. SERS confirms the presence of OPE-4S and shows a gradual increase of the signal intensity with increasing OPE-4S:AuNP ratios up to a ratio of about 4000, after which the SERS intensity does not increase significantly. For OPE-2S, no linking is observed below full coverage of the AuNPs indicating that the observed aggregate formation at high OPE-2S:AuNP ratios, above full AuNP coverage, is most likely of a physical nature (van der Waals forces or π-π interactions). PMID:26471461

  14. Molecular Architecture of  Yeast Chromatin Assembly Factor 1

    PubMed Central

    Kim, Daegeun; Setiaputra, Dheva; Jung, Taeyang; Chung, Jaehee; Leitner, Alexander; Yoon, Jungmin; Aebersold, Ruedi; Hebert, Hans; Yip, Calvin K.; Song, Ji-Joon

    2016-01-01

    Chromatin Assembly Complex 1 (CAF-1) is a major histone chaperone involved in deposition of histone H3 and H4 into nucleosome. CAF-1 is composed of three subunits; p150, p60 and p48 for human and Cac1, Cac2 and Cac3 for yeast. Despite of its central role in chromatin formation, structural features of the full CAF-1 in complex with histones and other chaperones have not been well characterized. Here, we dissect molecular architecture of yeast CAF-1 (yCAF-1) by cross-linking mass spectrometry (XL-MS) and negative stain single-particle electron microscopy (EM). Our work revealed that Cac1, the largest subunit of yCAF-1, might serve as a major histone binding platform linking Cac2 and Cac3. In addition, EM analysis showed that yCAF-1 adopts a bilobal shape and Cac1 connecting Cac2 and Cac3 to generate a platform for binding histones. This study provides the first structural glimpse of the full CAF-1 complex and a structural framework to understand histone chaperoning processes. PMID:27221973

  15. Controlling Molecular Motion, Assembly and Coupling as a Step towards Molecular Actuators

    NASA Astrophysics Data System (ADS)

    Murphy, Colin James

    changes in the supramolecular self-assembly of thioethers. Chapter 9 details how the ordering and length of surface-bound hydrogen-bonded chains of methanol are dictated by the underlying surface and examines an unreported chiral meta-stable methanol hexamer. Single-molecule measurements can answer many of the current questions in the field of molecular machines and lead to control of molecular motion. Development of mechanisms to direct molecular motion and to couple this motion to external systems is crucial for the rational design of new molecular machinery with functionalities such as mass transport, propulsion, separations, sensing, signaling and chemical reactions.

  16. Molecular Composite Coatings on Nafion Using Layer-by-Layer Self-Assembly.

    PubMed

    Lefaux, Christophe J; Kim, Byoung-Suhk; Venkat, Narayanan; Mather, Patrick T

    2015-05-20

    Controlled growth of nanometer-scale multilayered coatings of negatively charged sulfonated poly(benzobisimidazole) (SPBI), complexed with positively charged poly(2-vinylpyridine) (P2VP) on quartz, and Nafion membrane as substrates has been explored. Both polymers, SPBI and P2VP, possess a net charge in methanol as a result of the dissolution of SPBI by complexation with triethylamine (TEA) and the protonation of P2VP with HCl, respectively, and thereby can form a multilayered molecular composite of alternating anionic SPBI and cationic P2VP via an electrostatic layer-by-layer (LbL) self-assembly. UV-vis absorption spectrophotometry was used to monitor the buildup and growth rate of such SPBI/P2VP multilayer films. Atomic force microscopy (AFM) was used to determine the roughness and thickness of the resulting SPBI/P2VP multilayers. As a result, it was found that a steady-state linear growth regime for the LbL self-assembled SPBI/P2VP multilayer films and coatings onto quartz and Nafion membranes was observed after completion of the first few deposition cycles, indicating the successful formation of the SPBI/P2VP multilayered assembly in methanol solutions. In addition, the SPBI/P2VP multilayer films in the perpendicular direction (flat view) demonstrated isotropic orientation distribution on the Nafion membrane, while the SPBI/P2VP multilayer films examined by X-ray scattering in the parallel direction (edge view) revealed anisotropic orientation, the combined observations indicating confinement of SPBI rods to the plane of the coating. We further found that the SPBI/P2VP multilayer coated Nafion possesses good thermal stability, as indicated by isothermal gravimetric analysis at 310 °C, and it was further observed that SPBI/P2VP multilayer coatings using the LbL self-assembly technique on Nafion membrane significantly increased the membrane stiffness, despite the small coating thickness employed. PMID:25923689

  17. Etomica: an object-oriented framework for molecular simulation.

    PubMed

    Schultz, Andrew J; Kofke, David A

    2015-03-30

    We describe the design of an object-oriented library of software components that are suitable for constructing simulations of systems of interacting particles. The emphasis of the discussion is on the general design of the components and how they interact, and less on details of the programming interface or its implementation. Example code is provided as an aid to understanding object-oriented programming structures and to demonstrate how the framework is applied. PMID:25565378

  18. Oriented assembled TiO2 hierarchical nanowire arrays with fast electron transport properties.

    PubMed

    Sheng, Xia; He, Dongqing; Yang, Jie; Zhu, Kai; Feng, Xinjian

    2014-01-01

    Developing high surface area nanostructured electrodes with rapid charge transport is essential for artificial photosynthesis, solar cells, photocatalysis, and energy storage devices. Substantial research efforts have been recently focused on building one-dimensional (1D) nanoblocks with fast charge transport into three-dimensional (3D) hierarchical architectures. However, except for the enlargement in surface area, there is little experimental evidence of fast electron transport in these 3D nanostructure-based solar cells. In this communication, we report single-crystal-like 3D TiO2 branched nanowire arrays consisting of 1D branch epitaxially grown from the primary trunk. These 3D branched nanoarrays not only demonstrate 71% enlargement in large surface area (compared with 1D nanowire arrays) but also exhibit fast charge transport property (comparable to that in 1D single crystal nanoarrays), leading to 52% improvement in solar conversion efficiency. The orientated 3D assembly strategy reported here can be extended to assemble other metal oxides with one or multiple components and thus represents a critical avenue toward high-performance optoelectronics. PMID:24628675

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

    PubMed

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

    2016-04-01

    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]styryl-benzene (DSA-Ph) in mixtures with aluminum-tris(8-hydroxyquinoline) (Alq3) by spectroscopic ellipsometry and IR dichroism. We find that molecular orientation is controlled by the ratio of the substrate temperature during deposition and the glass transition temperature of the mixture. 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. PMID:26922903

  20. 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. PMID:23005623

  1. Oriented growth of porphyrin-based molecular wires on ionic crystals analysed by nc-AFM

    PubMed Central

    Zimmerli, Lars; Kawai, Shigeki; Meyer, Ernst; Fendt, Leslie-Anne; Diederich, Francois

    2011-01-01

    Summary The growth of molecular assemblies at room temperature on insulating surfaces is one of the main goals in the field of molecular electronics. Recently, the directed growth of porphyrin-based molecular wires on KBr(001) was presented. The molecule–surface interaction associated with a strong dipole moment of the molecules was sufficient to bind them to the surface; while a stabilization of the molecular assemblies was reached due to the intermolecular interaction by π–π binding. Here, we show that the atomic structure of the substrate can control the direction of the wires and consequently, complex molecular assemblies can be formed. The electronic decoupling of the molecules by one or two monolayers of KBr from the Cu(111) substrate is found to be insufficient to enable comparable growth conditions to bulk ionic materials. PMID:21977413

  2. Influence of spherical assembly of copper ferrite nanoparticles on magnetic properties: orientation of magnetic easy axis.

    PubMed

    Chatterjee, Biplab K; Bhattacharjee, Kaustav; Dey, Abhishek; Ghosh, Chandan K; Chattopadhyay, Kalyan K

    2014-06-01

    The magnetic properties of copper ferrite (CuFe2O4) nanoparticles prepared via sol-gel auto combustion and facile solvothermal method are studied focusing on the effect of nanoparticle arrangement. Randomly oriented CuFe2O4 nanoparticles (NP) are obtained from the sol-gel auto combustion method, while the solvothermal method allows us to prepare iso-oriented uniform spherical ensembles of CuFe2O4 nanoparticles (NS). X-ray diffractometry (XRD), atomic absorption spectroscopy (AAS), infra-red (IR) spectroscopy, Raman spectroscopy, scanning electron microscopy (SEM), transmission electron microscopy (TEM), (57)Fe Mössbauer spectroscopy and vibrating sample magnetometer (VSM) are used to investigate the composition, microstructure and magnetic properties of as-prepared ferrite nanoparticles. The field-dependent magnetization measurement for the NS sample at low temperature exhibits a step-like rectangular hysteresis loop (M(R)/M(S) ~ 1), suggesting cubic anisotropy in the system, whereas for the NP sample, typical features of uniaxial anisotropy (M(R)/M(S) ~ 0.5) are observed. The coercive field (HC) for the NS sample shows anomalous temperature dependence, which is correlated with the variation of effective anisotropy (K(E)) of the system. A high-temperature enhancement of H(C) and K(E) for the NS sample coincides with a strong spin-orbit coupling in the sample as evidenced by significant modification of Cu/Fe-O bond distances. The spherical arrangement of nanocrystals at mesoscopic scale provokes a high degree of alignment of the magnetic easy axis along the applied field leading to a step-like rectangular hysteresis loop. A detailed study on the temperature dependence of magnetic anisotropy of the system is carried out, emphasizing the influence of the formation of spherical iso-oriented assemblies. PMID:24714977

  3. Examples of Molecular Self-Assembly at Surfaces.

    PubMed

    Whitelam, Stephen

    2015-10-14

    The self-assembly of molecules at surfaces can be caused by a range of physical mechanisms. Assembly can be driven by intermolecular forces, or molecule-surface forces, or both; it can result in structures that are in equilibrium or that are kinetically trapped. Here we review examples of self-assembly at surfaces focusing on a physical understanding of what causes patterns seen in experiment. Some apparently disparate systems can be described in similar physical terms, indicating that simple factors - such as the geometry and energy scale of intermolecular binding - are key to understanding the self-assembly of those systems. PMID:25873520

  4. Molecular microbial diversity of a spacecraft assembly facility

    NASA Technical Reports Server (NTRS)

    Venkateswaran, K.; Satomi, M.; Chung, S.; Kern, R.; Koukol, R.; Basic, C.; White, D.

    2001-01-01

    In ongoing investigations to map and archive the microbial footprints in various components of the spacecraft and its accessories, we have examined the microbial populations of the Jet Propulsion Laboratory's Spacecraft Assembly Facility (JPL-SAF). Witness plates made up of spacecraft materials, some painted with spacecraft qualified paints, were exposed for approximately 7 to 9 months at JPL-SAF and examined the particulate materials collected for the incidence of total cultivable aerobic heterotrophs and heat-tolerant (80 degrees C for 15-min.) spore-formers. The results showed that the witness plates coated with spacecraft qualified paints attracted more dust particles than the non-coated stainless steel witness plates. Among the four paints tested, witness plates coated with NS43G accumulated the highest number of particles, and hence attracted more cultivable microbes. The conventional microbiological examination revealed that the JPL-SAF harbors mainly Gram-positive microbes and mostly spore-forming Bacillus species. Most of the isolated microbes were heat resistant to 80 degrees C and proliferate at 60 degrees C. The phylogenetic relationships among 23 cultivable heat-tolerant microbes were examined using a battery of morphological, physiological, molecular and chemotaxonomic characterizations. By 16S rDNA sequence analysis, the isolates fell into seven clades: Bacillus licheniformis, B. pumilus, B. cereus, B. circulans, Staphylococcus capitis, Planococcus sp. and Micrococcus lylae. In contrast to the cultivable approach, direct DNA isolation, cloning and 16S rDNA sequencing analysis revealed equal representation of both Gram-positive and Gram-negative microorganisms.

  5. Nanoimprint-Induced Molecular Orientation in Semiconducting Polymer Nanostructures

    SciTech Connect

    Hlaing, H.; Ocko, B.; Lu, X.; Hofmann, T.; Yager, K.G.; Black, C.T.

    2011-09-01

    The morphology and orientation of thin films of the polymer poly-3(hexylthiophene) - important parameters influencing electronic and photovoltaic device performance - have been significantly altered through nanoimprinting with 100 nm spaced grooves. Grazing-incidence small-angle X-ray scattering studies demonstrate the excellent fidelity of the pattern transfer, while wide-angle scattering convincingly shows an imprinting-induced {pi}-{pi} reorientation and polymer backbone alignment along the imprinted grooves. Surprisingly, temperature-dependent scattering measurements indicate that the imprinted induced orientation and alignment remain intact even at temperatures where the imprinted topographical features nearly vanish.

  6. Ordered nanocolumn-array organic semiconductor thin films with controllable molecular orientation

    NASA Astrophysics Data System (ADS)

    Yang, Bingchu; Duan, Haichao; Zhou, Conghua; Gao, Yongli; Yang, Junliang

    2013-12-01

    Ordered nanocolumn-array phthalocynine semiconductor thin films with controllable molecular orientation were fabricated by combining molecular template growth (MTG) and glancing angle deposition (GLAD) techniques. The pre-deposited planar perylene-3,4,9,10-tetracarboxylic-3,4,9,10-dianhydride (PTCDA) molecular template layer induces phthalocynine molecules arrange with a lying-down molecular orientation, in which the π-π stacking is vertical to the substrate improving the charge transport along the vertical direction; While the GLAD technique supports the formation of nanocolumn-array thin films, supplying a much larger exposed surface area than the conventional compact thin films. The ordered nanocolumn-array thin films with controllable molecular orientation fabricated by combining MTG and GLAD techniques show the potentials to fabricate ordered bulk heterojunction for improving the performance in organic photovoltaics.

  7. Molecular orientation effect on the differential cross sections for the electron-impact double ionization of oriented water molecules

    SciTech Connect

    Champion, C.; Dal Cappello, C.; Oubaziz, D.; Aouchiche, H.; Popov, Yu. V.

    2010-03-15

    Double ionization of isolated water molecules fixed in space is here investigated in a theoretical approach based on the first Born approximation. Secondary electron angular distributions are reported for particular (e,3e) kinematical conditions and compared in terms of shape and magnitude. Strong dependence of the fivefold differential cross sections on the molecular target orientation is clearly observed in (e,3-1e) as well as (e,3e) channels. Furthermore, for the major part of the kinematics considered, we identified the different mechanisms involved in the double ionization of water molecule, namely, the direct shake-off process as well as the two-step1 process. They are both discussed and analyzed with respect to the molecular target orientation.

  8. Contesting Discrimination Based on Sexual Orientation at the ICAE Sixth World Assembly: "Difference" Is a Fundamental Human Right."

    ERIC Educational Resources Information Center

    Hill, Robert J.

    2001-01-01

    Gives a brief history of the field of international adult education regarding sexual orientation, including events at the Sixth World Assembly. Presents 13 strategies for the elimination of homophobia and discrimination. Asserts that difference is a fundamental human right. (Contains 26 references.) (SK)

  9. Propargyl Vinyl Ethers and Tertiary Skipped Diynes: Two Pluripotent Molecular Platforms for Diversity-Oriented Synthesis.

