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1

Endogenous Damage-Associated Molecular Pattern Molecules at the Crossroads of Inflammation and Cancer1  

PubMed Central

Inflammatory mediators play important roles in the development and progression of cancer. Cellular stress, damage, inflammation, and necrotic cell death cause release of endogenous damage-associated molecular pattern (DAMP) molecules or alarmins, which alert the host of danger by triggering immune responses and activating repair mechanisms through their interaction with pattern recognition receptors. Recent studies show that abnormal persistence of these molecules in chronic inflammation and in tumor microenvironments underlies carcinogenesis and tumor progression, indicating that DAMP molecules and their receptors could provide novel targets for therapy. This review focuses on the role of DAMP molecules high-mobility group box 1 and S100 proteins in inflammation, tumor growth, and early metastatic events.

Srikrishna, Geetha; Freeze, Hudson H

2009-01-01

2

Programmable motion and patterning of molecules on solid surfaces.  

PubMed

Adsorbed on a solid surface, a molecule can migrate and carry an electric dipole moment. A nonuniform electric field can direct the motion of the molecule. A collection of the same molecules may aggregate into a monolayer island on the solid surface. Place such molecules on a dielectric substrate surface, beneath which an array of electrodes is buried. By varying the voltages of the electrodes individually, it is possible to program molecular patterning, direct an island to move in a desired trajectory, or merge several islands into a larger one. The dexterity may lead to new technologies, such as reconfigurable molecular patterning and programmable molecular cars. This paper develops a phase field model to simulate the molecular motion and patterning under the combined actions of dipole moments, intermolecular forces, entropy, and electrodes. PMID:15138299

Suo, Z; Hong, W

2004-05-25

3

Single molecule magnets: from thin films to nano-patterns.  

PubMed

Single molecule magnets (SMM) are a class of molecules exhibiting magnetic properties similar to those observed in conventional bulk magnets, but of molecular origin. SMMs have been proposed as potential candidates for several technological applications that require highly controlled thin films and patterns. Here we present an overview of the most important approaches for thin film growth and micro(nano)-patterning of SMM, giving special attention to Mn(12) based molecules. We present both conventional approaches to thin film growth (Langmuir-Blodgett, chemical approach, dip and dry, laser evaporation), patterning (micro-contact printing, deposition on patterned surface, moulding of homogeneous films) and new methods specifically developed for SMM (lithographically controlled wetting, lithographically controlled de-mixing). PMID:18231680

Cavallini, Massimiliano; Facchini, Massimo; Albonetti, Cristiano; Biscarini, Fabio

2008-02-14

4

DAMP Molecule S100A9 Acts as a Molecular Pattern to Enhance Inflammation during Influenza A Virus Infection: Role of DDX21-TRIF-TLR4-MyD88 Pathway  

PubMed Central

Pathogen-associated molecular patterns (PAMPs) trigger host immune response by activating pattern recognition receptors like toll-like receptors (TLRs). However, the mechanism whereby several pathogens, including viruses, activate TLRs via a non-PAMP mechanism is unclear. Endogenous “inflammatory mediators” called damage-associated molecular patterns (DAMPs) have been implicated in regulating immune response and inflammation. However, the role of DAMPs in inflammation/immunity during virus infection has not been studied. We have identified a DAMP molecule, S100A9 (also known as Calgranulin B or MRP-14), as an endogenous non-PAMP activator of TLR signaling during influenza A virus (IAV) infection. S100A9 was released from undamaged IAV-infected cells and extracellular S100A9 acted as a critical host-derived molecular pattern to regulate inflammatory response outcome and disease during infection by exaggerating pro-inflammatory response, cell-death and virus pathogenesis. Genetic studies showed that the DDX21-TRIF signaling pathway is required for S100A9 gene expression/production during infection. Furthermore, the inflammatory activity of extracellular S100A9 was mediated by activation of the TLR4-MyD88 pathway. Our studies have thus, underscored the role of a DAMP molecule (i.e. extracellular S100A9) in regulating virus-associated inflammation and uncovered a previously unknown function of the DDX21-TRIF-S100A9-TLR4-MyD88 signaling network in regulating inflammation during infection.

Tsai, Su-Yu; Segovia, Jesus A.; Chang, Te-Hung; Morris, Ian R.; Berton, Michael T.; Tessier, Philippe A.; Tardif, Melanie R.; Cesaro, Annabelle; Bose, Santanu

2014-01-01

5

Structure factor and rheology of chain molecules from molecular dynamics  

NASA Astrophysics Data System (ADS)

Equilibrium and non-equilibrium molecular dynamics were performed to determine the relationship between the static structure factor, the molecular conformation, and the rheological properties of chain molecules. A spring-monomer model with Finitely Extensible Nonlinear Elastic and Lennard-Jones force field potentials was used to describe chain molecules. The equations of motion were solved for shear flow with SLLOD equations of motion integrated with Verlet's algorithm. A multiple time scale algorithm extended to non-equilibrium situations was used as the integration method. Concentric circular patterns in the structure factor were obtained, indicating an isotropic Newtonian behavior. Under simple shear flow, some peaks in the structure factor were emerged corresponding to an anisotropic pattern as chains aligned along the flow direction. Pure chain molecules and chain molecules in solution displayed shear-thinning regions. Power-law and Carreau-Yasuda models were used to adjust the generated data. Results are in qualitative agreement with rheological and light scattering experiments.

Castrejón-González, Omar; Castillo-Tejas, Jorge; Manero, Octavio; Alvarado, Juan F. J.

2013-05-01

6

Relativistic Molecular Orbital Calculations for Diatomic Molecules  

Microsoft Academic Search

The relativistic molecular orbital calculations have been made for diatomic molecules by the use of the discrete variational Xa method. The validity of the method has been tested for CO mole- cule and good agreement is obtained between the relativistic and nonrelativistic calculations. The relativistic results for UO molecule are compared with the nonrelativistic ones and the importance of the

Takeshi MUKOYAMA; Hirohiko ADACHI

7

Patterns and conformations in molecularly thin films  

NASA Astrophysics Data System (ADS)

Molecularly thin films have been a subject of great interest for the last several years because of their large variety of industrial applications ranging from micro-electronics to bio-medicine. Additionally, molecularly thin films can be used as good models for biomembrane and other systems where surfaces are critical. Many different kinds of molecules can make stable films. My research has considered three such molecules: a polymerizable phospholipid, a bent-core molecules, and a polymer. One common theme of these three molecules is chirality. The phospolipid molecules studied here are strongly chiral, which can be due to intrinsically chiral centers on the molecules and also due to chiral conformations. We find that these molecules give rise to chiral patterns. Bent-core molecules are not intrinsically chiral, but individual molecules and groups of molecules can show chiral structures, which can be changed by surface interactions. One major, unconfirmed hypothesis for the polymer conformation at surface is that it forms helices, which would be chiral. Most experiments were carried out at the air/water interface, in what are called Langmuir films. Our major tools for studying these films are Brewster Angle Microscopy (BAM) coupled with the thermodynamic information that can be deduced from surface pressure isotherms. Phospholipids are one of the important constituents of liposomes -- a spherical vesicle com-posed of a bilayer membrane, typically composed of a phospholipid and cholesterol bilayer. The application of liposomes in drug delivery is well-known. Crumpling of vesicles of polymerizable phospholipids has been observed. With BAM, on Langmuir films of such phospholipids, we see novel spiral/target patterns during compression. We have found that both the patterns and the critical pressure at which they formed depend on temperature (below the transition to a i¬‘uid layer). Bent-core liquid crystals, sometimes knows as banana liquid crystals, have drawn increasing attention because of the richness in phases that they exhibit. Due to the unique coupling between dipole properties and the packing constraints placed by the bent shape, these molecules are emerging as strong candidates in electromechanical devices. However, most applications require that the molecules be aligned, which has proved difficult. Our group has tested such molecules both as Langmuir layers and, when transferred to a solid, as alignment layers with some limited success. However, these molecules do not behave well with the surfaces and the domains at the air/water interface tend to form ill-controlled multilayer structures since attraction with the surfaces is relatively weak. New bent-core molecules obtained from Prof. Dr. C. Tsehiemke from Department of Chemistry Institute of Organic Chemistry, Martin-Luther-University, Germany, have a hydrophilic group at one end. We expect this molecule to behave better on the surface because of the stronger attraction of the hydrophilic group towards the surface than for the bent-core molecules without the hydrophilic group. Polydimethylsiloxane (PDMS) is a polymer which finds many applications in modifying surface properties. It is used in manufacturing lubricants, protective coatings, hair conditioner and glass-coating. However its properties are not well understood. This polymer has been proposed to follow either helical or caterpillar conformations on a surface. The orientational order of CH3 side groups can test for these conformations (they would be predominantly up/down for the caterpillar conformation, but rotating through the entire 360 degree for the helical one). Thus previous work on the Langmuir polymer films at the air/water interface were complemented by deuterium NMR studies to probe their conformations at a surface. These experiments were performed using humid porous solids, in order to provide sufficient surface area for the technique. Previous tests in this group at room temperature were suggestive but inconclusive because of the rapid averaging motion of the molecules. Here, we attempt t

Basnet, Prem B.

8

Molecular-beam spectroscopy of interhalogen molecules  

SciTech Connect

A molecular-beam electric-resonance spectrometer employing a supersonic nozzle source has been used to obtain hyperfine spectra of /sup 79/Br/sup 35/Cl. Analyses of these spectra and of microwave spectra published by other authors have yielded new values for the electric dipole moment and for the nuclear quadrupole coupling constants in this molecule. The new constants are significantly different from the currently accepted values. Van der Waals clusters containing chlorine monofluoride have been studied under various expansion conditions by the molecular-beam electric-deflection method. The structural possibilities indicated by the results are discussed, and cluster geometries are proposed.

Sherrow, S.A.

1983-08-01

9

Dynamic spiral patterns in Langmuir monolayers of chiral molecules  

NASA Astrophysics Data System (ADS)

Experiments with Langmuir monolayers of chiral molecules on a water surface report a collective propeller-like precession of the molecules due to the evaporation of water [1]. If the molecular orientation is pinned along an edge, the precession leads to a series of stripes along the edge. This pattern formation has been explained by a dynamic equation due to the Lehmann effect [2]. Here, we consider how the patterns change if the monolayer contains vortices, topological defects which pin the molecular orientation. We model an annular ring with a single vortex at its center, and show that the director field forms a spiral centered at the defect, which reverses handedness between the inner and outer boundaries. We also simulate a system with one vortex and one anti-vortex on a lattice, and find that the defects form spirals with opposite handedness. These analytic and computational results are in good agreement with preliminary experiments [3]. [1] Y. Tabe, H. Yokoyama, Nat. Mater. 2, 806 (2003). [2] D. Svensek, H. Pleiner, H. R. Brand, Phys. Rev. Lett. 96, 140601 (2006). [3] K. A. Suresh, private communication.

Lopatina, Lena; Selinger, Jonathan V.

2007-03-01

10

Rotation and Anisotropic Molecular Orbital Effect in a Single H2TPP Molecule Transistor  

NASA Astrophysics Data System (ADS)

Electron transport through a single molecule is determined not only by the intrinsic properties of the molecule but also by the configuration of the molecule with respect to the lead electrodes. Here, we show how electron transport through a single H2TPP molecule is modulated by changes in the configuration. The Coulomb stability diagram of a single H2TPP molecule transistor exhibited a few different patterns in different measurement scans. Furthermore, the sample exhibited negative differential resistance, the magnitude of which changed with the pattern in the Coulomb stability diagram. Such behavior can be explained by the rotation of the molecule with anisotropic molecular orbitals in the gap electrodes induced by electrical stress. Moreover, we find that the energy separations between molecular orbitals are also affected by the rotation, confirming that the metal-molecule interface configuration renormalizes the electronic levels in the molecule.

Sakata, Shuichi; Yoshida, Kenji; Kitagawa, Yuichi; Ishii, Kazuyuki; Hirakawa, Kazuhiko

2013-12-01

11

Surface microfluidic patterning and transporting organic small molecules.  

PubMed

A microfluidic method is developed to pattern organic small molecules directly in air. When heated to above its melting point, a powder melts into liquid drops which propagate along the pattern area. The method can further be applied to transport other dye molecules, to create multicolored patterns in one step. The fluorescence microscopy image shows rhodamine B (red), fluorescein (green), and calcein blue (blue) doped N-ethyl-d-glucamine on 100-?m Au lines. PMID:24623611

Wang, Hong; Wang, Wenchong; Li, Liqiang; Zhu, Juan; Wang, Wenxin; Zhang, Deqing; Xie, Zhaoxiong; Fuchs, Harald; Lei, Yong; Chi, Lifeng

2014-07-01

12

Assembling molecular electronic junctions one molecule at a time.  

PubMed

Diffusion of metal atoms onto a molecular monolayer attached to a conducting surface permits electronic contact to the molecules with minimal heat transfer or structural disturbance. Surface-mediated metal deposition (SDMD) involves contact between "cold" diffusing metal atoms and molecules, due to shielding of the molecules from direct exposure to metal vapor. Measurement of the current through the molecular layer during metal diffusion permits observation of molecular conductance for junctions containing as few as one molecule. Discrete conductance steps were observed for 1-10 molecules within a monolayer during a single deposition run, corresponding to "recruitment" of additional molecules as the contact area between the diffusing Au layer and molecules increases. For alkane monolayers, the molecular conductance measured with SDMD exhibited an exponential dependence on molecular length with a decay constant (?) of 0.90 per CH(2) group, comparable to that observed by other techniques. Molecular conductance values were determined for three azobenzene molecules, and correlated with the offset between the molecular HOMO and the contact Fermi level, as expected for hole-mediated tunneling. Current-voltage curves were obtained during metal deposition showed no change in shape for junctions containing 1, 2, and 10 molecules, implying minimal intermolecular interactions as single molecule devices transitioned into several molecules devices. SDMD represents a "soft" metal deposition method capable of providing single molecule conductance values, then providing quantitative comparisons to molecular junctions containing 10(6) to 10(10) molecules. PMID:21995487

Bonifas, Andrew P; McCreery, Richard L

2011-11-01

13

Molecular electronics with single molecules in solid-state devices  

Microsoft Academic Search

The ultimate aim of molecular electronics is to understand and master single-molecule devices. Based on the latest results on electron transport in single molecules in solid-state devices, we focus here on new insights into the influence of metal electrodes on the energy spectrum of the molecule, and on how the electron transport properties of the molecule depend on the strength

Kasper Moth-Poulsen; Thomas Bjørnholm

2009-01-01

14

Design of a Molecular Assembly Line Based on Biological Molecules.  

National Technical Information Service (NTIS)

A general scheme towards a 'molecular assembly line' based on biological molecules is proposed, as well as its potential uses as a universal polymer scaffold in programmed assembly and molecular electronics. It is based on the principles of the biological...

B. Chow

2003-01-01

15

Patterns and conformations in molecularly thin films  

Microsoft Academic Search

Molecularly thin films have been a subject of great interest for the last several years because of their large variety of industrial applications ranging from micro-electronics to bio-medicine. Additionally, molecularly thin films can be used as good models for biomembrane and other systems where surfaces are critical. Many different kinds of molecules can make stable films. My research has considered

Prem B. Basnet

2010-01-01

16

Mitochondrial damage-associated molecular patterns and vascular function.  

PubMed

Immune system activation occurs not only due to foreign stimuli, but also due to endogenous molecules. As such, endogenous molecules that are released into the circulation due to cell death and/or injury alarm the immune system that something has disturbed homeostasis and a response is needed. Collectively, these molecules are known as damage-associated molecular patterns (DAMPs). Mitochondrial DAMPs (mtDAMPs) are potent immunological activators due to the bacterial ancestry of mitochondria. Mitochondrial DAMPs are recognized by specific pattern recognition receptors of the innate immune system, some of which are expressed in the cardiovascular system. Cell death leads to release of mtDAMPs that may induce vascular changes by mechanisms that are currently not well understood. This review will focus on recently published evidence linking mtDAMPs and immune system activation to vascular dysfunction and cardiovascular disease. PMID:24569027

Wenceslau, Camilla Ferreira; McCarthy, Cameron G; Szasz, Theodora; Spitler, Kathryn; Goulopoulou, Styliani; Webb, R Clinton

2014-05-01

17

Emerging role of damage-associated molecular patterns derived from mitochondria in inflammation.  

PubMed

Cell death and injury often lead to release or exposure of intracellular molecules called damage-associated molecular patterns (DAMPs) or cell death-associated molecules. These molecules are recognized by the innate immune system by pattern recognition receptors - the same receptors that detect pathogen-associated molecular patterns, thus revealing similarities between pathogen-induced and non-infectious inflammatory responses. Many DAMPs are derived from the plasma membrane, nucleus, endoplasmic reticulum and cytosol. Recently, mitochondria have emerged as other organelles that function as a source of DAMPs. Here, we highlight the significance of mitochondrial DAMPs and discuss their contribution to inflammation and development of human pathologies. PMID:21334975

Krysko, Dmitri V; Agostinis, Patrizia; Krysko, Olga; Garg, Abhishek D; Bachert, Claus; Lambrecht, Bart N; Vandenabeele, Peter

2011-04-01

18

Reactive Molecular Dynamics of Hypervelocity Collisions of PETN Molecules  

Microsoft Academic Search

Born-Oppenheimer direct dynamics classical trajectory simulations of bimolecular collisions of PETN molecules have been performed to investigate the fundamental mechanisms of hypervelocity chemistry relevant to initiating reactions immediately behind the shock wavefront in energetic molecular crystals. The solid-state environment specifies the initial orientations of colliding molecules. The threshold velocities for initiating chemistry for a variety of crystallographic orientations were correlated

A. C. Landerville; I. I. Oleynik; C. T. White

2009-01-01

19

Receptor-mediated signalling in plants: molecular patterns and programmes  

PubMed Central

A highly evolved surveillance system in plants is able to detect a broad range of signals originating from pathogens, damaged tissues, or altered developmental processes, initiating sophisticated molecular mechanisms that result in defence, wound healing, and development. Microbe-associated molecular pattern molecules (MAMPs), damage-associated molecular pattern molecules (DAMPs), virulence factors, secreted proteins, and processed peptides can be recognized directly or indirectly by this surveillance system. Nucleotide binding-leucine rich repeat proteins (NB-LRR) are intracellular receptors and have been targeted by breeders for decades to elicit resistance to crop pathogens in the field. Receptor-like kinases (RLKs) or receptor like proteins (RLPs) are membrane bound signalling molecules with an extracellular receptor domain. They provide an early warning system for the presence of potential pathogens and activate protective immune signalling in plants. In addition, they act as a signal amplifier in the case of tissue damage, establishing symbiotic relationships and effecting developmental processes. The identification of several important ligands for the RLK-type receptors provided an opportunity to understand how plants differentiate, how they distinguish beneficial and detrimental stimuli, and how they co-ordinate the role of various types of receptors under varying environmental conditions. The diverse roles of extra-and intracellular plant receptors are examined here and the recent findings on how they promote defence and development is reviewed.

Tor, Mahmut; Lotze, Michael T.; Holton, Nicholas

2009-01-01

20

Efficient Molecular Imaging Techniques Using Optically Active Molecules  

Microsoft Academic Search

Efficient imaging techniques aimed at the increasing of the image contrast of a structure, surrounded by a scattering medium, using optically active and high index of refraction molecules as molecular contrast agents, are presented. Specifically, an enhanced degree of linear polarization (DOLP) target detection and imaging is obtained by doping the surrounding medium with molecular contrast agents consisting of aqueous

George C. Giakos; S. Atreya Paturi; Keerthisrivatsav Valluru; P. Bathini; V. Adya; Srinivas Sukumar; K. Ambadipudi; B. Mandadi; M. Becker; S. Athawale; P. Farajipour; S. Marotta; D. Sheffer; G. Livanos; M. Zervakis

2010-01-01

21

Structural understanding of stabilization patterns in engineered bispecific Ig-like antibody molecules  

SciTech Connect

Bispecific immunoglobulin-like antibodies capable of engaging multiple antigens represent a promising new class of therapeutic agents. Engineering of these molecules requires optimization of the molecular properties of one of the domain components. Here, we present a detailed crystallographic and computational characterization of the stabilization patterns in the lymphotoxin-beta receptor (LT{beta}R) binding Fv domain of an anti-LT{beta}R/anti-TNF-related apoptosis inducing ligand receptor-2 (TRAIL-R2) bispecific immunoglobulin-like antibody. We further describe a new hierarchical structure-guided approach toward engineering of antibody-like molecules to enhance their thermal and chemical stability.

Jordan, Jacob L.; Arndt, Joseph W.; Hanf, Karl; Li, Guohui; Hall, Janine; Demarest, Stephen; Huang, Flora; Wu, Xiufeng; Miller, Brian; Glaser, Scott; Fernandez, Erik J.; Wang, Deping; Lugovskoy, Alexey; (UV); (Biogen)

2010-01-12

22

Signal transduction molecule patterns indicating potential glioblastoma therapy approaches  

PubMed Central

Purpose The expression of an array of signaling molecules, along with the assessment of real-time cell proliferation, has been performed in U87 glioma cell line and in patients’ glioblastoma established cell cultures in order to provide a better understanding of cellular and molecular events involved in glioblastoma pathogenesis. Experimental therapy was performed using a phosphatidylinositol-3?-kinase (PI3K) inhibitor. Patients and methods xMAP technology was employed to assess expression levels of several signal transduction molecules and real-time xCELLigence platform for cell behavior. Results PI3K inhibition induced the most significant effects on global signaling pathways in patient-derived cell cultures, especially on members of the mitogen-activated protein-kinase family, P70S6 serine-threonine kinase, and cAMP response element-binding protein expression and further prevented tumor cell proliferation. Conclusion The PI3K pathway might be a prime target for glioblastoma treatment.

Cruceru, Maria Linda; Enciu, Ana-Maria; Popa, Adrian Claudiu; Albulescu, Radu; Neagu, Monica; Tanase, Cristiana Pistol; Constantinescu, Stefan N

2013-01-01

23

A random rotor molecule: Vibrational analysis and molecular dynamics simulations  

NASA Astrophysics Data System (ADS)

Molecular structures that permit intramolecular rotational motion have the potential to function as molecular rotors. We have employed density functional theory and vibrational frequency analysis to study the characteristic structure and vibrational behavior of the molecule (4',4''''-(bicyclo[2,2,2]octane-1,4-diyldi-4,1-phenylene)-bis-2,2':6',2''-terpyridine. IR active vibrational modes were found that favor intramolecular rotation. To demonstrate the rotor behavior of the isolated single molecule, ab initio molecular dynamics simulations at various temperatures were carried out. This molecular rotor is expected to be thermally triggered via excitation of specific vibrational modes, which implies randomness in its direction of rotation.

Li, Yu; Zhang, Rui-Qin; Shi, Xing-Qiang; Lin, Zijing; Van Hove, Michel A.

2012-12-01

24

Patterned gallium surfaces as molecular mirrors.  

PubMed

An entirely new means of printing molecular information on a planar film, involving casting nanoscale impressions of the template protein molecules in molten gallium, is presented here for the first time. The metallic imprints not only replicate the shape and size of the proteins used as template. They also show specific binding for the template species. Such a simple approach to the creation of antibody-like properties in metallic mirrors can lead to applications in separations, microfluidic devices, and the development of new optical and electronic sensors, and will be of interest to chemists, materials scientists, analytical specialists, and electronic engineers. PMID:17689239

Bossi, Alessandra; Rivetti, Claudio; Mangiarotti, Laura; Whitcombe, Michael J; Turner, Anthony P F; Piletsky, Sergey A

2007-09-30

25

An extracellular adhesion molecule complex patterns dendritic branching and morphogenesis.  

PubMed

Robust dendrite morphogenesis is a critical step in the development of reproducible neural circuits. However, little is known about the extracellular cues that pattern complex dendrite morphologies. In the model nematode Caenorhabditis elegans, the sensory neuron PVD establishes stereotypical, highly branched dendrite morphology. Here, we report the identification of a tripartite ligand-receptor complex of membrane adhesion molecules that is both necessary and sufficient to instruct spatially restricted growth and branching of PVD dendrites. The ligand complex SAX-7/L1CAM and MNR-1 function at defined locations in the surrounding hypodermal tissue, whereas DMA-1 acts as the cognate receptor on PVD. Mutations in this complex lead to dramatic defects in the formation, stabilization, and organization of the dendritic arbor. Ectopic expression of SAX-7 and MNR-1 generates a predictable, unnaturally patterned dendritic tree in a DMA-1-dependent manner. Both in vivo and in vitro experiments indicate that all three molecules are needed for interaction. PMID:24120131

Dong, Xintong; Liu, Oliver W; Howell, Audrey S; Shen, Kang

2013-10-10

26

Molecular orbital theory of ballistic electron transport through molecules  

NASA Astrophysics Data System (ADS)

Electron transport through molecules occurs, for instance, in STM imaging and in conductance measurements on molecular electronic devices (MEDs). To model these phenomena, we use a non-Hermitian model Hamiltonian [1] for the description of open systems that exchange current density with their environment. We derive qualitative, molecular-orbital-based rules relating molecular structure and conductance. We show how side groups attached to molecular conductors [2] can completely suppress the conductance. We discuss interference effects in aromatic molecules [3] that can also inhibit electron transport. Rules are developed [1] for the prediction of Fano resonances. All these phenomena are explained with a molecular orbital theory [1,4] for molecules attached to macroscopic reservoirs. [1] F. Goyer, M. Ernzerhof, and M. Zhuang, JCP 126, 144104 (2007); M. Ernzerhof, JCP 127, 204709 (2007). [2] M. Ernzerhof, M. Zhuang, and P. Rocheleau, JCP 123, 134704 (2005); G. C. Solomon, D Q. Andrews, R P. Van Duyne, and M A. Ratner, JACS 130, 7788 (2008). [3] M. Ernzerhof, H. Bahmann, F. Goyer, M. Zhuang, and P. Rocheleau, JCTC 2, 1291 (2006); G. C. Solomon, D. Q. Andrews, R. P. Van Duyne, and M. A. Ratner, JCP 129, 054701 (2008). [4] B.T. Pickup, P.W. Fowler, CPL 459, 198 (2008); P. Rocheleau and M. Ernzerhof, JCP, submitted.

Ernzerhof, Matthias; Rocheleau, Philippe; Goyer, Francois

2009-03-01

27

Molecular Patterns of Alkyl-Aryl Amides Self-assembled on a Graphite Surface  

NASA Astrophysics Data System (ADS)

A series of amides having an alkyl chain and an aromatic head group has been prepared and their self-assembled molecular patterns on a graphite surface have been observed by scanning tunneling microscopy (STM). The molecular patterns generated appear to be defined by the relative location of the alkyl chain and aromatic ring with respect to the amide group. Thus, the molecular axis of amides derived from aromatic carboxylates and alkylamines appears to be inclined toward the lamella boundary at an angle of approximately 70°, forming mirror-image chiral domains. In contrast, the amides obtained from aromatic amines and alkyl carboxylate give a centro-symmetric molecular pattern where the molecular axis is at right angles to the lamella boundary. The relationship between the molecular ordering pattern and the structural feature of constituent molecules has been discussed.

Nanjo, Hiroshi; Qian, Pu; Yokoyama, Toshiro; Suzuki, Toshishige M.

2003-10-01

28

Molecular surface analysis by laser ionization of desorbed molecules  

SciTech Connect

While elemental analysis of surfaces has progressed dramatically over the past ten years, quantitative molecular surface analysis remains difficult. This is particularly true in the analysis of complex materials such as polymers and rubbers which contain a wide compliment of additives and pigments to enhance their material characteristics. For mass spectrometric analysis the difficulty is two fold. First, desorption of surface molecules must be accompanied with minimal fragmentation and collateral surface damage. Second, the desorbed molecules must be ionized for subsequent mass analysis with high efficiency and without significant cracking. This paper focuses on the second of these problems.

Pellin, M.J.; Lykke, K.R.; Wurz, P.; Parker, D.H.

1992-01-01

29

Molecular surface analysis by laser ionization of desorbed molecules  

SciTech Connect

While elemental analysis of surfaces has progressed dramatically over the past ten years, quantitative molecular surface analysis remains difficult. This is particularly true in the analysis of complex materials such as polymers and rubbers which contain a wide compliment of additives and pigments to enhance their material characteristics. For mass spectrometric analysis the difficulty is two fold. First, desorption of surface molecules must be accompanied with minimal fragmentation and collateral surface damage. Second, the desorbed molecules must be ionized for subsequent mass analysis with high efficiency and without significant cracking. This paper focuses on the second of these problems.

Pellin, M.J.; Lykke, K.R.; Wurz, P.; Parker, D.H.

1992-07-01

30

Nanoscale Patterning and Immobilization of Bio-Molecules.  

National Technical Information Service (NTIS)

A support for immobilizing target molecules comprises a substrate having a plurality of binding regions for binding select target molecules, with target-molecule-capturing agent immobilized at the binding regions. The binding regions are intersperse among...

A. J. Hunt E. Meyhofer J. D. Hoff L. J. Cheng L. J. Guo

2005-01-01

31

Variational path integral molecular dynamics study of a water molecule  

NASA Astrophysics Data System (ADS)

In the present study, a variational path integral molecular dynamics method developed by the author [Chem. Phys. Lett. 482, 165 (2009)] is applied to a water molecule on the adiabatic potential energy surface. The method numerically generates an exact wavefunction using a trial wavefunction of the target system. It has been shown that even if a poor trial wavefunction is employed, the exact quantum distribution is numerically extracted, demonstrating the robustness of the variational path integral method.

Miura, Shinichi

2013-08-01

32

Molecular patterning of the mammalian dentition.  