    PubMed

    Tejedor, David; López-Tosco, Sara; Méndez-Abt, Gabriela; Cotos, Leandro; García-Tellado, Fernando

    2016-04-19

    During the last years, we have been involved in the development of a diversity-oriented synthetic strategy aimed at transforming simple, linear, and densely functionalized molecular platforms into collections of topologically diverse scaffolds incorporating biologically relevant structural motifs such as N- and O- heterocycles, multifunctionalized aromatic rings, fused macrocycles, etc. The strategy merges the concepts of pluripotency (the property of an array of chemical functionalities to express different chemical outcomes under different chemical environments) and domino chemistry (chemistry based on processes involving two or more bond-forming transformations that take place while the initial reaction conditions are maintained, with the subsequent reaction resulting as a consequence of the functionality installed in the previous one) to transform common multifunctional substrates into complex and diverse molecular frameworks. This design concept constitutes the ethos of the so-called branching cascade strategy, a branch of diversity-oriented synthesis focused on scaffold diversity generation. Two pluripotent molecular platforms have been extensively studied under this merging (branching) paradigm: C4-O-C3 propargyl vinyl ethers (PVEs) and C7 tertiary skipped diynes (TSDs). These are conveniently constructed from simple and commercially available raw materials (alkyl propiolates, ketones, aldehydes, acid chlorides) through multicomponent manifolds (ABB' three-component reaction for PVEs; A2BB' four-component reaction for TSDs) or a simple two-step procedure (for PVEs). Their modular origin facilitates their structural/functional diversification without increasing the number of synthetic steps for their assembly. These two pluripotent molecular platforms accommodate a well-defined and dense array of through-bond/through-space interrelated functionalities on their structures, which defines their primary reactivity principles and establishes the reactivity profile

  10. An energy investigation into 1D/2D oriented-attachment assemblies of 1D Ag nanocrystals.

    PubMed

    Lv, Weiqiang; Yang, Xuemei; Wang, Wei; Niu, Yinghua; Liu, Zhongping; He, Weidong

    2014-09-15

    In the field of oriented-attachment crystal growth, one-dimensional nanocrystals are frequently employed as building blocks to synthesize two-dimensional or large-aspect-ratio one-dimensional nanocrystals. Despite recent extensive experimental advances, the underlying inter-particle interaction in the synthesis still remains elusive. In this report, using Ag as a platform, we investigate the van der Waals interactions associated with the side-by-side and end-to-end assemblies of one-dimensional nanorods. The size, aspect ratio, and inter-particle separation of the Ag precursor nanorods are found to have dramatically different impacts on the van der Waals interactions in the two types of assemblies. Our work facilitates the fundamental understanding of the oriented-attachment assembling mechanism based on one-dimensional nanocrystals. PMID:24954815

  11. Role of ionization in orientation dependence of molecular high-order harmonic generation

    NASA Astrophysics Data System (ADS)

    Chen, Y. J.; Hu, Bambi

    2009-12-01

    We investigate the orientation dependence of high-order harmonic generation (HHG) from O2 and CO2 molecules using the strong-field approximation (SFA). Our simulations reveal the important modulation of the ionization to the HHG orientation dependence, especially at larger orientation angles. By virtue of a simplified model arising from the SFA, we show that this modulation can be read from the harmonic order where the HHG spectra at different orientation angles intersect. These results give suggestions on probing the molecular structure and dynamics using HHG.

  12. Vapor deposition of a smectic liquid crystal: highly anisotropic, homogeneous glasses with tunable molecular orientation.

    PubMed

    Gómez, Jaritza; Jiang, Jing; Gujral, Ankit; Huang, Chengbin; Yu, Lian; Ediger, M D

    2016-03-01

    Physical vapor deposition (PVD) has been used to prepare glasses of itraconazole, a smectic A liquid crystal. Glasses were deposited onto subtrates at a range of temperatures (Tsubstrate) near the glass transition temperature (Tg), with Tsubstrate/Tg ranging from 0.70 to 1.02. Infrared spectroscopy and spectroscopic ellipsometry were used to characterize the molecular orientation using the orientational order parameter, Sz, and the birefringence. We find that the molecules in glasses deposited at Tsubstrate = Tg are nearly perpendicular to the substrate (Sz = +0.66) while at lower Tsubstrate molecules are nearly parallel to the substrate (Sz = -0.45). The molecular orientation depends on the temperature of the substrate during preparation, allowing layered samples with differing orientations to be readily prepared. In addition, these vapor-deposited glasses are macroscopically homogeneous and 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. Vapor deposition of liquid crystals is likely a general approach for the preparation of highly anisotropic glasses with tunable molecular orientation for use in organic electronics and optoelectronics. PMID:26875700

  13. Ultrafast Electron Transfer at Organic Semiconductor Interfaces: Importance of Molecular Orientation.

    PubMed

    Ayzner, Alexander L; Nordlund, Dennis; Kim, Do-Hwan; Bao, Zhenan; Toney, Michael F

    2015-01-01

    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 C60 acceptor yields a rate that is 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. PMID:26263084

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

    DOE PAGESBeta

    Ayzner, Alexander L.; Nordlund, Dennis; Kim, Do -Hwan; Bao, Zhenan; Toney, Michael F.

    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 C60 acceptor yields a rate that is approximatelymore » 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

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

    SciTech Connect

    Ayzner, Alexander L.; Nordlund, Dennis; Kim, Do -Hwan; Bao, Zhenan; Toney, Michael F.

    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 C60 acceptor yields a rate that is 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.

  16. Quantitative Sum-Frequency Generation Vibrational Spectroscopy of Molecular Surfaces and Interfaces: Lineshape, Polarization and Orientation

    SciTech Connect

    Wang, Hongfei; Velarde, Luis; Gan, Wei; Fu, Li

    2015-04-01

    Sum-frequency generation vibrational spectroscopy (SFG) can provide detailed information and understanding of molecular vibrational spectroscopy, orientational and conformational structure, and interactions of molecular surfaces and interfaces, through quantitative measurement and analysis. In this review, we present the current status and discuss the main developments on the measurement of intrinsic SFG spectral lineshape, formulations for polarization measurement and orientation analysis of the SFG-VS spectra. The main focus is to present a coherent formulation and discuss the main concepts or issues that can help to make SFG-VS a quantitative analytical and research tool in revealing the chemistry and physics of complex molecular surface and interface.

  17. Computer Simulation for Molecular Orientation of Vanadyl Phthalocyanine in Epitaxial Form

    NASA Astrophysics Data System (ADS)

    Tada, Hirokazu; Mashiko, Shinro

    1995-07-01

    Molecular orientation of vanadyl phthalocyanine (VOPc) adsorbed on KBr and KCl was studied by molecular mechanics simulation. A VOPc molecule with an oxygen atom oriented upward with respect to the substrate surface was found to be more stable than that oriented downward. The central vanadium atom preferred to stay on potassium cations rather than on halogen anions, which is contrary to our expectation. The lattices optimized in this study agree well with the experimental results. In the epitaxial form on KBr and KCl, the angle between the [100] axis of the substrates and the molecular axis passing through two bridge-nitrogen atoms was 39° and 45°, respectively. The dovetail molecular packing was observed on KCl, while some voids existed between molecules in the optimized packing on KBr.

  18. Topological defects in liquid crystals as templates for molecular self-assembly

    NASA Astrophysics Data System (ADS)

    Wang, Xiaoguang; Miller, Daniel; Bukusoglu, Emre; de Pablo, Juan; Abbott, Nicholas

    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 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 can direct processes of molecular self-assembly in a manner that is strongly analogous to other classes of macromolecular templates.

  19. Influence of solute-solvent coordination on the orientational relaxation of ion assemblies in polar solvents

    NASA Astrophysics Data System (ADS)

    Ji, Minbiao; Hartsock, Robert W.; Sung, Zheng; Gaffney, Kelly J.

    2012-01-01

    We have investigated the rotational dynamics of lithium thiocyanate (LiNCS) dissolved in various polar solvents with time and polarization resolved vibrational spectroscopy. LiNCS forms multiple distinct ionic structures in solution that can be distinguished with the CN stretch vibrational frequency of the different ionic assemblies. By varying the solvent and the LiNCS concentration, the number and type of ionic structures present in solution can be controlled. Control of the ionic structure provides control over the volume, shape, and dipole moment of the solute, critical parameters for hydrodynamic and dielectric continuum models of friction. The use of solutes with sizes comparable to or smaller than the solvent molecules also helps amplify the sensitivity of the measurement to the short-ranged solute-solvent interaction. The measured orientational relaxation dynamics show many clear and distinct deviations from simple hydrodynamic behavior. All ionic structures in all solvents exhibit multi-exponential relaxation dynamics that do not scale with the solute volume. For Lewis base solvents such as benzonitrile, dimethyl carbonate, and ethyl acetate, the observed dynamics strongly show the effect of solute-solvent complex formation. For the weak Lewis base solvent nitromethane, we see no evidence for solute-solvent complex formation, but still see strong deviation from the predictions of simple hydrodynamic theory.

  20. Universality and specificity in molecular orientation in anisotropic gels prepared by diffusion method.

    PubMed

    Maki, Yasuyuki; Furusawa, Kazuya; Yasuraoka, Sho; Okamura, Hideki; Hosoya, Natsuki; Sunaga, Mari; Dobashi, Toshiaki; Sugimoto, Yasunobu; Wakabayashi, Katsuzo

    2014-08-01

    Molecular orientation in anisotropic gels of chitosan, Curdlan and DNA obtained by dialysis of those aqueous solutions in gelation-inducing solutions was investigated. In this diffusion method (or dialysis method), the gel formation was induced by letting small molecules diffuse in or out of the polymer solutions through the surface. For the gels of DNA and chitosan, the polymer chains aligned perpendicular to the diffusion direction. The same direction of molecular orientation was observed for the Curdlan gel prepared in the dialysis cell. On the other hand, a peculiar nature was observed for the Curdlan gel prepared in the dialysis tube: the molecular orientation was perpendicular to the diffusion direction in the outermost layer of the gel, while the orientation was parallel to the diffusion direction in the inner translucent layer. The orientation parallel to the diffusion direction is attributed to a small deformation of the inner translucent layer caused by a slight shrinkage of the central region after the gel formation. At least near the surface of the gel, the molecular orientation perpendicular to the diffusion direction is a universal characteristic for the gels prepared by the diffusion method. PMID:24751255

  1. Bulk and Surface Molecular Orientation Distribution in Injection-molded Liquid Crystalline Polymers: Experiment and Simulation

    SciTech Connect

    Fang, J.; Burghardt, W; Bubeck, R; Burgard, S; Fischer, D

    2010-01-01

    Bulk and surface distributions of molecular orientation in injection-molded plaques of thermotropic liquid crystalline polymers (TLCPs) have been studied using a combination of techniques, coordinated with process simulations using the Larson-Doi 'polydomain' model. Wide-angle X-ray scattering was used to map out the bulk orientation distribution. Fourier Transform Infrared Attenuated Total Reflectance (FTIR-ATR) and Near-Edge X-ray Absorption Fine Structure (NEXAFS) were utilized to probe the molecular orientation states to within about {approx}5 {micro}m and {approx}2 nm, respectively, of the sample surface. These noninvasive, surface-sensitive techniques yield reasonable self-consistency, providing complementary validation of the robustness of these methods. An analogy between Larson-Doi and fiber orientation models has allowed the first simulations of TLCP injection molding. The simulations capture many fine details in the bulk orientation distribution across the sample plaque. Direct simulation of surface orientation at the level probed by FTIR-ATR and NEXAFS was not possible due to the limited spatial resolution of the simulations. However, simulation results extracted from the shear-dominant skin region are found to provide a qualitatively accurate indicator of surface orientation. Finally, simulations capture the relation between bulk and surface orientation states across the different regions of the sample plaque.

  2. Polyribosomes Are Molecular 3D Nanoprinters That Orchestrate the Assembly of Vault Particles

    PubMed Central

    2014-01-01

    Ribosomes are molecular machines that function in polyribosome complexes to translate genetic information, guide the synthesis of polypeptides, and modulate the folding of nascent proteins. Here, we report a surprising function for polyribosomes as a result of a systematic examination of the assembly of a large ribonucleoprotein complex, the vault particle. Structural and functional evidence points to a model of vault assembly whereby the polyribosome acts like a 3D nanoprinter to direct the ordered translation and assembly of the multi-subunit vault homopolymer, a process which we refer to as polyribosome templating. Structure-based mutagenesis and cell-free in vitro expression studies further demonstrated the critical importance of the polyribosome in vault assembly. Polyribosome templating prevents chaos by ensuring efficiency and order in the production of large homopolymeric protein structures in the crowded cellular environment and might explain the origin of many polyribosome-associated molecular assemblies inside the cell. PMID:25354757

  3. Regulating the Rate of Molecular Self-Assembly for Targeting Cancer Cells.

    PubMed

    Zhou, Jie; Du, Xuewen; Xu, Bing

    2016-05-01

    Besides tight and specific ligand-receptor interactions, the rate regulation of the formation of molecular assemblies is one of fundamental features of cells. But the latter receives little exploration for developing anticancer therapeutics. Here we show that a simple molecular design of the substrates of phosphatases-tailoring the number of phosphates on peptidic substrates-is able to regulate the rate of molecular self-assembly of the enzyme reaction product. Such a rate regulation allows selective inhibition of osteosarcoma cells over hepatocytes, which promises to target cancer cells in a specific organ. Moreover, our result reveals that the direct measurement of the rate of the self-assembly in a cell-based assay provides precise assessment of the cell targeting capability of self-assembly. This work, as the first report establishing rate regulation of a multiple-step process to inhibit cells selectively, illustrates a fundamentally new approach for controlling the fate of cells. PMID:27062481

  4. Topological defects in liquid crystals as templates for molecular self-assembly.

    PubMed

    Wang, Xiaoguang; Miller, Daniel S; Bukusoglu, Emre; de Pablo, Juan J; Abbott, Nicholas L

    2016-01-01

    Topological defects in liquid crystals (LCs) have been widely used to organize colloidal dispersions and template polymerization, leading to a range of assemblies, elastomers and gels. However, little is understood about molecular-level assembly processes within defects. Here, we report 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, we observed signatures of molecular self-assembly of amphiphilic molecules in topological defects, including cooperativity, reversibility and controlled growth. We also show that nanoscopic o-rings synthesized from Saturn-ring disclinations and other molecular assemblies templated by defects can be preserved by using photocrosslinkable amphiphiles. Our results reveal that, in analogy to other classes of macromolecular templates such as polymer-surfactant complexes, topological defects in LCs are a versatile class of three-dimensional, dynamic and reconfigurable templates that can direct processes of molecular self-assembly. PMID:26390324

  5. Zebrafish vimentin: molecular characterization, assembly properties and developmental expression.

    PubMed

    Cerdà, J; Conrad, M; Markl, J; Brand, M; Herrmann, H

    1998-11-01

    To provide a basis for the investigation of the intermediate filament (IF) protein vimentin in one of the most promising experimental vertebrate systems, the zebrafish (Danio rerio), we have isolated a cDNA clone of high sequence identity to and with the characteristic features of human vimentin. Using this clone we produced recombinant zebrafish vimentin and studied its assembly behaviour. Unlike other vimentins, zebrafish vimentin formed unusually thick filaments when assembled at temperatures below 21 degrees C. At 37 degrees C few filaments were observed, which often also terminated in aggregated masses, indicating that its assembly was severely disturbed at this temperature. Between 21 and 34 degrees C apparently normal IFs were generated. By viscometry, the temperature optimum of assembly was determined to be around 28 degrees C. At this temperature, zebrafish vimentin partially rescued, in mixing experiments, the temperature-dependent assembly defect of trout vimentin. Therefore it is apparently able to "instruct" the misorganized trout vimentin such that it can enter normal IFs. This feature, that assembly is best at the normal body temperature of various species, puts more weight on the assumption that vimentin is vital for some aspects of generating functional adult tissues. Remarkably, like in most other vertebrates, zebrafish vimentin appears to be an abundant factor in the lens and the retina as well as transiently, during development, in various parts of the central and peripheral nervous system. Therefore, promising cell biological investigations may now be performed with cells involved in the generation of the vertebrate eye and brain, and, in particular, the retina. Moreover, the power of genetics of the zebrafish system may be employed to investigate functional properties of vimentin in vivo. PMID:9860133

  6. StrateGene: object-oriented programming in molecular biology.

    PubMed

    Carhart, R E; Cash, H D; Moore, J F

    1988-03-01

    This paper describes some of the ways that object-oriented programming methodologies have been used to represent and manipulate biological information in a working application. When running on a Xerox 1100 series computer, StrateGene functions as a genetic engineering workstation for the management of information about cloning experiments. It represents biological molecules, enzymes, fragments, and methods as classes, subclasses, and members in a hierarchy of objects. These objects may have various attributes, which themselves can be defined and classified. The attributes and their values can be passed from the classes of objects down to the subclasses and members. The user can modify the objects and their attributes while using them. New knowledge and changes to the system can be incorporated relatively easily. The operations on the biological objects are associated with the objects themselves. This makes it easier to invoke them correctly and allows generic operations to be customized for the particular object. PMID:3164229

  7. Photoreactive self-assembled monolayer for the stabilization of tilt orientation of a director in vertically aligned nematic liquid crystals.