PubMed

Four conserved signaling pathways, including the bone morphogenetic proteins (Bmp), fibroblast growth factors (Fgf), sonic hedgehog (Shh), and wingless-related (Wnt) pathways, are each repeatedly used throughout tooth development. Inactivation of any of these resulted in early tooth developmental arrest in mice. The mutations identified thus far in human patients with tooth agenesis also affect these pathways. Recent studies show that these signaling pathways interact through positive and negative feedback loops to regulate not only morphogenesis of individual teeth but also tooth number, shape, and spatial pattern. Increased activity of each of the Fgf, Shh, and canonical Wnt signaling pathways revitalizes development of the physiologically arrested mouse diastemal tooth germs whereas constitutive activation of canonical Wnt signaling in the dental epithelium is able to induce supernumerary tooth formation even in the absence of Msx1 and Pax9, two transcription factors required for normal tooth development beyond the early bud stage. Bmp4 and Msx1 act in a positive feedback loop to drive sequential tooth formation whereas the Osr2 transcription factor restricts Msx1-mediated expansion of the mesenchymal odontogenic field along both the buccolingual and anteroposterior axes to pattern mouse molar teeth in a single row. Moreover, the ectodermal-specific ectodysplasin (EDA) signaling pathway controls tooth number and tooth shape through regulation of Fgf20 expression in the dental epithelium, whereas Shh suppresses Wnt signaling through a negative feedback loop to regulate spatial patterning of teeth. In this article, we attempt to integrate these exciting findings in the understanding of the molecular networks regulating tooth development and patterning. PMID:24355560

Lan, Yu; Jia, Shihai; Jiang, Rulang

2014-01-01

33

Integrin function: molecular hierarchies of cytoskeletal and signaling molecules  

PubMed Central

Integrin receptors play important roles in organizing the actin- containing cytoskeleton and in signal transduction from the extracellular matrix. The initial steps in integrin function can be analyzed experimentally using beads coated with ligands or anti- integrin antibodies to trigger rapid focal transmembrane responses. A hierarchy of transmembrane actions was identified in this study. Simple integrin aggregation triggered localized transmembrane accumulation of 20 signal transduction molecules, including RhoA, Rac1, Ras, Raf, MEK, ERK, and JNK. In contrast, out of eight cytoskeletal molecules tested, only tensin coaccumulated. Integrin aggregation alone was also sufficient to induce rapid activation of the JNK pathway, with kinetics of activation different from those of ERK. The tyrosine kinase inhibitors herbimycin A or genistein blocked both the accumulation of 19 out of 20 signal transduction molecules and JNK- and ERK-mediated signaling. Cytochalasin D had identical effects, whereas three other tyrosine kinase inhibitors did not. The sole exception among signaling molecules was the kinase pp125FAK which continued to coaggregate with alpha 5 beta 1 integrins even in the presence of these inhibitors. Tyrosine kinase inhibition also failed to block the ability of ligand occupancy plus integrin aggregation to trigger transmembrane accumulation of the three cytoskeletal molecules talin, alpha-actinin, and vinculin; these molecules accumulated even in the presence of cytochalasin D. However, it was necessary to fulfill all four conditions, i.e., integrin aggregation, integrin occupancy, tyrosine kinase activity, and actin cytoskeletal integrity, to achieve integrin- mediated focal accumulation of other cytoskeletal molecules including F- actin and paxillin. Integrins therefore mediate a transmembrane hierarchy of molecular responses.

1995-01-01

34

Selective Attachment of Nucleic Acid Molecules to Patterned Self-Assembled Surfaces.  

National Technical Information Service (NTIS)

Patterns of pre-formed hybridizable nucleic acid oligomers are formed upon a substrate. The substrate is coated with molecules, such as aminosilanes, whose reactivity with nucleic acid molecules can be transformed by irradiation. The coated substrate expo...

L. A. Chrisey W. J. Dressick J. M. Calvert

1994-01-01

35

Apparatus and method of determining molecular weight of large molecules  

DOEpatents

A mass spectrometer determines the mass of multiply charged high molecular weight molecules. This spectrometer utilizes an ion detector which is capable of simultaneously measuring the charge z and transit time of a single ion as it passes through the detector. From this transit time, the velocity of the single ion may then be derived, thus providing the mass-to-charge ratio m/z for a single ion which has been accelerated through a known potential. Given z and m/z, the mass m of the single ion can then be calculated. Electrospray ions with masses in excess of 1 MDa and charge numbers greater than 425 e{sup {minus}} are readily detected. The on-axis single ion detection configuration enables a duty cycle of nearly 100% and extends the practical application of electrospray mass spectrometry to the analysis of very large molecules with relatively inexpensive instrumentation. 14 figs.

Fuerstenau, S.; Benner, W.H.; Madden, N.M.; Searles, W.

1998-06-23

36

Reactive molecular dynamics of hypervelocity collisions of PETN molecules.  

PubMed

Born-Oppenheimer direct dynamics classical trajectory simulations of bimolecular collisions of PETN molecules have been performed to investigate the fundamental mechanisms of hypervelocity chemistry relevant to initiating reactions immediately behind the shock wavefront in energetic molecular crystals. The solid-state environment specifies the initial orientations of colliding molecules. The threshold velocities for initiating chemistry for a variety of crystallographic orientations were correlated with available experimental data on anisotropic shock sensitivity of PETN. Collisions normal to the planes (001) and (110) were found to be most sensitive with threshold velocities on the order of characteristic particle velocities in detonating PETN. The production of NO2 is the dominant reaction pathway in most of the reactive cases. The simulations show that the reactive chemistry, driven by dynamics rather than temperature during hypervelocity collisions, can occur at a very short time scale (10(-13) s) under highly nonequilibrium conditions. PMID:19817467

Landerville, A C; Oleynik, I I; White, C T

2009-11-01

37

Reactive Molecular Dynamics of Hypervelocity Collisions of PETN Molecules  

NASA Astrophysics Data System (ADS)

Born-Oppenheimer direct dynamics classical trajectory simulations of bimolecular collisions of PETN molecules have been performed to investigate the fundamental mechanisms of hypervelocity chemistry relevant to initiating reactions immediately behind the shock wavefront in energetic molecular crystals. The solid-state environment specifies the initial orientations of colliding molecules. The threshold velocities for initiating chemistry for a variety of crystallographic orientations were correlated with available experimental data on anisotropic shock sensitivity of PETN. Collisions normal to the planes (001) and (110) were found to be most sensitive with threshold velocities on the order of characteristic particle velocities in detonating PETN. The production of NO2 is the dominant reaction pathway in most of the reactive cases. The simulations show that the reactive chemistry, driven by dynamics rather than temperature during hypervelocity collisions, can occur at a very short time scale (10-13 s) under highly nonequilibrium conditions.

Landerville, A. C.; Oleynik, I. I.; White, C. T.

2009-10-01

38

Apparatus and method of determining molecular weight of large molecules  

DOEpatents

A mass spectrometer determines the mass of multiply charged high molecular weight molecules. This spectrometer utilizes an ion detector which is capable of simultaneously measuring the charge z and transit time of a single ion as it passes through the detector. From this transit time, the velocity of the single ion may then be derived, thus providing the mass-to-charge ratio m/z for a single ion which has been accelerated through a known potential. Given z and m/z, the mass m of the single ion can then be calculated. Electrospray ions with masses in excess of 1 MDa and charge numbers greater than 425 e.sup.- are readily detected. The on-axis single ion detection configuration enables a duty cycle of nearly 100% and extends the practical application of electrospray mass spectrometry to the analysis of very large molecules with relatively inexpensive instrumentation.

Fuerstenau, Stephen (Montrose, CA); Benner, W. Henry (Danville, CA); Madden, Norman (Livermore, CA); Searles, William (Fremont, CA)

1998-01-01

39

Molecular spectral line surveys and the organic molecules in the interstellar molecular clouds  

NASA Astrophysics Data System (ADS)

It is known that more than 140 interstellar and circumstellar molecules have so far been detected, mainly by means of the radio astronomy observations. Many organic molecules are also detected, including alcohols, ketons, ethers, aldehydes, and others, that are distributed from dark clouds and hot cores in the giant molecular clouds. It is believed that most of the organic molecules in space are synthesized through the grain surface reactions, and are evaporated from the grain surface when they are heated up by the UV radiation from adjacent stars. On the other hand the recent claim on the detection of glycine have raised an important issue how difficult it is to confirm secure detection of weak spectra from less abundant organic molecules in the interstellar molecular cloud. I will review recent survey observations of organic molecules in the interstellar molecular clouds, including independent observations of glycine by the 45 m radio telescope in Japan, and will discuss the procedure to securely identify weak spectral lines from organic molecules and the importance of laboratory measurement of organic species.

Ohishi, Masatoshi

2008-10-01

40

Microscopic approach to the kinetics of pattern formation of charged molecules on surfaces.  

PubMed

A microscopic formalism based on computing many-particle densities is applied to the analysis of the diffusion-controlled kinetics of pattern formation in oppositely charged molecules on surfaces or adsorbed at interfaces with competing long-range Coulomb and short-range Lennard-Jones interactions. Particular attention is paid to the proper molecular treatment of energetic interactions driving pattern formation in inhomogeneous systems. The reverse Monte Carlo method is used to visualize the spatial molecular distribution based on the calculated radial distribution functions (joint correlation functions). We show the formation of charge domains for certain combinations of temperature and dynamical interaction parameters. The charge segregation evolves into quasicrystalline clusters of charges, due to the competing long- and short-range interactions. The clusters initially co-exist with a gas phase of charges that eventually add to the clusters, generating "fingers" or line of charges of the same sign, very different than the nanopatterns expected by molecular dynamics in systems with competing interactions in two dimensions, such as strain or dipolar versus van der Waals interactions. PMID:20866821

Kuzovkov, V N; Zvejnieks, G; Kotomin, E A; Olvera de la Cruz, M

2010-08-01

41

Rapid searches for complex patterns in biological molecules.  

PubMed Central

The intrinsic redundancy of genetic information makes searching for patterns in biological sequences a difficult task. We have designed an interactive self-documenting computer program called QUEST that allows rapid searching of large DNA and protein data banks for highly redundant consensus sequences or character patterns. QUEST uses a concise language for specifying character patterns containing several levels of ambiguity and pattern arrangement. Examples of the use of this program for sequence data are given. Details of the algorithm and pattern optimization are explained.

Abarbanel, R M; Wieneke, P R; Mansfield, E; Jaffe, D A; Brutlag, D L

1984-01-01

42

Polarizable Atomic Multipole-based Molecular Mechanics for Organic Molecules  

PubMed Central

An empirical potential based on permanent atomic multipoles and atomic induced dipoles is reported for alkanes, alcohols, amines, sulfides, aldehydes, carboxylic acids, amides, aromatics and other small organic molecules. Permanent atomic multipole moments through quadrupole moments have been derived from gas phase ab initio molecular orbital calculations. The van der Waals parameters are obtained by fitting to gas phase homodimer QM energies and structures, as well as experimental densities and heats of vaporization of neat liquids. As a validation, the hydrogen bonding energies and structures of gas phase heterodimers with water are evaluated using the resulting potential. For 32 homo- and heterodimers, the association energy agrees with ab initio results to within 0.4 kcal/mol. The RMS deviation of hydrogen bond distance from QM optimized geometry is less than 0.06 Å. In addition, liquid self-diffusion and static dielectric constants computed from molecular dynamics simulation are consistent with experimental values. The force field is also used to compute the solvation free energy of 27 compounds not included in the parameterization process, with a RMS error of 0.69 kcal/mol. The results obtained in this study suggest the AMOEBA force field performs well across different environments and phases. The key algorithms involved in the electrostatic model and a protocol for developing parameters are detailed to facilitate extension to additional molecular systems.

Ren, Pengyu; Wu, Chuanjie; Ponder, Jay W.

2011-01-01

43

Patterns of energy levels and spectra for polyatomic molecules  

SciTech Connect

Laser spectroscopy has revealed a remarkable intricacy in the rotational, vibrational, and electronic energy levels for polyatomic molecules. The infrared spectra of SF/sub 6/, CF/sub 4/, and related molecules contain several levels of structure on top of structure which resembles a fractal in some ways. The purpose of this article will be to exhibit some of this structure and introduce the simplest theoretical interpretations of it which are presently available.

Harter, W.G.

1983-01-01

44

Molecular dynamics simulations of lubricant spreading on lubricant-patterned substrates  

NASA Astrophysics Data System (ADS)

The spreading of nonfunctional perfluoropolyether (PFPE) on PFPE-patterned substrates is examined using molecular dynamics simulations. During the spreading process, mobile molecules will encounter, pass by, and embrace the bonded ones. The movement of mobile molecules is hindered by the bonded ones. The spreading exhibits a slow evolution with time, a steep profile with a precursor film from a side view and a complicated profile from a top-down view. The atomic-scale mechanism is analyzed by the driving term, such as the van der Waals interaction and surface diffusion, and the resistance term, such as the interaction between bonded and mobile molecules or, furthermore, the combined interaction from the adjacent bonded molecules. Besides, the spreading profiles of PFPE on PFPE-patterned substrates with different coverage ratios are compared, which indicate that the coverage ratio has significant effects on the PFPE spreading behavior.

Li, Xin; Hu, Yuanzhong; Ma, Tianbao; Wang, Hui; Zhang, Jun

2006-10-01

45

Molecular dynamics integration and molecular vibrational theory. II. Simulation of nonlinear molecules.  

PubMed

A series of molecular dynamics (MD) simulations of nonlinear molecules has been performed to test the efficiency of newly introduced semianalytical second-order symplectic time-reversible MD integrators that combine MD and the standard theory of molecular vibrations. The simulation results indicate that for the same level of accuracy, the new algorithms allow significantly longer integration time steps than the standard second-order symplectic leap-frog Verlet method. Since the computation cost per integration step using new MD integrators with longer time steps is approximately the same as for the standard method, a significant speed-up in MD simulation is achieved. PMID:15910018

Praprotnik, Matej; Janezic, Dusanka

2005-05-01

46

Sensing of protein molecules through nanopores: a molecular dynamics study  

NASA Astrophysics Data System (ADS)

Solid-state nanopores have been shown to be suitable for single molecule detection. While numerous modeling investigations exist for DNA within nanopores, there are few simulations of protein translocations. In this paper, we use atomistic molecular dynamics to investigate the translocation of proteins through a silicon nitride nanopore. The nanopore dimensions and profile are representative of experimental systems. We are able to calculate the change in blockade current and friction coefficient for different positions of the protein within the pore. The change in ionic current is found to be negligible until the protein is fully within the pore and the current is lowest when the protein is in the pore center. Using a simple theory that gives good quantitative agreement with the simulation results we are able to show that the variation in current with position is a function of the pore shape. In simulations that guide the protein through the nanopore we identify the effect that confinement has on the friction coefficient of the protein. This integrated view of translocation at the nanoscale provides useful insights that can be used to guide the design of future devices.

Kannam, Sridhar Kumar; Kim, Sung Cheol; Rogers, Priscilla R.; Gunn, Natalie; Wagner, John; Harrer, Stefan; Downton, Matthew T.

2014-04-01

47

Molecular multipole moments of water molecules in ice Ih  

NASA Astrophysics Data System (ADS)

We have used an induction model including dipole, dipole-quadrupole, quadrupole-quadrupole polarizability and first hyperpolarizability as well as fixed octopole and hexadecapole moments to study the electric field in ice. The self-consistent induction calculations gave an average total dipole moment of 3.09 D, a 67% increase over the dipole moment of an isolated water molecule. A previous, more approximate induction model study by Coulson and Eisenberg [Proc. R. Soc. Lond. A 291, 445 (1966)] suggested a significantly smaller average value of 2.6 D. This value has been used extensively in recent years as a reference point in the development of various polarizable interaction potentials for water as well as for assessment of the convergence of water cluster properties to those of bulk. The reason for this difference is not due to approximations made in the computational scheme of Coulson and Eisenberg but rather due to the use of less accurate values for the molecular multipoles in these earlier calculations.

Batista, Enrique R.; Xantheas, Sotiris S.; Jónsson, Hannes

1998-09-01

48

Exploration of target molecules for molecular imaging of inflammatory bowel disease  

SciTech Connect

Highlights: {sup {yields}18}F-FDG PET could discriminate each inflamed area of IBD model mice clearly. {sup {yields}18}F-FDG PET could not discriminate the difference of pathogenic mechanism. {yields} Cytokines and cytokine receptors expression was different by pathogenic mechanism. {yields} Cytokines and cytokine receptors would be new target molecules for IBD imaging. -- Abstract: Molecular imaging technology is a powerful tool for the diagnosis of inflammatory bowel disease (IBD) and the efficacy evaluation of various drug therapies for it. However, it is difficult to elucidate directly the relationships between the responsible molecules and IBD using existing probes. Therefore, the development of an alternative probe that is able to elucidate the pathogenic mechanism and provide information on the appropriate guidelines for treatment is earnestly awaited. In this study, we investigated pathognomonic molecules in the intestines of model mice. The accumulation of fluorine-18 fluorodeoxyglucose ({sup 18}F-FDG) in the inflamed area of the intestines of dextran sulfate sodium (DSS)- or indomethacin (IND)-induced IBD model mice was measured by positron emission tomography (PET) and autoradiography to confirm the inflamed area. The results suggested that the inflammation was selectively induced in the colons of mice by the administration of DSS, whereas it was induced mainly in the ilea and the proximal colons of mice by the administration of IND. To explore attractive target molecules for the molecular imaging of IBD, we evaluated the gene expression levels of cytokines and cytokine receptors in the inflamed area of the intestines of both model mice. We found that the expression levels of cytokines and cytokine receptors were significantly increased during the progression of IBD, whereas the expression levels were decreased as the mucosa began to heal. In particular, the expression levels of these molecules had already changed before the symptoms of IBD appeared. In addition, the alterations of cytokine and cytokine receptor expression levels indicated differences in the expression pattern depending on the pathogenic mechanism or the region of inflammation (e.g., TNF-{alpha}). Our results suggest that these cytokines or cytokine receptors participate in the pathogenesis of IBD and are valuable biomarkers for the detection of the different circumstances underlying inflammation by the molecular imaging method. Finally, the development of an imaging probe for our target molecules is expected to improve our understanding of the inflammatory conditions of IBD.

Higashikawa, Kei; Akada, Naoki; Yagi, Katsuharu [Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, Okayama 700-8530 (Japan)] [Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, Okayama 700-8530 (Japan); Watanabe, Keiko; Kamino, Shinichiro; Kanayama, Yousuke; Hiromura, Makoto [Multiple Molecular Imaging Research Laboratory, RIKEN Center for Molecular Imaging Science, Kobe 650-0047 (Japan)] [Multiple Molecular Imaging Research Laboratory, RIKEN Center for Molecular Imaging Science, Kobe 650-0047 (Japan); Enomoto, Shuichi, E-mail: senomoto@pharm.okayama-u.ac.jp [Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, Okayama 700-8530 (Japan) [Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, Okayama 700-8530 (Japan); Multiple Molecular Imaging Research Laboratory, RIKEN Center for Molecular Imaging Science, Kobe 650-0047 (Japan)

2011-07-08

49

Adenovirus-mediated gene transfer of pathogen-associated molecular patterns for cancer immunotherapy  

Microsoft Academic Search

The delivery of stimulatory signals to dendritic cells (DCs) in the tumor microenvironment could be an effective means to break tumor-induced tolerance. The work presented here evaluates the immunostimulatory properties of pathogen-associated molecular patterns (PAMPs), microbial molecules which bind Toll-like receptors and deliver activating signals to immune cells, when expressed in tumor cells using adenoviral (Ad) vectors. In vitro, transduction

C Tosch; M Geist; C Ledoux; C Ziller-Remi; S Paul; P Erbs; N Corvaia; P Von Hoegen; J-M Balloul; H Haegel

2009-01-01

50

Molecular patterns in melanoma and therapeutic targets.  

PubMed

Malignant melanoma is one of the most lethal cancers whose treatment options are limited once it has metastasized. Recent advances in molecular technology have improved our understanding of the underlying mechanisms of melanoma pathogenesis. In this article, we highlight several pathways that have been implicated in melanoma-genesis. While a cure is not yet within grasp, the picture on the horizon is less hazy and the next decade promises to yield exciting new therapeutic discoveries. PMID:20930694

Chua, R A; Arbiser, J L

2010-10-01

51

Optical Active Molecules used as Molecular Contrast Agents for Enhanced Imaging  

Microsoft Academic Search

A novel technique aimed at increasing the image contrast of a structure surrounded by a scattering medium, using optically active molecules as molecular contrast agents, is presented. Specifically, enhanced target detection was obtained by doping the surrounding medium with molecular contrast agents, consisting of aqueous glucose molecules, in conjunction to advanced polarimetric imaging techniques. The outcome of this study opens

G. C. Giakos; S. Atreya Paturi; K. Valluru; P. Bathini; K. Ambadipudi; V. Adya; S. Sukumar; D. Sheffer

2008-01-01

52

Fine tuning of the electronic structure of ?-conjugated molecules for molecular electronics.  

PubMed

Molecular components with their inherent scalability are expected to be promising supplements for nanoscale electronic devices. Here we report on how to specifically tune the electronic structure of chemisorbed molecules and thus to gain control of molecular transport properties. The electronic structure of our prototype ?-conjugated carboxylic acid anchored on the Cu(110) surface is modified systematically by inserting nitrogen atoms in a six-membered aromatic ring, a carboxylic functional group at the aromatic ring or both. Depending on the specific nature of the substituent, the relative position of the occupied or unoccupied electronic states with respect to the Fermi level can be specifically controlled and thus the transport properties of the studied molecular systems are modified intentionally, as proven by our scanning tunneling spectroscopy measurements. On the basis of the insight gained by our systematic experiment and first-principles calculations we are also able to predict the specific molecular character (? or ?) of the orbitals involved in the transport process of a carboxylate-Cu(110) system, depending on the functionalization pattern employed. PMID:21346307

Caciuc, V; Lennartz, M C; Atodiresei, N; Karthäuser, S; Blügel, S

2011-04-01

53

Molecular anhydrobiology: identifying molecules implicated in invertebrate anhydrobiosis.  

PubMed

Studies in anhydrobiotic plants have defined many genes which are upregulated during desiccation, but comparable studies in invertebrates are at an early stage. To develop a better understanding of invertebrate anhydrobiosis, we have begun to characterise dehydration-inducible genes and their proteins in anhydrobiotic nematodes and bdelloid rotifers; this review emphasises recent findings with a hydrophilic nematode protein. Initial work with the fungivorous nematode Aphelenchus avenae led to the identification of two genes, both of which were markedly induced on slow drying (90-98% relative humidity, 24 hr) and also by osmotic stress, but not by heat or cold or oxidative stresses. The first of these genes encodes a novel protein we have named anhydrin; it is a small, basic polypeptide, with no counterparts in sequence databases, which is predicted to be natively unstructured and highly hydrophilic. The second is a member of the Group 3 LEA protein family; this and other families of LEA proteins are widely described in plants, where they are most commonly associated with the acquisition of desiccation tolerance in maturing seeds. Like anhydrin, the nematode LEA protein, Aav-LEA-1, is highly hydrophilic and a recombinant form has been shown to be unstructured in solution. In vitro functional studies suggest that Aav-LEA-1 is able to stabilise other proteins against desiccation-induced aggregation, which is in keeping with a role of LEA proteins in anhydrobiosis. In vivo, however, Aav-LEA-1 is apparently processed into smaller forms during desiccation. A processing activity was found in protein extracts of dehydrated, but not hydrated, nematodes; these shorter polypeptides are also active anti-aggregants and we hypothesise that processing LEA protein serves to increase the number of active molecules available to the dehydrating animal. Other LEA-like proteins are being identified in nematodes and it seems likely therefore that they will play a major role in the molecular anhydrobiology of invertebrates, as they are thought to do in plants. PMID:21676820

Goyal, Kshamata; Walton, Laura J; Browne, John A; Burnell, Ann M; Tunnacliffe, Alan

2005-11-01

54

Nanoscopic management of molecular packing and orientation of small molecules by a combination of linear and branched alkyl side chains.  

PubMed

We synthesized a series of acceptor-donor-acceptor-type small molecules (SIDPP-EE, SIDPP-EO, SIDPP-OE, and SIDPP-OO) consisting of a dithienosilole (SI) electron-donating moiety and two diketopyrrolopyrrole (DPP) electron-withdrawing moieties each bearing linear n-octyl (O) and/or branched 2-ethylhexyl (E) alkyl side chains. X-ray diffraction patterns revealed that SIDPP-EE and SIDPP-EO films were highly crystalline with pronounced edge-on orientation, whereas SIDPP-OE and SIDPP-OO films were less crystalline with a radial distribution of molecular orientations. Near-edge X-ray absorption fine structure spectroscopy disclosed an edge-on orientation with a molecular backbone tilt angle of ?22° for both SIDPP-EE and SIDPP-EO. Our analysis of the molecular packing and orientation indicated that the shorter 2-ethylhexyl groups on the SI core promote tight ?-? stacking of the molecular backbone, whereas n-octyl groups on the SI core hinder close ?-? stacking to some degree. Conversely, the longer linear n-octyl groups on the DPP arms facilitate close intermolecular packing via octyl-octyl interdigitation. Quantum mechanics/molecular mechanics molecular dynamics simulations determined the optimal three-dimensional positions of the flexible alkyl side chains of the SI and DPP units, which elucidates the structural cause of the molecular packing and orientation explicitly. The alkyl-chain-dependent molecular stacking significantly affected the electrical properties of the molecular films. The edge-on oriented molecules showed high hole mobilities in organic field-effect transistors, while the radially oriented molecules exhibited high photovoltaic properties in organic photovoltaic cells. These results demonstrate that appropriate positioning of alkyl side chains can modulate crystallinity and molecular orientation in SIDPP films, which ultimately have a profound impact on carrier transport and photovoltaic performance. PMID:24861723

Jung, Minwoo; Yoon, Youngwoon; Park, Jae Hoon; Cha, Wonsuk; Kim, Ajeong; Kang, Jinback; Gautam, Sanjeev; Seo, Dongkyun; Cho, Jeong Ho; Kim, Hyunjung; Choi, Jong Yong; Chae, Keun Hwa; Kwak, Kyungwon; Son, Hae Jung; Ko, Min Jae; Kim, Honggon; Lee, Doh-Kwon; Kim, Jin Young; Choi, Dong Hoon; Kim, BongSoo

2014-06-24

55

Molecular vibrations of methane molecules in the structure I clathrate hydrate from ab initio molecular dynamics simulation  

NASA Astrophysics Data System (ADS)

Vibrational frequencies of guest molecules in clathrate hydrates reflect the molecular environment and dynamical behavior of molecules. A detailed understanding of the mechanism for the vibrational frequency changes of the guest molecules in the clathrate hydrate cages is still incomplete. In this study, molecular vibrations of methane molecules in a structure I clathrate hydrate are calculated from ab initio molecular dynamics simulation. The vibrational spectra of methane are computed by Fourier transform of autocorrelation functions, which reveal distinct separation of each vibrational mode. Calculated symmetric and asymmetric stretching vibrational frequencies of methane molecules are lower in the large cages than in the small cages (8 and 16 cm-1 for symmetric and asymmetric stretching, respectively). These changes are closely linked with the C-H bond length. The vibrational frequencies for the bending and rocking vibrational modes nearly overlap in each of the cages.

Hiratsuka, Masaki; Ohmura, Ryo; Sum, Amadeu K.; Yasuoka, Kenji

2012-01-01

56

Molecular vibrations of methane molecules in the structure I clathrate hydrate from ab initio molecular dynamics simulation.  

PubMed

Vibrational frequencies of guest molecules in clathrate hydrates reflect the molecular environment and dynamical behavior of molecules. A detailed understanding of the mechanism for the vibrational frequency changes of the guest molecules in the clathrate hydrate cages is still incomplete. In this study, molecular vibrations of methane molecules in a structure I clathrate hydrate are calculated from ab initio molecular dynamics simulation. The vibrational spectra of methane are computed by Fourier transform of autocorrelation functions, which reveal distinct separation of each vibrational mode. Calculated symmetric and asymmetric stretching vibrational frequencies of methane molecules are lower in the large cages than in the small cages (8 and 16 cm(-1) for symmetric and asymmetric stretching, respectively). These changes are closely linked with the C-H bond length. The vibrational frequencies for the bending and rocking vibrational modes nearly overlap in each of the cages. PMID:22299892

Hiratsuka, Masaki; Ohmura, Ryo; Sum, Amadeu K; Yasuoka, Kenji

2012-01-28

57

Elements of the theory of molecular spectra. [multiatomic molecules  

NASA Technical Reports Server (NTRS)

The basic aspects of the theory concerning the spectra of multiatomic molecules are presented. The classification of the forms of motions in a molecule, the methods for determining the corresponding Schroudinger levels, the spectral types and the selection rules are discussed in order to identify their presence and state in outer space.

Gribov, L. A.

1979-01-01

58

Single Molecule Switches and Molecular Self-Assembly: Low Temperature STM Investigations and Manipulations  

SciTech Connect

This dissertation is devoted to single molecule investigations and manipulations of two porphyrin-based molecules, chlorophyll-a and Co-popphyrin. The molecules are absorbed on metallic substrates and studied at low temperatures using a scanning tunneling microscope. The electronic, structural and mechanical properties of the molecules are investigated in detail with atomic level precision. Chlorophyll-a is the key ingredient in photosynthesis processes while Co-porphyrin is a magnetic molecule that represents the recent emerging field of molecular spintronics. Using the scanning tunneling microscope tip and the substrate as electrodes, and the molecules as active ingredients, single molecule switches made of these two molecules are demonstrated. The first switch, a multiple and reversible mechanical switch, is realized by using chlorophyll-a where the energy transfer of a single tunneling electron is used to rotate a C-C bond of the molecule's tail on a Au(111) surface. Here, the det

Iancu, Violeta

2006-08-01

59

Molecular imprinted polymer-coated optical fiber sensor for the identification of low molecular weight molecules.  