    PubMed

    Oh, Su Yeon; Kang, Shin-Woong

    2013-12-16

    Photo-reactive self-assembled monolayer (PR-SAM) is employed to mediate alignment of liquid crystals (LC) and stabilize the tilt orientation of a nematic director for a vertically aligned liquid crystal. Bifunctional PR-SAM formed by silane coupling reaction to oxide surfaces efficiently induces a homeotropic alignment and stabilizes LC director by the photo-polymerization under applied electric field. As a result, the substantial enhancement of electro-optic performance has been achieved after the PR-SAM assisted stabilization of tilt orientation of director. This approach for pretilt stabilization has multifarious advantages over the conventional PSVA. PMID:24514711

  8. Molecular Arrangement in Self-Assembled Azobenzene-Containing Thiol Monolayers at the Individual Domain Level Studied through Polarized Near-Field Raman Spectroscopy

    PubMed Central

    Chaigneau, Marc; Picardi, Gennaro; Ossikovski, Razvigor

    2011-01-01

    6-[4-(phenylazo)phenoxy]hexane-1-thiol self-assembled monolayers deposited on a gold surface form domain-like structures possessing a high degree of order with virtually all the molecules being identically oriented with respect to the surface plane. We show that, by using polarized near-field Raman spectroscopy, it is possible to derive the Raman scattering tensor of the ordered layer and consequently, the in-plane molecular orientation at the individual domain level. More generally, this study extends the application domain of the near-field Raman scattering selection rules from crystals to ordered organic structures. PMID:21541056

  9. Molecular Self-Assembly Strategy for Generating Catalytic Hybrid Polypeptides

    PubMed Central

    Ikezoe, Yasuhiro; Pike, Douglas H.; Nanda, Vikas; Matsui, Hiroshi

    2016-01-01

    Recently, catalytic peptides were introduced that mimicked protease activities and showed promising selectivity of products even in organic solvents where protease cannot perform well. However, their catalytic efficiency was extremely low compared to natural enzyme counterparts presumably due to the lack of stable tertiary fold. We hypothesized that assembling these peptides along with simple hydrophobic pockets, mimicking enzyme active sites, could enhance the catalytic activity. Here we fused the sequence of catalytic peptide CP4, capable of protease and esterase-like activities, into a short amyloidogenic peptide fragment of Aβ. When the fused CP4-Aβ construct assembled into antiparallel β-sheets and amyloid fibrils, a 4.0-fold increase in the hydrolysis rate of p-nitrophenyl acetate (p-NPA) compared to neat CP4 peptide was observed. The enhanced catalytic activity of CP4-Aβ assembly could be explained both by pre-organization of a catalytically competent Ser-His-acid triad and hydrophobic stabilization of a bound substrate between the triad and p-NPA, indicating that a design strategy for self-assembled peptides is important to accomplish the desired functionality. PMID:27116246

  10. Molecular self-assembly strategy for generating catalytic hybrid polypeptides

    DOE PAGESBeta

    Maeda, Yoshiaki; Fang, Justin; Ikezoe, Yasuhiro; Pike, Douglas H.; Nanda, Vikas; Matsui, Hiroshi

    2016-04-26

    Recently, catalytic peptides were introduced that mimicked protease activities and showed promising selectivity of products even in organic solvents where protease cannot perform well. However, their catalytic efficiency was extremely low compared to natural enzyme counterparts presumably due to the lack of stable tertiary fold. We hypothesized that assembling these peptides along with simple hydrophobic pockets, mimicking enzyme active sites, could enhance the catalytic activity. Here we fused the sequence of catalytic peptide CP4, capable of protease and esterase-like activities, into a short amyloidogenic peptide fragment of Aβ. When the fused CP4-Aβ construct assembled into antiparallel β- sheets and amyloidmore » fibrils, a 4.0-fold increase in the hydrolysis rate of p-nitrophenyl acetate (p-NPA) compared to neat CP4 peptide was observed. Furthermore, the enhanced catalytic activity of CP4-Aβ assembly could be explained both by pre-organization of a catalytically competent Ser-His-acid triad and hydrophobic stabilization of a bound substrate between the triad and p-NPA, indicating that a design strategy for self-assembled peptides is important to accomplish the desired functionality.« less

  11. Molecular Self-Assembly Strategy for Generating Catalytic Hybrid Polypeptides.

    PubMed

    Maeda, Yoshiaki; Fang, Justin; Ikezoe, Yasuhiro; Pike, Douglas H; Nanda, Vikas; Matsui, Hiroshi

    2016-01-01

    Recently, catalytic peptides were introduced that mimicked protease activities and showed promising selectivity of products even in organic solvents where protease cannot perform well. However, their catalytic efficiency was extremely low compared to natural enzyme counterparts presumably due to the lack of stable tertiary fold. We hypothesized that assembling these peptides along with simple hydrophobic pockets, mimicking enzyme active sites, could enhance the catalytic activity. Here we fused the sequence of catalytic peptide CP4, capable of protease and esterase-like activities, into a short amyloidogenic peptide fragment of Aβ. When the fused CP4-Aβ construct assembled into antiparallel β-sheets and amyloid fibrils, a 4.0-fold increase in the hydrolysis rate of p-nitrophenyl acetate (p-NPA) compared to neat CP4 peptide was observed. The enhanced catalytic activity of CP4-Aβ assembly could be explained both by pre-organization of a catalytically competent Ser-His-acid triad and hydrophobic stabilization of a bound substrate between the triad and p-NPA, indicating that a design strategy for self-assembled peptides is important to accomplish the desired functionality. PMID:27116246

  12. Molecular Assemblies, Genes and Genomics Integrated Efficiently (MAGGIE)

    SciTech Connect

    Baliga, Nitin S

    2011-05-26

    Final report on MAGGIE. We set ambitious goals to model the functions of individual organisms and their community from molecular to systems scale. These scientific goals are driving the development of sophisticated algorithms to analyze large amounts of experimental measurements made using high throughput technologies to explain and predict how the environment influences biological function at multiple scales and how the microbial systems in turn modify the environment. By experimentally evaluating predictions made using these models we will test the degree to which our quantitative multiscale understanding wilt help to rationally steer individual microbes and their communities towards specific tasks. Towards this end we have made substantial progress towards understanding evolution of gene families, transcriptional structures, detailed structures of keystone molecular assemblies (proteins and complexes), protein interactions, biological networks, microbial interactions, and community structure. Using comparative analysis we have tracked the evolutionary history of gene functions to understand how novel functions evolve. One level up, we have used proteomics data, high-resolution genome tiling microarrays, and 5' RNA sequencing to revise genome annotations, discover new genes including ncRNAs, and map dynamically changing operon structures of five model organisms: For Desulfovibrio vulgaris Hildenborough, Pyrococcus furiosis, Sulfolobus solfataricus, Methanococcus maripaludis and Haiobacterium salinarum NROL We have developed machine learning algorithms to accurately identify protein interactions at a near-zero false positive rate from noisy data generated using tagfess complex purification, TAP purification, and analysis of membrane complexes. Combining other genome-scale datasets produced by ENIGMA (in particular, microarray data) and available from literature we have been able to achieve a true positive rate as high as 65% at almost zero false positives when

  13. Crystal orientation mechanism of ZnTe epilayers formed on different orientations of sapphire substrates by molecular beam epitaxy

    SciTech Connect

    Nakasu, T. Yamashita, S.; Aiba, T.; Hattori, S.; Sun, W.; Taguri, K.; Kazami, F.; Kobayashi, M.

    2014-10-28

    The electrooptic effect in ZnTe has recently attracted research attention, and various device structures using ZnTe have been explored. For application to practical terahertz wave detector devices based on ZnTe thin films, sapphire substrates are preferred because they enable the optical path alignment to be simplified. ZnTe/sapphire heterostructures were focused upon, and ZnTe epilayers were prepared on highly mismatched sapphire substrates by molecular beam epitaxy. Epitaxial relationships between the ZnTe thin films and the sapphire substrates with their various orientations were investigated using an X-ray diffraction pole figure method. (0001) c-plane, (1-102) r-plane, (1-100) m-plane, and (11-20) a-plane oriented sapphire substrates were used in this study. The epitaxial relationship between ZnTe and c-plane sapphire was found to be (111) ZnTe//(0001) sapphire with an in-plane orientation relationship of [−211] ZnTe//[1-100] sapphire. It was found that the (211)-plane ZnTe layer was grown on the m-plane of the sapphire substrates, and the (100)-plane ZnTe layer was grown on the r-plane sapphire. When the sapphire substrates were inclined from the c-plane towards the m-axis direction, the orientation of the ZnTe thin films was then tilted from the (111)-plane to the (211)-plane. The c-plane of the sapphire substrates governs the formation of the (111) ZnTe domain and the ZnTe epilayer orientation. These crystallographic features were also related to the atom arrangements of ZnTe and sapphire.

  14. Crystal orientation mechanism of ZnTe epilayers formed on different orientations of sapphire substrates by molecular beam epitaxy

    NASA Astrophysics Data System (ADS)

    Nakasu, T.; Yamashita, S.; Aiba, T.; Hattori, S.; Sun, W.; Taguri, K.; Kazami, F.; Kobayashi, M.

    2014-10-01

    The electrooptic effect in ZnTe has recently attracted research attention, and various device structures using ZnTe have been explored. For application to practical terahertz wave detector devices based on ZnTe thin films, sapphire substrates are preferred because they enable the optical path alignment to be simplified. ZnTe/sapphire heterostructures were focused upon, and ZnTe epilayers were prepared on highly mismatched sapphire substrates by molecular beam epitaxy. Epitaxial relationships between the ZnTe thin films and the sapphire substrates with their various orientations were investigated using an X-ray diffraction pole figure method. (0001) c-plane, (1-102) r-plane, (1-100) m-plane, and (11-20) a-plane oriented sapphire substrates were used in this study. The epitaxial relationship between ZnTe and c-plane sapphire was found to be (111) ZnTe//(0001) sapphire with an in-plane orientation relationship of [-211] ZnTe//[1-100] sapphire. It was found that the (211)-plane ZnTe layer was grown on the m-plane of the sapphire substrates, and the (100)-plane ZnTe layer was grown on the r-plane sapphire. When the sapphire substrates were inclined from the c-plane towards the m-axis direction, the orientation of the ZnTe thin films was then tilted from the (111)-plane to the (211)-plane. The c-plane of the sapphire substrates governs the formation of the (111) ZnTe domain and the ZnTe epilayer orientation. These crystallographic features were also related to the atom arrangements of ZnTe and sapphire.

  15. Tuning Open-Circuit Voltage in Organic Solar Cells with Molecular Orientation.

    PubMed

    Kitchen, Brent; Awartani, Omar; Kline, R Joseph; McAfee, Terry; Ade, Harald; O'Connor, Brendan T

    2015-06-24

    The role of molecular orientation of a polar conjugated polymer in polymer-fullerene organic photovoltaic (OPV) cells is investigated. A planar heterojunction (PHJ) OPV cell composed of poly(3-hexylthiophene) (P3HT) and [6,6]-phenyl C61-butyric acid methyl ester (PCBM) is used as a model system to isolate the effect of the interfacial orientation on the photovoltaic properties. The molecular orientation of the aggregate P3HT relative to the PCBM layer is varied from highly edge-on (conjugated ring plane perpendicular to the interface plane) to appreciably face-on (ring plane parallel to the interface). It is found that as the P3HT stacking becomes more face-on there is a positive correlation to the OPV open-circuit voltage (V(OC)), attributed to a shift in the highest occupied molecular orbital (HOMO) energy level of P3HT. In addition, the PHJ OPV cell with a broad P3HT stacking orientation distribution has a V(OC) comparable to an archetypal bulk heterojunction (BHJ) device. These results suggest that, in the BHJ OPV cell, the hole energy level in the charge transfer state is defined in part by the orientation distribution of the P3HT at the interface with PCBM. Finally, the photoresponses of the devices are also shown to have a dependence on P3HT stacking orientation. PMID:26027430

  16. Effects of substrate orientation on the growth of InSb nanostructures by molecular beam epitaxy

    NASA Astrophysics Data System (ADS)

    Chou, C. Y.; Torfi, A.; Pei, C.; Wang, W. I.

    2016-05-01

    In this work, the effects of substrate orientation on InSb quantum structure growth by molecular beam epitaxy (MBE) are presented. Motivated by the observation that (411) evolves naturally as a stable facet during MBE crystal growth, comparison studies have been carried out to investigate the effects of the crystal orientation of the underlying GaSb substrate on the growth of InSb by MBE. By depositing InSb on a number of different substrate orientations, namely: (100), (311), (411), and (511), a higher nanostructure density was observed on the (411) surface compared with the other orientations. This result suggests that the (411) orientation presents a superior surface in MBE growth to develop a super-flat GaSb buffer surface, naturally favorable for nanostructure growth.

  17. Effect of horizontal molecular orientation on triplet-exciton diffusion in amorphous organic films

    NASA Astrophysics Data System (ADS)

    Sawabe, T.; Takasu, I.; Yonehara, T.; Ono, T.; Yoshida, J.; Enomoto, S.; Amemiya, I.; Adachi, C.

    2012-09-01

    Triplet harvesting is a candidate technology for highly efficient and long-life white OLEDs, where green or red phosphorescent emitters are activated by the triplet-excitons diffused from blue fluorescent emitters. We examined two oxadiazole-based electron transport materials with different horizontal molecular orientation as a triplet-exciton diffusion layer (TDL) in triplet-harvesting OLEDs. The device characteristics and the transient electroluminescent analyses of the red phosphorescent emitter showed that the triplet-exciton diffusion was more effective in the highly oriented TDL. The results are ascribed to the strong orbital overlap between the oriented molecules, which provides rapid electron exchange (Dexter energy transfer) in the TDL.

  18. Unforeseen distance-dependent SERS spectroelectrochemistry from surface-tethered Nile Blue: the role of molecular orientation.

    PubMed

    Wilson, Andrew J; Willets, Katherine A

    2016-08-15

    Covalent immobilization of redox-active dyes is an important strategy to evaluate structure-activity relationships in nanoscale electrochemistry by using optical readouts such as surface-enhanced Raman scattering (SERS). Here we investigate the role of the tether length in the SERS spectroelectrochemistry of surface-attached Nile Blue. Differential pulse voltammetry and a potential-dependent SERS derivative analysis reveal that the Nile Blue molecules adopt a different orientation with respect to the electrode surface as the number of carbons in a carboxylic acid-terminated alkanethiol monolayer is varied, which leads to unique SERS spectroelectrochemical behaviors. We use the relative molecular orientations and spectral characteristics to propose a model in which tethers shorter than the length of the molecule limit molecular motion under electrochemical perturbation, but tethers longer than the length of the molecule allow dye intercalation into the hydrophobic self-assembled monolayer, producing an unexpected decrease in the SERS intensity when the molecule is in the oxidized form. PMID:27337143

  19. Optimization of sub-cells orientation for assembly of a high-quality transmission sphere

    NASA Astrophysics Data System (ADS)

    Peng, Wei-Jei; Ho, Cheng-Fang; Yu, Zong-Ru; Huang, Chien-Yao; Kuo, Ching-Hsiang; Hsu, Wei-Yao

    2015-10-01

    The transmission sphere (TS) provides a high-quality reference wavefront which is common path with a test wavefront to generate interference fringes in a Fizeau interferometer. The optical path difference (OPD) of the reference wavefront should be controlled within peak-to-valley (PV) 5 λ (λ=0.6328 um), because too large OPD makes interference fringes distorted. Therefore, the tolerance analysis of the reference wavefront is very critical. Because the surface irregularity of lens can change the phase of a wavefront, surface deformation after mounting highly impacts on the wavefront error. For large optics, such as φ 6-inch in this study, surface deformation dominates the quality of the reference wavefront. For minimizing surface deformation after mounting, semi-kinematic mounting technology is used in sub-cells design to avoid over-constraint forces and unpredictable deformation. Then, the deformation due to gravity force of each surface can be constrained around PV 0.3 λ with Zernike trefoil in vertical setup TS; however, the superposition of the distorted wavefront may deteriorate the optical performance. A method of optimizing orientation of each lens around optical axis is presented in this paper. Sub-cells are designed to be rotational around optical axis respectively. The wavefront error of the reference beam of the worst case is improved significantly after optimization. Consequently, the method can effectively reduce the difficulty of lenses fabrication and mounting, and then the specification of the surface irregularity can be lower for cost saving. Based on the optimization in our study, a good reference wavefront can be acquired without any tight tolerance or complicated assembly.