PubMed

A biomimetic optical probe for detecting low molecular weight molecules (maltol, 3-hydroxy-2-methyl-4H-pyran-4-one, molecular weight of 126.11g/mol), was designed, fabricated, and characterized. The sensor couples a molecular imprinted polymer (MIP) and the Bragg grating refractometry technology into an optical fiber. The probe is fabricated first by inscribing tilted grating planes in the core of the fiber, and then by photopolymerization to immobilize a maltol imprinted MIP on the fiber cladding surface over the Bragg grating. The sensor response to the presence of maltol in different media is obtained by spectral interrogation of the fiber transmission signal. The results showed that the limit of detection of the sensor reached 1ng/mL in pure water with a sensitivity of 6.3×10(8)pm/M. The selectivity of the sensor against other compounds and its reusability were also studied experimentally. Finally, the unambiguous detection of concentrations as little as 10nM of maltol in complex media (real food samples) by the MIP-coated tilted fiber Bragg grating sensor was demonstrated. PMID:25059178

Lépinay, Sandrine; Ianoul, Anatoli; Albert, Jacques

2014-10-01

60

Molecular flux dependence of chemical patterning by microcontact printing.  

PubMed

We address the importance of the dynamic molecular ink concentration at a polymer stamp/substrate interface during microcontact displacement or insertion printing. We demonstrate that by controlling molecular flux, we can influence both the molecular-scale order and the rate of molecular exchange of self-assembled monolayers (SAMs) on gold surfaces. Surface depletion of molecular ink at a polymer stamp/substrate interface is driven predominantly by diffusion into the stamp interior; depletion occurs briefly at the substrate by SAM formation, but diffusion of molecules into the bulk of the stamp dominates over practical experimental time scales. As contact time is increased, the interface concentration varies significantly due to diffusion, affecting the quality and coverage of printed films. Controlling interfacial concentration improves printed film reproducibility and the fractional coverage of multicomponent films can be controlled to within a few percent. We first briefly review the important aspects of molecular ink diffusion at a stamp interface and how it relates to experimental duration. We then describe two examples that illustrate control over ink transfer during experiments: the role of contact time on monolayer reproducibility and molecular order, and the fine control of fractional monolayer coverage for the displacement printing of 1-adamantanethiolate SAMs by 1-dodecanethiol. PMID:24070334

Schwartz, Jeffrey J; Hohman, J Nathan; Morin, Elizabeth I; Weiss, Paul S

2013-10-23

61

Microcontact printing of axon guidance molecules for generation of graded patterns.  

PubMed

Microcontact printing (microCP) of proteins has been successfully used for patterning surfaces in various contexts. Here we describe a simple 'lift-off' method to print precise patterns of axon guidance molecules, which are used as substrate for growing chick retinal ganglion cell (RGC) axons. Briefly, the etched pattern of a silicon master is transferred to a protein-coated silicone cuboid (made from polydimethylsiloxane, PDMS), which is then used as a stamp on a glass coverslip. RGC explants are placed adjacent to the pattern and cultured overnight. Fluorescent labeling of the printed proteins allows the quantitative analysis of the interaction of axons and growth cones with single protein dots and of the overall outgrowth and guidance rate in variously designed patterns. Patterned substrates can be produced in 3-4 h and are stable for up to one week at 4 degrees C; the entire protocol can be completed in 3 d. PMID:17406418

von Philipsborn, Anne C; Lang, Susanne; Bernard, André; Loeschinger, Jürgen; David, Christian; Lehnert, Dirk; Bastmeyer, Martin; Bonhoeffer, Friedrich

2006-01-01

62

Cross Sections and Related Data for Electron Collisions with Hydrogen Molecules and Molecular Ions  

Microsoft Academic Search

Data are compiled and evaluated for collision processes of excitation, dissociation, ionization, attachment, and recombination of hydrogen molecules and molecular ions (H+2, H+3) by electron impact as well as for properties of their collision products.

H. Tawara; Y. Itikawa; H. Nishimura; M. Yoshino

1990-01-01

63

Three-dimensional Molecular Modeling with Single Molecule FRET  

PubMed Central

Single molecule fluorescence energy transfer experiments enable investigations of macromolecular conformation and folding by the introduction of fluorescent dyes at specific sites in the macromolecule. Multiple such experiments can be performed with different labeling site combinations in order to map complex conformational changes or interactions between multiple molecules. Distances that are derived from such experiments can be used for determination of the fluorophore positions by triangulation. When combined with a known structure of the macromolecule(s) to which the fluorophores are attached, a three-dimensional model of the system can be determined. However, care has to be taken to properly derive distance from fluorescence energy transfer efficiency and to recognize the systematic or random errors for this relationship. Here we review the experimental and computational methods used for three-dimensional modeling based on single molecule fluorescence resonance transfer, and describe recent progress in pushing the limits of this approach to macromolecular complexes.

Brunger, Axel T.; Strop, Pavel; Vrljic, Marija; Chu, Steven; Weninger, Keith R.

2011-01-01

64

A molecular dynamics simulation of the destruction of explosive molecules at high-velocity collisions  

Microsoft Academic Search

The infrared spectra and the energies of dissociation of R-NO2 bonds (R?C, N, and O) were calculated for explosive molecules (trinitrotoluene, hexogen, octogen, pentaerythrityl tetranitrate,\\u000a triaminotrinitrobenzene, and nitromethane). The time of kinetic energy redistribution over intramolecular vibrational modes\\u000a for these molecules (the V-V relaxation time) was calculated by the molecular dynamics simulation method. Molecular dynamics simulations were also used\\u000a to

A. A. Selezenev; A. Yu. Aleinikov; I. V. Briginas

2008-01-01

65

Molecular dynamics simulation studies on some topics of water molecules on hydrophobic surfaces  

Microsoft Academic Search

Molecular dynamics simulations have been used to study two topics of water molecules on hydrophobic surfaces. Some properties of the nanobubbles with different ingredients and behavior of single water chains in single-walled carbon nanochannels are exploited. Molecular simulations show that the density of the N2 and H2 are quite high, which is critical for the stability of the nanobubbles and

Hai-Ping FANG; Jun HU

2006-01-01

66

High energy sources and materials: High-temperature molecules and molecular energy storage  

Microsoft Academic Search

The objective of this research was the characterization of molecular species which are important because of (a) their occurrence in high-temperature environments, as for example in the vapor over refractory solids, and in combustion, flames, and propellant burning; (b) their relevance to clarification and\\/or extension of the basic theory of molecular properties. The molecules studied were usually highly reactive or

W. Weltner Jr.

1980-01-01

67

Selective inner-valence ionization of aligned polyatomic molecules for controlling molecular fragmentation  

NASA Astrophysics Data System (ADS)

We show experimentally and theoretically, using acetylene as an example, that the strong preponderance of ionization from specific molecular orbitals to the alignment of the molecular axis with respect to the laser polarization direction allows implementing a method for controlling fragmentation reactions of polyatomic molecules.

Xie, X.; Doblhoff-Dier, K.; Xu, H.; Roither, S.; Iwasaki, A.; Schöffler, M.; Kartashov, D.; Yamanouchi, K.; Baltuška, A.; Gräfe, S.; Kitzler, M.

2014-04-01

68

A comparison of the molecular surfaces of sandalwood odour molecules.. Conformational calculations on sandalwood odour VIII  

NASA Astrophysics Data System (ADS)

Molecular surface comparisons offer a possibility for investigating small differences in molecular shape between biologically active and inactive compounds of the same structural type. The method of comparison described here is based on volume matching followed by the calculation of comparable surface dots. Subsequently, the surfaces are matched. The method was applied to the stereoisomers of some sandalwood odour molecules.

Neumann, Andrea; Wei, Petra; Wolschann, Peter

1993-07-01

69

Simulations of excitonic coupling effects in chiral molecule: optical properties and molecular structure  

NASA Astrophysics Data System (ADS)

Simulations of the chirally induced excitonic optical rotation dispersion using molecular dynamics and self-consistent quantum chemical calculations within the restricted Hartree-Fock (RHF) and density functional theory (DFT) approaches were performed for the chiral molecule. As a chiral molecule we have used typical bis (Schiff bases) molecule. The geometry of the molecule was optimized for the ground state, taking into account the excited configuration interaction (CI) states. We have found that the DFT approach gives substantially better agreement with the experimental optical rotation dispersion (ORD) data comparing with the RHF ones. The possibility of applying the quantum chemical methods for simulations of chirally induced exciton coupling is shown.

Andraud, C.; Alexandre, M.; Lemercier, G.; Gruhn, W.; Kityk, I. V.

2002-01-01

70

Pattern formation in Langmuir-Blodgett films of tricycloquinazoline based discotic liquid crystal molecules  

NASA Astrophysics Data System (ADS)

The assembly of molecules on the surface has drawn considerable attention because of its potential to tailor the physicochemical, electronic, and magnetic properties of materials. The structure of aggregates of molecules can be influenced by the molecular interactions and the external parameters like temperature, pressure and ion contents. We have found a stable Langmuir monolayer of amphiphilic tricycloquinazoline based discotic liquid crystal (AmTCQ) molecules at air-water (A-W) interface. The monolayer exhibits gas phase, low density liquid phase and high density liquid phase. The structural evolution in Langmuir-Blodgett (LB) films of the AmTCQ molecules as a function of target surface pressure is studied using an atomic force microscope. We found aggregation of the discotic molecules leading to nucleation sites at a lower surface pressure. With the increasing surface pressure, each nucleation site grows to form a stable triangular structure. The shape and size of the triangular structure remain stable till the target surface pressure for LB films deposition exceeds the equilibrium surface pressure of the AmTCQ molecules. The number of triangles in the film increases with increasing target surface pressure of LB deposition. The target surface pressure of LB deposition acts as a controlling parameter for obtaining desired number of triangular domains in the film.

Karthik, C.; Manjuladevi, V.; Gupta, R. K.; Kumar, Sandeep

2014-07-01

71

Renormalization of molecular quasiparticle levels at metal-molecule interfaces: trends across binding regimes.  

PubMed

When an electron or a hole is added into an orbital of an adsorbed molecule the substrate electrons will rearrange in order to screen the added charge. This polarization effect reduces the electron addition and removal energies of the adsorbed molecule relative to those of the free molecule. Using a microscopic model of the metal-molecule interface, we illustrate the basic features of this renormalization mechanism through systematic GW, Hartree-Fock, and Kohn-Sham calculations for the molecular energy levels as function of the model parameters. We identify two different polarization mechanisms: (i) polarization of the metal (image charge formation) and (ii) polarization of the molecule via charge transfer across the interface. The importance of (i) and (ii) is found to increase with the metal density of states at the Fermi level and metal-molecule coupling strength, respectively. PMID:19257455

Thygesen, Kristian S; Rubio, Angel

2009-01-30

72

New Materials, Methods, and Molecules for Microelectronic and Molecular Electronic Devices  

NASA Astrophysics Data System (ADS)

This dissertation reports a variety of new methods and materials for the fabrication of electronic devices. Particular emphasis is placed on low-cost, solution based methods for flexible electronic device fabrication, and new substrates and molecules for molecular electronic tunnel junctions. Chapter 2 reports a low-cost, solution based method for depositing patterned metal circuitry onto a variety of flexible polymer substrates. Microcontact printing an aluminum (III) porphyrin complex activates selected areas of an oxidized polymer substrate to electroless copper metallization. Chapter 3 reports a new transparent conductive electrode for use in optoelectronic devices. A highly conductive, transparent silver nanowire network is embedded at the surface of an optical adhesive, which can be applied to a variety of rigid and flexible polymer substrates. Chapter 4 describes a new approach to the self-assembly of mesoscale components into two-dimensional arrays. Unlike most previously reported self-assembly motifs, this method is completely dry; eliminating solvent makes this method compatible with the assembly of electronic components. Chapter 5 describes a new class of self-assembled monolayer (SAM) on gold formed from dihexadecyldithiophosphinic acid ((C16) 2DTPA) adsorbate molecules. The binding and structure (C16) 2DTPA SAMs is dependent upon the roughness and morphology of the underlying gold substrate. Chapter 6 investigates the influence of chain length on the binding and structure of dialkyl-DTPA SAMs on smooth, template-stripped (TS) gold. Binding of the DTPA head group is independent of the length of the alkyl chain, while the structure of the organic layer has a counter-intuitive dependence: As the length of the alkyl chain increases, these SAMs become more disordered and liquid-like. Chapter 7 describes the fabrication of ultra smooth gold substrates using chemical mechanical polishing (CMP). These substrates are smooth, uniform, and prove to be ideal candidates for bottom electrodes within SAM-based molecular electronic tunnel junctions. Chapter 8 investigates the charge transport properties of new diphenyldithiophosphinic acid (Ph 2DTPA) SAMs on TS gold within metal-SAM//Ga2O3/EGaIn molecular tunnel junctions. A computational investigation provides insight into the electronic structure of the junction.

Miller, Michael Stephen

73

Electron transmission through molecules and molecular layers: Theory and Simulations  

NASA Astrophysics Data System (ADS)

Several aspects of electron transmission through molecular layers will be discussed. (a) The mechanism of electron tunneling through a narrow water barrier between two Pt(100) metal surfaces was studied by numerical simulations.[1] Assuming that the water configuration is static on the time scale of the electron motion, the tunneling probability show distinct resonance structures below the vacuum barrier. These resonances are shown to be associated with molecular cavities in which the electron is trapped between repulsive oxygen cores. The lifetimes of these resonances are found to be of the order 10 fs or less. (b) The concept of 'tunneling time' is revisited and this time is analyzed for a simple superexchange model of electron transfer.[2] This time is computed also for electron tunneling through water and its relation to the resonance features observed in that process and to their lifetime is discussed.[3] (c) Theoretical models that analyze thermal effects in resonance tunneling are presented.[4] References 1. U. Peskin, A. Edlund, I. Bar-On , M. Galperin and A. Nitzan, Transient resonance structures in electron tunneling through water, J. Chem. Phys. 111, 7558 (1999). 2. A. Nitzan, J. Jortner, J. Wilkie and M. Ratner, Tunneling time for electron transfer reactions, to be published. 3. M. Galperin and A. Nitzan, Tunneling time for electron transfer through water, to be published. 4. D. Segal, A. Nitzan, W. B. Davis, M. R. Wasielewski, and M. A. Ratner, Electron Transfer Rates in Bridged Molecular Systems II: A steady state analysis of coherent tunneling and thermal transitions, J. Phys. Chem., in press.

Nitzan, Abraham

2000-03-01

74

Method and algorithm of obtaining the molecular intrinsic characteristic contours (MICCs) of organic molecules.  

PubMed

The molecular intrinsic characteristic contour (MICC) is defined as the set of all the classical turning points of electron movement in a molecule. Studies on the MICCs of some medium organic molecules, such as dimethylether, acetone, and some homologues of alkanes, alkenes, and alkynes, as well as the electron density distributions on the MICCs, are shown for the first time. Results show that the MICC is an intrinsic approach to shape and size of a molecule. Unlike the van der Waals hard-sphere model, the MICC is a smooth contour, and it has a clear physical meaning. Detailed investigations on the cross-sections of MICCs have provided a kind of important information about atomic size changing in the process of forming molecules. Studies on electron density distribution on the MICC not only provide a new insight into molecular shape, but also show that the electron density distribution on the boundary surface relates closely with molecular properties and reactivities. For the homologues of alkanes, Rout(H), Dmin, and Dmax (the minimum and maximum of electron density on the MICC), all have very good linear relationships with minus of the molecular ionization potential. This work may serve as a basis for exploring a new reactivity indicator of chemical reactions and for studying molecular shape properties of large organic and biological molecules. PMID:15526323

Yang, Zhong-Zhi; Gong, Li-Dong; Zhao, Dong-Xia; Zhang, Ming-Bo

2005-01-15

75

Molecular dynamics simulation suggests possible interaction patterns at early steps of beta2-microglobulin aggregation.  

PubMed

Early events in aggregation of proteins are not easily accessible by experiments. In this work, we perform a 5-ns molecular dynamics simulation of an ensemble of 27 copies of beta(2)-microglobulin in explicit solvent. During the simulation, the formation of intermolecular contacts is observed. The simulation highlights the importance of apical residues and, in particular, of those at the N-terminus end of the molecule. The most frequently found pattern of interaction involves a head-to-head contact arrangement of molecules. Hydrophobic contacts appear to be important for the establishment of long-lived (on the simulation timescale) contacts. Although early events on the pathway to aggregation and fibril formation are not directly related to the end-state of the process, which is reached on a much longer timescale, simulation results are consistent with experimental data and in general with a parallel arrangement of intermolecular beta-strand pairs. PMID:17158575

Fogolari, Federico; Corazza, Alessandra; Viglino, Paolo; Zuccato, Pierfrancesco; Pieri, Lidia; Faccioli, Pietro; Bellotti, Vittorio; Esposito, Gennaro

2007-03-01

76

Molecular Dynamics Simulation Suggests Possible Interaction Patterns at Early Steps of ?2-Microglobulin Aggregation  

PubMed Central

Early events in aggregation of proteins are not easily accessible by experiments. In this work, we perform a 5-ns molecular dynamics simulation of an ensemble of 27 copies of ?2-microglobulin in explicit solvent. During the simulation, the formation of intermolecular contacts is observed. The simulation highlights the importance of apical residues and, in particular, of those at the N-terminus end of the molecule. The most frequently found pattern of interaction involves a head-to-head contact arrangement of molecules. Hydrophobic contacts appear to be important for the establishment of long-lived (on the simulation timescale) contacts. Although early events on the pathway to aggregation and fibril formation are not directly related to the end-state of the process, which is reached on a much longer timescale, simulation results are consistent with experimental data and in general with a parallel arrangement of intermolecular ?-strand pairs.

Fogolari, Federico; Corazza, Alessandra; Viglino, Paolo; Zuccato, Pierfrancesco; Pieri, Lidia; Faccioli, Pietro; Bellotti, Vittorio; Esposito, Gennaro

2007-01-01

77

Molecular beam study of the scattering behavior of water molecules from a graphite surface.  

PubMed

Gas flow in nanospaces is greatly affected by the scattering behavior of gas molecules on solid surfaces, resulting in unique mass transport properties. In this paper, the molecular beam scattering experiment of water molecules on a graphite surface was conducted to understand their scattering dynamics in an incident energy range that corresponds to their thermal velocity distribution at room temperature (35-130 meV). Because of the large adsorption energy (?100 meV), the scattering behavior is quite sensitive to the incident energy even within this narrow energy range. For relatively large incident energies, the direct-inelastic and trapping-desorption channels have comparable contributions to the scattering process on the surface at 300 K. In contrast, when the incident energy decreases well below the adsorption energy on the surface, the trapping-desorption channel becomes dominant, changing the scattering pattern from directional to diffusive scattering. As a result, the tangential momentum accommodation coefficient (TMAC), which significantly impacts the mass transport in nanospaces, largely depends on the incident energy. A decrease in the incident energy from 130 to 35 meV doubles the TMAC (0.42 to 0.86). In addition to the incident energy, the TMAC shows a strong dependence on the surface temperature. With increasing the surface temperature from 300 to 500 K, the scattering becomes more directional because of the increasing contribution of the direct-inelastic channel, which reduces the TMAC for the incident beam energy of 35 meV to 0.48. PMID:24901371

Miyoshi, Nobuya; Osuka, Kenichi; Kinefuchi, Ikuya; Takagi, Shu; Matsumoto, Yoichiro

2014-07-01

78

Molecular wires in single-molecule junctions: charge transport and vibrational excitations.  

PubMed

We investigate the effect of vibrations on the electronic transport through single-molecule junctions, using the mechanically controlled break junction technique. The molecules under investigation are oligoyne chains with appropriate end groups, which represent both an ideally linear electrical wire and an ideal molecular vibrating string. Vibronic features can be detected as satellites to the electronic transitions, which are assigned to longitudinal modes of the string by comparison with density functional theory data. PMID:20521299

Ballmann, Stefan; Hieringer, Wolfgang; Secker, Daniel; Zheng, Qinglin; Gladysz, John A; Görling, Andreas; Weber, Heiko B

2010-07-12

79

Molecular Resolution Imaging of Protein Molecules in Liquid Using Frequency Modulation Atomic Force Microscopy  

NASA Astrophysics Data System (ADS)

We demonstrated molecular resolution imaging of biological samples such as bacteriorhodopsin protein molecules in purple membrane and isolated chaperonin (GroEL) protein molecules, both adsorbed on mica using frequency modulation atomic force microscope (FM-AFM) in liquid. We also showed that the frequency noise of FM-AFM in liquid can be greatly reduced by the reduction of the noise-equivalent deflection of an optical beam deflection sensor.

Yamada, Hirofumi; Kobayashi, Kei; Fukuma, Takeshi; Hirata, Yoshiki; Kajita, Teruyuki; Matsushige, Kazumi

2009-09-01

80

Recognition of damage-associated molecular patterns related to nucleic acids during inflammation and vaccination  

PubMed Central

All mammalian cells are equipped with large numbers of sensors for protection from various sorts of invaders, who, in turn, are equipped with molecules containing pathogen-associated molecular patterns (PAMPs). Once these sensors recognize non-self antigens containing PAMPs, various physiological responses including inflammation are induced to eliminate the pathogens. However, the host sometimes suffers from chronic infection or continuous injuries, resulting in production of self-molecules containing damage-associated molecular patterns (DAMPs). DAMPs are also responsible for the elimination of pathogens, but promiscuous recognition of DAMPs through sensors against PAMPs has been reported. Accumulation of DAMPs leads to massive inflammation and continuous production of DAMPs; that is, a vicious circle leading to the development of autoimmune disease. From a vaccinological point of view, the accurate recognition of both PAMPs and DAMPs is important for vaccine immunogenicity, because vaccine adjuvants are composed of several PAMPs and/or DAMPs, which are also associated with severe adverse events after vaccination. Here, we review as the roles of PAMPs and DAMPs upon infection with pathogens or inflammation, and the sensors responsible for recognizing them, as well as their relationship with the development of autoimmune disease or the immunogenicity of vaccines.

Jounai, Nao; Kobiyama, Kouji; Takeshita, Fumihiko; Ishii, Ken J.

2012-01-01

81

Millimeter-Wave Spectroscopic and Collisional Studies of Molecules and Molecular Ions  

NASA Astrophysics Data System (ADS)

Molecular spectroscopy in the millimeter- and submillimeter-wave regions is an important tool in molecular physics. Information on molecular motions and interactions is obtained from spectroscopic studies of energy levels and collisions. This information and the data from which it is derived are essential in remote sensing of the atmosphere and the interstellar medium. Remote sensing at submillimeter wavelengths is now possible, making higher frequency and quantum number measurements of known interstellar species like water, propionitrile and ethyl alcohol necessary. Remote sensing improvements have also facilitated the need for spectral data on suspected interstellar molecules like propylene. The desire to extract quantitative information from atmospheric remote sensing has resulted in the need for a better understanding of the molecular interactions that cause pressure broadening. The use of a cold molecular ion to magnify the effects of intermolecular interactions has serious implications for pressure broadening theory. The measurement and analysis of rotational spectra of the asymmetric rotors water and propionitrile and the internal rotors propylene and ethyl alcohol are presented. These investigations provide the data and analysis necessary for astronomical observation. The ethyl alcohol investigation is the first experimental millimeter-wave study of a molecule with an asymmetric internal rotor. This study provides the data necessary for detailed theoretical modeling of this type of problem. A novel new experimental technique for generating and studying molecular ions is presented. The first temperature dependent microwave pressure broadening study of a molecular ion colliding with a neutral molecule, HCO^{+} on H_2 , is presented.

Pearson, John Christoffersen

1995-01-01

82

A quantum mechanical/molecular mechanical approach to the investigation of particle-molecule interactions  

NASA Astrophysics Data System (ADS)

A quantum mechanical/molecular mechanical aerosol model is developed to describe the interaction between gas phase molecules and atmospheric particles. The model enables the calculation of interaction energies and time-dependent properties. We use the model to investigate how a succinic acid molecule interacts with an aqueous particle. We show how the interaction energies and linear response properties (excitation energies, transition moments, and polarizabilities) depend on the distance between aerosol particle and molecule and on their relative orientation. The results are compared with those obtained previously using a dielectric continuum model [Sloth et al., J. Phys. Chem. (submitted)].

Sloth, Marianne; Bilde, Merete; Mikkelsen, Kurt V.

2003-06-01

83

Disruption of small double stranded DNA molecules on carbon nanotubes: A molecular dynamics study  

NASA Astrophysics Data System (ADS)

The behaviour of double stranded DNA molecules (dsDNA) attached to single walled carbon nanotubes (SWCNTs) was investigated by molecular dynamics simulations. We observe that disruption of short dsDNA helices is accelerated by the presence of SWCNT due to the establishment of ?-stacking interactions between the nucleobases and the sidewall of the nanotubes. These results are in good agreement with experimental evidences and confirm the mechanism of assembly between a single stranded DNA molecule and a SWCNT. Longer DNA molecules maintain the structure of a double helix although with the hydrogen-bonding network slightly altered on the relatively short time scale.

Alegret, Núria; Santos, Eva; Rodríguez-Fortea, Antonio; Rius, F. Xavier; Poblet, Josep M.

2012-02-01

84

Vibrationally resolved molecular frame photoelectron angular distributions of diatomic and polyatomic molecules  

NASA Astrophysics Data System (ADS)

Vibrationally resolved molecular frame photoelectron angular distributions (MFPADs) of fixed-in-space molecules have been evaluated for diatomic and polyatomic molecules. Calculations have been performed by using an extension of the static-exchange density functional theory formerly developed by P. Decleva [1] and coworkers and extended in order to include the nuclear motion in the Born-Oppenheimer approximation. The method proved to be very accurate for diatomic molecules [2, 3, 5], particularly at high energy of the photoelectron. In this work, we present the results obtained for the inner shell photoionization of C2H2, NH3, CH4, CF4, BF3 and SF6.

Plésiat, Etienne; Decleva, Piero; Martín, Fernando

2014-04-01

85

Carbon Nanotube Biosensors for Space Molecule Detection and Clinical Molecular Diagnostics  

NASA Technical Reports Server (NTRS)

Both space molecule detection and clinical molecule diagnostics need to develop ultra sensitive biosensors for detection of less than attomole molecules such as amino acids for DNA. However all the electrode sensor systems including those fabricated from the existing carbon nanotubes, have a background level of nA (nanoAmp). This has limited DNA or other molecule detection to nA level or molecules whose concentration is, much higher than attomole level. A program has been created by NASA and NCI (National Cancer Institute) to exploit the possibility of carbon nanotube based biosensors to solve this problem for both's interest. In this talk, I will present our effort on the evaluation and novel design of carbon nanotubes as electrode biosensors with strategies to minimize background currents while maximizing signal intensity.The fabrication of nanotube electrode arrays, immobilization of molecular probes on nanotube electrodes and in vitro biosensor testing will also be discussed.

Han, Jie

2001-01-01

86

Identification of low molecular weight molecules as new components of the nacre organic matrix.  

PubMed

Nacre of Pinctada margaritifera displays a number of interesting biological activities on bone, mainly concentrated in a water-soluble organic matrix representing 0.24% of the nacre weight. Dialysis of that matrix through 8 kDa and 1 kDa cut-off membranes showed that 60% of it is made of small molecules of molecular masses below 1 kDa. Reversed-phase high-performance liquid chromatography of the small molecule fractions and subsequent electrospray ionization mass spectrometric analysis of 19 fractions thereof indicated the presence of at least 110 different molecules, in the range 100 Da-700 Da. Evidence for aggregate-forming properties of the small molecules was given. Amino acid analysis revealed that most of the small molecules were not peptides and tandem mass spectrometric gas-phase fragmentations clearly indicated a structural relationship between several molecules. Intriguingly, differences of a single Dalton between mono-charged ions peaks were observed. Further, approximately 40 analytes could be arranged in a ladder-like manner with mass spaces of 57 Da. Some of the water-soluble peptide sequences obtained after MS/MS fragmentation revealed that the 57 Da shift corresponds to the repetition of glycine residues. Furthermore, the exchange of glycine against alanine explains the 14 Da shift observed between some peptides. These data show for the first time that small molecules, especially peptides, are prevalent components of nacre. The molecular species described in this report might have a functional role in nacre. PMID:16828570

Bédouet, Laurent; Rusconi, Filippo; Rousseau, Marthe; Duplat, Denis; Marie, Arul; Dubost, Lionel; Le Ny, Karine; Berland, Sophie; Péduzzi, Jean; Lopez, Evelyne

2006-08-01

87

Energy-Level Related Nuclear-Spin Effects and Super-Hyperfine Spectral Patterns: how Molecules do Self-Nmr  

NASA Astrophysics Data System (ADS)

At several points in his defining works on molecular spectroscopy, Herzberg notes that ``because nuclear moments ldots are so very slight ldots transitions between species ldots are very strictly forbiddenldots '' Herzberg's most recent statement of such selection rules pertained to spherical top spin-species. It has since been shown that spherical top species (as well as those of lower symmetry molecules) converge exponentially with momentum quanta J and K to degenerate level clusters wherein even ``very slight'' nuclear fields and moments cause pervasive resonance and total spin species mixing. Ultra-high resolution spectra of Borde, et .al and Pfister et .al shows how SF_6 and SiF_4 Fluorine nuclear spin levels rearrange from total-spin multiplets to NMR-like patterns as their superfine structure converges. Similar super-hyperfine effects are anticipated for lower symmetry molecules exhibiting converging superfine level-clusters. Examples include PH_3 molecules and asymmetric tops. Following this we consider models that treat nuclear spins as coupled rotors undergoing generalized Hund-case transitions from spin-lab-momentum coupling to various spin-rotor correlations. G. A. Herzberg, Electronic Spectra of Polyatomic Molecules, (Von Norstrand Rheinhold 1966) p. 246. W G. Harter and C. W Patterson, Phys. Rev. A 19, 2277 (1979) W. G. Harter, Phys. Rev. A 24, 192 (1981). Ch. J. Borde, J. Borde, Ch. Breant, Ch. Chardonnet, A. Van Lerberghe, and Ch. Salomon, in Laser Spectroscopy VII, T. W Hensch and Y. R. Shen, eds. (Springer-Verlag, Berlin, 1985). O. Pfister, F. Guernet, G. Charton, Ch. Chardonnet, F. Herlemont, and J. Legrand, J. Opt. Soc. Am. B 10, 1521 (1993). O. Pfister, Ch. Chardonnet, and Ch. J. Bordè, Phys. Rev. Lett. 76, 4516 (1996) S. N. Yurchenko, W. Thiel, S. Patchkovskii, and P. Jensen, Phys. Chem. Chem. Phys.7, 573 (2005)

Harter, William; Mitchell, Justin

2009-06-01

88

Coherent electron transport through an azobenzene molecule: A light-driven molecular switch  

Microsoft Academic Search

We apply a first-principles computational approach to study a light-sensitive molecular switch. The molecule that comprises the switch can convert between a trans and a cis configuration upon photo-excitation. We find that the conductance of the two isomers vary dramatically, which suggests that this system has potential application as a molecular device. A detailed analysis of the band structure of

Hai-Ping Cheng; Chu Chang; Mao-Hua Du; Xiao-Guang Zhang; Adrian Roitberg; Jeffrey Krause

2004-01-01

89

Imiging molecular dynamics of dissociative electron attachment to polyatomic molecules: ammonia, methane, and methanol  

NASA Astrophysics Data System (ADS)

Momentum imaging experiment is performed to study molecular dynamics of dissociative electron attachment(DEA) to the ammonia, methane, and methanol molecules for their well known resonances. The momentum spheres of the negative ion fragments, H^-,NH^-,NH2^- from ammonia, H^-,CH^-,CH2^- from methane, H^-,O^-,CH3O^- from methanol, show unique angular distribution in their respective resonances, indicating each resonance involves different molecular dynamics.