  20. 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. PMID:16117022

  1. Orientation Dependence in Molecular Dynamics Simulations of Shocked Single Crystals

    SciTech Connect

    Germann, Timothy C.; Holian, Brad Lee; Lomdahl, Peter S.; Ravelo, Ramon

    2000-06-05

    We use multimillion-atom molecular dynamics simulations to study shock wave propagation in fcc crystals. As shown recently, shock waves along the <100> direction form intersecting stacking faults by slippage along {l_brace}111{r_brace} close-packed planes at sufficiently high shock strengths. We find even more interesting behavior of shocks propagating in other low-index directions: for the <111> case, an elastic precursor separates the shock front from the slipped (plastic) region. Shock waves along the <110> direction generate a leading solitary wave train, followed (at sufficiently high shock speeds) by an elastic precursor, and then a region of complex plastic deformation. (c) 2000 The American Physical Society.

  2. Molecular orientation of silane at the surface of colloidal silica.

    PubMed

    Söderholm, K J; Shang, S W

    1993-06-01

    The objective of this study was to investigate the silica-silane bond formation present at the filler interface of dental composites. Diffuse reflectance infrared Fourier transform spectroscopy was used, and the spectra of pyrogenic silica (Cab-O-Sil) treated with different concentrations of gamma-methacryloxypropyltrimethoxysilane (MPS) were analyzed. The outcome of the study suggested that the gamma-methacryloxypropyltrimethoxysilane (MPS) molecules oriented parallel to the colloidal silica surface (Cab-O-Sil) and formed two types of bonds. One of these bonds was a siloxane bridge formed by a condensation reaction between the silanol groups of both the silica surface and the hydrolyzed silane. Water formed during this reaction and soon became recaptured by the silanol groups of the silica surface. These water molecules were not available for additional hydrolyzation reactions of the unhydrolyzed silane under the experimental conditions. The intensity of the isolated OH-groups decreased because of this reaction. Simultaneous with the condensation reaction, the carbonyl group of the MPS molecule formed hydrogen bonds. This hydrogen bond formation resulted in a peak shift of the carbonyl band from 1718-1720 cm-1 to 1700-1702 cm-1. This hydrogen bond formation also occurred with the isolated OH-groups. After consumption of the isolated OH-groups, no additional surface reaction occurred because no further OH-groups were available for additional condensation reactions or hydrogen bond formation. The findings suggest that the amount of silane needed for filler treatment depends on the number of isolated OH-groups available on the filler surface. PMID:8388415

  3. A molecular mechanism of mitotic centrosome assembly in Drosophila

    PubMed Central

    Conduit, Paul T; Richens, Jennifer H; Wainman, Alan; Holder, James; Vicente, Catarina C; Pratt, Metta B; Dix, Carly I; Novak, Zsofia A; Dobbie, Ian M; Schermelleh, Lothar; Raff, Jordan W

    2014-01-01

    Centrosomes comprise a pair of centrioles surrounded by pericentriolar material (PCM). The PCM expands dramatically as cells enter mitosis, but it is unclear how this occurs. In this study, we show that the centriole protein Asl initiates the recruitment of DSpd-2 and Cnn to mother centrioles; both proteins then assemble into co-dependent scaffold-like structures that spread outwards from the mother centriole and recruit most, if not all, other PCM components. In the absence of either DSpd-2 or Cnn, mitotic PCM assembly is diminished; in the absence of both proteins, it appears to be abolished. We show that DSpd-2 helps incorporate Cnn into the PCM and that Cnn then helps maintain DSpd-2 within the PCM, creating a positive feedback loop that promotes robust PCM expansion around the mother centriole during mitosis. These observations suggest a surprisingly simple mechanism of mitotic PCM assembly in flies. DOI: http://dx.doi.org/10.7554/eLife.03399.001 PMID:25149451

  4. Vacuum sublimed α ,ω-dihexylsexithiophene thin films: Correlating electronic structure and molecular orientation

    NASA Astrophysics Data System (ADS)

    Duhm, S.; Salzmann, I.; Koch, N.; Fukagawa, H.; Kataoka, T.; Hosoumi, S.; Nebashi, K.; Kera, S.; Ueno, N.

    2008-08-01

    In order to correlate the molecular orientation of organic thin films with charge injection barriers at organic/metal interfaces, the electronic structure and molecular orientation of vacuum sublimed thin films of α ,ω-dihexylsexithiophene (DH6T) on the substrates Ag(111), highly oriented pyrolytic graphite (HOPG), and tetratetracontane (TTC) precovered Ag(111) were investigated. Results from metastable atom electron spectroscopy, ultraviolet photoelectron spectroscopy, and x-ray diffraction were used to derive growth models (including molecular orientation and conformation) of DH6T on the different substrates. On Ag(111), DH6T exhibits a transition from lying molecules in the monolayer/bilayer range to almost standing upright molecules in multilayers. This is accompanied by a shift of the molecular energy levels to a lower binding energy by 0.65 eV with respect to the vacuum level. The unit cell of standing DH6T on lying DH6T on Ag(111) is estimated to be similar to the DH6T bulk phase. On HOPG, DH6T grows in the bulk phase with lying orientation, starting already from the monolayer coverage. DH6T on TTC precovered Ag(111) grows in an almost lying orientation and a conformation that allows a strong overlap of the hexyl chains of DH6T with the alkyl chains of TTC. In all cases, the electronic structure and, particulary, the ionization energy of DH6T is dependent on the orientation of DH6T, i.e., lying DH6T has higher ionization energy than standing DH6T.

  5. Recent emergence of photon upconversion based on triplet energy migration in molecular assemblies.

    PubMed

    Yanai, Nobuhiro; Kimizuka, Nobuo

    2016-04-01

    An emerging field of triplet energy migration-based photon upconversion (TEM-UC) is reviewed. Highly efficient photon upconversion has been realized in a wide range of chromophore assemblies, such as non-solvent liquids, ionic liquids, amorphous solids, gels, supramolecular assemblies, molecular crystals, and metal-organic frameworks (MOFs). The control over their assembly structures allows for unexpected air-stability and maximum upconversion quantum yield at weak solar irradiance that has never been achieved by the conventional molecular diffusion-based mechanism. The introduction of the "self-assembly" concept offers a new perspective in photon upconversion research and triplet exciton science, which show promise for numerous applications ranging from solar energy conversion to chemical biology. PMID:26947379

  6. The spindle assembly checkpoint promotes chromosome bi-orientation: A novel Mad1 role in chromosome alignment.

    PubMed

    Akera, Takashi; Watanabe, Yoshinori

    2016-01-01

    Faithful chromosome segregation relies on dynamic interactions between spindle microtubules and chromosomes. Especially, all chromosomes must be aligned at the equator of the spindle to establish bi-orientation before they start to segregate. The spindle assembly checkpoint (SAC) monitors this process, inhibiting chromosome segregation until all chromosomes achieve bi-orientation. The original concept of 'checkpoints' was proposed as an external surveillance system that does not play an active role in the process it monitors. However, accumulating evidence from recent studies suggests that SAC components do play an active role in chromosome bi-orientation. In this review, we highlight a novel Mad1 role in chromosome alignment, which is the first conserved mechanism that links the SAC and kinesin-mediated chromosome gliding. PMID:26752263

  7. Orientation and morphology of self-assembled oligothiophene semiconductors and development of hybrid nanostructures for photovoltaic devices

    NASA Astrophysics Data System (ADS)

    Tevis, Ian David

    This dissertation examines the self-assembly of electronically active small molecules for heterojunction photovoltaic devices and the synthesis of nanoscale hybrid materials with a focus on orientation and morphology. A hairpin-shaped self-assembling molecule featuring two semiconducting sexithiophene arms connected through a diamidocyclohexane linker was found to form p-type semiconducting nanowires through H-aggregation as well as J-aggregated bundles. This molecule was incorporated into heterojunction photovoltaics with phenyl-(C61/C71)-butyric acid methyl ester through spin-coating. The sexithiophene assembled during drying to form a percolating network of nanowires and fullerenes. Thermal annealing enhanced efficiencies by increasing domain sizes and organizing the fullerenes into the groves of the nanofibers to produce 0.48% efficient devices. A p-type quarterthiophene derivative was designed and synthesized to assemble through pi-pi stacking and hydrogen bonding and its assembly was explored. Solutions of the quarterthiophene drop-cast on poly(tetrafluoroethylene) dried quickly to form bundled fibers parallel to the substrate. Slower drying and higher concentrations led to the formation of rhombohedra and randomly oriented hexagonal prisms, respectively. Liquid-liquid interfacial precipitation was used with a porous aluminum oxide membrane between a solution of quarterthiophene and toluene to orient the hexagonal prisms perpendicular to the membrane. Depositing the molecule from solution onto a UV/Ozone treated transparent conducting oxide subtrated affored prisms and sheets with perpendicular pi-pi stacking was anisotropy observed by 2D-GISAXS. This perpendicular pi-pi stacking orientation and sheet formation on a planar electrode shortens charge transport distances and minimizes film defects, which could lead to improved photovoltaic devices. Interpenetrating donor and acceptor hybrid materials with perpendicular orientation for enhanced morphological

  8. The Nodes of Ranvier: Molecular Assembly and Maintenance.

    PubMed

    Rasband, Matthew N; Peles, Elior

    2016-03-01

    Action potential (AP) propagation in myelinated nerves requires clustered voltage gated sodium and potassium channels. These channels must be specifically localized to nodes of Ranvier where the AP is regenerated. Several mechanisms have evolved to facilitate and ensure the correct assembly and stabilization of these essential axonal domains. This review highlights the current understanding of the axon intrinsic and glial extrinsic mechanisms that control the formation and maintenance of the nodes of Ranvier in both the peripheral nervous system (PNS) and central nervous system (CNS). PMID:26354894

  9. Following the nanostructural molecular orientation guidelines for sulfur versus thiophene units in small molecule photovoltaic cells

    NASA Astrophysics Data System (ADS)

    Kim, Yu Jin; Park, Chan Eon

    2016-03-01

    In bulk heterojunction (BHJ) organic photovoltaics, particularly those using small molecules, electron donor and/or electron acceptor materials form a distributed network in the photoactive layer where critical photo-physical processes occur. Extensive research has recently focused on the importance of sulfur atoms in the small molecules. Little is known about the three-dimensional orientation of these sulfur atom-containing molecules. Herein, we report on our research concerning the heterojunction textures of the crystalline molecular orientation of small compounds having sulfur-containing units in the side chains, specifically, compounds known as DR3TSBDT that contain the alkylthio group and DR3TBDTT that does not. The improved performance of the DR3TBDTT-based devices, particularly in the photocurrent and the fill factor, was attributed to the large population of donor compound crystallites with a favorable face-on orientation along the perpendicular direction. This orientation resulted in efficient charge transport and a reduction in charge recombination. These findings underscore the great potential of small-molecule solar cells and suggest that even higher efficiencies can be achieved through materials development and molecular orientation control.In bulk heterojunction (BHJ) organic photovoltaics, particularly those using small molecules, electron donor and/or electron acceptor materials form a distributed network in the photoactive layer where critical photo-physical processes occur. Extensive research has recently focused on the importance of sulfur atoms in the small molecules. Little is known about the three-dimensional orientation of these sulfur atom-containing molecules. Herein, we report on our research concerning the heterojunction textures of the crystalline molecular orientation of small compounds having sulfur-containing units in the side chains, specifically, compounds known as DR3TSBDT that contain the alkylthio group and DR3TBDTT that does not

  10. Detection of Alzheimer's amyloid beta aggregation by capturing molecular trails of individual assemblies

    SciTech Connect

    Vestergaard, Mun'delanji Hamada, Tsutomu; Saito, Masato; Yajima, Yoshifumi; Kudou, Monotori; Tamiya, Eiichi; Takagi, Masahiro

    2008-12-12

    Assembly of Amyloid beta (A{beta}) peptides, in particular A{beta}-42 is central to the formation of the amyloid plaques associated with neuro-pathologies such as Alzheimer's disease (AD). Molecular assembly of individual A{beta}-42 species was observed using a simple fluorescence microscope. From the molecular movements (aka Brownian motion) of the individual peptide assemblies, we calculated a temporal evolution of the hydrodynamic radius (R{sub H}) of the peptide at physiological temperature and pH. The results clearly show a direct relationship between R{sub H} of A{beta}-42 and incubation period, corresponding to the previously reported peptide's aggregation kinetics. The data correlates highly with in solution-based label-free electrochemical detection of the peptide's aggregation, and A{beta}-42 deposited on a solid surface and analysed using atomic force microscopy (AFM). To the best of our knowledge, this is the first analysis and characterisation of A{beta} aggregation based on capturing molecular trails of individual assemblies. The technique enables both real-time observation and a semi-quantitative distribution profile of the various stages of A{beta} assembly, at microM peptide concentration. Our method is a promising candidate for real-time observation and analysis of the effect of other pathologically-relevant molecules such as metal ions on pathways to A{beta} oligomerisation and aggregation. The method is also a promising screening tool for AD therapeutics that target A{beta} assembly.

  11. Control of molecular orientation in TTF TCNQ co-evaporated films by applying an electric field

    NASA Astrophysics Data System (ADS)

    Kato, N. A.; Fujimura, M.; Kuniyoshi, S.; Kudo, K.; Hara, M.; Tanaka, K.

    1998-06-01

    We have investigated the effect of an electric field on the molecular orientation of tetrathiafulvalene-tetracyanoquinodimethane (TTF-TCNQ) co-evaporated films, using an optical microscope, a scanning tunnelling microscope and X-ray diffraction. It is found that with an electric field applied TTF-TCNQ grows with the b-axis parallel to the electric field.

  12. 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

  13. Molecular orientation in soft matter thin films studied by resonant soft X-ray reflectivity

    SciTech Connect

    Mezger, Markus; Jerome, Blandine; Kortright, Jeffrey B.; Valvidares, Manuel; Gullikson, Eric; Giglia, Angelo; Mahne, Nicola; Nannarone, Stefano

    2011-01-12

    We present a technique to study depth profiles of molecular orientation in soft matter thin films with nanometer resolution. The method is based on dichroism in resonant soft X-ray reflectivity using linear s- and p-polarization. It combines the chemical sensitivity of Near-Edge X-ray Absorption Fine Structure spectroscopy to specific molecular bonds and their orientation relative to the polarization of the incident beam with the precise depth profiling capability of X-ray reflectivity. We demonstrate these capabilities on side chain liquid crystalline polymer thin films with soft X-ray reflectivity data at the carbon K edge. Optical constants of the anisotropic refractive index ellipsoid were obtained from a quantitative analysis using the Berreman formalism. For films up to 50 nm thickness we find that the degree of orientation of the long axis exhibits no depth variation and isindependent of the film thickness.

  14. An Elaborate Supramolecular Assembly for a Smart Nanodevice for Ratiometric Molecular Recognition and Logic Gates.

    PubMed

    Xie, Yu-Jie; Wu, Wen-Yu; Chen, Hao; Li, Xiang; Zhang, Hao-Li; Liu, Liang-Liang; Shao, Xing-Xin; Shan, Chang-Fu; Liu, Wei-Sheng; Tang, Yu

    2016-06-01

    Ingenious approaches to supramolecular assembly for fabricating smart nanodevices is one of the more significant topics in nanomaterials research. Herein, by using surface quaternized cationic carbon dots (CDots) as the assembly and fluorescence platform, anionic sulfonatocalix[4]arene with modifiable lower and upper rims as a connector, as well as in situ coordination of Tb(3+) ions, we propose an elaborate supramolecular assembly strategy for the facile fabrication of a multifunctional nanodevice. The dynamic equilibrium characteristics of the supramolecular interaction can eventually endow this nanodevice with functions of fluorescent ratiometric molecular recognition and as a nano-logic gate with two output channels. PMID:27106796

  15. Fabrication and Characterization of Oriented Carbon Atom Wires Assembled on Gold

    SciTech Connect

    Xue,K.H.; Wu,L.; Chen, S.-P.; Wanga, L.X.; Wei, R.-B.; Xu, S.-M.; Cui, L.; Mao, B.-W.; Tian, Z.-Q.; Zen, C.-H.; Sun, S.-G.; Zhu, Y.-M.