Adaniya, Hidehito; Slaughter, Daniel; Weber, Thorsten; Belkacem, Ali

2011-06-01

90

Molecular release from patterned nanoporous gold thin films  

NASA Astrophysics Data System (ADS)

Nanostructured materials have shown significant potential for biomedical applications that require high loading capacity and controlled release of drugs. Nanoporous gold (np-Au), produced by an alloy corrosion process, is a promising novel material that benefits from compatibility with microfabrication, tunable pore morphology, electrical conductivity, well-established gold-thiol conjugate chemistry, and biocompatibility. While np-Au's non-biological applications are abundant, its performance in the biomedical field is nascent. In this work, we employ a combination of techniques including nanoporous thin film synthesis, quantitative electron microscopy, fluorospectrometry, and electrochemical surface characterization to study loading capacity and molecular release kinetics as a function of film properties and discuss underlying mechanisms. The sub-micron-thick sputter-coated nanoporous gold films provide small-molecule loading capacities up to 1.12 ?g cm-2 and molecular release half-lives between 3.6 hours to 12.8 hours. A systematic set of studies reveals that effective surface area of the np-Au thin films on glass substrates plays the largest role in determining loading capacity. The release kinetics on the other hand depends on a complex interplay of micro- and nano-scale morphological features.Nanostructured materials have shown significant potential for biomedical applications that require high loading capacity and controlled release of drugs. Nanoporous gold (np-Au), produced by an alloy corrosion process, is a promising novel material that benefits from compatibility with microfabrication, tunable pore morphology, electrical conductivity, well-established gold-thiol conjugate chemistry, and biocompatibility. While np-Au's non-biological applications are abundant, its performance in the biomedical field is nascent. In this work, we employ a combination of techniques including nanoporous thin film synthesis, quantitative electron microscopy, fluorospectrometry, and electrochemical surface characterization to study loading capacity and molecular release kinetics as a function of film properties and discuss underlying mechanisms. The sub-micron-thick sputter-coated nanoporous gold films provide small-molecule loading capacities up to 1.12 ?g cm-2 and molecular release half-lives between 3.6 hours to 12.8 hours. A systematic set of studies reveals that effective surface area of the np-Au thin films on glass substrates plays the largest role in determining loading capacity. The release kinetics on the other hand depends on a complex interplay of micro- and nano-scale morphological features. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr01288g

Kurtulus, Ozge; Daggumati, Pallavi; Seker, Erkin

2014-05-01

91

Molecular dynamics of immiscible fluids in chemically patterned nanochannels  

NASA Astrophysics Data System (ADS)

Molecular dynamics simulations of chain molecules are used to elucidate physical phenomena involved in flows of dense immiscible fluids in nanochannels. We first consider a force driven flow in which the channel walls are homogeneous and wetting to one fluid and nonwetting to the other fluid. The coating of the walls by the wetting fluid provides a fluctuating surface that confines the flow of the nonwetting fluid. The resulting dissipation yields stationary Poiseuille-like flows in contrast to the accelerating nature of flow in the absence of the coating. We then consider walls consisting of patches whose wetting preferences to a fluid alternate along the walls. In the resulting flow, the immiscible components exhibit periodic structures in their velocity fields such that the crests are located at the wettability steps in contrast to the behavior of a single fluid for which the crest occurs in the wetting region. We demonstrate that for a single fluid, the modulated velocity field scales with the size of the chain molecules.

Cieplak, Marek; Banavar, Jayanth R.

2008-03-01

92

Methods for the determination of molecular mobility of adsorbed molecules based on high resolution NMR  

Microsoft Academic Search

Based on the increased resolution achieved in NMR on adsorbed molecules, various methods are proposed to determine the mobility of adsorbed species. 1H NMR linewidths are shown to reflect intramolecular dipolar relaxation and can therefore be used for mobility estimates. This method is applicable to extremely low loadings. Thus we measured a significant decrease in molecular mobility for 1-butene adsorbed

U. Schwerk; D. Michel

1996-01-01

93

Molecular isomerization and fragmentation of polyatomic molecules controlled by inner-valence recollision-ionization  

NASA Astrophysics Data System (ADS)

Control over various fragmentation reactions of a series of polyatomic molecules (acetylene, ethylene, 1,3-butadiene) by the optical waveform of intense few-cycle laser pulses is demonstrated experimentally. We show both experimentally and theoretically that the responsible mechanism is inelastic ionization from inner-valence molecular orbitals by recolliding electron wave packets.

Xie, X.; Doblhoff-Dier, K.; Roither, S.; Schöffler, M.; Kartashov, D.; Xu, H.; Rathje, T.; Paulus, G. G.; Baltuška, A.; Gräfe, S.; Kitzler, M.

2014-04-01

94

Hydration shells of molecules in molecular association: A mechanism for biomolecular recognition  

PubMed Central

It has become clear that water should not be treated as an inert environment, but rather as an integral and active component of molecules. Here, we consider molecules and their hydration shells together as single entities. We show that: (1) the rate of association of molecules should be determined by the energetic barriers arising from interactions between their hydration shells; (2) replacing non-polar atoms of molecular surfaces with polar atoms increases these barriers; (3) reduction of the hydration shells during molecular association is the driving force for association not only of non-polar, but of polar molecules as well; (4) in most cases the dehydration of polar atoms during molecular association thermodynamically counteracts association; (5) on balance the thermodynamic stability of associated complexes is basically determined by the action of these two opposing factors: reduction of the hydration shells and dehydration of polar atoms; (6) molecular crowding reduces the energetic barriers counteracting association and changes the thermodynamic stability of associated complexes. These results lead to a mechanism for biomolecular recognition in the context of which the formation of unique structures is provided by rapidly forming kinetic traps with a biologically necessary lifetime but with a marginal thermodynamic stability. The mechanism gives definitive answers to questions concerning the heart of specific interactions between biomolecules, their folding and intracellular organization. Predictions are given that can be subjected to direct experimental tests.

Lim, Valery I.; Curran, James F.; Garber, Maria B.

2013-01-01

95

Effect of Temperature on Water Molecules in a Model Epoxy Molding Compound: Molecular Dynamics Simulation Approach  

Microsoft Academic Search

The effect of temperature on the distribution and transport of water molecules in a model epoxy molding com- pound (EMC) system is investigated using atomistic molecular dynamics simulation with 4 and 7 wt% water content at various temperatures, such as 298, 323, 353, and 373 K. The thermal expansion of the hydrated model EMC was evaluated as 1-5% of its

Seung Geol Lee; Ji Il Choi; Wonsang Koh; Seung Soon Jang; Jongman Kim; Gene Kim

2011-01-01

96

Fabrication of a highly oriented line structure on an aluminum surface and the nanoscale patterning on the nanoscale structure using highly functional molecules  

SciTech Connect

The surface of an Al plate was treated with a combination of chemical and electrochemical processes for fabrication of surface nanoscale structures on Al plates. Chemical treatments by using acetone and pure water under supersonic waves were conducted on an Al surface. Additional electrochemical process in H{sub 2}SO{sub 4} solution created a finer and oriented nanoscale structure on the Al surface. Dynamic force microscopy (DFM) measurement clarified that the nanoscale highly oriented line structure was successfully created on the Al surface. The line distance was estimated approximately 30-40 nm. At the next stage, molecular patterning on the highly oriented line structure by functional molecules such as copper phthalocyanine (CuPc) and fullerene C{sub 60} was also conducted. CuPc or C{sub 60} molecules were deposited on the highly oriented line structure on Al. A toluene droplet containing CuPc molecules was cast on the nanostructured Al plate and was extended on the surface. CuPc or C{sub 60} deposition on the nanostructured Al surface proceeded by evaporation of toluene. DFM and x-ray photoemission spectroscopy measurements demonstrated that a unique molecular pattern was fabricated so that the highly oriented groove channels were filled with the functional molecules.

Watanabe, Y.; Kato, H.; Takemura, S.; Watanabe, H.; Hayakawa, K.; Kimura, S.; Okumura, D.; Sugiyama, T.; Hiramatsu, T.; Nanba, N.; Nishikawa, O.; Taniguchi, M. [Department of Electrical, Electronic and Information Engineering, College of Engineering, Kanto Gakuin University, 1-50-1 Mutsuurahigashi, Kanazawa-ku, Yokohama 236-8501 (Japan); Department of Biology and Chemistry, Kanazawa Institute of Technology, 7-1 Ohgigaoka, Nonoichi, Ishikawa 921-8501 (Japan)

2009-07-15

97

Ultra high resolution molecular beam cars spectroscopy with application to planetary atmospheric molecules  

NASA Technical Reports Server (NTRS)

The measurement of high resolution pulsed and continuous wave (CW) coherent anti-Stokes Raman spectroscopy (CARS) measurements in pulsed and steady state supersonic expansions were demonstrated. Pulsed molecular beam sources were characterized, and saturation of a Raman transition and, for the first time, the Raman spectrum of a complex molecular cluster were observed. The observation of CW CARS spectra in a molecular expansion and the effects of transit time broadening is described. Supersonic expansion is established as a viable technique for high resolution Raman spectroscopy of cold molecules with resolutions of 100 MH2.

Byer, R. L.

1982-01-01

98

Organization of copper-phthalocyanine molecules on mono-molecular organic buffer layers  

NASA Astrophysics Data System (ADS)

After 17,19-dotetracontadiyne (DTDY) mono-molecular layer was formed onto highly ordered pyrolytic graphite by vacuum deposition, copper-phthalocyanine (CuPc) was successively deposited on the DTDY layer. Depending on the coverage of CuPc molecules on the DTDY layer, the CuPc changed in their aggregation states. When a small amount of CuPc molecule was deposited, one-dimensional alignment of CuPc molecules was formed along a line of the DTDY columnar axis. With increasing the amount of deposited CuPc, two-dimensional domains were formed and exhibit the point-on-line coincidence with respect to the underlying DTDY layer. The one-dimensional alignment of CuPc was observed also along a column axis of the n-tetratriacontane mono-molecular layer prepared in the same way.

Takajo, Daisuke; Nemoto, Takashi; Ozaki, Hiroyuki; Mazaki, Yasuhiro; Isoda, Seiji

2004-11-01

99

Above-threshold ionization of diatomic molecules in an intense laser field: Molecular alignment effects  

NASA Astrophysics Data System (ADS)

In this work, we study the photoelectron spectra of the diatomic molecule O2 in the direction perpendicular to the laser polarization. Compared with atoms, molecules have additional parameters, e.g., the orientation of the molecule and the symmetry of the initial electronic state, and thus give rise to richer strong-field phenomena. Our simulations show that for parallel and perpendicular alignments of the laser polarization with respect to the molecular axis, the photoelectron spectra display above-threshold ionization (ATI) peaks with a specific 2?? separation in which the absorption of an even number of photons is absent. However, for other alignment angles, the even-order ATI peaks appear. According to our analysis, the physical mechanism of the alignment effect of the even-order ATI peaks can be attributed to the symmetry of the molecular ground-state wave function with respect to the photoelectron emission direction.

Hu, ZiLong; Lai, XuanYang; Liu, XiaoJun; Chen, Jing

2014-04-01

100

Single-molecule chemical reaction reveals molecular reaction kinetics and dynamics.  

PubMed

Understanding the microscopic elementary process of chemical reactions, especially in condensed phase, is highly desirable for improvement of efficiencies in industrial chemical processes. Here we show an approach to gaining new insights into elementary reactions in condensed phase by combining quantum chemical calculations with a single-molecule analysis. Elementary chemical reactions in liquid-phase, revealed from quantum chemical calculations, are studied by tracking the fluorescence of single dye molecules undergoing a reversible redox process. Statistical analyses of single-molecule trajectories reveal molecular reaction kinetics and dynamics of elementary reactions. The reactivity dynamic fluctuations of single molecules are evidenced and probably arise from either or both of the low-frequency approach of the molecule to the internal surface of the SiO2 nanosphere or the molecule diffusion-induced memory effect. This new approach could be applied to other chemical reactions in liquid phase to gain more insight into their molecular reaction kinetics and the dynamics of elementary steps. PMID:24963600

Zhang, Yuwei; Song, Ping; Fu, Qiang; Ruan, Mingbo; Xu, Weilin

2014-01-01

101

Molecular release from patterned nanoporous gold thin films.  

PubMed

Nanostructured materials have shown significant potential for biomedical applications that require high loading capacity and controlled release of drugs. Nanoporous gold (np-Au), produced by an alloy corrosion process, is a promising novel material that benefits from compatibility with microfabrication, tunable pore morphology, electrical conductivity, well-established gold-thiol conjugate chemistry, and biocompatibility. While np-Au's non-biological applications are abundant, its performance in the biomedical field is nascent. In this work, we employ a combination of techniques including nanoporous thin film synthesis, quantitative electron microscopy, fluorospectrometry, and electrochemical surface characterization to study loading capacity and molecular release kinetics as a function of film properties and discuss underlying mechanisms. The sub-micron-thick sputter-coated nanoporous gold films provide small-molecule loading capacities up to 1.12 ?g cm(-2) and molecular release half-lives between 3.6 hours to 12.8 hours. A systematic set of studies reveals that effective surface area of the np-Au thin films on glass substrates plays the largest role in determining loading capacity. The release kinetics on the other hand depends on a complex interplay of micro- and nano-scale morphological features. PMID:24842586

Kurtulus, Ozge; Daggumati, Pallavi; Seker, Erkin

2014-05-29

102

Molecular Threading: Mechanical Extraction, Stretching and Placement of DNA Molecules from a Liquid-Air Interface  

PubMed Central

We present “molecular threading”, a surface independent tip-based method for stretching and depositing single and double-stranded DNA molecules. DNA is stretched into air at a liquid-air interface, and can be subsequently deposited onto a dry substrate isolated from solution. The design of an apparatus used for molecular threading is presented, and fluorescence and electron microscopies are used to characterize the angular distribution, straightness, and reproducibility of stretched DNA deposited in arrays onto elastomeric surfaces and thin membranes. Molecular threading demonstrates high straightness and uniformity over length scales from nanometers to micrometers, and represents an alternative to existing DNA deposition and linearization methods. These results point towards scalable and high-throughput precision manipulation of single-molecule polymers.

Kemmish, Kent; Hamalainen, Mark; Bowell, Charlotte; Bleloch, Andrew; Klejwa, Nathan; Lehrach, Wolfgang; Schatz, Ken; Stark, Heather; Marblestone, Adam; Church, George; Own, Christopher S.; Andregg, William

2013-01-01

103

Molecular Nanoshearing: An Innovative Approach to Shear off Molecules with AC-Induced Nanoscopic Fluid Flow  

PubMed Central

Early diagnosis of disease requires highly specific measurement of molecular biomarkers from femto to pico-molar concentrations in complex biological (e.g., serum, blood, etc.) samples to provide clinically useful information. While reaching this detection limit is challenging in itself, these samples contain numerous other non-target molecules, most of which have a tendency to adhere to solid surfaces via nonspecific interactions. Herein, we present an entirely new methodology to physically displace nonspecifically bound molecules from solid surfaces by utilizing a newly discovered “tuneable force”, induced by an applied alternating electric field, which occurs within few nanometers of an electrode surface. This methodology thus offers a unique ability to shear-off loosely bound molecules from the solid/liquid interface. Via this approach, we achieved a 5-fold reduction in nonspecific adsorption of non-target protein molecules and a 1000-fold enhancement for the specific capture of HER2 protein in human serum.

Shiddiky, Muhammad J. A.; Vaidyanathan, Ramanathan; Rauf, Sakandar; Tay, Zhikai; Trau, Matt

2014-01-01

104

Interactions of Liquid Crystal-Forming Molecules with Phospholipid Bilayers Studied by Molecular Dynamics Simulations  

PubMed Central

Recent experiments have shown that liquid crystals can be used to image mammalian cell membranes and to amplify structural reorganization in phospholipid-laden liquid crystal-aqueous interfaces. In this work, molecular dynamics simulations were employed to explore the interactions between commonly used liquid crystal-forming molecules and phospholipid bilayers. In particular, umbrella sampling was used to obtain the potential of mean force of 4-cyano-4?-pentylbiphenyl (5CB) and 4?-(3,4-difluor-phenyl)-4-pentyl-bicylohexyl (5CF) molecules partitioning into a dipalmitoylphosphatidylcholine bilayer. In addition, results of simulations are presented for systems consisting of a fully hydrated bilayer with 5CB or 5CF molecules at the lowest (4.5 mol %) and highest (20 mol %) concentrations used in recent laboratory experiments. It is found that mesogens preferentially partition from the aqueous phase into the membrane; the potential of mean force exhibits highly favorable free energy differences for partitioning (?18 kBT for 5CB and ?26 kBT for 5CF). The location and orientation of mesogens associated with the most stable free energies in umbrella sampling simulations of dilute systems were found to be consistent with those observed in liquid-crystal-rich bilayers. It is found that the presence of mesogens in the bilayer enhances the order of lipid acyl tails, and changes the spatial and orientational arrangement of lipid headgroup atoms. These effects are more pronounced at higher liquid-crystal concentrations. In comparing the behavior of 5CB and 5CF, a stronger spatial correlation (i.e., possibly leading to aggregation) is observed between 5CB molecules within a bilayer than between 5CF molecules. Also, the range of molecular orientations and positions along the bilayer normal is larger for 5CB molecules. At the same time, 5CF molecules were found to bind more strongly to lipid headgroups, thereby slowing the lateral motion of lipid molecules.

Kim, Evelina B.; Lockwood, Nathan; Chopra, Manan; Guzman, Orlando; Abbott, Nicholas L.; de Pablo, Juan J.

2005-01-01

105

Hydroxyl and water molecule orientations in trypsin: comparison to molecular dynamic structures.  

PubMed

A comparison is presented of experimentally observed hydroxyl and water hydrogens in trypsin determined from neutron density maps with the results of a 140ps molecular dynamics (MD) simulation. Experimental determination of hydrogen and deuterium atom positions in molecules as large as proteins is a unique capability of neutron diffraction. The comparison addresses the degree to which a standard force-field approach can adequately describe the local electrostatic and van der Waals forces that determine the orientations of these hydrogens. The molecular dynamics simulation, based on the all-atom AMBER force-field, allowed free rotation of all hydroxyl groups and movement of water molecules making up a bath surrounding the protein. The neutron densities, derived from 2.1A D2O-H2O difference Fourier maps, provide a database of 27 well-ordered hydroxyl hydrogens. Virtually all of the simulated hydroxyl orientations are within a standard deviation of the experimentally-observed positions, including several examples in which both the simulation and the neutron density indicate that a hydroxyl group is shifted from a 'standard' rotamer. For the most highly ordered water molecules, the hydrogen distributions calculated from the trajectory were in good agreement with neutron density; simulated water molecules that displayed multiple hydrogen bonding networks had correspondingly broadened neutron density profiles. This comparison was facilitated by development of a method to construct a pseudo 2A density map based on the hydrogen atom distributions from the simulation. The degree of internal water molecules is shown to result primarily from the electrostatic environment surrounding that water molecule as opposed to the cavity size available to the molecule. A method is presented for comparing the discrete observations sampled in a dynamics trajectory with the time-averaged data obtained from X-ray or neutron diffraction studies. This method is particularly useful for statically-disordered water molecules, in which the average location assigned from a trajectory may represent a site of relatively low occupancy. PMID:9092457

McDowell, R S; Kossiakoff, A A

1996-01-01

106

Molecular Mechanisms of Reversible and Irreversible Trapping of >Large DNA Molecules Undergoing Gel Electrophoresis  

NASA Astrophysics Data System (ADS)

Megabase-size DNA becomes trapped in agarose gels during electrophoresis if the electric field is greater than 2 V/cm. Fluorescence microscopy reveals that megabase molecules invariably arrest during the U-shape phase of their caterpillar cycle, adhering to the gel near the vertex of the U. The electric field dependence of the molecular sizes trapped in the gel has been determined and indicates a critical force above which molecules trap. The size of unligated ?-ladders sheared during electrophoresis at a given field is the same as the size of molecules trapped at that field and suggests that both processes occur through nick melting near the vertex of the U. Consistently, molecules nicked by exposure to UV radiation trapped more readily than un-exposed ones. To further characterize the nature of the molecule-gel interaction near the vertex, the electric force on tethered DNA molecules within a gel has been measured using laser tweezers, yielding an effective charge of 0.16 e^-/phos. This figure translates into a critical tension at the vertex of 15 pN, a force sufficient to melt nicks bent around corners in the gel path near the vertex, and to trap a molecule.

Bustamante, Carlos

1998-05-01

107

Distribution patterns of small-molecule ligands in the protein universe and implications for origin of life and drug discovery  

PubMed Central

Background Extant life depends greatly on the binding of small molecules (such as ligands) with macromolecules (such as proteins), and one ligand can bind multiple proteins. However, little is known about the global patterns of ligand-protein mapping. Results By examining 2,186 well-defined small-molecule ligands and thousands of protein domains derived from a database of druggable binding sites, we show that a few ligands bind tens of protein domains or folds, whereas most ligands bind only one, which indicates that ligand-protein mapping follows a power law. Through assigning the protein-binding orders (early or late) for bio-ligands, we demonstrate that the preferential attachment principle still holds for the power-law relation between ligands and proteins. We also found that polar molecular surface area, H-bond acceptor counts, H-bond donor counts and partition coefficient are potential factors to discriminate ligands from ordinary molecules and to differentiate super ligands (shared by three or more folds) from others. Conclusion These findings have significant implications for evolution and drug discovery. First, the chronology of ligand-protein binding can be inferred by the power-law feature of ligand-protein mapping. Some nucleotide-containing ligands, such as ATP, ADP, GDP, NAD, FAD, dihydro-nicotinamide-adenine-dinucleotide phosphate (NDP), nicotinamide-adenine-dinucleotide phosphate (NAP), flavin mononucleotide (FMN) and AMP, are found to be the earliest cofactors bound to proteins, agreeing with the current understanding of evolutionary history. Second, the finding that about 30% of ligands are shared by two or more domains will help with drug discovery, such as in finding new functions from old drugs, developing promiscuous drugs and depending more on natural products.

Ji, Hong-Fang; Kong, De-Xin; Shen, Liang; Chen, Ling-Ling; Ma, Bin-Guang; Zhang, Hong-Yu

2007-01-01

108

Development of molecular patterning and immobilization techniques for scanning tunnelling microscopy and atomic force microscopy  

Microsoft Academic Search

A preliminary study has been carried out to evaluate the possibility of patterning biological molecules on surfaces for scanning tunnelling microscopy and atomic force microscopy. The approach uses the concept of treating surfaces that are suitable for semiconductor lithography with bridging molecules that can be patterned to micrometre and nanometre scales. Indium tin oxide and flame-treated gold have been selected

P. Connolly; J. Cooper; G. R. Moores; Jie Shen; G. Thompson

1991-01-01

109

Computer-aided molecular modeling and design of DNA-inserting molecules.  

PubMed

Intercalators are molecules capable of sliding between base pairs without disturbing the overall stacking pattern. In addition, there may exist molecules capable of inserting into a base pair thereby disrupting the hydrogen bonds and replacing them with new hydrogen bonds. A molecule probably capable of inserting, i.e., an insertor, is the diketopiperazine cyclo-[Gly-Gly] (1). A barbiturate (2), alloxan (3), a pyrimidine derivative (4) and a hydantoin (5) were also studied as possible insertors. Furthermore, molecules such as ethyleneurea (6), succinimide (7), as well as a malonamide derivative (8) and oxamide derivatives (9-11) were studied in order to investigate the arrangement and the number of hydrogen bonds necessary for insertion. Molecules 12-14 were designed and studied for their capacity to act as bisinsertors and/or bisintercalators. These molecules feature two diketopiperazine moieties which are connected via a diphenyl(thio)ether, i.e., 12 and 13, or a bisphenol A spacer, i.e., 14. The latter molecule (14) seems a promising candidate as a bisinsertor. PMID:1583538

van der Klein-de Gunst, F J; van Boom, J H; Liskamp, R M

1992-02-01

110

Microfluidic parallel patterning and cellular delivery of molecules with a nanofountain probe.  

PubMed

This brief report describes a novel tool for microfluidic patterning of biomolecules and delivery of molecules into cells. The microdevice is based on integration of nanofountain probe (NFP) chips with packaging that creates a closed system and enables operation in liquid. The packaged NFP can be easily coupled to a micro/nano manipulator or atomic force microscope for precise position and force control. We demonstrate here the functionality of the device for continuous direct-write parallel patterning on a surface in air and in liquid. Because of the small volume of the probes (~3 pL), we can achieve flow rates as low as 1 fL/s and have dispensed liquid drops with submicron to 10 µm diameters in a liquid environment. Furthermore, we demonstrate that this microdevice can be used for delivery of molecules into single cells by transient permeabilization of the cell membrane (i.e., electroporation). The significant advantage of NFP-based electroporation compared with bulk electroporation and other transfection techniques is that it allows for precise and targeted delivery while minimizing stress to the cell. We discuss the ongoing development of the tool toward automated operation and its potential as a multifunctional device for microarray applications and time-dependent single-cell studies. PMID:23897012

Kang, Wonmo; McNaughton, Rebecca L; Yavari, Fazel; Minary-Jolandan, Majid; Safi, Asmahan; Espinosa, Horacio D

2014-02-01

111

Vascular bed origin dictates flow pattern regulation of endothelial adhesion molecule expression.  

PubMed

Endothelial cell phenotypes markedly differ, depending upon function and vascular bed of origin. Differences might account for specific susceptibility to pathological conditions. As leukocyte adhesion to activated endothelium is the initiating event in a range of diseases, we compared the influence of vascular bed-specific flow patterns on adhesion molecule expression in human saphenous vein (HSVEC) and coronary artery endothelial cells (HCAEC). In vitro, immune cell attachment was increased 1.6-fold when tumor necrosis factor (TNF)-alpha-stimulated HSVEC were exposed to coronary artery flow in place of physiological venous flow and 1.9-fold higher compared with attachment to cytokine-stimulated HCAEC exposed to coronary artery flow. This was associated with increased concentrations of soluble E-selectin, VCAM-1, and ICAM-1 in supernatants of HSVEC exposed to coronary artery flow compared with HCAEC exposed to the same flow pattern. Venous and coronary artery flow both increased TNF-alpha-induced E-selectin and ICAM-1 expression on HSVEC, but only coronary artery flow increased VCAM-1 expression. In marked contrast to HSVEC, venous and coronary artery flow attenuated TNF-alpha-induced E-selectin and VCAM-1 expression on HCAEC, whereas coronary artery flow further induced ICAM-1 on cytokine-stimulated HCAEC. With the exception of cytokine-induced ICAM-1, adhesion molecule expression on HSVEC exposed to coronary artery flow exceeded expression on HCAEC. Thus ICAM-1 expression involves complex flow-dependent and -independent pathways with marked dissimilarities between the two endothelial cell types studied. Interestingly, Kruppel-like factor (KLF) 4 overexpression in HCAEC and HSVEC significantly reduced TNF-alpha-induced E-selectin and VCAM-1 expression in static conditions, while ICAM-1 expression remained constant. Furthermore, both flow patterns induced KLF2 and KLF4 expression in HCAEC and HSVEC. Venous and coronary artery flow differentially influence endothelial adhesion molecule and transcription factor expression, depending on the vascular bed of origin. Differences in adhesion molecule expression and subsequent immune cell adhesion between HSVEC and HCAEC may contribute to different susceptibility to pathological conditions. PMID:17209004

Methe, Heiko; Balcells, Mercedes; Alegret, Maria del Carmen; Santacana, Marina; Molins, Blanca; Hamik, Anne; Jain, Mukesh K; Edelman, Elazer R

2007-05-01

112

Molecules, cancer, and the surgeon. A review of molecular biology and its implications for surgical oncology.  

PubMed Central

Interactions between molecules control intra- and intercellular physiology. Cancer is emerging as a disease in which individual molecules are either overproduced, mutated, expressed at inappropriate stages of development, or lost due to inheritance or aberrant mitotic division. The major players in this contest of cellular control are growth factors, growth factor receptors (GFRs), signal transducers, and dominant or suppressor/recessive oncogenes. The tumors most frequently removed by surgeons have been reported to have changes in one or another of these types of molecules. The concept of multistage carcinogenesis, whereby malignancy arises after a sequence of changes that are cumulative, and passed from progenitor to daughter cells, is also being defined as a sequence of molecular, genetic, and chromosomal alterations. Molecular antineoplastic therapy is in early stages of development at the laboratory bench. The future may see patients screened for cancer susceptibility, evaluated for adjuvant therapy, and chosen for particular treatment based on molecular analysis. The types of cancer operations and the scope of surgical resection may change as molecular techniques enhance oncologic treatment.

Arbeit, J M

1990-01-01

113

Nonnegative principal component analysis for cancer molecular pattern discovery.  

PubMed

As a well-established feature selection algorithm, principal component analysis (PCA) is often combined with the state-of-the-art classification algorithms to identify cancer molecular patterns in microarray data. However, the algorithm's global feature selection mechanism prevents it from effectively capturing the latent data structures in the high-dimensional data. In this study, we investigate the benefit of adding nonnegative constraints on PCA and develop a nonnegative principal component analysis algorithm (NPCA) to overcome the global nature of PCA. A novel classification algorithm NPCA-SVM is proposed for microarray data pattern discovery. We report strong classification results from the NPCA-SVM algorithm on five benchmark microarray data sets by direct comparison with other related algorithms. We have also proved mathematically and interpreted biologically that microarray data will inevitably encounter overfitting for an SVM/PCA-SVM learning machine under a Gaussian kernel. In addition, we demonstrate that nonnegative principal component analysis can be used to capture meaningful biomarkers effectively. PMID:20671323

Han, Xiaoxu

2010-01-01

114

Molecular Dynamics Simulation of Multivalent-Ion Mediated Attraction between DNA Molecules  

NASA Astrophysics Data System (ADS)

All atom molecular dynamics simulations with explicit water were done to study the interaction between two parallel double-stranded DNA molecules in the presence of the multivalent counterions putrescine (2+), spermidine (3+), spermine (4+) and cobalt hexamine (3+). The inter-DNA interaction potential is obtained with the umbrella sampling technique. The attractive force is rationalized in terms of the formation of ion bridges, i.e., multivalent ions which are simultaneously bound to the two opposing DNA molecules. The lifetime of the ion bridges is short on the order of a few nanoseconds.

Dai, Liang; Mu, Yuguang; Nordenskiöld, Lars; van der Maarel, Johan R. C.

2008-03-01

115

Imaging Polyatomic Molecules in Three Dimensions Using Molecular Frame Photoelectron Angular Distributions  

NASA Astrophysics Data System (ADS)

We demonstrate a method for determining the full three-dimensional molecular-frame photoelectron angular distribution in polyatomic molecules using methane as a prototype. Simultaneous double Auger decay and subsequent dissociation allow measurement of the initial momentum vectors of the ionic fragments and the photoelectron in coincidence, allowing full orientation by observing a three-ion decay pathway, (H+, H+, CH2+). We find the striking result that at low photoelectron energies the molecule is effectively imaged by the focusing of photoelectrons along bond directions.

Williams, J. B.; Trevisan, C. S.; Schöffler, M. S.; Jahnke, T.; Bocharova, I.; Kim, H.; Ulrich, B.; Wallauer, R.; Sturm, F.; Rescigno, T. N.; Belkacem, A.; Dörner, R.; Weber, Th.; McCurdy, C. W.; Landers, A. L.

2012-06-01

116

Imaging polyatomic molecules in three dimensions using molecular frame photoelectron angular distributions.  

PubMed

We demonstrate a method for determining the full three-dimensional molecular-frame photoelectron angular distribution in polyatomic molecules using methane as a prototype. Simultaneous double Auger decay and subsequent dissociation allow measurement of the initial momentum vectors of the ionic fragments and the photoelectron in coincidence, allowing full orientation by observing a three-ion decay pathway, (H+, H+, CH2(+)). We find the striking result that at low photoelectron energies the molecule is effectively imaged by the focusing of photoelectrons along bond directions. PMID:23003951

Williams, J B; Trevisan, C S; Schöffler, M S; Jahnke, T; Bocharova, I; Kim, H; Ulrich, B; Wallauer, R; Sturm, F; Rescigno, T N; Belkacem, A; Dörner, R; Weber, Th; McCurdy, C W; Landers, A L

2012-06-01

117

Imaging Polyatomic Molecules in Three Dimensions using Molecular Frame Photoelectron Angular Distributions  

NASA Astrophysics Data System (ADS)

We demonstrate a method for determining the full three-dimensional molecular frame photoelectron angular distribution in polyatomic molecules using methane as a prototype. Simultaneous double Auger decay and subsequent dissociation allow measurement of the initial momentum vectors of the ionic fragments and the photoelectron in coincidence, allowing full orientation by observing a three-ion decay pathway, [H^+, H^+, CH2^+]. We find the striking result that at low photoelectron energies the molecule is effectively imaged by the focusing of photoelectrons along bond directions.

Williams, J. B.; Landers, A. L.; Trevisan, C.; Jahnke, T.; Schoeffler, M. S.; Doerner, R.; Bocharova, I.; Sturm, F.; McCurdy, C. W.; Belkacem, A.; Weber, Th.

2012-06-01

118

A virus-like molecule in the early stage of encoded molecular evolution  

NASA Astrophysics Data System (ADS)

The recent advances of the evolutionary molecular engineering revealed the effectiveness of bonding strategy for assignment of the phenotype to its genotype, which non-enveloped viruses such as simple bacteriophages adopt. On the other hand, cellular organisms adopt another kind of the strategy, namely the compartmentalzation of both genotype and phenotype molecules in a single compartment enclosed with a cell membrane. The simplest strategy is that adopted by ribozymes in the RNA world. A single molecule carries both genotype and its phenotype. Based on the definition of “virus”-type and “cell”-type of the assignment strategy, we propose a virus-early/cell-late model of the history of life.

Nemoto, Naoto; Yanagawa, Hiroshi; Husimi, Yuzuru

1996-10-01

119

Patterned domains of supported phospholipid bilayer using microcontact printing of Pll-g-PEG molecules.  

PubMed

In this work, we propose a reliable microcontact printing (?CP) process for generating Patterned Supported Phospholipids Bilayer (P-SPB) confined by Poly-L-(lysine)-grafted-polyethylene(glycol) (Pll-g-PEG) molecular barriers. The efficiency of Pll-g-PEG for inhibiting the fusion process of incubated liposome was first analyzed by Quartz Micro Balance (QCM) measurements. The quality and stability of Pll-g-PEG patterns were then both verified by fluorescence microscopy and Atomic Force Microscopy (AFM) in liquid media. The micro domains of P-SPB produced were stable in liquid environment during several weeks and also during AFM imaging. This exceptional stability is a clear improvement compared to previous studies involving proteins as confinement barriers. PMID:21978556

Chalmeau, Jerome; le Grimellec, Christian; Sternick, John; Vieu, Christophe

2012-01-01

120

Electronic mapping of molecular orbitals at the molecule-metal interface.  

PubMed

The molecule-metal interface formed by pyridine-2,5-dicarboxylic acid chemically bonded to the Cu(110) surface is investigated by scanning tunneling microscopy and first-principles calculations. Our current-voltage spectroscopy studies reveal an electronic mapping of molecular orbitals as a function of tip position. By combining experimental and theoretical investigations, individual molecular orbitals are characterized by their energy and spatial distribution. The importance of adsorption geometries and conformational changes on the electron transport properties is highlighted. PMID:20867996

Lennartz, M C; Caciuc, V; Atodiresei, N; Karthäuser, S; Blügel, S

2010-08-01

121

Understanding molecular structure dependence of exciton diffusion in conjugated small molecules  

NASA Astrophysics Data System (ADS)

First-principles simulations are carried out to understand molecular structure dependence of exciton diffusion in a series of small conjugated molecules arranged in a disordered, crystalline, and blend structure. Exciton diffusion length (LD), lifetime, and diffusivity in four diketopyrrolopyrrole derivatives are calculated and the results compare very well with experimental values. The correlation between exciton diffusion and molecular structure is examined in detail. In the disordered molecule structure, a longer backbone length leads to a shorter exciton lifetime and a higher exciton diffusivity, but it does not change LD substantially. Removal of the end alkyl chains or the extra branch on the side alkyl chains reduces LD. In the crystalline structure, exciton diffusion exhibits a strong anisotropy whose origin can be elucidated from the intermolecular transition density interaction point of view. In the blend structure, LD increases with the crystalline ratios, which are estimated and consistent with the experimental results.

Li, Zi; Zhang, Xu; Woellner, Cristiano F.; Lu, Gang

2014-04-01

122

Conformational populations of ligand-sized molecules by replica exchange molecular dynamics and temperature reweighting  

PubMed Central

The use of the replica exchange (RE) molecular dynamics (MD) method for the efficient estimation of conformational populations of ligand-sized molecules in solution is investigated. We compare the computational efficiency of the traditional constant temperature MD technique to that of the parallel RE molecular dynamics method for a series of alkanes and rilpivirine (TMC278), an inhibitor against HIV-1 reverse transcriptase, with implicit solvation. We show that conformational populations are accurately estimated by both methods, however replica exchange estimates converge at a faster rate especially for rilpivirine which is characterized by multiple stable states separated by high free energy barriers. Furthermore convergence is enhanced when the weighted histogram analysis method (WHAM) is employed to estimate populations from the data collected from multiple RE temperature replicas. For small drug-like molecules with energetic barriers separating the stable states, the use of RE with WHAM is an efficient computational approach for estimating the contribution of ligand conformational reorganization to binding affinities.

Okumura, Hisashi; Gallicchio, Emilio; Levy, Ronald M.

2009-01-01

123

Dynamic decomposition of aliphatic molecules on Al(111) from ab initio molecular dynamics  

NASA Astrophysics Data System (ADS)

Ab initio molecular dynamics based on density functional theory within the generalized gradient approximation was used to explore decomposition on Al(111) of butanol-alcohol and butanoic-acid, two important boundary additives in Al processing. Each molecule was oriented with its functional group closest to the surface and then given an initial velocity toward the surface. Decomposition occurred upon collision with Al(111) resulting in the formation of adhered fragments that represent the very initial stages in additive film formation during plastic deformation where nascent Al is liberated. Bonding interactions over the simulation time frames were explored with contours of the electron localization function. Results of the simulations were compared with existing experimental studies of chemical decomposition on clean Al surfaces and found to be in qualitative accord. The effects of other initial molecular orientations on decomposition were explored in ancillary calculations where the molecules were rotated through 90° and 180° prior to collision with Al(111).

Zhong, Jun; Hector, Louis G., Jr.; Adams, James B.

2009-03-01

124

Molecular effects in the neutrino mass determination from beta-decay of the tritium molecule  

SciTech Connect

Molecular final state energies and transition probabilities have been computed for beta-decay of the tritium molecule. The results are of sufficient accuracy to make a determination of the electron neutrino rest mass with an error not exceeding a few tenths of an electron volt. Effects of approximate models of tritium beta-decay on the neutrino mass determination are discussed. 14 refs., 3 figs., 1 tab.

Fackler, O.; Jeziorski, B.; Kolos, W.; Szalewicz, K.; Monkhorst, H.J.; Mugge, M.

1986-03-01

125

Pyrimidinone-Peptoid Hybrid Molecules with Distinct Effects on Molecular Chaperone Function and Cell Proliferation  

PubMed Central

The Hsp70 molecular chaperones are ATPases that play critical roles in the pathogenesis of many human diseases, including breast cancer. Hsp70 ATP hydrolysis is relatively weak, but is stimulated by J domain-containing proteins. We identified pyrimidinone-peptoid hybrid molecules that inhibit cell proliferation with greater potency than previously described Hsp70 modulators. In many cases, anti-proliferative activity correlated with inhibition of J domain stimulation of Hsp70.

Wright, Christine M.; Chovatiya, Raj J.; Jameson, Nora E.; Turner, David M.; Zhu, Guangyu; Werner, Stefan; Huryn, Donna M.; Pipas, James M.; Day, Billy W.; Wipf, Peter; Brodsky, Jeffrey L.

2008-01-01

126

Pattern of adhesion molecule expression in labial salivary glands from patients with primary Sjögren's syndrome.  

PubMed

The aim of this work was to examine the pattern of distribution of adhesion molecules in minor salivary glands from patients with primary Sjögren's syndrome (SS). Labial salivary gland (LSG) biopsies from 31 patients with primary SS and 21 normal subjects were examined. Cryostat sections were examined with monoclonal antibodies to different adhesion molecules using an indirect immunoperoxidase technique. There was an increased expression of ICAM-1, class IMHC, HLA-DR & DQ (p<0.05) on endothelial cells, lymphocytes, fibroblasts and salivary epithelial cells (HLA-DR far exceeds ICAM-1 (limited) epithelial expression). ELAM-1 and to a lesser extent VCAM-1 were demonstrated over some of the endothelial cells in patients, but not in controls (p<0.01). Many of the endothelial cells expressing ICAM-1, DR, DQ, ELAM-1 were high endothelial venules. CD44 was strongly expressed over epithelial cells, endothelial and infiltrating mononuclear cells, while LFA-3 was present mainly on epithelial cells, and faintly on infiltrating inflammatory cells. There was no difference between patients and controls with regard to CD44 or LFA-3 expression. The ligands for the above mentioned adhesion molecules, namely LFA-1?, LFA-1ß, LECAM-1, VLA-4ß(CD49d), CD44 and CD2 were demonstrated (variably) on the surface of infiltrating lymphocytes. CD11b and CD11c were detected over monocytes/macrophages. A proportion of lymphocytes expressed VCAM-1 and CD11c and may function as antigen presenting cells. In some biopsies these molecules were localized at the center of lymphoid follicles with the appearance of dendritic cells. Although the majority of lymphocytes were activated and strongly expressing DR and ICAM-1, they were IL-2R? (CD25) negative. We conclude that adhesion molecules are prominent in LSG of patients with primary SS. They may play a major role by mediating the lymphocytic infiltration to the glands, retaining the lymphocytes in the glands and regulating the different immune responses in the local microenvironment of this chronic inflammatory disease. PMID:22823269

Aziz, K E; McCluskey, P J; Wakefield, D

1995-01-01

127

Selective deposition of organic molecules onto DPPC templates--a molecular dynamics study.  

PubMed

The site-selective deposition of organic molecules onto template structures to create ordered micro/nanoscale arrangements has drawn more and more attention because of the broad possibility, for example, application in organic electronic devices. Here we present a molecular dynamics study toward the selective deposition of organic molecules 3(5)-(9-anthryl) pyrazole (ANP), perylene and sexiphenyl (6P) onto template structures made of the phospholipid L-?-dipalmitoyl-phosphatidylcholine (DPPC) in alternating liquid expanded (LE) and liquid condensed (LC) states. The simulation results indicate, first of all, that the molecules immerge into both LE and LC phases instead of staying on top of them. Furthermore, the simulations replicate the empirically observed higher diffusion constants of the organic molecules on LE phase compared to LC phase of the underlying DPPC layer. Additionally, we propose a possible mechanism for the diffusion barrier between LE/LC phase needed to explain the experimental findings of the selective deposition. Altogether, this study supports the notions suggested by the experiments on the causes of the selective deposition while giving a deeper insight into the molecular processes involved. PMID:23044270

Hirtz, Michael; Kumar, Naresh; Franke, Jörn-Holger; Hao, Juanyuan; Lu, Nan; Fuchs, Harald; Chi, Lifeng

2013-01-01

128

Laser Coulomb Explosion Imaging of molecular dynamics in CO2 molecule  

NASA Astrophysics Data System (ADS)

Molecular structure dynamics and dissociation pathways of CO2 molecule initiated by interaction with strong laser field were investigated by Laser Coulomb Explosion Imaging (LCEI) technique. Momentum imaging of ions in tree-body fragmentation break-up channels O^++C^++O^+ (1,1,1) and O^2++C^2++O^2+ (2,2,2) was used to determine full geometry of CO2 ionic states before explosion. Varying laser pulse length from sub-7 fs to 200 fs at the same laser field intensity we were able to follow the evolution of the molecular structure and observe dramatic change in total kinetic energy of O^2++C^2++O^2+ channel with increasing pulse length. We observed significantly bent structure of parent ion and low kinetic energy of the (2,2,2) channel for long pulses, compared to the very close to linear geometry, and very high kinetic energy for sub-7 fs laser pulse. This observation supports the idea that a phenomenon known as enhanced ionization takes place for CO2 molecule with the same mechanism as in hydrogen molecule. It also lets us put temporal and spatial limits on this process, and in the future, probing molecular structure within the critical distance range, establish connection between changing geometry and dissociation pathways.

Legare, Francois; Bocharova, Irina; Litvinyuk, Igor; Sanderson, Joseph; Karimi, Reza

2009-05-01

129

Structure transition and swapping pattern of clathrate hydrates driven by external guest molecules.  

PubMed

We first report here that under strong surrounding gas of external CH4 guest molecules the sII and sH methane hydrates are structurally transformed to the crystalline framework of sI, leading to a favorable change of the lattice dimension of the host-guest networks. The high power decoupling 13C NMR and Raman spectroscopies were used to identify structure transitions of the mixed CH4 + C2H6 hydrates (sII) and hydrocarbons (methylcyclohexane, isopentane) + CH4 hydrates (sH). The present findings might be expected to provide rational evidences regarding the preponderant occurrence of naturally occurring sI methane hydrates in marine sediments. More importantly, we note that the unique and cage-specific swapping pattern of multiguests is expected to provide a new insight for better understanding the inclusion phenomena of clathrate materials. PMID:16984168

Yeon, Sun-Hwa; Seol, Jiwoong; Lee, Huen

2006-09-27

130

Building foundations for molecular electronics: Growth of organic molecules on alkali halides as prototypical insulating substrates  

NASA Astrophysics Data System (ADS)

The epitaxy and growth of a series of organic molecules deposited on insulating surfaces were investigated by noncontact atomic force microscopy (nc-AFM). The molecules studied, C60, 3,4,9,10-perylene tetracarboxylic dianhydride (PTCDA), 3,4,9,10-perylene tetracarboxlylic diimide (PTCDI), and copper (II) phthalocyanine (CuPc), were selected to investigate the effect of different molecular geometries, charge distributions and intermolecular interactions and as interesting candidates in molecular electronic applications. As it is known that the properties of molecules are influenced by their structural arrangements, an understanding of the interactions of molecules with substrates of interest as well as the dominant processes involved in growth are of great interest. Model insulating substrates KBr and NaCl were used for growth studies, due to the necessity of insulators in electrically isolating device regions. Dewetting processes were observed in several of these systems: C 60 on KBr and NaCl, PTCDA on NaCl and PTCDI on NaCl. The specific influences of de- wetting are discussed for each system, in particular the morphological impact of dewetting and the driving of dewetting by strained metastable monolayers. For C60 deposits, interesting branched structures are formed in the process of dewetting which are remarkably stable once formed, yet do not represent the equilibrium growth morphology. A determination of the large cell coincident epitaxy reveals a small, yet significant discrepancy between the observed overlayer and calculated stable adsorption sites indicating a dominance of the intermolecular interaction over the molecule---substrate interaction. For both PTCDA and PTCDI on NaCl, strained metastable monolayer epitaxies were observed giving rise to a transition in both interface structure and morphology: a dewetting transition. A comparison of the observed molecular scale structures and growth modalities is made in order to build a framework for understanding the prevalence of dewetting for molecules on ionic surfaces. Finally, in order to better understand the connection between molecular scale structures and interesting opto-electronic properties, the application of a hybrid-electrostatic characterization technique by nc-AFM is discussed. Using this technique, the opto-electrostatic response of three different PTCDA arrangements on a nanotemplated NaCl surface are shown to differ according to the degree of intermolecular interaction permitted by the structure.

Burke, Sarah A.

131

Single-molecule study of molecular mobility in the cytoplasm of Escherichia coli  

NASA Astrophysics Data System (ADS)

The cytoplasm of bacterial cells is filled with individual molecules and molecular complexes that rely on diffusion to bring them together for interaction. The mobility of molecules in the cytoplasm has been characterized by several techniques mainly using fluorescent probes and ensemble methods. In order to probe the microenvrionment inside the cytoplasm as viewed by an individual molecule, we have studied single green fluorescent proteins (GFPs) diffusing in the cytoplasm of Escherichia coli cells at observation at rates ranging from 60 to 1000 Hz. Over long times the diffusion shows confinement due to the geometry of the cells themselves. A simulation in model cells using the actual distribution of cell sizes found in the experiments describes accurately the experimental results as well as reveals a short time diffusion coefficient that agrees well with that determined by ensemble methods. Higher short time diffusion coefficients can be obtained by filling the simulated cell with small spheres modeling cytoplasmic molecules and, depending on the density of particles included in the modeled cytoplasm, can approach the diffusion coefficient of GFPs found in water. Thus, single-molecule tracking combined with analysis using simple simulation of Brownian motion is able to reveal the main contributors to the GFP mobility in the cytoplasm of E. coli.

Lill, Yoriko; Kaserer, Wallace A.; Newton, Salete M.; Lill, Markus; Klebba, Phillip E.; Ritchie, Ken

2012-08-01

132

Can azulene-like molecules function as substitution-free molecular rectifiers?  

PubMed

The feasibility of employing azulene-like molecules as a new type of high performance substitution-free molecular rectifier has been explored using NEGF-DFT calculation. The electronic transport behaviors of metal-molecule-metal junctions consisting of various azulene-like dithiol molecules are investigated, which reveals that the azulene-like molecules exhibit high conductance and bias-dependent rectification effects. Among all the substitution-free azulene-like structures, cyclohepta[b]cyclopenta[g]naphthalene exhibits the highest rectification ratio, revealing that the all fused aromatic ring structure and an appropriate separation between the pentagon and heptagon rings are essential for achieving both high conductance and high rectification ratio. The rectification ratio can be increased by substituting the pentagon ring with electron-withdrawing group and/or the heptagon ring with electron donating groups. Further increase of the rectification ratio may also be obtained by lithium adsorption on the pentagon ring. This work reveals that azulene-like molecules may be used as a new class of highly conductive unimolecular rectifiers. PMID:21822508

Zhou, Kai-Ge; Zhang, Yong-Hui; Wang, Le-Jia; Xie, Ke-Feng; Xiong, Yu-Qing; Zhang, Hao-Li; Wang, Cheng-Wei

2011-09-21

133

Allele-Specific Behavior of Molecular Networks: Understanding Small-Molecule Drug Response in Yeast  

PubMed Central

The study of systems genetics is changing the way the genetic and molecular basis of phenotypic variation, such as disease susceptibility and drug response, is being analyzed. Moreover, systems genetics aids in the translation of insights from systems biology into genetics. The use of systems genetics enables greater attention to be focused on the potential impact of genetic perturbations on the molecular states of networks that in turn affects complex traits. In this study, we developed models to detect allele-specific perturbations on interactions, in which a genetic locus with alternative alleles exerted a differing influence on an interaction. We utilized the models to investigate the dynamic behavior of an integrated molecular network undergoing genetic perturbations in yeast. Our results revealed the complexity of regulatory relationships between genetic loci and networks, in which different genetic loci perturb specific network modules. In addition, significant within-module functional coherence was found. We then used the network perturbation model to elucidate the underlying molecular mechanisms of individual differences in response to 100 diverse small molecule drugs. As a result, we identified sub-networks in the integrated network that responded to variations in DNA associated with response to diverse compounds and were significantly enriched for known drug targets. Literature mining results provided strong independent evidence for the effectiveness of these genetic perturbing networks in the elucidation of small-molecule responses in yeast.

Li, Chunquan; Hao, Dapeng; Zhang, Shaojun; Zhou, Meng; Su, Fei; Chen, Xi; Zhi, Hui; Li, Xia

2013-01-01

134

Molecular plasticity of ?-catenin: New insights from single-molecule measurements and MD simulation  

PubMed Central

The multifunctional protein, ?-catenin, has essential roles in cell adhesion and, through the Wnt signaling pathway, in controlling cell differentiation, development, and generation of cancer. Could distinct molecular forms of ?-catenin underlie these two functions? Our single-molecule force spectroscopy of armadillo ?-catenin, with molecular dynamics (MD) simulation, suggests a model in which the cell generates various forms of ?-catenin, in equilibrium. We find ?-catenin and the transcriptional factor Tcf4 form two complexes with different affinities. Specific cellular response is achieved by the ligand binding to a particular matching preexisting conformer. Our MD simulation indicates that complexes derive from two conformers of the core region of the protein, whose preexisting molecular forms could arise from small variations in flexible regions of the ?-catenin main binding site. This mechanism for the generation of the various forms offers a route to tailoring future therapeutic strategies.

Ritco-Vonsovici, Monica; Ababou, Abdessamad; Horton, Michael

2007-01-01

135

Finite temperature infrared spectroscopy of polycyclic aromatic hydrocarbon molecules: Path-integral molecular dynamics  

NASA Astrophysics Data System (ADS)

The vibrational spectra of the naphthalene, pyrene, and coronene molecules have been computed in the 0-3500 cm-1 infrared range using classical and quantum molecular dynamics simulations based on a dedicated tight-binding potential energy surface. The ring-polymer molecular dynamics (RPMD) and partially adiabatic centroid molecular dynamics (CMD) methods have been employed to account for quantum nuclear effects. The contributions of quantum delocalization to the line shift and broadening are significant in the entire spectral range and of comparable magnitude as pure thermal effects. While the two methods generally produce similar results, the CMD method may converge slower at low temperature with increasing Trotter discretization number. However, and contrary to the CMD method, the RPMD approach suffers from serious resonance problems at high frequencies and low temperatures.

Calvo, F.; Parneix, P.; van-Oanh, N.-T.

2010-03-01

136

Finite temperature infrared spectroscopy of polycyclic aromatic hydrocarbon molecules: path-integral molecular dynamics.  

PubMed

The vibrational spectra of the naphthalene, pyrene, and coronene molecules have been computed in the 0-3500 cm(-1) infrared range using classical and quantum molecular dynamics simulations based on a dedicated tight-binding potential energy surface. The ring-polymer molecular dynamics (RPMD) and partially adiabatic centroid molecular dynamics (CMD) methods have been employed to account for quantum nuclear effects. The contributions of quantum delocalization to the line shift and broadening are significant in the entire spectral range and of comparable magnitude as pure thermal effects. While the two methods generally produce similar results, the CMD method may converge slower at low temperature with increasing Trotter discretization number. However, and contrary to the CMD method, the RPMD approach suffers from serious resonance problems at high frequencies and low temperatures. PMID:20370124

Calvo, F; Parneix, P; Van-Oanh, N-T

2010-03-28

137

Molecular-crowding effects on single-molecule RNA folding/unfolding thermodynamics and kinetics.  

PubMed

The effects of "molecular crowding" on elementary biochemical processes due to high solute concentrations are poorly understood and yet clearly essential to the folding of nucleic acids and proteins into correct, native structures. The present work presents, to our knowledge, first results on the single-molecule kinetics of solute molecular crowding, specifically focusing on GAAA tetraloop-receptor folding to isolate a single RNA tertiary interaction using time-correlated single-photon counting and confocal single-molecule FRET microscopy. The impact of crowding by high-molecular-weight polyethylene glycol on the RNA folding thermodynamics is dramatic, with up to ??G° ? -2.5 kcal/mol changes in free energy and thus >60-fold increase in the folding equilibrium constant (Keq) for excluded volume fractions of 15%. Most importantly, time-correlated single-molecule methods permit crowding effects on the kinetics of RNA folding/unfolding to be explored for the first time (to our knowledge), which reveal that this large jump in Keq is dominated by a 35-fold increase in tetraloop-receptor folding rate, with only a modest decrease in the corresponding unfolding rate. This is further explored with temperature-dependent single-molecule RNA folding measurements, which identify that crowding effects are dominated by entropic rather than enthalpic contributions to the overall free energy change. Finally, a simple "hard-sphere" treatment of the solute excluded volume is invoked to model the observed kinetic trends, and which predict ??G° ? -5 kcal/mol free-energy stabilization at excluded volume fractions of 30%. PMID:24850865

Dupuis, Nicholas F; Holmstrom, Erik D; Nesbitt, David J

2014-06-10

138

Structural distributions from single-molecule measurements as a tool for molecular mechanics  

NASA Astrophysics Data System (ADS)

A mechanical view provides an attractive alternative for predicting the behavior of complex systems since it circumvents the resource-intensive requirements of atomistic models; however, it remains extremely challenging to characterize the mechanical responses of a system at the molecular level. Here, the structural distribution is proposed to be an effective means to extracting the molecular mechanical properties. End-to-end distance distributions for a series of short poly-L-proline peptides with the sequence PnCG3K-biotin (n = 8, 12, 15 and 24) were used to experimentally illustrate this new approach. High-resolution single-molecule Förster-type resonance energy transfer (FRET) experiments were carried out and the conformation-resolving power was characterized and discussed in the context of the conventional constant-time binning procedure for FRET data analysis. It was shown that the commonly adopted theoretical polymer models—including the worm-like chain, the freely jointed chain, and the self-avoiding chain—could not be distinguished by the averaged end-to-end distances, but could be ruled out using the molecular details gained by conformational distribution analysis because similar polymers of different sizes could respond to external forces differently. Specifically, by fitting the molecular conformational distribution to a semi-flexible polymer model, the effective persistence lengths for the series of short poly-L-proline peptides were found to be size-dependent with values of ˜190 Å, ˜67 Å, ˜51 Å, and ˜76 Å for n = 8, 12, 15, and 24, respectively. A comprehensive computational modeling was carried out to gain further insights for this surprising discovery. It was found that P8 exists as the extended all-trans isomaer whereas P12 and P15 predominantly contained one proline residue in the cis conformation. P24 exists as a mixture of one-cis (75%) and two-cis (25%) isomers where each isomer contributes to an experimentally resolvable conformational mode. This work demonstrates the resolving power of the distribution-based approach, and the capacity of integrating high-resolution single-molecule FRET experiments with molecular modeling to reveal detailed structural information about the conformation of molecules on the length scales relevant to the study of biological molecules.