    2009-02-17

    Carbon atom wires (CAWs) are of the sp-hybridized allotrope of carbon. To augment the extraordinary features based on sp-hybridization, we developed an approach to make CAWs be self-assembled and orderly organized on Au substrate. The self-assembling process was investigated in situ by using scanning tunneling microscopy (STM) and electrochemical quartz crystal microbalance (EQCM). The properties of the assembled film were characterized by voltammetry, Raman spectroscopy, electron energy loss spectroscopy (EELS), and the contact angle measurements. Experimental results indicated that the assembled CAW film was of the good structural integrity and well organized, with the sp-hybridized features enhanced.

  16. Molecular mechanisms underlying KVS-1-MPS-1 complex assembly.

    PubMed

    Wang, Yi; Sesti, Federico

    2007-11-01

    Formation of heteromeric complexes between voltage-gated K(+) (Kv) channels and accessory (beta) subunits is a widespread means to generate heterogeneity of K(+) current in the nervous system. Here we investigate the principles that determine the interactions of Caenorhabditis elegans MPS-1, a bifunctional beta-subunit that possesses kinase activity, with Kv channels. MPS-1 belongs to the evolutionarily conserved family of KCNE beta-subunits that modulate the functional properties of a variety of Kv channels and that, when defective, can cause congenital and acquired disease in Homo sapiens. In Chinese hamster ovary cells, MPS-1 forms stable complexes with different alpha-subunits. The transmembrane domain of MPS-1 is necessary and sufficient for MPS-1 complex formation. The hydropathicity of the transmembrane domain is an important factor controlling MPS-1 assembly. A highly hydrophobic MPS-1 mutant fails to interact with its endogenous channel partners when transgenically expressed in living worms. The hydropathic mechanism does not require specific points of contact between interacting proteins. This may allow MPS-1 to assemble with various Kv channels, presumably modifying the electrical properties of each. PMID:17604313

  17. Method of assembly of molecular-sized nets and scaffolding

    DOEpatents

    Michl, Josef; Magnera, Thomas F.; David, Donald E.; Harrison, Robin M.

    1999-01-01

    The present invention relates to methods and starting materials for forming molecular-sized grids or nets, or other structures based on such grids and nets, by creating molecular links between elementary molecular modules constrained to move in only two directions on an interface or surface by adhesion or bonding to that interface or surface. In the methods of this invention, monomers are employed as the building blocks of grids and more complex structures. Monomers are introduced onto and allowed to adhere or bond to an interface. The connector groups of adjacent adhered monomers are then polymerized with each other to form a regular grid in two dimensions above the interface. Modules that are not bound or adhered to the interface are removed prior to reaction of the connector groups to avoid undesired three-dimensional cross-linking and the formation of non-grid structures. Grids formed by the methods of this invention are useful in a variety of applications, including among others, for separations technology, as masks for forming regular surface structures (i.e., metal deposition) and as templates for three-dimensional molecular-sized structures.

  18. Method of assembly of molecular-sized nets and scaffolding

    DOEpatents

    Michl, J.; Magnera, T.F.; David, D.E.; Harrison, R.M.

    1999-03-02

    The present invention relates to methods and starting materials for forming molecular-sized grids or nets, or other structures based on such grids and nets, by creating molecular links between elementary molecular modules constrained to move in only two directions on an interface or surface by adhesion or bonding to that interface or surface. In the methods of this invention, monomers are employed as the building blocks of grids and more complex structures. Monomers are introduced onto and allowed to adhere or bond to an interface. The connector groups of adjacent adhered monomers are then polymerized with each other to form a regular grid in two dimensions above the interface. Modules that are not bound or adhered to the interface are removed prior to reaction of the connector groups to avoid undesired three-dimensional cross-linking and the formation of non-grid structures. Grids formed by the methods of this invention are useful in a variety of applications, including among others, for separations technology, as masks for forming regular surface structures (i.e., metal deposition) and as templates for three-dimensional molecular-sized structures. 9 figs.

  19. Chemical vapor deposition graphene as structural template to control interfacial molecular orientation of chloroaluminium phthalocyanine

    NASA Astrophysics Data System (ADS)

    Ying Mao, Hong; Wang, Rui; Wang, Yu; Chao Niu, Tian; Qiang Zhong, Jian; Yang Huang, Ming; Chen Qi, Dong; Ping Loh, Kian; Thye Shen Wee, Andrew; Chen, Wei

    2011-08-01

    Chemical vapor deposition (CVD) graphene has been used as an effective structural template to manipulate molecular orientation of organic thin film of chloroaluminium phthalocyanine (ClAlPc) on indium tin oxide (ITO) electrode. As revealed by in-situ near-edge x-ray adsorption fine structure measurement, ClAlPc molecules on the CVD graphene modified ITO electrode adopt a well-aligned lying-down configuration with their molecular π-plane nearly parallel to the electrode surface, in contrast to the random orientation of ClAlPc molecules on the bare ITO electrode. This lying-down configuration results in an optimized stacking of the molecular π-plane perpendicular to the electrode surface and hence facilitates efficient charge transport along this direction.

  20. ADVANCED HEAT EXCHANGERS USING TUNABLE NANOSCALE-MOLECULAR ASSEMBLY

    SciTech Connect

    Kwang J. Kim; Thomas W. Bell; Srinivas Vemuri; Sailaja Govindaraju

    2004-01-01

    Steam condensation heat transfer on smooth horizontal tubes and enhanced tubes (TURBO-CDI and TURBO-CSL) along with nanoscale hydrophobic coated tubes was studied experimentally. Hydrophobic coatings have been created through self-assembled mono layers (SAMs) on copper alloy (99.9% Cu, 0.1% P) surfaces to enhance steam condensation through dropwise condensation. In general, a SAM system with a long-chain, hydrophobic group is nano-resistant, meaning that such a system forms a protective hydrophobic layer with negligible heat transfer resistance but a much stronger bond. When compared to complete filmwise condensation, the SAM coating on a plain tube increased the condensation heat transfer rate by a factor of 3 for copper alloy surfaces, under vacuum pressure (33.86 kPa) and by a factor of about 8 times when operated at atmospheric pressure (101 kPa). Lifetime of maintaining dropwise condensation is greatly dependent on the processing conditions.

  1. Self-assembled molecular films incorporating a ligand

    DOEpatents

    Bednarski, Mark D.; Wilson, Troy E.; Mastandra, Mark S.

    1996-01-01

    Functionalized monomers are presented which can be used in the fabrication of molecular films for controlling adhesion, detection of receptor-ligand binding and enzymatic reactions; new coatings for lithography; and for semiconductor materials. The monomers are a combination of a ligand, a linker, optionally including a polymerizable group, and a surface attachment group. The processes and an apparatus for making films from these monomers, as well as methods of using the films are also provided.

  2. Self-assembled molecular films incorporating a ligand

    DOEpatents

    Bednarski, M.D.; Wilson, T.E.; Mastandra, M.S.

    1996-04-23

    Functionalized monomers are presented which can be used in the fabrication of molecular films for controlling adhesion, detection of receptor-ligand binding and enzymatic reactions; new coatings for lithography; and for semiconductor materials. The monomers are a combination of a ligand, a linker, optionally including a polymerizable group, and a surface attachment group. The processes and an apparatus for making films from these monomers, as well as methods of using the films are also provided. 7 figs.

  3. Directed Self-Assembly of Micron-Sized Gold Nanoplatelets into Oriented Flexible Stacks with Tunable Interplate Distance.

    PubMed

    Vutukuri, Hanumantha Rao; Badaire, Stéphane; de Winter, D A Matthijs; Imhof, Arnout; van Blaaderen, Alfons

    2015-08-12

    A growing demand for control over the interparticle spacing and the orientation of anisotropic metallic particles into self-assembled structures is fuelled by their use in potential applications such as in plasmonics, catalysis, sensing, and optoelectronics. Here, we present an improved high yield synthesis method to fabricate micron- and submicron-sized gold nanoplatelets with a thickness less than 20 nm using silver nanoplatelets as seeds. By tuning the depth of the secondary minimum in the DLVO interaction potential between these particles, we are able to assemble the platelets into dynamic and flexible stacks containing thousands of platelets arranged face-to-face with well-defined spacing. Moreover, we demonstrate that the length of the stacks, and the interplate distance can be controlled between tens and hundreds of nm with the ionic strength. We use a high frequency external electric field to control the orientation of the stacks and direct the stacks into highly organized 2D and 3D assemblies that strongly polarize light. PMID:26237212

  4. Following the nanostructural molecular orientation guidelines for sulfur versus thiophene units in small molecule photovoltaic cells.

    PubMed

    Kim, Yu Jin; Park, Chan Eon

    2016-03-31

    In bulk heterojunction (BHJ) organic photovoltaics, particularly those using small molecules, electron donor and/or electron acceptor materials form a distributed network in the photoactive layer where critical photo-physical processes occur. Extensive research has recently focused on the importance of sulfur atoms in the small molecules. Little is known about the three-dimensional orientation of these sulfur atom-containing molecules. Herein, we report on our research concerning the heterojunction textures of the crystalline molecular orientation of small compounds having sulfur-containing units in the side chains, specifically, compounds known as that contain the alkylthio group and that does not. The improved performance of the -based devices, particularly in the photocurrent and the fill factor, was attributed to the large population of donor compound crystallites with a favorable face-on orientation along the perpendicular direction. This orientation resulted in efficient charge transport and a reduction in charge recombination. These findings underscore the great potential of small-molecule solar cells and suggest that even higher efficiencies can be achieved through materials development and molecular orientation control. PMID:26987868

  5. A Molecular Toolkit to Visualize Native Protein Assemblies in the Context of Human Disease

    PubMed Central

    Gilmore, Brian L.; Winton, Carly E.; Demmert, Andrew C.; Tanner, Justin R.; Bowman, Sam; Karageorge, Vasilea; Patel, Kaya; Sheng, Zhi; Kelly, Deborah F.

    2015-01-01

    We present a new molecular toolkit to investigate protein assemblies natively formed in the context of human disease. The system employs tunable microchips that can be decorated with switchable adaptor molecules to select for target proteins of interest and analyze them using molecular microscopy. Implementing our new streamlined microchip approach, we could directly visualize BRCA1 gene regulatory complexes from patient-derived cancer cells for the first time. PMID:26395823

  6. Directed nanoscale self-assembly of molecular wires interconnecting nodal points using Monte Carlo simulations

    SciTech Connect

    Boscoboinik, A. M.; Manzi, S. J.; Tysoe, W. T.; Pereyra, V. D.; Boscoboinik, J. A.

    2015-09-10

    The influence of directing agents in the self-assembly of molecular wires to produce two-dimensional electronic nanoarchitectures is studied here using a Monte Carlo approach to simulate the effect of arbitrarily locating nodal points on a surface, from which the growth of self-assembled molecular wires can be nucleated. This is compared to experimental results reported for the self-assembly of molecular wires when 1,4-phenylenediisocyanide (PDI) is adsorbed on Au(111). The latter results in the formation of (Au-PDI)n organometallic chains, which were shown to be conductive when linked between gold nanoparticles on an insulating substrate. The present study analyzes, by means of stochastic methods, the influence of variables that affect the growth and design of self-assembled conductive nanoarchitectures, such as the distance between nodes, coverage of the monomeric units that leads to the formation of the desired architectures, and the interaction between the monomeric units. As a result, this study proposes an approach and sets the stage for the production of complex 2D nanoarchitectures using a bottom-up strategy but including the use of current state-of-the-art top-down technology as an integral part of the self-assembly strategy.

  7. Organization of Inorganic Nanomaterials via Programmable DNA Self-Assembly and Peptide Molecular Recognition

    PubMed Central

    Carter, Joshua D.; LaBean, Thomas H.

    2011-01-01

    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 multi-nanoparticle 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. PMID:21314176

  8. Directed nanoscale self-assembly of molecular wires interconnecting nodal points using Monte Carlo simulations

    DOE PAGESBeta

    Boscoboinik, A. M.; Manzi, S. J.; Tysoe, W. T.; Pereyra, V. D.; Boscoboinik, J. A.

    2015-09-10

    The influence of directing agents in the self-assembly of molecular wires to produce two-dimensional electronic nanoarchitectures is studied here using a Monte Carlo approach to simulate the effect of arbitrarily locating nodal points on a surface, from which the growth of self-assembled molecular wires can be nucleated. This is compared to experimental results reported for the self-assembly of molecular wires when 1,4-phenylenediisocyanide (PDI) is adsorbed on Au(111). The latter results in the formation of (Au-PDI)n organometallic chains, which were shown to be conductive when linked between gold nanoparticles on an insulating substrate. The present study analyzes, by means of stochasticmore » methods, the influence of variables that affect the growth and design of self-assembled conductive nanoarchitectures, such as the distance between nodes, coverage of the monomeric units that leads to the formation of the desired architectures, and the interaction between the monomeric units. As a result, this study proposes an approach and sets the stage for the production of complex 2D nanoarchitectures using a bottom-up strategy but including the use of current state-of-the-art top-down technology as an integral part of the self-assembly strategy.« less

  9. Molecular Architecture and Assembly of the Eukaryotic Proteasome

    PubMed Central

    Tomko, Robert J.; Hochstrasser, Mark

    2013-01-01

    The eukaryotic ubiquitin-proteasome system is responsible for most cellular quality-control and regulatory protein degradation. Its substrates, which are usually modified by polymers of ubiquitin, are ultimately degraded by the 26S proteasome. This 2.6 MDa protein complex is separated into a barrel-shaped proteolytic 20S core particle (CP) of 28 subunits capped on one or both ends by a 19S regulatory particle (RP) comprising at least 19 subunits. The RP coordinates substrate recognition, removal of substrate polyubiquitin chains, and substrate unfolding and translocation into the CP for degradation. While many atomic structures of the CP have been determined, the RP has resisted high-resolution analysis. Recently, however, a combination of cryo-electron microscopy (cryo-EM), biochemical analysis, and crystal structure determination of several RP subunits has yielded a near-atomic resolution view of much of the complex. Major new insights into chaperone-assisted proteasome assembly have also recently been made. Here we review these novel findings. PMID:23495936

  10. Sample handling for kinetics and molecular assembly in flow cytometry

    SciTech Connect

    Sklar, L.A. |; Seamer, L.C.; Kuckuck, F.; Prossnitz, E.; Edwards, B.; Posner, G.

    1998-07-01

    Flow cytometry discriminates particle associated fluorescence from the fluorescence of the surrounding medium. It permits assemblies of macromolecular complexes on beads or cells to be detected in real-time with precision and specificity. The authors have investigated two types of robust sample handling systems which provide sub-second resolution and high throughput: (1) mixers which use stepper-motor driven syringes to initiate chemical reactions in msec time frames; and (2) flow injection controllers with valves and automated syringes used in chemical process control. In the former system, the authors used fast valves to overcome the disparity between mixing 100 {micro}ls of sample in 100 msecs and delivering sample to a flow cytometer at 1 {micro}l/sec. Particles were detected within 100 msec after mixing, but turbulence was created which lasted for 1 sec after injection of the sample into the flow cytometer. They used optical criteria to discriminate particles which were out of alignment due to the turbulent flow. Complex sample handling protocols involving multiple mixing steps and sample dilution have also been achieved. With the latter system they were able to automate sample handling and delivery with intervals of a few seconds. The authors used a fluidic approach to defeat turbulence caused by sample introduction. By controlling both sheath and sample with individual syringes, the period of turbulence was reduced to {approximately} 200 msecs. Automated sample handling and sub-second resolution should permit broad analytical and diagnostic applications of flow cytometry.

  11. Precise Characterisation of Molecular Orientation in a Single Crystal Field-Effect Transistor Using Polarised Raman Spectroscopy.

    PubMed

    Wood, Sebastian; Rigas, Grigorios-Panagiotis; Zoladek-Lemanczyk, Alina; Blakesley, James C; Georgakopoulos, Stamatis; Mas-Torrent, Marta; Shkunov, Maxim; Castro, Fernando A

    2016-01-01

    Charge transport in organic semiconductors is strongly dependent on the molecular orientation and packing, such that manipulation of this molecular packing is a proven technique for enhancing the charge mobility in organic transistors. However, quantitative measurements of molecular orientation in micrometre-scale structures are experimentally challenging. Several research groups have suggested polarised Raman spectroscopy as a suitable technique for these measurements and have been able to partially characterise molecular orientations using one or two orientation parameters. Here we demonstrate a new approach that allows quantitative measurements of molecular orientations in terms of three parameters, offering the complete characterisation of a three-dimensional orientation. We apply this new method to organic semiconductor molecules in a single crystal field-effect transistor in order to correlate the measured orientation with charge carrier mobility measurements. This approach offers the opportunity for micrometre resolution (diffraction limited) spatial mapping of molecular orientation using bench-top apparatus, enabling a rational approach towards controlling this orientation to achieve optimum device performance. PMID:27619423

  12. Molecular-Orientation-Induced Rapid Roughening and Morphology Transition in Organic Semiconductor Thin-Film Growth

    PubMed Central

    Yang, Junliang; Yim, Sanggyu; Jones, Tim S.

    2015-01-01

    We study the roughening process and morphology transition of organic semiconductor thin film induced by molecular orientation in the model of molecular semiconductor copper hexadecafluorophthalocyanine (F16CuPc) using both experiment and simulation. The growth behaviour of F16CuPc thin film with the thickness, D, on SiO2 substrate takes on two processes divided by a critical thickness: (1) D ≤ 40 nm, F16CuPc thin films are composed of uniform caterpillar-like crystals. The kinetic roughening is confirmed during this growth, which is successfully analyzed by Kardar-Parisi-Zhang (KPZ) model with scaling exponents α = 0.71 ± 0.12, β = 0.36 ± 0.03, and 1/z = 0.39 ± 0.12; (2) D > 40 nm, nanobelt crystals are formed gradually on the caterpillar-like crystal surface and the film growth shows anomalous growth behaviour. These new growth behaviours with two processes result from the gradual change of molecular orientation and the formation of grain boundaries, which conversely induce new molecular orientation, rapid roughening process, and the formation of nanobelt crystals. PMID:25801646

  13. Self-Assembly of One-Dimensional Nanocrystal Superlattice Chains Mediated by Molecular Clusters.

    PubMed

    Zhang, Xianfeng; Lv, Longfei; Ji, Li; Guo, Guannan; Liu, Limin; Han, Dandan; Wang, Biwei; Tu, Yaqi; Hu, Jianhua; Yang, Dong; Dong, Angang

    2016-03-16

    Self-assembly of nanocrystal (NC) building blocks into mesoscopic superstructures with well-defined symmetry and geometry is essential for creating new materials with rationally designed properties. Despite the tremendous progress in colloidal assembly, it remains a fundamental challenge to assemble isotropic spherical NCs into one-dimensional (1D) ordered superstructures. Here, we report a new and general methodology that utilizes molecular clusters to induce the anisotropic assembly of NCs in solution, yielding polymer-like, single-NC-wide linear chains comprising as many as ∼1000 close-packed NCs. This cluster-assisted assembly process is applicable to various metallic, semiconductor, and magnetic NCs of different sizes and shapes. Mechanistic investigation reveals that the solvent-induced association of clusters plays a key role in driving the anisotropic assembly of NCs. Our work opens a solution-based route for linearly assembling NCs and represents an important step toward the bottom-up construction of 1D ordered NC superstructures. PMID:26936281

  14. Molecular Recognition: Use of Metal-Containing Molecular Clefts for Supramolecular Self-Assembly and Host-Guest Formation

    SciTech Connect

    Crowley, James D.; Bosnich, Brice

    2008-10-03

    Molecular clefts consisting of a rigid spacer linked to two parallel cofacially disposed terpy-M-X (M = Pd{sup 2+}, Pt{sup 2+}) units, which can vary in separation from 6.6 to 7.2 {angstrom}, have been used as molecular receptors and for self-assembly with linear and triangular linkers to produce rectangles and trigonal prisms, respectively. Aromatic molecules form multiple host-guest adducts with the molecular cleft receptors and with the rectangles and trigonal prisms. Planar complexes of Pt{sup 2+} also form host-guest adducts. The forces that control this molecular recognition, namely, {pi}-{pi} interactions, charge-induced dipole interactions, charge-charge forces, weak metal-metal interactions and solvation effects, are discussed and assigned to the various adducts.

  15. Critical CuI buffer layer surface density for organic molecular crystal orientation change

    SciTech Connect

    Ahn, Kwangseok; Kim, Jong Beom; Lee, Dong Ryeol; Kim, Hyo Jung; Lee, Hyun Hwi

    2015-01-21

    We have determined the critical surface density of the CuI buffer layer inserted to change the preferred orientation of copper phthalocyanine (CuPc) crystals grown on the buffer layer. X-ray reflectivity measurements were performed to obtain the density profiles of the buffer layers and out-of-plane and 2D grazing-incidence X-ray diffraction measurements were performed to determine the preferred orientations of the molecular crystals. Remarkably, it was found that the preferred orientation of the CuPc film is completely changed from edge-on (1 0 0) to face-on (1 1 −2) by a CuI buffer layer with a very low surface density, so low that a large proportion of the substrate surface is bare.

  16. Anisotropic Molecular Orientation of Poly [4, 4'-oxydiphenylene- 1, 2, 3, 4-cyclobutanetetracarboximide] Films Irradiated by Linearly Polarized UV Light

    NASA Astrophysics Data System (ADS)

    Sakamoto, Kenji; Usami, Kiyoaki; Araya, Takeshi; Ushioda, Sukekatsu

    1999-12-01

    We have investigated the anisotropic molecular orientation of poly [4, 4'-oxydiphenylene-1, 2, 3, 4-cyclobutanetetracarboximide] (CBDA-ODA) films induced by irradiation with linearly polarized ultraviolet light (LPUVL). The molecular orientation was monitored by measuring the polarized infrared (IR) absorption spectra of a 10-nm-thick film. The anisotropy of the molecular orientation exceeded that of a rubbed film with the same film thickness. From the LPUVL exposure dependence of IR absorption we found that preferential cleavage occurs to the cyclobutane ring in the polyimide backbone structure oriented parallel to the polarization direction of LPUVL. Then the orientation of the cleaved polyimide molecule is randomized. We conclude that the large anisotropy of the LPUVL-exposed film is caused by the anisotropic cleavage of the cyclobutane rings and the orientational randomization of the cleaved polyimide molecules.

  17. Dynamics of Molecular Orientation Observed Using Angle Resolved Photoemission Spectroscopy during Deposition of Pentacene on Graphite.

    PubMed

    Park, Sang Han; Kwon, Soonnam

    2016-04-19

    A real-time method to observe both the structural and the electronic configuration of an organic molecule during deposition is reported for the model system of pentacene on graphite. Structural phase transition of the thin films as a function of coverage is monitored by using in situ angle resolved photoemission spectroscopy (ARPES) results to observe the change of the electronic configuration at the same time. A photoemission theory that uses independent atomic center approximations is introduced to identify the molecular orientation from the ARPES technique. This study provides a practical insight into interpreting ARPES data regarding dynamic changes of molecular orientation during initial growth of molecules on a well-defined surface. PMID:26999332

  18. Rational peptide design for functional materials via molecular self-assembly

    NASA Astrophysics Data System (ADS)

    Rajagopal, Karthikan

    Supra-molecular self-assembly of rationally designed peptides is a promising approach to construct functional materials. This thesis specifically focuses on hydrogels, an important class of materials with potential for applications in tissue engineering, drug delivery and micro-fluidic systems. The objective is to design short peptides that would specifically adopt a stimulus dependent conformation that is strongly amenable to self-assembly resulting in material formation. With this concept the rational design of a 20 amino acid peptide (MAX1) that folds into an amphiphilic beta-hairpin structure and then self-assembles to form a rigid hydrogel under alkaline conditions is presented. The molecular level conformation of MAX1 was characterized using circular dichroism and FTIR spectroscopies. The mesoscale structure of the hydrogel assessed using confocal and transmission electron micron microscopies and neutron scattering techniques shows that peptide self-assembly results in the formation of fibrils that are homogeneously 3 nm in diameter. The mechanical properties of the hydrogel probed using oscillatory rheology shows that MAX1 forms a stiff hydrogel. Since the self-assembly process is coupled to the intra-molecularly folded state of the peptide, stimulus responsiveness can be specifically engineered into the sequence by rational design. This was demonstrated in the design of peptides that form hydrogels in response to a specific stimulus such as temperature, pH or ionic strength. The significance of peptide design in the context of self-assembly and its relationship to the nanostructure was studied by designing a series of peptides derived from MAX1. Evolving from these studies is an understanding of the relationship between molecular level peptide structure and the nanoscale supra-molecular morphology. Based on this, it has been shown that alternate morphologies distinct from those observed with the gel forming peptides, such as non-twisting laminates or tube

  19. Self-assembly of intramolecular charge-transfer compounds into functional molecular systems.

    PubMed

    Li, Yongjun; Liu, Taifeng; Liu, Huibiao; Tian, Mao-Zhong; Li, Yuliang

    2014-04-15

    Highly polarized compounds exhibiting intramolecular charge transfer (ICT) are used widely as nonlinear optical (NLO) materials and red emitters and in organic light emitting diodes. Low-molecular-weight donor/acceptor (D/A)-substituted ICT compounds are ideal candidates for use as the building blocks of hierarchically structured, multifunctional self-assembled supramolecular systems. This Account describes our recent studies into the development of functional molecular systems with well-defined self-assembled structures based on charge-transfer (CT) interactions. From solution (sensors) to the solid state (assembled structures), we have fully utilized intrinsic and stimulus-induced CT interactions to construct these functional molecular systems. We have designed some organic molecules capable of ICT, with diversity and tailorability, that can be used to develop novel self-assembled materials. These ICT organic molecules are based on a variety of simple structures such as perylene bisimide, benzothiadiazole, tetracyanobutadiene, fluorenone, isoxazolone, BODIPY, and their derivatives. The degree of ICT is influenced by the nature of both the bridge and the substituents. We have developed new methods to synthesize ICT compounds through the introduction of heterocycles or heteroatoms to the π-conjugated systems or through extending the conjugation of diverse aromatic systems via another aromatic ring. Combining these ICT compounds featuring different D/A units and different degrees of conjugation with phase transfer methodologies and solvent-vapor techniques, we have self-assembled various organic nanostructures, including hollow nanospheres, wires, tubes, and ribbonlike architectures, with controllable morphologies and sizes. For example, we obtained a noncentrosymmetric microfiber structure that possessed a permanent dipole along its fibers' long axis and a transition dipole perpendicular to it; the independent NLO responses of this material can be separated and

  20. Molecular assemblies and membrane domains in multivesicular endosome dynamics

    SciTech Connect

    Falguieres, Thomas; Luyet, Pierre-Philippe; Gruenberg, Jean

    2009-05-15

    Along the degradation pathway, endosomes exhibit a characteristic multivesicular organization, resulting from the budding of vesicles into the endosomal lumen. After endocytosis and transport to early endosomes, activated signaling receptors are incorporated into these intralumenal vesicles through the action of the ESCRT machinery, a process that contributes to terminate signaling. Then, the vesicles and their protein cargo are further transported towards lysosomes for degradation. Evidence also shows that intralumenal vesicles can undergo 'back-fusion' with the late endosome limiting membrane, a route exploited by some pathogens and presumably followed by proteins and lipids that need to be recycled from within the endosomal lumen. This process depends on the late endosomal lipid lysobisphosphatidic acid and its putative effector Alix/AIP1, and is presumably coupled to the invagination of the endosomal limiting membrane at the molecular level via ESCRT proteins. In this review, we discuss the intra-endosomal transport routes in mammalian cells, and in particular the different mechanisms involved in membrane invagination, vesicle formation and fusion in a space inaccessible to proteins known to control intracellular membrane traffic.

  1. Molecular assemblies and membrane domains in multivesicular endosome dynamics.

    PubMed

    Falguières, Thomas; Luyet, Pierre-Philippe; Gruenberg, Jean

    2009-05-15

    Along the degradation pathway, endosomes exhibit a characteristic multivesicular organization, resulting from the budding of vesicles into the endosomal lumen. After endocytosis and transport to early endosomes, activated signaling receptors are incorporated into these intralumenal vesicles through the action of the ESCRT machinery, a process that contributes to terminate signaling. Then, the vesicles and their protein cargo are further transported towards lysosomes for degradation. Evidence also shows that intralumenal vesicles can undergo "back-fusion" with the late endosome limiting membrane, a route exploited by some pathogens and presumably followed by proteins and lipids that need to be recycled from within the endosomal lumen. This process depends on the late endosomal lipid lysobisphosphatidic acid and its putative effector Alix/AIP1, and is presumably coupled to the invagination of the endosomal limiting membrane at the molecular level via ESCRT proteins. In this review, we discuss the intra-endosomal transport routes in mammalian cells, and in particular the different mechanisms involved in membrane invagination, vesicle formation and fusion in a space inaccessible to proteins known to control intracellular membrane traffic. PMID:19133258

  2. High-Throughput Analysis of Molecular Orientation on Surfaces by NEXAFS Imaging of Curved Sample Arrays

    PubMed Central

    Baio, Joe E.; Jaye, Cherno; Fischer, Daniel A.; Weidner, Tobias

    2015-01-01

    Near-edge X-ray absorption fine structure (NEXAFS) spectroscopy provides detailed information about the orientation and alignment of thin films. NEXAFS is a synchrotron-based technique—the availability of beam-time per user is typically limited to no more than a few weeks per year. The limited availability is currently a true barrier for using NEXAFS in combinatorial studies of molecular alignment. We have recently demonstrated how large area full field NEXAFS imaging allows users to pursue combinatorial studies of surface chemistry. Now we report an extension of this approach which allows the acquisition of orientation information from a single NEXAFS image. An array with 80 elements (samples), containing eight series of different surface modifications, was mounted on a curved substrate allowing the collection of NEXAFS spectra with a range of orientations with respect to the X-ray beam. Images collected from this array show how hyperspectral NEXAFS data collected from curved surfaces can be used for high-throughput molecular orientation analysis. PMID:25046426

  3. Controlling Nanostructures by Templated Templates: Inheriting Molecular Orientation in Binary Heterostructures.

    PubMed

    Breuer, Tobias; Witte, Gregor

    2015-09-16

    Precise preparation strategies are required to fabricate molecular nanostructures of specific arrangement. In bottom-up approaches, where nanostructures are gradually formed by piecing together individual parts to the final structure, the self-ordering mechanisms of the involved structures are utilized. In order to achieve the desired structures regarding morphology, grain size, and orientation of the individual moieties, templates can be applied, which influence the formation process of subsequent structures. However, this strategy is of limited use for complex architectures because the templates only influence the structure formation at the interface between the template and the first compound. Here, we discuss the implementation of so-called templated templates and analyze to what extent orientations of the initial layers are inherited in the top layers of another compound to enable structural control in binary heterostructures. For that purpose, we prepared crystalline templates of the organic semiconductors pentacene and perfluoropentacene in different exclusive orientations. We observe that for templates of both individual materials the molecular orientation is inherited in the top layers of the respective counterpart. This behavior is also observed for various other molecules, indicating the robustness of this approach. PMID:26305339

  4. Photodissociation of laboratory oriented molecules: Revealing molecular frame properties of nonaxial recoil

    SciTech Connect

    Brom, Alrik J. van den; Rakitzis, T. Peter; Janssen, Maurice H.M.