Hanson, Jeffrey A.; Brokaw, Jason; Hayden, Carl C.; Chu, Jhih-Wei; Yang, Haw

2012-03-01

139

Structural distributions from single-molecule measurements as a tool for molecular mechanics  

PubMed Central

A mechanical view provides an attractive alternative for predicting the behavior of complex systems since it circumvents the resource-intensive requirements of atomistic models; however, it remains extremely challenging to characterize the mechanical responses of a system at the molecular level. Here, the structural distribution is proposed to be an effective means to extracting the molecular mechanical properties. End-to-end distance distributions for a series of short poly-L-proline peptides with the sequence PnCG3K-biotin (n = 8, 12, 15 and 24) were used to experimentally illustrate this new approach. High-resolution single-molecule Förster-type resonance energy transfer (FRET) experiments were carried out and the conformation-resolving power was characterized and discussed in the context of the conventional constant-time binning procedure for FRET data analysis. It was shown that the commonly adopted theoretical polymer models—including the worm-like chain, the freely jointed chain, and the self-avoiding chain—could not be distinguished by the averaged end-to-end distances, but could be ruled out using the molecular details gained by conformational distribution analysis because similar polymers of different sizes could respond to external forces differently. Specifically, by fitting the molecular conformational distribution to a semi-flexible polymer model, the effective persistence lengths for the series of short poly-L-proline peptides were found to be size-dependent with values of ~190 Å, ~67 Å, ~51 Å, and ~76 Å for n = 8, 12, 15, and 24, respectively. A comprehensive computational modeling was carried out to gain further insights for this surprising discovery. It was found that P8 exists as the extended all-trans isomaer whereas P12 and P15 predominantly contained one proline residue in the cis conformation. P24 exists as a mixture of one-cis (75%) and two-cis (25%) isomers where each isomer contributes to an experimentally resolvable conformational mode. This work demonstrates the resolving power of the distribution-based approach, and the capacity of integrating high-resolution single-molecule FRET experiments with molecular modeling to reveal detailed structural information about the conformation of molecules on the length scales relevant to the study of biological molecules.

Hanson, Jeffrey A.; Brokaw, Jason; Hayden, Carl C.; Chu, Jhih-Wei; Yang, Haw

2011-01-01

140

Efficient GW methods implemented in molecular orbital space: Ionization energy and electron affinity of conjugated molecules  

NASA Astrophysics Data System (ADS)

An efficient all-electron non-selfconsistent GW (G^0W^0) method is proposed, which is based on the full random-phase approximation and implemented in the molecular-orbital space with algorithms for reducing the error coming from the incompleteness of the basis set. The convergence of its result with regard to the size of the basis set is examined. Based on this, we further implement a quasiparticle self-consistent GW (QSGW) approach with Gaussian basis functions. The high computational efficiency allows us to deal with larger molecules from the first principles, and we applied our methods to calculate the ionization energy (IE) and electron affinity (EA) of ten conjugated molecules with up to 32 atoms. The G^0W^0 result improves the Hartree-Fock result significantly, especially for EA, and, furthermore, the QSGW improves the G^0W^0 and gives results of both IE and EA in very good agreement with the available experimental data and also with the results from the ?SCF calculation using the B3LYP functional. This indicates that our all-electron ab initio GW calculation can describe very well molecular electronic structures, making the QSGW approach a good candidate for investigating electronic and transport properties of molecular systems.

Ke, San-Huang

2012-02-01

141

Molecular weight dependence of emission intensity and emitting sites distribution within single conjugated polymer molecules.  

PubMed

We investigated exciton migration, trapping and emission processes occurring within a single conjugated polymer molecule by means of superresolution fluorescence localization microscopy. This methodology allowed us to locate the spatial distribution of emitting sites within single chains with nanometre precision. The study was done on individual poly[2-methoxy-5-(2'-ethyl-hexyloxy)-1,4-phenylene vinylene] (MEH-PPV) molecules with average molecular weights ranging from 215,000 to 1,440,000 and with narrow weight distributions. We found that the mean emission intensity increases proportionally to the polymer molecular weight. The localization experiments suggest that the emitting sites are distributed nearly uniformly within a single chain and that the sites are on average 10 nm apart, irrespective of the molecular weight of the polymer. Furthermore, spatial contours formed by all the combined emitting sites within one chain show elongated shapes, in agreement with a rod-like structure of MEH-PPV in a collapsed state. PMID:21113536

Habuchi, Satoshi; Onda, Suguru; Vacha, Martin

2011-02-01

142

Fast molecular shocks. I - Reformation of molecules behind a dissociative shock  

NASA Technical Reports Server (NTRS)

The physical and chemical processes that operate in the cooling gas behind a fast, dissociative, single-fluid shock propagating in a dense interstellar cloud are discussed. The treatment extends previous theoretical work on fast molecular shocks by including the effects of the conversion of Ly-alpha photons into radiation of the two-photon continuum and into H2 Lyman band emission lines, the effects of CO photodissociation following line absorption, and the formation and destruction of molecules containing the elements nitrogen, silicon, and sulphur, and of the complex hydrocarbons. Abundance profiles for the molecular species of interest are presented. After molecular hydrogen begins to reform, by means of gas phase and grain surface processes, the neutral species OH, H2O, O2, CO, CN, HCN, N2, NO, SO, and SiO reach substantial abundances. The molecular ions HeH(+), OH(+), SO(+), CH(+), H2(+), and H3(+), are produced while the gas is still hot and partially ionized. Emissions from them provide a possible diagnostic probe of fast molecular shocks.

Neufeld, David A.; Dalgarno, A.

1989-01-01

143

Molecular tailoring approach for geometry optimization of large molecules: Energy evaluation and parallelization strategies  

NASA Astrophysics Data System (ADS)

A linear-scaling scheme for estimating the electronic energy, gradients, and Hessian of a large molecule at ab initio level of theory based on fragment set cardinality is presented. With this proposition, a general, cardinality-guided molecular tailoring approach (CG-MTA) for ab initio geometry optimization of large molecules is implemented. The method employs energy gradients extracted from fragment wave functions, enabling computations otherwise impractical on PC hardware. Further, the method is readily amenable to large scale coarse-grain parallelization with minimal communication among nodes, resulting in a near-linear speedup. CG-MTA is applied for density-functional-theory-based geometry optimization of a variety of molecules including ?-tocopherol, taxol, ?-cyclodextrin, and two conformations of polyglycine. In the tests performed, energy and gradient estimates obtained from CG-MTA during optimization runs show an excellent agreement with those obtained from actual computation. Accuracy of the Hessian obtained employing CG-MTA provides good hope for the application of Hessian-based geometry optimization to large molecules.

Ganesh, V.; Dongare, Rameshwar K.; Balanarayan, P.; Gadre, Shridhar R.

2006-09-01

144

Chemoinformatic Analysis of Combinatorial Libraries, Drugs, Natural Products and Molecular Libraries Small Molecule Repository  

PubMed Central

A multiple criteria approach is presented, that is used to perform a comparative analysis of four recently developed combinatorial libraries to drugs, Molecular Libraries Small Molecule Repository (MLSMR) and natural products. The compound databases were assessed in terms of physicochemical properties, scaffolds and fingerprints. The approach enables the analysis of property space coverage, degree of overlap between collections, scaffold and structural diversity and overall structural novelty. The degree of overlap between combinatorial libraries and drugs was assessed using the R-NN curve methodology, which measures the density of chemical space around a query molecule embedded in the chemical space of a target collection. The combinatorial libraries studied in this work exhibit scaffolds that were not observed in the drug, MLSMR and natural products collections. The fingerprint-based comparisons indicate that these combinatorial libraries are structurally different to current drugs. The R-NN curve methodology revealed that a proportion of molecules in the combinatorial libraries are located within the property space of the drugs. However, the R-NN analysis also showed that there are a significant number of molecules in several combinatorial libraries that are located in sparse regions of the drug space.

Singh, Narender; Guha, Rajarshi; Giulianotti, Marc; Pinilla, Clemencia; Houghten, Richard; Medina-Franco, Jose L.

2009-01-01

145

A Molecular Dynamics Study on Slow Ion Interactions with the Polycyclic Aromatic Hydrocarbon Molecule Anthracene  

NASA Astrophysics Data System (ADS)

Atomic collisions with polycyclic aromatic hydrocarbon (PAH) molecules are astrophysically particularly relevant for collision energies of less than 1 keV. In this regime, the interaction dynamics are dominated by elastic interactions. We have employed a molecular dynamics simulation based on analytical interaction potentials to model the interaction of low energy hydrogen and helium projectiles with isolated anthracene (C14H10) molecules. This approach allows for a very detailed investigation of the elastic interaction dynamics on an event by event basis. From the simulation data the threshold projectile kinetic energies above which direct C atom knock out sets in were determined. Anthracene differential energy transfer cross sections and total (dissociation) cross sections were computed for a wide range of projectile kinetic energies. The obtained results are interpreted in the context of PAH destruction in astrophysical environments.

Postma, J.; Hoekstra, R.; Tielens, A. G. G. M.; Schlathölter, T.

2014-03-01

146

Nanotubule and Tour Molecule Based Molecular Electronics: Suggestion for a Hybrid Approach  

NASA Technical Reports Server (NTRS)

Recent experimental and theoretical attempts and results indicate two distinct broad pathways towards future molecular electronic devices and architectures. The first is the approach via Tour type ladder molecules and their junctions which can be fabricated with solution phase chemical approaches. Second are fullerenes or nanotubules and their junctions which may have better conductance, switching and amplifying characteristics but can not be made through well controlled and defined chemical means. A hybrid approach combining the two pathways to take advantage of the characteristics of both is suggested. Dimension and scale of such devices would be somewhere in between isolated molecule and nanotubule based devices but it maybe possible to use self-assembly towards larger functional and logicalunits.

Srivastava, Deepak; Saini, Subhash (Technical Monitor)

1998-01-01

147

Bond orientation properties in lipid molecules of membranes: molecular dynamics simulations  

NASA Astrophysics Data System (ADS)

Atomistic molecular dynamics simulations have been carried out for 16 different fully hydrated phosphatidylcholine lipid bilayers, having 16 or 18 carbon atoms in fully saturated sn ? 1 chain and from 18 to 22 carbon atoms in sn ? 2 chain with different degree of unsaturation, with the purpose to investigate the effect of unsaturation on physical properties of lipid bilayers. Special attention has been paid to profiles of C-C and C-H bond order parameters of lipid molecules and the orientational fluctuations of these bond vectors. It was shown that the study of anisotropy degree of bond orientations probability distributions allows distinguishing extended regions with different types of angular fluctuations of bonds in a membrane formed by lipid molecules with unsaturated chains.

Rabinovich, Alexander L.; Lyubartsev, Alexander P.

2014-05-01

148

Small Molecule Activators of the Heat Shock Response: Chemical Properties, Molecular Targets, and Therapeutic Promise  

PubMed Central

All cells have developed various mechanisms to respond and adapt to a variety of environmental challenges, including stresses that damage cellular proteins. One such response, the heat shock response (HSR), leads to the transcriptional activation of a family of molecular chaperone proteins that promote proper folding or clearance of damaged proteins within the cytosol. In addition to its role in protection against acute insults, the HSR also regulates lifespan and protects against protein misfolding that is associated with degenerative diseases of aging. As a result, identifying pharmacological regulators of the HSR has become an active area of research in recent years. Here, we review progress made in identifying small molecule activators of the HSR, what cellular targets these compounds interact with to drive response activation, and how such molecules may ultimately be employed to delay or reverse protein misfolding events that contribute to a number of diseases.

West, James D.; Wang, Yanyu; Morano, Kevin A.

2012-01-01

149

Multiligand Specificity of Pathogen-associated Molecular Pattern-binding Site in Peptidoglycan Recognition Protein*  

PubMed Central

The peptidoglycan recognition protein PGRP-S is an innate immunity molecule that specifically interacts with microbial peptidoglycans and other pathogen-associated molecular patterns. We report here two structures of the unique tetrameric camel PGRP-S (CPGRP-S) complexed with (i) muramyl dipeptide (MDP) at 2.5 ? resolution and (ii) GlcNAc and ?-maltose at 1.7? resolution. The binding studies carried out using surface plasmon resonance indicated that CPGRP-S binds to MDP with a dissociation constant of 10?7 m, whereas the binding affinities for GlcNAc and ?-maltose separately are in the range of 10?4 m to 10?5 m, whereas the dissociation constant for the mixture of GlcNAc and maltose was estimated to be 10?6 m. The data from bacterial suspension culture experiments showed a significant inhibition of the growth of Staphylococcus aureus cells when CPGRP-S was added to culture medium. The ELISA experiment showed that the amount of MDP-induced production of TNF-? and IL-6 decreased considerably after the introduction of CPGRP-S. The crystal structure determinations of (i) a binary complex with MDP and (ii) a ternary complex with GlcNAc and ?-maltose revealed that MDP, GlcNAc, and ?-maltose bound to CPGRP-S in the ligand binding cleft, which is situated at the interface of molecules C and D of the homotetramer formed by four protein molecules A, B, C, and D. In the binary complex, the muramyl moiety of MDP is observed at the C-D interface, whereas the peptide chain protrudes into the center of tetramer. In the ternary complex, GlcNAc and ?-maltose occupy distinct non-overlapping positions belonging to different subsites.

Sharma, Pradeep; Dube, Divya; Sinha, Mau; Mishra, Biswajit; Dey, Sharmistha; Mal, Gorakh; Pathak, Krishan M. L.; Kaur, Punit; Sharma, Sujata; Singh, Tej P.

2011-01-01

150

Monte Carlo simulation of molecular flux on simple spacecraft surfaces due to self- and ambient-scatter of outgassing molecules  

Microsoft Academic Search

A computer program was developed for the Monte Carlo simulation of molecular flux impingement on simple spacecraft surfaces due to self- and ambient-scatter of outgassing molecules. The molecules are assumed to be elastic spheres with a Maxwellian velocity distribution. Binary elastic collision processes were adopted in a hard-sphere collision model. A Test Particle Monte Carlo (TPMC) methodology was used for

Chien Fan; Clifford Gee; Michael Fong

1993-01-01

151

Vibrational Excitation of Diatomic Molecular Ions in Strong Field Ionization of Diatomic Molecules  

SciTech Connect

A model based on the strong-field and Born-Oppenheimer approximations qualitatively describes the distribution over vibrational states formed in a diatomic molecular ion following ionization of the neutral molecule by intense laser pulses. Good agreement is found with a recent experiment [X. Urbain et al., Phys. Rev. Lett. 92, 163004 (2004)]. In particular, the observed deviation from a Franck-Condon-like distribution is reproduced. Additionally, we demonstrate control of the vibrational distribution by a variation of the peak intensity or a change of frequency of the laser pulse.

Kjeldsen, Thomas K.; Madsen, Lars Bojer [Department of Physics and Astronomy, University of Aarhus, 8000 Aarhus C (Denmark)

2005-08-12

152

Molecular Dynamics Simulation of Squeeze-Film Damping in the Free-Molecule Regime  

NASA Astrophysics Data System (ADS)

A molecular dynamics (MD) simulation tool was developed for the prediction of squeeze-film damping on a micro beam/plate resonator oscillating in a highly rarefied gas environment. This tool was then employed to identify important parameters that characterize the damping and to study the dependence of the quality factor of the resonator on these parameters. Particular focus is on air flows that are in the free-molecule regime. An excellent agreement between the predicted quality factor and the measurement data in the low pressure range has been achieved and favorable comparisons with other models have also been demonstrated.

Hong, Gang; Ye, Wenjing

2008-12-01

153

Attached molecular motor in a trapped single molecule assay as a bidimensional Brownian multistable system  

NASA Astrophysics Data System (ADS)

To elucidate the physical properties of the force generation mechanism in molecular motors, we have obtained an analytical solution of the bidimensional Fokker-Plank equation which describes a common setup used in single molecule experiments. As a first application of this general result, we have shown that the size of the trapping system affects the dwell time of a multistable particle linearly. A quantitative application to skeletal actomyosin complex, using direct observation of force generation dynamics in the literature, shows that the size of the trapping system used was important for increasing the dwell time of the myosin head stable states to an observable time scale.

Marcucci, L.; Yanagida, T.

2013-06-01

154

Time reversible and symplectic integrators for molecular dynamics simulations of rigid molecules.  

PubMed

Molecular dynamics integrators are presented for translational and rotational motion of rigid molecules in microcanonical, canonical, and isothermal-isobaric ensembles. The integrators are all time reversible and are also, in some approaches, symplectic for the microcanonical ensembles. They are developed utilizing the quaternion representation on the basis of the Trotter factorization scheme using a Hamiltonian formalism. The structure is similar to that of the velocity Verlet algorithm. Comparison is made with standard integrators in terms of stability and it is found that a larger time step is stable with the new integrators. The canonical and isothermal-isobaric molecular dynamics simulations are defined by using a chain thermostat approach according to generalized Nosé-Hoover and Andersen methods. PMID:15974658

Kamberaj, H; Low, R J; Neal, M P

2005-06-01

155

Expression patterns of claudins, tight junction adhesion molecules, in the inner ear.  

PubMed

Tight junctions (TJs) are indispensable for the establishment of compositionally distinct fluid compartments in the inner ear, but our knowledge of the claudins, TJ adhesion molecules, in the inner ear is still fragmentary. We examined the expression and distribution of claudin-1 to claudin-18 (except for claudin-7, -13 and -17) in the inner ear by immunofluorescence microscopy. In the cochlea, the organ of Corti expressed claudin-1, -2, -3, -9, -10, -12, -14 and -18. In the stria vascularis, claudin-1, -2, -3, -8, -9, -10, -12, -14 and -18 were expressed in the marginal cells, whereas the basal cells were positive only for claudin-11. In Reissner's membrane and the spiral limbus, the expression of claudin-1, -2, -3, -8, -9, -10, -12, -14 and -18 was detected. Furthermore, in the vestibule, claudin-1, -3, -9, -12, -14 and -18 were expressed in the sensory epithelia, whereas in the dark cell area claudin-1, -3, -8, -9, -12, -14 and -18 were detectable. These findings, i.e., very complex expression patterns of claudin species in the inner ear, would reflect the importance and the complexity of the barrier function of TJs in the inner ear. PMID:14698084

Kitajiri, Shin-iciro; Furuse, Mikio; Morita, Kazumasa; Saishin-Kiuchi, Yumiko; Kido, Hirofumi; Ito, Juichi; Tsukita, Shoichiro

2004-01-01

156

Expression pattern of osteopontin in endometrial carcinoma: correlation with expression of the adhesion molecule CEACAM1.  

PubMed

Osteopontin (OPN) and CEACAM1 have diverse biological functions in the uterus and placenta throughout the estrous cycle and pregnancy and have been shown to interact with integrin beta3. OPN is a glycoprotein of the extracellular matrix, which has been shown to mediate cellular migration and invasion and to contribute to tumorigenesis in several types of cancers. Recently we showed the expression pattern of OPN in gestational trophoblastic tumors. CEACAM1 is an adhesion molecule of the carcinoembryonic antigen family that we have recently found to be expressed in endometrial cancer and that has been shown to be down-regulated in colorectal, prostate, and breast cancer. In this study, immunohistochemistry and immunofluorescence with specific antibodies were performed on a series of 20 normal endometrial samples, 17 endometrial hyperplasias, and 43 endometrial carcinomas (28 endometrioid, 10 serous, and 5 clear cell carcinomas) to investigate the expression pattern and cell-type specific localization of OPN and to correlate it with the expression of CEACAM1. In addition, Western blot was performed on normal human endometrium and endometrial neoplasia. Strong OPN expression with a consistent cytoplasmic localization in epithelial glandular cells was observed in the normal human endometrium in 80% of the samples of the proliferative and secretory phase (score 8-12). Similar results could be found in endometrial hyperplasias. Strong expression of OPN could be observed in 29 (67.4%) of the 43 analyzed endometrial carcinomas. Of the 43 analyzed tumors, 18 (41.8%) were in the high score (8-12) category with a strong OPN expression level; 11 of 43 (25.5%) showed a moderate score (4-7) category. In endometrioid carcinoma with increasing malignancy grade, increasing areas with low OPN expression level or complete loss of OPN expression could be observed. In contrast, serous tumors showed a strong OPN expression level. Similar results could be found in Western blot analysis. CEACAM1 showed similar results and could be found to be coexpressed with OPN in normal human endometrium and in endometrial neoplasia as we showed using immunofluorescence. In this study, the different expression patterns of OPN in endometrial tumors could additionally support the biological diversity of endometrioid and serous carcinomas together with other markers. We suggest that OPN might play a different role in the pathogenesis of endometrial cancer (possibly as a functional complex with CEACAM1) and could be relevant for invasive growth of such lesions. PMID:16633066

Briese, Juliane; Schulte, Heinrich M; Bamberger, Christoph M; Löning, Thomas; Bamberger, Ana-Maria

2006-04-01

157

Positive patterning of ferritin and fibronectin molecules on silicon by the atomic force microscopic anodic oxidation technique.  

PubMed

Oxide dots fabricated on silicon (111) by the Atomic Force Microscopy (AFM) anodic oxidation technique was used for the patterning of two different proteins namely, ferritin and fibronectin. Si surfaces were oxidized by the SC1 process and then modified with octadecyltrichlorosilane (OTS) for passivation. Oxide dots were fabricated by applying a bias voltage between the AFM probe and the silicon surface. Furthermore, surface functionalization of oxide dots was achieved through gamma-aminopropyltriethoxysilane (gamma-APTES) and glutaraldehye modification to establish a covalent bond between aldehydes and amino groups of protein molecules. Topographies after each modification steps were monitored by AFM. We were able to achieve positive patterning of ferritin molecules up to an average density of 6 x 10(9)/cm2 on gamma-APTES-covered dots, while 9 x 10(8)/cm2 of ferritin molecules remained on the OTS surface. In contrast to this observation, fibronectin molecules were patterned successfully only on oxide dots, and we did not observe any fibronectin molecules on the OTS surface. PMID:21780372

Shanmugam, Kumaran; Yoshinobu, Tatsuo; Moon, Wonchul; Iwasaki, Hiroshi

2011-05-01

158

Single molecule vibrationally mediated chemistry. Towards state-specific strategies for molecular handling  

NASA Astrophysics Data System (ADS)

Tunnelling electrons may scatter inelastically with an adsorbate, releasing part of their energy through the excitation of molecular vibrations. The resolution of inelastic processes with a low temperature scanning tunnelling microscope (STM) provides a valuable tool to chemically characterize single adsorbates and their adsorption mechanisms. Here, we present a molecular scale picture of single molecule vibrational chemistry, as resolved by STM. To understand the way a reaction proceed it is needed knowledge about both the excitation and damping of a molecular vibration. The excitation is mediated by the specific coupling between electronic molecular resonances present at the Fermi level and vibrational states of the adsorbate. Thus, the two-dimensional mapping of the inelastic signal with an STM provides the spatial distribution of the adsorbate electronic states (near the Fermi level) which are predominantly coupled to the particular vibrational mode observed. The damping of the vibration follows a competition between different mechanisms, mediated via the creation of electron-hole pairs or via anharmonic coupling between vibrational states. This latter case give rise to effective energy transfer mechanisms which eventually may focus vibrational energy in a specific reaction coordinate. In this single-molecule work-bench, STM provides alternative tools to understand reactivity in the limit of low excitation rate, which demonstrate the existence of state-specific excitation strategies which may lead to selectivity in the product of a reaction. The author acknowledges his co-workers in the work presented here, H. Conrad, N. Lorente, H.-P. Rust, and Z. Song, as well as collaborations with J. Gómez Herrero, J.J. Jackiw, D. Sánchez-Portal and P.S. Weiss.

Pascual, J. I.

2005-08-01

159

LC-MS with electron ionization of cold molecules in supersonic molecular beams  

NASA Astrophysics Data System (ADS)

A new approach is described for the combination of electron ionization and LC-MS based on sample ionization as vibrationally cold molecules in a supersonic molecular beam (Cold EI). Cold EI of sample compounds in liquid solutions (methanol, acetonitrile, water, etc.) is achieved through spray formation, followed by soft thermal vaporization of the sample particles prior to their supersonic expansion and direct electron ionization of the sample compounds while they are contained in a supersonic molecular beam (SMB). Cold EI mass spectra were demonstrated to combine an enhanced molecular ion and improved mass spectral information (in comparison with standard EI), plus all the library searchable fragments. Cold EI enables the ionization of a broad range of compounds, including the full range of non-polar samples. Four orders of magnitude linear dynamic range is demonstrated and a detection limit of 2 pg was achieved for a 774 amu compound in single ion monitoring mode at m/z = 774. The method and apparatus are under continuous development and we feel that it can excel particularly in the analysis of unknown samples, while enabling fast LC-MS analysis through automated mass spectral deconvolution of coeluting LC peaks. In addition, the same MS system can also serve as an advanced GC-MS with supersonic molecular beams.

Granot, Ori; Amirav, Aviv

2005-06-01

160

Initial partition and aggregation of uncharged polyaromatic molecules at the oil-water interface: a molecular dynamics simulation study.  

PubMed

Initial partitioning and aggregation of several uncharged polyaromatic (PA) molecules with the same polyaromatic core but different terminal moieties at oil-water interfaces from the bulk oil phase were studied by molecular dynamics simulation. The partition of the PA molecules between the bulk organic phase and oil-water interface was highly dependent on the terminal moiety structure of the PA molecules and aromaticity of the organic phase. The polarity ratio between the oil and water phases showed a significant influence on adsorption of the PA molecules at the oil-water interface. The presence of hydrophobic aromatic moieties in PA molecules hindered the adsorption process. Larger aromatic rings in PA molecules lowered the interfacial activity due to strong intermolecular ?-? interactions and molecular aggregation in the bulk oil phase. The presence of a terminal carboxylic functional group on the side chain enhanced the adsorption of the PA molecules at the oil-water interface. The fused ring plane of the uncharged PA molecules was found to preferentially adsorb at the oil-water interface in a head-on or side-on orientation with the polyaromatic core staying in the nonaqueous phase (i.e., the principal plane of the molecule perpendicular to the oil-water interface). The results obtained from this study could provide a scientific direction for the design of proper chemical demulsifiers for PA molecule-mediated emulsions formed under specific process conditions of temperature, pressure, and pH. PMID:24397444

Teklebrhan, Robel B; Ge, Lingling; Bhattacharjee, Subir; Xu, Zhenghe; Sjöblom, Johan

2014-01-30

161

A molecular-beacon-based screen for small molecule inhibitors of miRNA maturation.  

PubMed

miRNAs are small non-coding RNAs that regulate about 60% of mammalian genes by modulating their transcript levels. Network scale studies of miRNA-mediated regulatory circuits demonstrate the central importance of this class of small RNA in the maintenance of biological robustness. More recently, several reports have described the deregulation of numerous miRNA to be causally associated with many diseases, including cancer. These studies have highlighted the potential for development of therapeutic modalities against miRNA. Previous screening protocols, for small molecules targeting miRNA function, are either costly or technically too complex to be applied in a high-throughput manner in standard chemical laboratories. We describe a simple in vitro screening method using a DNA-based molecular beacon that overcomes the limitations associated with earlier screens. We used this method to identify inhibitors of miR-27a function from a library of 14 aminoglycosides as a pilot study. Inhibitory molecules identified were further scrutinized to identify the validity of screen. With this proof of concept we illustrate the utility of a scalable molecular-beacon-based screening strategy for miRNA inhibitors. PMID:23402670

Bose, Debojit; Jayaraj, Gopal Gunanathan; Kumar, Santosh; Maiti, Souvik

2013-05-17

162

Molecular architecture governs the kinetics of single molecule unfolding under force  

NASA Astrophysics Data System (ADS)

Proteins are a paradigm of complexity due to the broad energy scales involved in holding their folded structure intact under thermal fluctuations. Moreover, a subset of all proteins is known to withstand stretching forces on the order of 100 pN on the timescale of seconds. The dynamic mechanism by which these proteins support stress on the molecular level remains largely unknown. With the advent of single molecule techniques using the atomic force microscope (AFM), we measure the kinetics of unfolding as a function of a constant force for the archetypal mechanically stable proteins: the degradation protein ubiquitin and the 27th immunoglobulin domain (I27) in muscle. Instead of filtering the data, we develop a maximum likelihood method to analyze all force-clamp unfolding dwell times in order to deduce the underlying kinetics. We find that the large pool of data for both proteins is best fit with stretched exponential distributions, whose exponent depends on the molecular architecture of the protein. Our analysis of previously published kinetic data on ubiquitin as a function of force [PNAS, Garcia-Manyes et. al., 2009] follows stretched exponential kinetics at all forces. Rescaling the data by the exponent shows that the characteristic timescale for the rupture of the molecules increases slower than exponentially with the force, challenging the Bell model. The observed complex kinetics may therefore be of evolutionary importance, as it increases the protein's mechanical resilience. We discuss competing microscopic mechanisms by which the complex kinetic profiles may arise.