    2004-12-15

    We report the photodissociation of laboratory oriented OCS molecules. A molecular beam of OCS molecules is hexapole state-selected and spatially oriented in the electric field of a velocity map imaging lens. The oriented OCS molecules are dissociated at 230 nm with the linear polarization set at 45 deg. to the orientation direction of the OCS molecules. The CO({nu}=0,J) photofragments are quantum state-selectively ionized by the same 230 nm pulse and the angular distribution is measured using the velocity map imaging technique. The observed CO({nu}=0,J) images are strongly asymmetric and the degree of asymmetry varies with the CO rotational state J. From the observed asymmetry in the laboratory frame we can directly extract the molecular frame angles between the final photofragment recoil velocity and the permanent dipole moment and the transition dipole moment. The data for CO fragments with high rotational excitation reveal that the dissociation dynamics is highly nonaxial, even though conventional wisdom suggests that the nearly limiting {beta} parameter results from fast axial recoil dynamics. From our data we can extract the relative contribution of parallel and perpendicular transitions at 230 nm excitation.

  5. Extended orientational correlation study for molecular liquids containing distorted tetrahedral molecules: application to methylene halides.

    PubMed

    Pothoczki, Szilvia; Temleitner, László; Pusztai, László

    2010-04-28

    The method of Rey [Rey, J. Chem. Phys. 126, 164506 (2007)] for describing how molecules orient toward each other in systems with perfect tetrahedral molecules is extended to the case of distorted tetrahedral molecules of c(2v) symmetry by means of introducing 28 subgroups. Additionally, the original analysis developed for perfect tetrahedral molecules, based on six groups, is adapted for molecules with imperfect tetrahedral shape. Deriving orientational correlation functions have been complemented with detailed analyses of dipole-dipole correlations. This way, (up to now) the most complete structure determination can be carried out for such molecular systems. In the present work, these calculations have been applied for particle configurations resulting from reverse Monte Carlo computer modeling. These particle arrangements are fully consistent with structure factors from neutron and x-ray diffraction measurements. Here we present a complex structural study for methylene halide (chloride, bromide, and iodide) molecular liquids, as possibly the best representative examples. It has been found that the most frequent orientations of molecules are of the 2:2 type over the entire distance range in these liquids. Focusing on the short range orientation, neighboring molecules turn toward each other with there "H,Y"-"H,Y" (Y: Cl, Br, I) edges, apart from CH(2)Cl(2) where the H,H-H,Cl arrangement is the most frequent. In general, the structure of methylene chloride appears to be different from the structure of the other two liquids. PMID:20441292

  6. Molecular Beam Epitaxial Growth of GaAs on (631) Oriented Substrates

    SciTech Connect

    Cruz Hernandez, Esteban; Rojas Ramirez, Juan-Salvador; Contreras Hernandez, Rocio; Lopez Lopez, Maximo; Pulzara Mora, Alvaro; Mendez Garcia, Victor H.

    2007-02-09

    In this work, we report the study of the homoepitaxial growth of GaAs on (631) oriented substrates by molecular beam epitaxy (MBE). We observed the spontaneous formation of a high density of large scale features on the surface. The hilly like features are elongated towards the [-5, 9, 3] direction. We show the dependence of these structures with the growth conditions and we present the possibility of to create quantum wires structures on this surface.

  7. Mapping molecular orientational distributions for biological sample in 3D (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    HE, Wei; Ferrand, Patrick; Richter, Benjamin; Bastmeyer, Martin; Brasselet, Sophie

    2016-04-01

    Measuring molecular orientation properties is very appealing for scientists in molecular and cell biology, as well as biomedical research. Orientational organization at the molecular scale is indeed an important brick to cells and tissues morphology, mechanics, functions and pathologies. Recent work has shown that polarized fluorescence imaging, based on excitation polarization tuning in the sample plane, is able to probe molecular orientational order in biological samples; however this applies only to information in 2D, projected in the sample plane. To surpass this limitation, we extended this approach to excitation polarization tuning in 3D. The principle is based on the decomposition of any arbitrary 3D linear excitation in a polarization along the longitudinal z-axis, and a polarization in the transverse xy-sample plane. We designed an interferometer with one arm generating radial polarization light (thus producing longitudinal polarization under high numerical aperture focusing), the other arm controlling a linear polarization in the transverse plane. The amplitude ratio between the two arms can vary so as to get any linear polarized excitation in 3D at the focus of a high NA objective. This technique has been characterized by polarimetry imaging at the back focal plane of the focusing objective, and modeled theoretically. 3D polarized fluorescence microscopy is demonstrated on actin stress fibers in non-flat cells suspended on synthetic polymer structures forming supporting pillars, for which heterogeneous actin orientational order could be identified. This technique shows a great potential in structural investigations in 3D biological systems, such as cell spheroids and tissues.

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

    PubMed Central

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

    2016-01-01

    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. PMID:26998516

  9. Monte Carlo study of the molecular mechanisms of surface-layer protein self-assembly

    NASA Astrophysics Data System (ADS)

    Horejs, Christine; Mitra, Mithun K.; Pum, Dietmar; Sleytr, Uwe B.; Muthukumar, Murugappan

    2011-03-01

    The molecular mechanisms guiding the self-assembly of proteins into functional or pathogenic large-scale structures can be only understood by studying the correlation between the structural details of the monomer and the eventual mesoscopic morphologies. Among the myriad structural details of protein monomers and their manifestations in the self-assembled morphologies, we seek to identify the most crucial set of structural features necessary for the spontaneous selection of desired morphologies. Using a combination of the structural information and a Monte Carlo method with a coarse-grained model, we have studied the functional protein self-assembly into S(surface)-layers, which constitute the crystallized outer most cell envelope of a great variety of bacterial cells. We discover that only few and mainly hydrophobic amino acids, located on the surface of the monomer, are responsible for the formation of a highly ordered anisotropic protein lattice. The coarse-grained model presented here reproduces accurately many experimentally observed features including the pore formation, chemical description of the pore structure, location of specific amino acid residues at the protein-protein interfaces, and surface accessibility of specific amino acid residues. In addition to elucidating the molecular mechanisms and explaining experimental findings in the S-layer assembly, the present work offers a tool, which is chemical enough to capture details of primary sequences and coarse-grained enough to explore morphological structures with thousands of protein monomers, to promulgate design rules for spontaneous formation of specific protein assemblies.

  10. 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. PMID:26998516

  11. Monte Carlo study of the molecular mechanisms of surface-layer protein self-assembly.

    PubMed

    Horejs, Christine; Mitra, Mithun K; Pum, Dietmar; Sleytr, Uwe B; Muthukumar, Murugappan

    2011-03-28

    The molecular mechanisms guiding the self-assembly of proteins into functional or pathogenic large-scale structures can be only understood by studying the correlation between the structural details of the monomer and the eventual mesoscopic morphologies. Among the myriad structural details of protein monomers and their manifestations in the self-assembled morphologies, we seek to identify the most crucial set of structural features necessary for the spontaneous selection of desired morphologies. Using a combination of the structural information and a Monte Carlo method with a coarse-grained model, we have studied the functional protein self-assembly into S(surface)-layers, which constitute the crystallized outer most cell envelope of a great variety of bacterial cells. We discover that only few and mainly hydrophobic amino acids, located on the surface of the monomer, are responsible for the formation of a highly ordered anisotropic protein lattice. The coarse-grained model presented here reproduces accurately many experimentally observed features including the pore formation, chemical description of the pore structure, location of specific amino acid residues at the protein-protein interfaces, and surface accessibility of specific amino acid residues. In addition to elucidating the molecular mechanisms and explaining experimental findings in the S-layer assembly, the present work offers a tool, which is chemical enough to capture details of primary sequences and coarse-grained enough to explore morphological structures with thousands of protein monomers, to promulgate design rules for spontaneous formation of specific protein assemblies. PMID:21456703

  12. Understanding Molecular Interactions within Chemically Selective Layered Polymer Assemblies

    SciTech Connect

    Gary J. Blanchard

    2009-06-30

    This work focuses on two broad issues. These are (1) the molecular origin of the chemical selectivity achieved with ultrathin polymer multilayers, and (2) how the viscoelastic properties of the polymer layers are affected by exposure to solvent and analytes. These issues are inter-related, and to understand them we need to design experiments that probe both the energetic and kinetic aspects of interfacial adsorption processes. This project focuses on controling the chemical structure, thickness, morphology and sequential ordering of polymer layers bound to interfaces using maleimide-vinyl ether and closely related alternating copolymerization chemistry and efficient covalent cross-linking reactions that allow for layer-by-layer polymer deposition. This chemistry has been developed during the funding cycle of this Grant. We have measure the equilibrium constants for interactions between specific layers within the polymer interfaces and size-controlled, surface-functionalized gold nanoparticles. The ability to control both size and functionality of gold nanoparticle model analytes allows us to evaluate the average “pore size” that characterizes our polymer films. We have measured the “bulk” viscosity and shear modulus of the ultrathin polymer films as a function of solvent overlayer identity using quartz crystal microbalance complex impedance measurements. We have measured microscopic viscosity at specific locations within the layered polymer interfaces with time-resolved fluorescence lifetime and depolarization techniques. We combine polymer, cross-linking and nanoparticle synthetic expertise with a host of characterization techniques, including QCM gravimetry and complex impedance analysis, steady state and time-resolved spectroscopies.

  13. 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. PMID:27088305

  14. Designed self-assembly of molecular necklaces using host-stabilized charge-transfer interactions.

    PubMed

    Ko, Young Ho; Kim, Kyungpil; Kang, Jin-Koo; Chun, Hyungphil; Lee, Jae Wook; Sakamoto, Shigeru; Yamaguchi, Kentaro; Fettinger, James C; Kim, Kimoon

    2004-02-25

    A novel approach to the noncovalent synthesis of molecular necklaces successfully led to the first quantitative self-assembly of a molecular necklace [6]MN, in which five small rings are threaded on a large ring, from 10 components. Our strategy involves the host-guest complex formation between the molecular host cucurbit[8]uril (CB[8]) and a guest molecule in which an electron donor and an electron acceptor unit are connected by a rigid linker with a proper angle, to form a cyclic oligomer through the host-stabilized intermolecular charge-transfer (CT) complex formation. In the structure of the molecular necklace [6]MN, five molecules of the guest form a cyclic framework by the intermolecular CT interactions, on which five CB[8] molecules are threaded with an arrangement reminiscent of a five-fold propeller. The molecular necklace measures approximately 3.7 nm in diameter and approximately 1.8 nm in thickness. PMID:14971915

  15. Synthetic Molecular Machines for Active Self-Assembly: Prototype Algorithms, Designs, and Experimental Study

    NASA Astrophysics Data System (ADS)

    Dabby, Nadine L.

    Computer science and electrical engineering have been the great success story of the twentieth century. The neat modularity and mapping of a language onto circuits has led to robots on Mars, desktop computers and smartphones. But these devices are not yet able to do some of the things that life takes for granted: repair a scratch, reproduce, regenerate, or grow exponentially fast--all while remaining functional. This thesis explores and develops algorithms, molecular implementations, and theoretical proofs in the context of "active self-assembly" of molecular systems. The long-term vision of active self-assembly is the theoretical and physical implementation of materials that are composed of reconfigurable units with the programmability and adaptability of biology's numerous molecular machines. En route to this goal, we must first find a way to overcome the memory limitations of molecular systems, and to discover the limits of complexity that can be achieved with individual molecules. One of the main thrusts in molecular programming is to use computer science as a tool for figuring out what can be achieved. While molecular systems that are Turing-complete have been demonstrated [Winfree, 1996], these systems still cannot achieve some of the feats biology has achieved. One might think that because a system is Turing-complete, capable of computing "anything," that it can do any arbitrary task. But while it can simulate any digital computational problem, there are many behaviors that are not "computations" in a classical sense, and cannot be directly implemented. Examples include exponential growth and molecular motion relative to a surface. Passive self-assembly systems cannot implement these behaviors because (a) molecular motion relative to a surface requires a source of fuel that is external to the system, and (b) passive systems are too slow to assemble exponentially-fast-growing structures. We call these behaviors "energetically incomplete" programmable

  16. Manipulation of Self-Assembled Nanostructure Dimensions in Molecular Janus Particles.

    PubMed

    Liu, Hao; Luo, Jiancheng; Shan, Wenpeng; Guo, Dong; Wang, Jing; Hsu, Chih-Hao; Huang, Mingjun; Zhang, Wei; Lotz, Bernard; Zhang, Wen-Bin; Liu, Tianbo; Yue, Kan; Cheng, Stephen Z D

    2016-07-26

    The ability to manipulate self-assembly of molecular building blocks is the key to achieving precise "bottom-up" fabrications of desired nanostructures. Herein, we report a rational design, facile synthesis, and self-assembly of a series of molecular Janus particles (MJPs) constructed by chemically linking α-Keggin-type polyoxometalate (POM) nanoclusters with functionalized polyhedral oligomeric silsesquioxane (POSS) cages. Diverse nanostructures were obtained by tuning secondary interactions among the building blocks and solvents via three factors: solvent polarity, surface functionality of POSS derivatives, and molecular topology. Self-assembled morphologies of KPOM-BPOSS (B denotes isobutyl groups) were found dependent on solvent polarity. In acetonitrile/water mixtures with a high dielectric constant, colloidal nanoparticles with nanophase-separated internal lamellar structures quickly formed, which gradually turned into one-dimensional nanobelt crystals upon aging, while stacked crystalline lamellae were dominantly observed in less polar methanol/chloroform solutions. When the crystallizable BPOSS was replaced with noncrystallizable cyclohexyl-functionalized CPOSS, the resulting KPOM-CPOSS also formed colloidal spheres; however, it failed to further evolve into crystalline nanobelt structures. In less polar solvents, KPOM-CPOSS crystallized into isolated two-dimensional nanosheets, which were composed of two inner crystalline layers of Keggin POM covered by two monolayers of amorphous CPOSS. In contrast, self-assembly of KPOM-2BPOSS was dominated by crystallization of the BPOSS cages, which was hardly sensitive to solvent polarity. The BPOSS cages formed the crystalline inner bilayer, sandwiched by two outer layers of Keggin POM clusters. These results illustrate a rational strategy to purposely fabricate self-assembled nanostructures with diverse dimensionality from MJPs with controlled molecular composition and topology. PMID:27337531

  17. Programmable concatenation of conductively linked gold nanorods using molecular assembly and femtosecond irradiation

    NASA Astrophysics Data System (ADS)

    Fontana, Jake; Flom, Steve; Naciri, Jawad; Ratna, Banahalli

    The ability to tune the resonant frequency in plasmonic nanostructures is fundamental to developing novel optical properties and ensuing materials. Recent theoretical insights show that the plasmon resonance can be exquisitely controlled through the conductive concatenation of plasmonic nanoparticles. Furthermore these charge transfer systems may mimic complex and hard to build nanostructures. Here we experimentally demonstrate a directed molecular assembly approach to controllably concatenate gold nanorods end to end into discrete linear structures, bridged with gold nanojunctions, using femtosecond laser light. By utilizing high throughput and nanometer resolution this approach offers a pragmatic assembly strategy for charge transfer plasmonic systems.

  18. Long-range orientational order, local-field anisotropy, and mean molecular polarizability in liquid crystals

    SciTech Connect

    Aver'yanov, E. M.

    2009-01-15

    The problems on the relation of the mean effective molecular polarizability {gamma}-bar to the long-range orientational order of molecules (the optical anisotropy of the medium) in uniaxial and biaxial liquid crystals, the local anisotropy on mesoscopic scales, and the anisotropy of the Lorentz tensor L and the local-field tensor f are formulated and solved. It is demonstrated that the presence of the long-range orientational order of molecules in liquid crystals imposes limitations from below on the molecular polarizability {gamma}-bar, which differs for uniaxial and biaxial liquid crystals. The relation between the local anisotropy and the molecular polarizability {gamma}-bar is investigated for calamitic and discotic uniaxial liquid crystals consisting of lath- and disk-shaped molecules. These liquid crystals with identical macroscopic symmetry differ in the local anisotropy and the relationships between the components L{sub parallel} < L{sub perpendicular} , f{sub parallel} < f{sub perpendicular} (calamitic) and L{sub parallel} > L{sub perpendicular} , f{sub parallel} > f{sub perpendicular} (discotic) for an electric field oriented parallel and perpendicular to the director. The limitations from below and above on the molecular polarizability {gamma}-bar due to the anisotropy of the tensors L and f are established for liquid crystals of both types. These limitations indicate that the molecular polarizability {gamma}-bar depends on the phase state and the temperature. The factors responsible for the nonphysical consequences of the local-field models based on the approximation {gamma}-bar = const are revealed. The theoretical inferences are confirmed by the experimental data for a number of calamitic nematic liquid crystals with different values of birefringence and the discotic liquid crystal Col{sub ho}.