Brujic, Jasna

2010-03-01

163

The peptide-receptive transition state of MHC-1 molecules: Insight from structure and molecular dynamics  

SciTech Connect

MHC class I (MHC-I) proteins of the adaptive immune system require antigenic peptides for maintenance of mature conformation and immune function via specific recognition by MHC-I-restricted CD8(+) T lymphocytes. New MHC-I molecules in the endoplasmic reticulum are held by chaperones in a peptide-receptive (PR) transition state pending release by tightly binding peptides. In this study, we show, by crystallographic, docking, and molecular dynamics methods, dramatic movement of a hinged unit containing a conserved 3(10) helix that flips from an exposed 'open' position in the PR transition state to a 'closed' position with buried hydrophobic side chains in the peptide-loaded mature molecule. Crystallography of hinged unit residues 46-53 of murine H-2L(d) MHC-I H chain, complexed with mAb 64-3-7, demonstrates solvent exposure of these residues in the PR conformation. Docking and molecular dynamics predict how this segment moves to help form the A and B pockets crucial for the tight peptide binding needed for stability of the mature peptide-loaded conformation, chaperone dissociation, and Ag presentation.

Robinson H.; Mage, M.; Dolan, M.; Wang, R.; Boyd, L.; Revilleza, M.; Natarajan, K.; Myers, N.; Hansen, T.; Margulies, D.

2012-05-01

164

The recognition of lysozyme by patterned molecularly imprinted polymers  

Microsoft Academic Search

Microelectro-mechanical-system (MEMS) microsensing devices have recently been extensively researched for their application in biomedical diagnostics. Molecularly imprinted polymers with highly specific binding to targets and their low cost have potential for use in devices as sensing materials. Both techniques were combined to synthesize localized molecularly imprinted polymers (MIPs) by microcontact printing for integration in a micrototal analysis system (?TAS).

Hung-Yin Lin; Dorcas; Cheng-Pu Lin; Gwo-Bin Lee; Tse-Chuan Chou

2005-01-01

165

Theoretical descriptions of electron transport through single molecules: Developing design tools for molecular electronic devices  

NASA Astrophysics Data System (ADS)

There are vast numbers of organic compounds that could be considered for use in molecular electronics. Hence there is a need for efficient and economical screening tools. Here we develop theoretical methods to describe electron transport through individual molecules, the ultimate goal of which is to establish design tools for molecular electronic devices. To successfully screen a compound for its use as a device component requires a proper representation of the quantum mechanics of electron transmission. In this work we report the development of tools for the description of electron transmission that are: Charge self-consistent, valid in the presence of a finite applied potential field and (in some cases) explicitly time-dependent. In addition, the tools can be extended to any molecular system, including biosystems, because they are free of restrictive parameterizations. Two approaches are explored: (1) correlation of substituent parameter values (sigma), (commonly found in organic chemistry textbooks) to properties associated with electron transport, (2) explicit tracking of the time evolution of the wave function of a nonstationary electron. In (1) we demonstrate that the a correlate strongly with features of the charge migration process, establishing them as useful indicators of electronic properties. In (2) we employ a time-dependent description of electron transport through molecular junctions. To date, the great majority of theoretical treatments of electron transport in molecular junctions have been of the time-independent variety. Time dependence, however, is critical to such properties as switching speeds in binary computer components and alternating current conductance, so we explored methods based on time-dependent quantum mechanics. A molecular junction is modeled as a single molecule sandwiched between two clusters of close-packed metal atoms or other donor and acceptor groups. The time dependence of electron transport is investigated by initially localizing an electron on the donor and following the time development of the corresponding non-stationary wavefunction of the time-independent Hamiltonian. We demonstrate that the time-dependent treatment of electron transport predicts physically intuitive results, while providing insights not available from time-independent methods.

Carroll, Natalie R.

166

Manipulating the motion of large molecules: Information from the molecular frame  

NASA Astrophysics Data System (ADS)

Large molecules have complex potential-energy surfaces with many local minima. They exhibit multiple stereoisomers, even at the low temperatures (˜1 K) in a molecular beam, with rich intra- and intermolecular dynamics. Over the last years, we have developed methods to manipulate the motion of large, complex molecules and to select their quantum states. We have exploited this state-selectivity, for example, to spatially separate individual structural isomers of complex molecules [1] and to demonstrate unprecedented degrees of laser alignment and mixed-field orientation of these molecules [2]. Such clean, well-defined samples strongly benefit, or simply allow, novel experiments on the dynamics of complex molecules, for instance, femtosecond pump-probe measurements, X-ray or electron diffraction of molecular ensembles (including diffraction-from-within experiments), or tomographic reconstructions of molecular orbitals. These samples could also be very advantageous for metrology applications, such as, for example, matter-wave interferometry or the search for electroweak interactions in chiral molecules. Moreover, they provide an extreme level of control for stereo-dynamically controlled reaction dynamics. We have recently exploited these state-selected and oriented samples to measure photoelectron angular distributions in the molecular frame (MFPADs) from non-resonant femtosecond-laser photoionization [3] and using the X-ray Free-Electron-Laser LCLS. We have also investigated X-ray diffraction imaging and, using ion momentum imaging, the induced radiation damage of these samples using the LCLS. This work was carried out within a collaboration for which J. Küpper, H. Chapman, and D. Rolles are spokespersons. The collaboration consists of CFEL (DESY, MPG, University Hamburg), Fritz-Haber-Institute Berlin, MPI Nuclear Physics Heidelberg, MPG Semi-conductor Lab, Aarhus University, FOM AMOLF Amsterdam, Lund University, MPI Medical Research Heidelberg, TU Berlin, Max Born Institute Berlin, and SLAC Menlo Park, CA, USA. The experiments were carried out using CAMP (designed and built by the MPG-ASG at CFEL) [4] at the LCLS (operated by Stanford University on behalf of the US DOE) [5]. [4pt] [1] Filsinger, Erlekam, von Helden, Küpper, Meijer, Phys. Rev. Lett. 100, 133003 (2008); Filsinger, Küpper, Meijer, Hansen, Maurer, Nielsen, Holmegaard, Stapelfeldt, Angew. Chem. Int. Ed. 48, 6900 (2009)[0pt] [2] Holmegaard, Nielsen, Nevo, Stapelfeldt, Filsinger, Küpper, Meijer, Phys. Rev. Lett. 102, 023001 (2009); Filsinger, Küpper, Meijer, Holmegaard, Nielsen, Nevo, Hansen, Stapelfeldt, J. Chem. Phys. 131, 064309, (2009); Nevo, Holmegaard, Nielsen, Hansen, Stapelfeldt, Filsinger, Meijer, Küpper, Phys. Chem. Chem. Phys. 11, 9912 (2009)[0pt] [3] Holmegaard, Hansen, Kalhøj, Kragh, Stapelfeldt, Filsinger, Küpper, Meijer, Dimitrovski, Abu-samha, Martiny, Madsen, Nature Phys. 6, 428 (2010)[0pt] [4] Strüder et al. Nucl Instrum Meth A 614, 483 (2010)[0pt] [5] Emma et al. Nat Photonics 4, 641 (2010)

Küpper, Jochen

2011-06-01

167

Molecular ions and protonated molecules observed in the atmospheric solids analysis probe analysis of steroids.  

PubMed

Atmospheric pressure chemical ionisation (APCI) has often been used to ionise steroids in mass spectrometry, usually when interfaced to high-performance liquid chromatography (HPLC). However, in positive ion mode, a dehydrated protonated molecule is often observed with a loss of structural information. The recently introduced technique of atmospheric solids analysis probe (ASAP) has the advantage that the sample can be analysed directly and does not need to be interfaced to HPLC. Existing ionisation sources such as direct analysis in real time (DART) and desorption electrospray ionisation (DESI) have shown the advantage of direct analysis techniques in a variety of applications. ASAP can be performed on commercial atmospheric pressure ionisation (API) mass spectrometers with only simple modifications to API sources. The samples are vaporised by hot nitrogen gas from the electrospray desolvation heater and ionised by a corona discharge. A range of commercially available steroids were analysed by ASAP to investigate the mechanism of ionisation. ASAP analysis of steroids generally results in the formation of the parent molecular ion as either the radical cation M+* or the protonated molecule MH+. The formation of the protonated molecule is a result of proton transfer from ionised water clusters in the source. However, if the source is dry, then formation of the radical cation is the primary ionisation mechanism. PMID:20212333

Ray, Andrew D; Hammond, Janet; Major, Hilary

2010-01-01

168

Dressed-bound-state molecular strong-field approximation: Application to above-threshold ionization of heteronuclear diatomic molecules  

SciTech Connect

The molecular strong-field approximation (MSFA), which includes dressing of the molecular bound state, is introduced and applied to above-threshold ionization of heteronuclear diatomic molecules. Expressions for the laser-induced molecular dipole and polarizability as functions of the laser parameters (intensity and frequency) and molecular parameters [molecular orientation, dipole, and parallel and perpendicular polarizabilities of the highest occupied molecular orbital (HOMO)] are presented. Our previous MSFA theory, which incorporates the rescattering effects, is generalized from homonuclear to heteronuclear diatomic molecules. Angle- and energy-resolved high-order above-threshold ionization spectra of oriented heteronuclear diatomic molecules, exemplified by the carbon monoxide (CO) molecule, exhibit pronounced minima, which can be related to the shape of their HOMO-electron-density distribution. For the CO molecule we have found an analytical condition for the positions of these minima. We have also shown that the effect of the dressing of the HOMO is twofold: (i) the laser-induced Stark shift decreases the ionization yield and (ii) the laser-induced time-dependent dipole and polarizability change the oscillatory structure of the spectra.

Hasovic, E. [Faculty of Science, University of Sarajevo, Zmaja od Bosne 35, BA-71000 Sarajevo (Bosnia and Herzegowina); Max-Born-Institut, Max-Born-Strasse 2a, DE-12489 Berlin (Germany); Busuladzic, M. [Medical Faculty, University of Sarajevo, Cekalusa 90, BA-71000 Sarajevo (Bosnia and Herzegowina); Becker, W. [Max-Born-Institut, Max-Born-Strasse 2a, DE-12489 Berlin (Germany); Milosevic, D. B. [Faculty of Science, University of Sarajevo, Zmaja od Bosne 35, BA-71000 Sarajevo (Bosnia and Herzegowina); Max-Born-Institut, Max-Born-Strasse 2a, DE-12489 Berlin (Germany); Academy of Sciences and Arts of Bosnia and Herzegovina, Bistrik 7, BA-71000 Sarajevo (Bosnia and Herzegowina)

2011-12-15

169

The molecular transport and intercalation of guest molecules into hydrogen-bonded metal-organic frameworks (HMOFs)  

Microsoft Academic Search

The process of molecular transport and intercalation has been widely studied for many years, resulting in the discovery of molecular frameworks that are capable of hosting guest molecules or ions. Layered and porous metal-organic frameworks (MOFs) have been found to have applications in the field of catalysis, storage, separations, and ion-exchange. More recently, molecular components with peripheral hydrogen-bonding moieties have

Greg Anthony Hogan

2010-01-01

170

Molecular resonant dissociation of surface-adsorbed molecules by plasmonic nanoscissors.  

PubMed

The ability to break individual bonds or specific modes in chemical reactions is an ardently sought goal by chemists and physicists. While photochemistry based methodologies are very successful in controlling e.g. photocatalysis, photosynthesis and the degradation of plastic, it is hard to break individual molecular bonds for those molecules adsorbed on the surface because of the weak light-absorption in molecules and the redistribution of the resulting vibrational energy both inside the molecule and to its surrounding environment. Here we show how to overcome these obstacles with a plasmonic hot-electron mediated process and demonstrate a new method that allows the sensitive control of resonant dissociation of surface-adsorbed molecules by 'plasmonic' scissors. To that end, we used a high-vacuum tip-enhanced Raman spectroscopy (HV-TERS) setup to dissociate resonantly excited NC2H6 fragments from Malachite green. The surface plasmons (SPs) excited at the sharp metal tip not only enhance the local electric field to harvest the light incident from the laser, but crucially supply 'hot electrons' whose energy can be transferred to individual bonds. These processes are resonant Raman, which result in some active chemical bonds and then weaken these bonds, followed by dumping in lots of indiscriminant energy and breaking the weakest bond. The method allows for sensitive control of both the rate and probability of dissociation through their dependence on the density of hot electrons, which can be manipulated by tuning the laser intensity or tunneling current/bias voltage in the HV-TERS setup, respectively. The concepts of plasmonic scissors open up new versatile avenues for the deep understanding of in situ surface-catalyzed chemistry. PMID:24671142

Zhang, Zhenglong; Sheng, Shaoxiang; Zheng, Hairong; Xu, Hongxing; Sun, Mengtao

2014-05-01

171

Collision dynamics of methyl radicals and highly vibrationally excited molecules using crossed molecular beams  

SciTech Connect

The vibrational to translational (V{yields}T) energy transfer in collisions between large highly vibrationally excited polyatomics and rare gases was investigated by time-of-flight techniques. Two different methods, UV excitation followed by intemal conversion and infrared multiphoton excitation (IRMPE), were used to form vibrationally excited molecular beams of hexafluorobenzene and sulfur hexafluoride, respectively. The product translational energy was found to be independent of the vibrational excitation. These results indicate that the probability distribution function for V{yields}T energy transfer is peaked at zero. The collisional relaxation of large polyatomic molecules with rare gases most likely occurs through a rotationally mediated process. Photodissociation of nitrobenzene in a molecular beam was studied at 266 nm. Two primary dissociation channels were identified including simple bond rupture to produce nitrogen dioxide and phenyl radical and isomerization to form nitric oxide and phenoxy radical. The time-of-flight spectra indicate that simple bond rupture and isomerization occurs via two different mechanisms. Secondary dissociation of the phenoxy radicals to carbon monoxide and cyclopentadienyl radicals was observed as well as secondary photodissociation of phenyl radical to give H atom and benzyne. A supersonic methyl radical beam source is developed. The beam source configuration and conditions were optimized for CH{sub 3} production from the thermal decomposition of azomethane. Elastic scattering of methyl radical and neon was used to differentiate between the methyl radicals and the residual azomethane in the molecular beam.

Chu, P.M.Y.

1991-10-01

172

Testosterone Induces Molecular Changes in Dopamine Signaling Pathway Molecules in the Adolescent Male Rat Nigrostriatal Pathway  

PubMed Central

Adolescent males have an increased risk of developing schizophrenia, implicating testosterone in the precipitation of dopamine-related psychopathology. Evidence from adult rodent brain indicates that testosterone can modulate nigrostriatal dopamine. However, studies are required to understand the role testosterone plays in maturation of dopamine pathways during adolescence and to elucidate the molecular mechanism(s) by which testosterone exerts its effects. We hypothesized that molecular indices of dopamine neurotransmission [synthesis (tyrosine hydroxylase), breakdown (catechol-O-methyl transferase; monoamine oxygenase), transport [vesicular monoamine transporter (VMAT), dopamine transporter (DAT)] and receptors (DRD1-D5)] would be changed by testosterone or its metabolites, dihydrotestosterone and 17?-estradiol, in the nigrostriatal pathway of adolescent male rats. We found that testosterone and dihydrotestosterone increased DAT and VMAT mRNAs in the substantia nigra and that testosterone increased DAT protein at the region of the cell bodies, but not in target regions in the striatum. Dopamine receptor D2 mRNA was increased and D3 mRNA was decreased in substantia nigra and/or striatum by androgens. These data suggest that increased testosterone at adolescence may change dopamine responsivity of the nigrostriatal pathway by modulating, at a molecular level, the capacity of neurons to transport and respond to dopamine. Further, dopamine turnover was increased in the dorsal striatum following gonadectomy and this was prevented by testosterone replacement. Gene expression changes in the dopaminergic cell body region may serve to modulate both dendritic dopamine feedback inhibition and reuptake in the dopaminergic somatodendritic field as well as dopamine release and re-uptake dynamics at the presynaptic terminals in the striatum. These testosterone-induced changes of molecular indices of dopamine neurotransmission in males are primarily androgen receptor-driven events as estradiol had minimal effect. We conclude that nigrostriatal responsivity to dopamine may be modulated by testosterone acting via androgen receptors to alter gene expression of molecules involved in dopamine signaling during adolescence.

Purves-Tyson, Tertia D.; Owens, Samantha J.; Double, Kay L.; Desai, Reena; Handelsman, David J.; Weickert, Cynthia Shannon

2014-01-01

173

Large-area molecular patterning with polymer pen lithography.  

PubMed

The challenge of constructing surfaces with nanostructured chemical functionality is central to many areas of biology and biotechnology. This protocol describes the steps required for performing molecular printing using polymer pen lithography (PPL), a cantilever-free scanning probe-based technique that can generate sub-100-nm molecular features in a massively parallel fashion. To illustrate how such molecular printing can be used for a variety of biologically relevant applications, we detail the fabrication of the lithographic apparatus and the deposition of two materials, an alkanethiol and a polymer onto a gold and silicon surface, respectively, and show how the present approach can be used to generate nanostructures composed of proteins and metals. Finally, we describe how PPL enables researchers to easily create combinatorial arrays of nanostructures, a powerful approach for high-throughput screening. A typical protocol for fabricating PPL arrays and printing with the arrays takes 48-72 h to complete, including two overnight waiting steps. PMID:24263094

Eichelsdoerfer, Daniel J; Liao, Xing; Cabezas, Maria D; Morris, William; Radha, Boya; Brown, Keith A; Giam, Louise R; Braunschweig, Adam B; Mirkin, Chad A

2013-12-01

174

Affinity flow fractionation of cells via transient interactions with asymmetric molecular patterns.  

PubMed

Flow fractionation of cells using physical fields to achieve lateral displacement finds wide applications, but its extension to surface molecule-specific separation requires labeling. Here we demonstrate affinity flow fractionation (AFF) where weak, short-range interactions with asymmetric molecular patterns laterally displace cells in a continuous, label-free process. We show that AFF can directly draw neutrophils out of a continuously flowing stream of blood with an unprecedented 400,000-fold depletion of red blood cells, with the sorted cells being highly viable, unactivated, and functionally intact. The lack of background erythrocytes enabled the use of AFF for direct enumeration of neutrophils by a downstream detector, which could distinguish the activation state of neutrophils in blood. The compatibility of AFF with capillary microfluidics and its ability to directly separate cells with high purity and minimal sample preparation will facilitate the design of simple and portable devices for point-of-care diagnostics and quick, cost-effective laboratory analysis. PMID:23900203

Bose, Suman; Singh, Rishi; Hanewich-Hollatz, Mikhail; Shen, Chong; Lee, Chia-Hua; Dorfman, David M; Karp, Jeffrey M; Karnik, Rohit

2013-01-01

175

Molecular dynamics study of solvation differences between cis- and transplatin molecules in water  

NASA Astrophysics Data System (ADS)

The classical molecular dynamics (MD) simulations for the solvation properties of cis- and transplatins in water are performed with the Lennard-Jones plus Coulomb electrostatic potential parameters that are optimized with ab initio potential energies of the water-platin systems. Two hydration shells are found both for cis- and transplatins. The first shell of water molecules is closer to transplatin than cisplatin. The average number and lifetime of the intermolecular hydrogen bonds (HBs) estimated from the MD trajectories indicate that the Cl and NH3 ligands are the main groups involved in the intermolecular HBs with water. In comparison with cisplatin, there are more HBs around transplatin and these HBs show the longer lifetime. The distinctly different solvation structures between cis- and transplatins are further revealed with the spatially anisotropic distributions of the first hydration shells.

Fu, Cen-Feng; Tian, Shan Xi

2010-05-01

176

Operation mechanism of rotary molecular motor F1 probed by single-molecule techniques  

NASA Astrophysics Data System (ADS)

F1 is a rotary motor protein. Three catalytic ?-subunits in the stator ?3?3 ring are torque generators, and rotate the rotor ?-subunit by sequential and cooperative conformational changes coupled with adenosine triphosphate (ATP) hydrolysis reaction. F1 shows remarkable performances such as rotation rate faster than 10,000 rpm, high reversibility and efficiency in chemo-mechanical energy conversion. I will introduce basic characteristics of F1 revealed by single-molecule imaging and manipulation techniques based on optical microscopy and high-speed atomic force microscopy. I will also discuss the possible operation mechanism behind the F1, along with structurally-related hexameric ATPases, also mentioning the possibility of generating hybrid molecular motors.

Iino, Ryota

2013-03-01

177

Pattern Speeds of BIMA SONG Galaxies with Molecule-dominated Interstellar Mediums Using the Tremaine-Weinberg Method  

NASA Astrophysics Data System (ADS)

We apply the Tremaine-Weinberg method of pattern speed determination to data cubes of CO emission in six spiral galaxies from the BIMA Survey of Nearby Galaxies, each with an interstellar medium dominated by molecular gas. We compare derived pattern speeds with estimates based on other methods, usually involving the identification of a predicted behavior at one or more resonances of the pattern(s). In two cases (NGC 1068 and NGC 4736), we find evidence for a central bar pattern speed that is greater than that of the surrounding spiral and roughly consistent with previous estimates. However, the spiral pattern speed in both cases is much larger than previous determinations. For the barred spirals NGC 3627 and NGC 4321, the method is insensitive to the bar pattern speed (the bar in each is nearly parallel to the major axis; in this case the method will not work), but for the former galaxy the spiral pattern speed found agrees with previous estimates of the bar pattern speed, suggesting that these two structures are part of a single pattern. For the latter, the spiral pattern speed found is in agreement with several previous determinations. For the flocculent spiral NGC 4414 and the ``Evil Eye'' galaxy NGC 4826, the method does not support the presence of a large-scale coherent pattern. We also apply the method to a simulated barred galaxy in order to demonstrate its validity and to understand its sensitivity to various observational parameters. In addition, we study the results of applying the method to a simulated, clumpy axisymmetric disk with no wave present. The Tremaine & Weinberg method in this case may falsely indicate a well-defined pattern.

Rand, Richard J.; Wallin, John F.

2004-10-01

178

High-efficiency molecular counting in solution: Single-molecule detection in electrodynamically focused microdroplet streams  

SciTech Connect

We report fluorescence detection of individual rhodamine 6G molecules using a linear quadrupole to focus streams of microdroplets through the waist of a counterpropagating cw Ar{sup +} laser. Since the terminal velocity scales as the square of the droplet diameter, the droplet-laser interaction time was `tunable` between 5 and 200 ms by using water samples spiked with a small, variable (2-5% v/v) amount of glycerol. Fluorescence bursts from droplets containing single molecules were clearly distinguished from the blanks in real time with an average signal-to-noise ratio of about 10, limited primarily by photobleaching and droplet size fluctuations (<1%). The volume throughput rates associated with this approach (approx. 10 pL/s) are roughly 10{sup 3} higher than those associated with particle levitation techniques, with minimal sacrifice in sensitivity. Total molecular detection efficiencies of about 80% (at >99% confidence) were obtained for 100 and 15 fM rhodamine 6G solutions, in good agreement with detailed theoretical calculations and statistical limitations. 39 refs., 7 figs., 1 tab.

Lermer, N.; Barnes, M.D.; Kung, C.Y.; Whitten, W.B.; Ramsey, J.M. [Oak Ridge National Lab., TN (United States)] [Oak Ridge National Lab., TN (United States)

1997-06-01

179

Single molecule molecular inversion probes for targeted, high-accuracy detection of low-frequency variation  

PubMed Central

The detection and quantification of genetic heterogeneity in populations of cells is fundamentally important to diverse fields, ranging from microbial evolution to human cancer genetics. However, despite the cost and throughput advances associated with massively parallel sequencing, it remains challenging to reliably detect mutations that are present at a low relative abundance in a given DNA sample. Here we describe smMIP, an assay that combines single molecule tagging with multiplex targeted capture to enable practical and highly sensitive detection of low-frequency or subclonal variation. To demonstrate the potential of the method, we simultaneously resequenced 33 clinically informative cancer genes in eight cell line and 45 clinical cancer samples. Single molecule tagging facilitated extremely accurate consensus calling, with an estimated per-base error rate of 8.4 × 10?6 in cell lines and 2.6 × 10?5 in clinical specimens. False-positive mutations in the single molecule consensus base-calls exhibited patterns predominantly consistent with DNA damage, including 8-oxo-guanine and spontaneous deamination of cytosine. Based on mixing experiments with cell line samples, sensitivity for mutations above 1% frequency was 83% with no false positives. At clinically informative sites, we identified seven low-frequency point mutations (0.2%–4.7%), including BRAF p.V600E (melanoma, 0.2% alternate allele frequency), KRAS p.G12V (lung, 0.6%), JAK2 p.V617F (melanoma, colon, two lung, 0.3%–1.4%), and NRAS p.Q61R (colon, 4.7%). We anticipate that smMIP will be broadly adoptable as a practical and effective method for accurately detecting low-frequency mutations in both research and clinical settings.

Hiatt, Joseph B.; Pritchard, Colin C.; Salipante, Stephen J.; O'Roak, Brian J.; Shendure, Jay

2013-01-01

180

Expression patterns of the creatine metabolism-related molecules AGAT, GAMT and CT1 in adult zebrafish Danio rerio.  

PubMed

AGAT, GAMT and CT1, three creatine synthesis and transport-related molecules, have been widely studied in mammals. To explore their homologous genes in adult zebrafish Danio rerio, the gene expression patterns of these three genes in D. rerio were investigated. The results reveal that AGAT, GAMT and CT1 are expressed widely in diverse tissues of D. rerio where the homologous genes in mammals are also expressed. PMID:20409172

Wang, L; Chen, D; Yang, L; Huang, S; Zhang, Y; Zhang, H

2010-04-01

181

Researchers use changes in the patterns of sugar molecules to detect cells before they develop into esophageal cancer:  

Cancer.gov

Scientists working at Britain's Medical Research Council, in collaboration with researchers from New York University, have identified changes in the patterns of sugar molecules that line pre-cancerous cells in the esophagus, a condition called Barrett’s dysplasia, making it much easier to detect and remove these cells before they develop into esophageal cancer. These findings, reported in the journal Nature Medicine, have important implications for patients and may help to monitor their condition and prevent the development of cancer.

182

Cold and heat pattern of rheumatoid arthritis in traditional Chinese medicine: distinct molecular signatures indentified by microarray expression profiles in CD4-positive T cell.  

PubMed

The research is aimed to explore the distinct molecular signatures in discriminating the rheumatoid arthritis patients with traditional Chinese medicine (TCM) cold pattern and heat pattern. Twenty patients with typical TCM cold pattern and heat pattern were included. Microarray technology was used to reveal gene expression profiles in CD4+ T cells. The signal intensity of each expressed gene was globally normalized using the R statistics program. The ratio of cold pattern to heat pattern in patients with RA at more or less than 1:2 was taken as the differential gene expression criteria. Protein-protein interaction information for these genes from databases was searched, and the highly connected regions were detected by IPCA algorithm. The significant pathways were extracted from these subnetworks by Biological Network Gene Ontology tool. Twenty-nine genes differentially regulated between cold pattern and heat pattern were found. Among them, 7 genes were expressed significantly more in cold pattern. Biological network of protein-protein interaction information for these significant genes were searched and four highly connected regions were detected by IPCA algorithm to infer significant complexes or pathways in the biological network. Particularly, the cold pattern was related to Toll-like receptor signaling pathway. The following related pathways in heat pattern were included: Calcium signaling pathway; cell adhesion molecules; PPAR signaling pathway; fatty acid metabolism. These results suggest that better knowledge of the main biological processes involved at a given pattern in TCM might help to choose the most appropriate treatment. PMID:20658292

Lu, Cheng; Xiao, Cheng; Chen, Gao; Jiang, Miao; Zha, Qinglin; Yan, Xiaoping; Kong, Weiping; Lu, Aiping

2012-01-01

183

Planar microdevices enhance transport of large molecular weight molecules across retinal pigment epithelial cells.  

PubMed

Large molecular weight drug delivery to the posterior eye is challenging due to cellular barriers that hinder drug transport. Understanding how to enhance transport across the retinal barrier is important for the design of new drug delivery systems. A novel mechanism to enhance drug transport is the use of geometric properties, which has not been extensively explored in the retina. Planar SU-8/Poly(ethyleneglycol)dimethacrylate microdevices were constructed using photolithography to deliver FITC dextran across an in vitro retinal model. The model consists of retinal pigment epithelial (RPE) cells grown to confluence on transwell inserts, which provides an environment to investigate the influence of geometry on paracellular and transcellular delivery of encapsulated large molecules. Planar microdevices enhanced transport of large molecular weight dextrans across different models of RPE in a size dependent fashion. Increased drug permeation across the RPE was observed with the addition of microdevices as compared to a traditional bolus of FITC dextran. This phenomena was initiated by a non-toxic interaction between the microdevices and the retinal tight junction proteins. Suggesting that increased drug transport occurs via a paracellular pathway. These experiments provide evidence to support the future use of planar unidirectional microdevices for delivery of biologics in ocular applications. PMID:24789225

Wade, Jennifer S; Desai, Tejal A

2014-08-01

184

Molecular Quantum Spintronics: Supramolecular Spin Valves Based on Single-Molecule Magnets and Carbon Nanotubes  

PubMed Central

We built new hybrid devices consisting of chemical vapor deposition (CVD) grown carbon nanotube (CNT) transistors, decorated with TbPc2 (Pc = phthalocyanine) rare-earth based single-molecule magnets (SMMs). The drafting was achieved by tailoring supramolecular ?-? interactions between CNTs and SMMs. The magnetoresistance hysteresis loop measurements revealed steep steps, which we can relate to the magnetization reversal of individual SMMs. Indeed, we established that the electronic transport properties of these devices depend strongly on the relative magnetization orientations of the grafted SMMs. The SMMs are playing the role of localized spin polarizer and analyzer on the CNT electronic conducting channel. As a result, we measured magneto-resistance ratios up to several hundred percent. We used this spin valve effect to confirm the strong uniaxial anisotropy and the superparamagnetic blocking temperature (TB ~ 1 K) of isolated TbPc2 SMMs. For the first time, the strength of exchange interaction between the different SMMs of the molecular spin valve geometry could be determined. Our results introduce a new design for operable molecular spintronic devices using the quantum effects of individual SMMs.