  19. Monitoring intermediate filament assembly by small-angle x-ray scattering reveals the molecular architecture of assembly intermediates

    PubMed Central

    Sokolova, Anna V.; Kreplak, Laurent; Wedig, Tatjana; Mücke, Norbert; Svergun, Dmitri I.; Herrmann, Harald; Aebi, Ueli; Strelkov, Sergei V.

    2006-01-01

    Intermediate filaments (IFs), along with microtubules, microfilaments, and associated cross-bridging proteins, constitute the cytoskeleton of metazoan cells. While crystallographic data on the dimer representing the elementary IF “building block” have recently become available, little structural detail is known about both the mature IF architecture and its assembly pathway. Here, we have applied solution small-angle x-ray scattering to investigate the in vitro assembly of a 53-kDa human IF protein vimentin at pH 8.4 by systematically varying the ionic strength conditions, and complemented these experiments by electron microscopy and analytical ultracentrifugation. While a vimentin solution in 5 mM Tris·HCl (pH 8.4) contains predominantly tetramers, addition of 20 mM NaCl induces further lateral assembly evidenced by the shift of the sedimentation coeficient and yields a distinct octameric intermediate. Four octamers eventually associate into unit-length filaments (ULFs) that anneal longitudinally. Based on the small-angle x-ray scattering experiments supplemented by crystallographic data and additional structural constraints, 3D molecular models of the vimentin tetramer, octamer, and ULF were constructed. Within each of the three oligomers, the adjacent dimers are aligned exclusively in an approximately half-staggered antiparallel A11 mode with a distance of 3.2–3.4 nm between their axes. The ULF appears to be a dynamic and a relatively loosely packed structure with a roughly even mass distribution over its cross-section. PMID:17050693

  20. Molecular and electronic structure of osmium complexes confined to Au(111) surfaces using a self-assembled molecular bridge.

    PubMed

    de la Llave, Ezequiel; Herrera, Santiago E; Adam, Catherine; Méndez De Leo, Lucila P; Calvo, Ernesto J; Williams, Federico J

    2015-11-14

    The molecular and electronic structure of Os(II) complexes covalently bonded to self-assembled monolayers (SAMs) on Au(111) surfaces was studied by means of polarization modulation infrared reflection absorption spectroscopy, photoelectron spectroscopies, scanning tunneling microscopy, scanning tunneling spectroscopy, and density functional theory calculations. Attachment of the Os complex to the SAM proceeds via an amide covalent bond with the SAM alkyl chain 40° tilted with respect to the surface normal and a total thickness of 26 Å. The highest occupied molecular orbital of the Os complex is mainly based on the Os(II) center located 2.2 eV below the Fermi edge and the LUMO molecular orbital is mainly based on the bipyridine ligands located 1.5 eV above the Fermi edge. PMID:26567676

  1. Molecular and electronic structure of osmium complexes confined to Au(111) surfaces using a self-assembled molecular bridge

    SciTech Connect

    Llave, Ezequiel de la; Herrera, Santiago E.; Adam, Catherine; Méndez De Leo, Lucila P.; Calvo, Ernesto J.; Williams, Federico J.

    2015-11-14

    The molecular and electronic structure of Os(II) complexes covalently bonded to self-assembled monolayers (SAMs) on Au(111) surfaces was studied by means of polarization modulation infrared reflection absorption spectroscopy, photoelectron spectroscopies, scanning tunneling microscopy, scanning tunneling spectroscopy, and density functional theory calculations. Attachment of the Os complex to the SAM proceeds via an amide covalent bond with the SAM alkyl chain 40° tilted with respect to the surface normal and a total thickness of 26 Å. The highest occupied molecular orbital of the Os complex is mainly based on the Os(II) center located 2.2 eV below the Fermi edge and the LUMO molecular orbital is mainly based on the bipyridine ligands located 1.5 eV above the Fermi edge.

  2. Molecular and electronic structure of osmium complexes confined to Au(111) surfaces using a self-assembled molecular bridge

    NASA Astrophysics Data System (ADS)

    de la Llave, Ezequiel; Herrera, Santiago E.; Adam, Catherine; Méndez De Leo, Lucila P.; Calvo, Ernesto J.; Williams, Federico J.

    2015-11-01

    The molecular and electronic structure of Os(II) complexes covalently bonded to self-assembled monolayers (SAMs) on Au(111) surfaces was studied by means of polarization modulation infrared reflection absorption spectroscopy, photoelectron spectroscopies, scanning tunneling microscopy, scanning tunneling spectroscopy, and density functional theory calculations. Attachment of the Os complex to the SAM proceeds via an amide covalent bond with the SAM alkyl chain 40° tilted with respect to the surface normal and a total thickness of 26 Å. The highest occupied molecular orbital of the Os complex is mainly based on the Os(II) center located 2.2 eV below the Fermi edge and the LUMO molecular orbital is mainly based on the bipyridine ligands located 1.5 eV above the Fermi edge.

  3. Self-assembly of mixed lipids into bicelles and vesicles: molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Sharma, Hari; Wang, Zilu; Dormidontova, Elena

    Formation of complex supramolecular nanostructures, such as micelles, bicelles, vesicles (liposomes) etc. via self-assembly of simple molecules has provided a new pathway for the design and development of effective drug carriers. Solid nanoparticles or functional biopolymers, such as RNA, DNA, peptides can be encapsulated into these carriers for controlled delivery or selective targeting. We performed coarse grained molecular dynamics simulation using the MARTINI force field to study the self-assembly of a binary surfactant mixture composed of long and short phospholipids, DPPC and DHPC, in the ratio 3:1. We found that at low temperature lipids self-assemble into a bicelle (nanodisc) with the longer lipid mainly forming the interior and short lipid the rim of the bicelle. At higher temperature the nanodisc transforms into a vesicle with homogeneously distributed lipids. The structural changes of these nanodiscs and vesicles imposed by gold nanoparticle encapsulation and pegylation will be addressed.

  4. Self-assembled molecular rafts at liquid|liquid interfaces for four-electron oxygen reduction.

    PubMed

    Olaya, Astrid J; Schaming, Delphine; Brevet, Pierre-Francois; Nagatani, Hirohisa; Zimmermann, Tomas; Vanicek, Jiri; Xu, Hai-Jun; Gros, Claude P; Barbe, Jean-Michel; Girault, Hubert H

    2012-01-11

    The self-assembly of the oppositely charged water-soluble porphyrins, cobalt tetramethylpyridinium porphyrin (CoTMPyP(4+)) and cobalt tetrasulphonatophenyl porphyrin (CoTPPS(4-)), at the interface with an organic solvent to form molecular "rafts", provides an excellent catalyst to perform the interfacial four-electron reduction of oxygen by lipophilic electron donors such as tetrathiafulvalene (TTF). The catalytic activity and selectivity of the self-assembled catalyst toward the four-electron pathway was found to be as good as that of the Pacman type cofacial cobalt porphyrins. The assembly has been characterized by UV-visible spectroscopy, Surface Second Harmonic Generation, and Scanning Electron Microscopy. Density functional theory calculations confirm the possibility of formation of the catalytic CoTMPyP(4+)/ CoTPPS(4-) complex and its capability to bind oxygen. PMID:22107335

  5. Parity-selective enhancement of field-free molecular orientation in an intense two-color laser field

    SciTech Connect

    Yun, Hyeok; Nam, Chang Hee; Kim, Hyung Taek; Kim, Chul Min; Lee, Jongmin

    2011-12-15

    We investigated the characteristics of molecular orientation induced by a nonresonant two-color femtosecond laser field. By analyzing the rotational dynamics of asymmetric linear molecules, we revealed that the critical parameter in characterizing the molecular orientation was the hyperpolarizability of molecules that selected the excitation paths of rotational states between parity-changing and parity-conserving transitions. Especially, in the case of molecules with small hyperpolarizability, a significant enhancement of orientation was achieved at the half-rotational period, instead of the full-rotational period. This deeper understanding of the hyperpolarizability-dependent characteristics of molecular orientation in a two-color scheme can provide an effective method to achieve significantly enhanced field-free orientation for various polar molecules.

  6. Monitoring molecular orientational order in NLO push-pull based polymeric films via photoacoustic measurements

    NASA Astrophysics Data System (ADS)

    Torres-Zúñiga, V.; Castañeda-Guzmán, R.; Morales-Saavedra, O. G.; Pérez-Martínez, A. L.; Ogawa, T.

    2011-12-01

    The pulsed-laser photoacoustic-technique (PLPA) was implemented to characterize molecular orientational order and anisotropy in push-pull poled polymeric films as function of temperature and laser polarization. Traditionally, photoacoustic signals are considered to be directly proportional to the linear optical absorption in amorphous media. In this work, however, it is shown that photoacoustic signals can also be highly sensitive to the material anisotropy when convenient polarization dependent photoacoustic analyses are performed. Thus, variation of the molecular orientation in organic films, comprising rod-like polar chromophores, can be unambiguously monitored via rms-analyses performed on the amplitude of the generated opto-acoustical PLPA-signals as function of the incident laser polarization. This result can be useful for the characterization of organic-based nonlinear optical (NLO) poled films and, in general, in studies of anisotropic materials. In fact, in this work we were able to accurately determine the molecular order parameter ( ϕ) of a NLO-active spin-coated polymeric film containing optically active push-pull chromophores. These molecules, previously oriented via an electrical-poling procedure, are capable to exhibit strong second harmonic generation (SHG) effects. The PLPA-measurements were systematically compared to the linear UV-vis optical absorbance spectra while heating the poled film sample in order to monitor the thermally induced molecular disorder, so that the order parameter may be photo-acoustically evaluated via the PLPA-signals generated from the poled to the unpoled film phase. These PLPA-experiments were performed taking into account the UV-vis reference spectra for calibration and comparison purposes in the evaluation of the order parameter. A significant advantage of the PLPA-technique over commonly used optical spectral methodologies is its convenient applicability in samples exhibiting poor or null optical transmission.

  7. Transient molecular orientation and rheology in flow aligning thermotropic liquid crystalline polymers

    SciTech Connect

    Ugaz, Victor M.; Burghardt, Wesley R.; Zhou, Weijun; Kornfield, Julia A.

    2001-09-01

    Quantitative measurements of molecular orientation and rheology are reported for various transient shear flows of a nematic semiflexible copolyether. Unlike the case of lyotropic liquid crystalline polymers (LCPs), whose structure and rheology in shear are dominated by director tumbling, this material exhibits flow aligning behavior. The observed behavior is quite similar to that seen in a copolyester that we have recently studied [Ugaz and Burghardt (1998)], suggesting that flow aligning dynamics may predominate in main-chain thermotropes that incorporate significant chain flexibility. Since the flow aligning regime has received little attention in previous attempts to model the rheology of textured, polydomain LCPs, we attempt to determine whether available models are capable of predicting the orientation and stress response of this class of LCP. We first examine the predictions of the polydomain Ericksen model, an adaptation of Ericksen's transversely isotropic fluid model which accounts for the polydomain distribution of director orientation while neglecting distortional elasticity. This simple model captures a number of qualitative and quantitative features associated with the evolution of orientation and stress during shear flow inception, but cannot cope with reversing flows. To consider the possible role of distortional elasticity in the re-orientation dynamics upon reversal, we evaluate the mesoscopically averaged domain theory of Larson and Doi [Larson and Doi (1991)], which incorporates a phenomenological description of distortional elastic effects. To date, their approach to account for polydomain structure has only been applied to describe tumbling LCPs. We find that it captures the qualitative transient orientation response to flow reversals, but is less successful in describing the evolution of stresses. This is linked to the decoupling approximation adopted during the model's development. Finally, a modified polydomain Ericksen model is introduced

  8. Molecular Self-Assembly of Short Aromatic Peptides: From Biology to Nanotechnology and Material Science

    NASA Astrophysics Data System (ADS)

    Gazit, Ehud

    2013-03-01

    The formation of ordered amyloid fibrils is the hallmark of several diseases of unrelated origin. In spite of grave clinical consequence, the mechanism of amyloid formation is not fully understood. We have suggested, based on experimental and bioinformatic analysis, that aromatic interactions may provide energetic contribution as well as order and directionality in the molecular-recognition and self-association processes that lead to the formation of these assemblies. This is in line with the well-known central role of aromatic-stacking interactions in self-assembly processes. Our works on the mechanism of aromatic peptide self-assembly, lead to the discovery that the diphenylalanine recognition motif self-assembles into peptide nanotubes with a remarkable persistence length. Other aromatic homodipeptides could self-assemble in nano-spheres, nano-plates, nano-fibrils and hydrogels with nano-scale order. We demonstrated that the peptide nanostructures have unique chemical, physical and mechanical properties including ultra-rigidity as aramides, semi-conductive, piezoelectric and non-linear optic properties. We also demonstrated the ability to use these peptide nanostructures as casting mold for the fabrication of metallic nano-wires and coaxial nano-cables. The application of the nanostructures was demonstrated in various fields including electrochemical biosensors, tissue engineering, and molecular imaging. Finally, we had developed ways for depositing of the peptide nanostructures and their organization. We had use inkjet technology as well as vapour deposition methods to coat surface and from the peptide ``nano-forests''. We recently demonstrated that even a single phenylalanine amino-acid can form well-ordered fibrilar assemblies.

  9. DNA hybridization in nanostructural molecular assemblies enables detection of gene mutations without a fluorescent probe.

    PubMed

    Maruyama, Tatsuo; Park, Lian-Chun; Shinohara, Toshimitsu; Goto, Masahiro

    2004-01-01

    We have developed a simple single nucleotide polymorphisms (SNPs) analysis utilizing DNA hybridization in nanostructural molecular assemblies. The novel technique enables the detection of a single-base mismatch in a DNA sequence without a fluorescent probe. This report describes for the first time that DNA hybridization occurs in the nanostructural molecular assemblies (termed reverse micelles) formed in an organic medium. The restricted nanospace in the reverse micelles amplifies the differences in the hybridization rate between mismatched and perfectly matched DNA probes. For a model system, we hybridized a 20-mer based on the p53 gene sequence to 20-mer complementary oligonucleotides with various types of mismatches. Without any DNA labeling or electrochemical apparatus, we successfully detected the various oligonucleotide mismatches by simply measuring the UV absorbance at 260 nm. PMID:14715007

  10. Five-vertex Archimedean surface tessellation by lanthanide-directed molecular self-assembly

    PubMed Central

    Écija, David; Urgel, José I.; Papageorgiou, Anthoula C.; Joshi, Sushobhan; Auwärter, Willi; Seitsonen, Ari P.; Klyatskaya, Svetlana; Ruben, Mario; Fischer, Sybille; Vijayaraghavan, Saranyan; Reichert, Joachim; Barth, Johannes V.

    2013-01-01

    The tessellation of the Euclidean plane by regular polygons has been contemplated since ancient times and presents intriguing aspects embracing mathematics, art, and crystallography. Significant efforts were devoted to engineer specific 2D interfacial tessellations at the molecular level, but periodic patterns with distinct five-vertex motifs remained elusive. Here, we report a direct scanning tunneling microscopy investigation on the cerium-directed assembly of linear polyphenyl molecular linkers with terminal carbonitrile groups on a smooth Ag(111) noble-metal surface. We demonstrate the spontaneous formation of fivefold Ce–ligand coordination motifs, which are planar and flexible, such that vertices connecting simultaneously trigonal and square polygons can be expressed. By tuning the concentration and the stoichiometric ratio of rare-earth metal centers to ligands, a hierarchic assembly with dodecameric units and a surface-confined metal–organic coordination network yielding the semiregular Archimedean snub square tiling could be fabricated. PMID:23576764