Urdampilleta, Matias; Nguyen, Ngoc-Viet; Cleuziou, Jean-Pierre; Klyatskaya, Svetlana; Ruben, Mario; Wernsdorfer, Wolfgang

2011-01-01

185

Long-Lived, Energetic States of Small Molecules: Spectroscopy, Pattern Recognition, and Formation/Destruction Mechanisms.  

National Technical Information Service (NTIS)

Metastable, electronically excited states of atoms and small molecules have chemical and photophysical properties that are relevant to Air Force missions in communication, upper atmospheric modeling, and high speed vehicle detection; tracking, and identif...

R. W. Field R. J. Silbey

2002-01-01

186

Innate recognition of apoptotic cells: novel apoptotic cell-associated molecular patterns revealed by crossreactivity of anti-LPS antibodies  

PubMed Central

Cells dying by apoptosis are normally cleared by phagocytes through mechanisms that can suppress inflammation and immunity. Molecules of the innate immune system, the pattern recognition receptors (PRRs), are able to interact not only with conserved structures on microbes (pathogen-associated molecular patterns, PAMPs) but also with ligands displayed by apoptotic cells. We reasoned that PRRs might therefore interact with structures on apoptotic cells – apoptotic cell-associated molecular patterns (ACAMPs) – that are analogous to PAMPs. Here we show that certain monoclonal antibodies raised against the prototypic PAMP, lipopolysaccharide (LPS), can crossreact with apoptotic cells. We demonstrate that one such antibody interacts with a constitutively expressed intracellular protein, laminin-binding protein, which translocates to the cell surface during apoptosis and can interact with cells expressing the prototypic PRR, mCD14 as well as with CD14-negative cells. Anti-LPS cross reactive epitopes on apoptotic cells colocalised with annexin V- and C1q-binding sites on vesicular regions of apoptotic cell surfaces and were released associated with apoptotic cell-derived microvesicles (MVs). These results confirm that apoptotic cells and microbes can interact with the immune system through common elements and suggest that anti-PAMP antibodies could be used strategically to characterise novel ACAMPs associated not only with apoptotic cells but also with derived MVs.

Tennant, I; Pound, J D; Marr, L A; Willems, J J L P; Petrova, S; Ford, C A; Paterson, M; Devitt, A; Gregory, C D

2013-01-01

187

Photodissociation of a water molecule in ice: a molecular dynamics study  

NASA Astrophysics Data System (ADS)

UV irradiation of ice may be important for dust grain chemistry in dense clouds through (i) the photolysis of molecules in the icy mantles releasing reactive species that can react with eachother or other species present in the ice, (ii) desorption of atoms and molecules into the gas phase, and (iii) phase transformation of the ice. There have been a number of experiments studying the effects of UV irradiation of water ice. Ghormley and Hochanadel (1971) studied flash photolysis of crystalline hexagonal ice at 263 K and could detect OH radicals in the ice. In a study of different UV doses on the chemical composition of a number of pure ices at 10 K, Gerakines et al. (1996), OH, H2O2, and HO2 were detected after UV irradiation of amorphous ice. In their work on UV iradiation of amorphous D2O ice, Watanabe et al. (2000) found that D2 was efficiently formed upon irradiation of 9.8 eV photons, while Yabushita et al. (2004) detected H atoms desorbing from amorphous ice that had been irradiated by 6.4 eV photons. The amorphization of crystalline cubic ice at 16 K was shown to be quite efficient through Ly-? irradiation (Leto & Baratta 2003). In the work presented here the photodissociation dynamics of a water molecule in crystalline and amorphous pure water ices is studied computationally using classical molecular dynamics (Andersson et al. in press, Andersson et al. in prep). Photodissociation in the first bilayer of crystalline ice leads mainly to H atoms desorbing, while in the third bilayer trapping of H and OH dominates. Results for amorphous ice shows a similar depth dependence for the outcome of photodissociation. The probability of H atom desorption is however somewhat higher for the upper layers of amorphous ice compared to the corresponding layers in crystalline ice. The kinetic energy distribution of the desorbing H atoms is much broader than that for the corresponding gas-phase photodissociation due to loss of energy through collisional encounters with the ice water molecules. H atom desorption from amorphous ice shows a hotter kinetic energy distribution than the one for crystalline ice. The H atoms on average move about 10 Å before becoming trapped, while OH radicals typically move 2 Å, their motion through the ice being more restricted. OH formed from photodisscation at the surface has in some cases however been found to move more than 50 Å over the surface before being readsorbed. In accordance with experiments a blueshift of the absorption spectrum is obtained relative to gas-phase water.

Andersson, Stefan; Kroes, Geert-Jan; van Dishoeck, Ewine F.

188

Performance of an Arc-Heated Supersonic Molecular Beam and Its Application to Molecule-Molecule Collision Studies.  

National Technical Information Service (NTIS)

Bases for designs of the several components of an intermediate-energy high-intensity molecular beam are presented. Intermediate energies and high intensities are realized as a consequence of heating the beam gas in an electric arc and then converting the ...

E. L. Knuth N. M. Kuluva

1967-01-01

189

Hunting complex differential gene interaction patterns across molecular contexts  

PubMed Central

Heterogeneity in genetic networks across different signaling molecular contexts can suggest molecular regulatory mechanisms. Here we describe a comparative chi-square analysis (CP?2) method, considerably more flexible and effective than other alternatives, to screen large gene expression data sets for conserved and differential interactions. CP?2 decomposes interactions across conditions to assess homogeneity and heterogeneity. Theoretically, we prove an asymptotic chi-square null distribution for the interaction heterogeneity statistic. Empirically, on synthetic yeast cell cycle data, CP?2 achieved much higher statistical power in detecting differential networks than alternative approaches. We applied CP?2 to Drosophila melanogaster wing gene expression arrays collected under normal conditions, and conditions with overexpressed E2F and Cabut, two transcription factor complexes that promote ectopic cell cycling. The resulting differential networks suggest a mechanism by which E2F and Cabut regulate distinct gene interactions, while still sharing a small core network. Thus, CP?2 is sensitive in detecting network rewiring, useful in comparing related biological systems.

Song, Mingzhou; Zhang, Yang; Katzaroff, Alexia J.; Edgar, Bruce A.; Buttitta, Laura

2014-01-01

190

Hunting complex differential gene interaction patterns across molecular contexts.  

PubMed

Heterogeneity in genetic networks across different signaling molecular contexts can suggest molecular regulatory mechanisms. Here we describe a comparative chi-square analysis (CP?(2)) method, considerably more flexible and effective than other alternatives, to screen large gene expression data sets for conserved and differential interactions. CP?(2) decomposes interactions across conditions to assess homogeneity and heterogeneity. Theoretically, we prove an asymptotic chi-square null distribution for the interaction heterogeneity statistic. Empirically, on synthetic yeast cell cycle data, CP?(2) achieved much higher statistical power in detecting differential networks than alternative approaches. We applied CP?(2) to Drosophila melanogaster wing gene expression arrays collected under normal conditions, and conditions with overexpressed E2F and Cabut, two transcription factor complexes that promote ectopic cell cycling. The resulting differential networks suggest a mechanism by which E2F and Cabut regulate distinct gene interactions, while still sharing a small core network. Thus, CP?(2) is sensitive in detecting network rewiring, useful in comparing related biological systems. PMID:24482443

Song, Mingzhou; Zhang, Yang; Katzaroff, Alexia J; Edgar, Bruce A; Buttitta, Laura

2014-04-01

191

Molecular properties from combined QM/MM methods. 2. Chemical shifts in large molecules  

SciTech Connect

A method for calculating the chemical shielding tensor of any atom with the QM/MM approach has been developed. The method is described and applied to a number of model systems including the water dimer, NMA-water complexes, cytosine monophosphate, paired and stacked nucleic acid bases, imidazole-metal complexes, and 1{prime}-deoxyribose-metal ion complexes. The results demonstrate that with an appropriate QM/MM partition, good descriptions of the environmental effects on chemical shift tensors are obtained. The typical error compared to full QM calculations is 1--2 ppm for heavy atoms. At distances below 2.5 {angstrom}, such as occur in hydrogen bonding, larger errors arise due to the lack of Pauli repulsion and magnetic susceptibility of the nearby groups in the current QM/MM model; including the hydrogen bonded molecules as part of the QM region is a way of solving this problem. The method is also applied to a simple model of myoglobin-CO and it is shown that the significant influence from the distal histidine on the shielding of Fe and CO is well reproduced by a QM/MM calculation. Application to the chemical shift of the 1-N nitrogen in nicotinamide adenine dinucleotide (NAD{sup +}), relative to N-methyl nicotinamide, gives good results, indicating that accurate chemical shifts can be obtained for specific atoms in large molecules that cannot be treated by QM at the MP2 level. The effect of solvation on the chemical shift of water was also studied with the QM/MM approach in a molecular dynamics framework. The test calculations described in this paper demonstrate that the QM/MM method for estimating shielding tensors and chemical shifts is a useful approach for large systems.

Cui, Q.; Karplus, M.

2000-04-20

192

Molecular dynamics study of structure H clathrate hydrates of methane and large guest molecules.  

PubMed

Methane storage in structure H (sH) clathrate hydrates is attractive due to the relatively higher stability of sH as compared to structure I methane hydrate. The additional stability is gained without losing a significant amount of gas storage density as happens in the case of structure II (sII) methane clathrate. Our previous work has showed that the selection of a specific large molecule guest substance (LMGS) as the sH hydrate former is critical in obtaining the optimum conditions for crystallization kinetics, hydrate stability, and methane content. In this work, molecular dynamics simulations are employed to provide further insight regarding the dependence of methane occupancy on the type of the LMGS and pressure. Moreover, the preference of methane molecules to occupy the small (5(12)) or medium (4(3)5(6)6(3)) cages and the minimum cage occupancy required to maintain sH clathrate mechanical stability are examined. We found that thermodynamically, methane occupancy depends on pressure but not on the nature of the LMGS. The experimentally observed differences in methane occupancy for different LMGS may be attributed to the differences in crystallization kinetics and/or the nonequilibrium conditions during the formation. It is also predicted that full methane occupancies in both small and medium clathrate cages are preferred at higher pressures but these cages are not fully occupied at lower pressures. It was found that both small and medium cages are equally favored for occupancy by methane guests and at the same methane content, the system suffers a free energy penalty if only one type of cage is occupied. The simulations confirm the instability of the hydrate when the small and medium cages are empty. Hydrate decomposition was observed when less than 40% of the small and medium cages are occupied. PMID:18500878

Susilo, Robin; Alavi, Saman; Ripmeester, John A; Englezos, Peter

2008-05-21

193

Low molecular weight molecules of oyster nacre induce mineralization of the MC3T3-E1 cells.  

PubMed

The nacre layer from the pearl oyster shell is considered as a promising osteoinductive biomaterial. Nacre contains one or more signal molecules capable of stimulating bone formation. The identity and the mode of action of these molecules on the osteoblast differentiation were analyzed. Water-soluble molecules from nacre were fractionated according to dialysis, solvent extraction, and reversed-phase HPLC. The activity of a fraction composed of low molecular weight molecules in the mineralization of the MC3T3-E1 extracellular matrix was investigated. Mineralization of the preosteoblast cells was monitored according to alizarin red staining, Raman spectroscopy, scanning electron microscopy, and quantitative RT-PCR. Molecules isolated from nacre, ranging from 50 to 235 Da, induced a red alizarin staining of the preosteoblasts extracellular matrix after 16 days of culture. Raman spectroscopy demonstrated the presence of hydroxyapatite (HA) in samples treated with these molecules. Scanning electron microscopy pictures showed at the surface of the treated cells the occurrence of clusters of spherical particles resembling to HA. The treatment of cells with nacre molecules accelerated expression of collagen I and increased the mRNA expression of Runx2 and osteopontin. This study indicated that the nacre molecules efficient in bone cell differentiation are certainly different from proteins, and could be useful for in vivo bone repair. PMID:17729263

Rousseau, Marthe; Boulzaguet, Hélène; Biagianti, Julie; Duplat, Denis; Milet, Christian; Lopez, Evelyne; Bédouet, Laurent

2008-05-01

194

The similar expression pattern of MHC class I molecules in human and mouse cerebellar cortex.  

PubMed

The major histocompatibility complex (MHC) class I molecules are considered to be important in the immune system. However, the results reported in the past decade indicate that they also play important roles in the central nervous system. Here we examined the expression of MHC I and ?2-microglobulin (?2m) in human and mouse cerebellar cortex. The results show that MHC I molecules are expressed both in human and mouse cerebellar cortex during brain development. The expression of H-2K(b)/D(b) is gradually increased with the development of mouse cerebellar cortex, but finally decreased to a very low level. Similarly, the expression of HLA-B/C genes is increased in developing human cerebellar cortex, but decreased after birth. The spatial and temporal expression of ?2m overlaps mostly with that of HLA-B/C molecules, and they are co-expressed in Purkinje cells. Our findings provide a fundamental basis to reveal the functions of neuronal MHC class I molecules in the development of human cerebellum. PMID:24272393

Lv, Dan; Shi, Qian; Liu, Jiane; Zhang, Aifeng; Miao, Fengqin; He, Youji; Shen, Yuqing; Zhang, Jianqiong

2014-01-01

195

Direct molecular simulation of gradient-driven diffusion of large molecules using constant pressure  

NASA Astrophysics Data System (ADS)

Dual control volume grand canonical molecular dynamics (DCV-GCMD) is a boundary-driven nonequilibrium molecular-dynamics technique for simulating gradient-driven diffusion in multicomponent systems. Two control volumes are established at opposite ends of the simulation box. Constant temperature and chemical potential of diffusing species are imposed in the control volumes (i.e., constant-?1...?n-1?nVT). This results in stable chemical potential gradients and steady-state diffusion fluxes in the region between the control volumes. We present results and detailed analysis for a new constant-pressure variant of the DCV-GCMD method in which one of the diffusing species for which a steady-state diffusion flux exists does not have to be inserted or deleted. Constant temperature, pressure, and chemical potential of all diffusing species except one are imposed in the control volumes (i.e., constant-?1...?n-1NnPT). The constant-pressure method can be applied to situations in which insertion and deletion of large molecules would be prohibitively difficult. As an example, we used the method to simulate diffusion in a binary mixture of spherical particles with a 2:1 size ratio. Steady-state diffusion fluxes of both diffusing species were established. The constant-pressure diffusion coefficients agreed closely with the results of the standard constant-volume calculations. In addition, we show how the concentration, chemical potential, and flux profiles can be used to calculate local binary and Maxwell-Stefan diffusion coefficients. In the case of the 2:1 size ratio mixture, we found that the binary diffusion coefficients were asymmetric and composition dependent, whereas the Maxwell-Stefan diffusion coefficients changed very little with composition and were symmetric. This last result verified that the Gibbs-Duhem relation was satisfied locally, thus validating the assumption of local equilibrium.

Thompson, Aidan P.; Heffelfinger, Grant S.

1999-06-01

196

Direct Molecular Simulation of Gradient-Driven Diffusion of Large Molecules using Constant Pressure  

SciTech Connect

Dual control volume grand canonical molecular dynamics (DCV-GCMD) is a boundary-driven non-equilibrium molecular dynamics technique for simulating gradient driven diffusion in multi-component systems. Two control volumes are established at opposite ends of the simulation box. Constant temperature and chemical potential of diffusing species are imposed in the control volumes. This results in stable chemical potential gradients and steady-state diffusion fluxes in the region between the control volumes. We present results and detailed analysis for a new constant-pressure variant of the DCV-GCMD method in which one of the diffusing species for which a steady-state diffusion flux exists does not have to be inserted or deIeted. Constant temperature, pressure and chemical potential of all diffusing species except one are imposed in the control volumes. The constant-pressure method can be applied to situations in which insertion and deletion of large molecules would be prohibitively difficult. As an exampIe, we used the method to shnulate diffusion in a biruuy mixture of spherical particles with a 2:1 size ratio. Steady-state diffusion fluxes of both diffbsi.ng species were established. The constant-pressure diffision coefficients agreed closely with the results of the standard constant-volume calculations. In addition, we show how the concentration, chemical potential and flux profiles can be used to calculate kwd binary and Maxwell-Stefim diffusion coefficients. In the case of the 2:1 size ratio mixture, we found that the binary dlffision coefficients were asymmetric and composition dependent, whereas the Maxwell-Stefan diffision coefficients changed very little with composition and were symmetric. This last result verified that the Gibbs-Duhem relation was satisfied locally, thus validating the assumption of local equilibrium.

Heffelfinger, G.S.; Thompson, A.P.

1998-12-23

197

Inelastic Collision Processes of Methane and Ethane Molecules at a Pt(111) Surface Studied by Molecular Beam Scattering Techniques  

NASA Astrophysics Data System (ADS)

Despite distinct differences in molecular structures andchemical bonds of various alkanes, the inelastic collision processesof CH4 and C2H6 on a Pt(111) surface have been found tobe very similar. Both processes can be explained qualitatively by asimple classical binary collision model. Angular intensitydistributions of reflected molecules of both species indicate thatdirect inelastic collision is primarily governed by the molecularmass, the incident kinetic energy of the molecule and the surfacetemperature of the Pt(111). Other factors such as the molecularstructure and chemical bond play minor roles in the process. However,the degree of inelastic collision, that is, the energy transfer rateper collision, increases with the molecular mass. Helium atomscattering has revealed that the dissociation process on the surfaceis identical for both molecules depending on the incident energy andthe surface temperature, as methyl moiety, ethylidyne moiety andcomplete decomposition into carbon and hydrogen atoms,successively. At elevated surface temperatures, however, thermallyassisted hydrogen tunneling appears to dominate ethane dissociation.

Yagyu, Shinjiro; Kino, Yasunobu; Ikeuchi, Toshiyuki; Hiraoka, Tomomi; Kondo, Takahiro; Yamamoto, Shigehiko

1999-12-01

198

Patterning of polypyrrole using a fluoropolymer as an adsorption-protecting molecule  

NASA Astrophysics Data System (ADS)

Patterning of the conducting polymer polypyrrole (PPy) was achieved using perfluoropolyether (PFPE) as a mask material. The fluoropolymer PFPE has both hydrophobic and oleophobic properties that allowed the generation of passivated patterns against PPy deposition. We exploited these properties to achieve the selective micropattern deposition of PPy, by simple chemical oxidation in an aqueous solution. Using a microcontact printing method, circle patterns with exposed carboxyl groups were prepared, while other region was protected by PFPE. Chemical oxidation of PPy on the patterned substrate resulted in selective deposition of PPy onto only the carboxylate-terminated regions, with little deposition on the PFPE layer. Cross-sectional analysis of the pattern revealed that the PFPE layer would form a hole-like structure around the carboxylate-terminated surfaces, with PPy deposition only in the holes. The PFPE layer had little influence on surface smoothness, compared to other self-assembled monolayers. These results suggest that PFPE can be used as a protective material for the surface modification and patterning of various materials.

Kwon, Sunil; Ha, Jong-Wook; Noh, Jiwhan; Lee, Sang-Yup

2010-10-01

199

Non-equilibrium all-atom molecular dynamics simulations of free and tethered DNA molecules in nanochannel shear flows.  

PubMed

In order to gain insight into the mechanical and dynamical behaviour of free and tethered short chains of ss/ds DNA molecules in flow, and in parallel to investigate the properties of long chain molecules in flow fields, we have developed a series of quantum and molecular methods to extend the well developed equilibrium software CHARMM to handle non-equilibrium dynamics. These methods have been applied to cases of DNA molecules in shear flows in nanochannels. Biomolecules, both free and wall-tethered, have been simulated in the all-atom style in solvent-filled nanochannels. The new methods were demonstrated by carrying out NEMD simulations of free single-stranded DNA (ssDNA) molecules of 21 bases as well as double-stranded DNA (dsDNA) molecules of 21 base pairs tethered on gold surfaces in an ionic water shear flow. The tethering of the linker molecule (6-mercapto-1-hexanol) to perfect Au(111) surfaces was parametrized based on density functional theory (DFT) calculations. Force field parameters were incorporated into the CHARMM database. Gold surfaces are simulated in a Lennard-Jones style model that was fitted to the Morse potential model of bulk gold. The bonding force of attachment of the DNA molecules to the gold substrate linker molecule was computed to be up to a few nN when the DNA molecules are fully stretched at high shear rates. For the first time, we calculated the relaxation time of DNA molecules in picoseconds (ps) and the hydrodynamic force up to a few nanoNewtons (nN) per base pair in a nanochannel flow. The velocity profiles in the solvent due to the presence of the tethered DNA molecules were found to be nonlinear only at high shear flow rates. Free ssDNA molecules in a shear flow were observed to behave differently from each other depending upon their initial orientation in the flow field. Both free and tethered DNA molecules are clearly observed to be stretching, rotating and relaxing. Methods developed in this initial work can be incorporated into multiscale simulations including quantum mechanical, molecular and the microfluidic continuum regimes. The results may also be useful in extending existing macroscopic empirical models of DNA response dynamics in shear flows. PMID:21730387

Wang, Guan M; Sandberg, William C

2007-04-01

200

PRO_LIGAND: an approach to de novo molecular design. 2. Design of novel molecules from molecular field analysis (MFA) models and pharmacophores.  

PubMed

A computational approach for molecular design, PRO_LIGAND, has been developed within the PROMETHEUS molecular design and simulation system in order to provide a unified framework for the de novo generation of diverse molecules which are either similar or complementary to a specified target. In this instance, the target is a pharmacophore derived from a series of active structures either by a novel interpretation of molecular field analysis data or by a pharmacophore-mapping procedure based on clique detection. After a brief introduction to PRO_LIGAND, a detailed description is given of the two pharmacophore generation procedures and their abilities are demonstrated by the elucidation of pharmacophores for steroid binding and ACE inhibition, respectively. As a further indication of its efficacy in aiding the rational drug design process, PRO_LIGAND is then employed to build novel organic molecules to satisfy the physicochemical constraints implied by the pharmacophores. PMID:7966160

Waszkowycz, B; Clark, D E; Frenkel, D; Li, J; Murray, C W; Robson, B; Westhead, D R

1994-11-11

201

Genetic basis of dental agenesis - molecular genetics patterning clinical dentistry  

PubMed Central

Tooth agenesis is one of the most common congenital malformations in humans. Hypodontia can either occur as an isolated condition (non-syndromic hypodontia) or can be associated with a syndrome (syndromic hypodontia), highlighting the heterogeneity of the condition. Though much progress has been made to identify the developmental basis of tooth formation, knowledge of the etiological basis of inherited tooth loss is still lacking. To date, the mutation spectra of non-syndromic form of familial and sporadic tooth agenesis in humans have revealed defects in various such genes that encode transcription factors, MSX1 and PAX9 or genes that code for a protein involved in canonical Wnt signaling (AXIN2), and a transmembrane receptor of fibroblast growth factors (FGFR1). The aim of this paper is to review the current literature on the molecular mechanisms responsible for selective hypodontia in humans and to present a detailed overview of causative genes and syndromes associated with hypodontia. Key words:Tooth agenesis, hypodontia, growth factors, mutations.

Goswami, Mridula; Chhabra, Anuj

2014-01-01

202

Calculation of NMR-relaxation parameters for flexible molecules from molecular dynamics simulations.  

PubMed

Comparatively small molecules such as peptides can show a high internal mobility with transitions between several conformational minima and sometimes coupling between rotational and internal degrees of freedom. In those cases the interpretation of NMR relaxation data is difficult and the use of standard methods for structure determination is questionable. On the other hand, in the case of those system sizes, the timescale of both rotational and internal motions is accessible by molecular dynamics (MD) simulations using explicit solvent. Thus a comparison of distance averages ([r(-6)](-1/6) or [r(-3)](1/3)) over the MD trajectory with NOE (or ROE) derived distances is no longer necessary, the (back)calculation of the complete spectra becomes possible. In the present study we use two 200 ns trajectories of a heptapeptide of beta-amino acids in methanol at two different temperatures to obtain theoretical ROESY spectra by calculating the exact spectral densities for the interproton vectors and the full relaxation matrix. Those data are then compared with the experimental ones. This analysis permits to test some of the assumptions and approximations that generally have to be made to interpret NMR spectra, and to make a more reliable prediction of the conformational equilibrium that leads to the experimental spectrum. PMID:11563554

Peter, C; Daura, X; van Gunsteren, W F

2001-08-01

203

Real-space imaging of molecular structure and chemical bonding by single-molecule inelastic tunneling probe.  

PubMed

The arrangement of atoms and bonds in a molecule influences its physical and chemical properties. The scanning tunneling microscope can provide electronic and vibrational signatures of single molecules. However, these signatures do not relate simply to the molecular structure and bonding. We constructed an inelastic tunneling probe based on the scanning tunneling microscope to sense the local potential energy landscape of an adsorbed molecule with a carbon monoxide (CO)-terminated tip. The skeletal structure and bonding of the molecule are revealed from imaging the spatial variations of a CO vibration as the CO-terminated tip probes the core of the interactions between adjacent atoms. An application of the inelastic tunneling probe reveals the sharing of hydrogen atoms among multiple centers in intramolecular and extramolecular bonding. PMID:24855265

Chiang, Chi-lun; Xu, Chen; Han, Zhumin; Ho, W

2014-05-23

204

Mechanical properties of NRR domain from human Notch 1 studied by single molecule AFM force spectroscopy and steered molecular dynamics  

NASA Astrophysics Data System (ADS)

For proteins in living cells, forces are present from macroscopic to single molecule levels. Single molecule atomic force microscopy in force extension (FX-AFM) mode measures forces at which proteins undergo major conformational transitions with ˜ 10 pN force sensitivity (FX-AFM). Here, we present the results of the FX-AFM experiments on a construct comprising the NRR domain from human Notch 1. It is believed that understanding the mechanical properties of Notch at the single molecule level can help to understand its role in triggering some breast cancers. The experimental results on our Notch construct revealed several conformational transitions of this molecule under force. These results were confronted with the steered molecular dynamics simulations based on a simplified Go model. These results opened a path for further investigations of Notch constructs at various physiologically relevant conditions.

Dey, Ashim; Chen, Jianhan; Li, Hui; Zolkiewska, Anna; Wu, Hui-Chuan; Zolkiewski, Michal; Szoszkiewicz, Robert

2010-10-01

205

Ion and molecule sensors using molecular recognition in luminescent, conductive polymers. FY 1997 year-end progress report  

SciTech Connect

'The purpose of this project is to use molecular recognition strategies to develop sensor technology based on luminescent, conductive polymers that contain sites for binding specific molecules or ions in the presence of related molecules or ions. Selective binding of a particular molecule or ion of interest to these polymers will result in a large change in their luminescence and/or conductivity, which can be used to both qualitatively and quantitatively sense the presence of the bound molecules or ions. The main thrusts and accomplishments in the first year of this project involve developing polymer syntheses that yield conjugated polymers to which a wide variety of ligands for metal ion binding can be readily incorporated.'

Wasielewski, M.R.

1997-01-01

206

Specific features of propagation of femtosecond laser pulses through a molecular gaseous medium under conditions of efficient alignment of molecules  

SciTech Connect

The propagation of femtosecond laser pulses in a molecular gaseous medium is studied with the rotational dynamics of molecules under the action of these pulses taken into account. Based on the simultaneous numerical solution of the wave equation describing the laser pulse evolution and the Schroedinger equation that determines the quantum state evolution of the medium molecules, the rotational dynamics of molecules in the laser field and the laser pulse evolution are analysed with their mutual influence taken into account. Efficient dynamic alignment of molecules along the direction of laser radiation polarisation is observed, which causes variation in the spatiotemporal pulse profile, as well as significant broadening and deformation of its spectrum in the course of propagation through the medium. The physical mechanisms of the observed phenomena are analysed by using the approximate analytical solution of the problem, derived for the case of preliminary excitation of the medium by a pump pulse (the pump-probe scheme). (nonlinear optical phenomena)

Gulyaev, A V; Tikhonova, O V

2013-07-31

207

Toll-like receptors and damage-associated molecular patterns: novel links between inflammation and hypertension.  

PubMed

Low-grade systemic inflammation is a common manifestation of hypertension; however, the exact mechanisms that initiate this pathophysiological response, thereby contributing to further increases in blood pressure, are not well understood. Aberrant vascular inflammation and reactivity via activation of the innate immune system may be the first step in the pathogenesis of hypertension. One of the functions of the innate immune system is to recognize and respond to danger. Danger signals can arise from not only pathogenic stimuli but also endogenous molecules released following cell injury and/or death [damage-associated molecular patterns (DAMPs)]. In the short-term, activation of the innate immune system is beneficial in the vasculature by providing cytoprotective mechanisms and facilitating tissue repair following injury or infection. However, sustained or excessive immune system activation, such as in autoimmune diseases, may be deleterious and can lead to maladaptive, irreversible changes to vascular structure and function. An initial source of DAMPs that enter the circulation to activate the innate immune system could arise from modest elevations in peripheral vascular resistance. These stimuli could subsequently lead to ischemic- or pressure-induced events aggravating further cell injury and/or death, providing more DAMPs for innate immune system activation. This review will address and critically evaluate the current literature on the role of the innate immune system in hypertension pathogenesis. The role of Toll-like receptor activation on somatic cells of the vasculature in response to the release of DAMPs and the consequences of this activation on inflammation, vasoreactivity, and vascular remodeling will be specifically discussed. PMID:24163075

McCarthy, Cameron G; Goulopoulou, Styliani; Wenceslau, Camilla F; Spitler, Kathryn; Matsumoto, Takayuki; Webb, R Clinton

2014-01-15

208

The role of pathogen-associated molecular patterns in inflammatory responses against alginate based microcapsules.  

PubMed

Alginate-based microcapsules are used for immunoisolation of cells to release therapeutics on a minute-to-minute basis. Unfortunately, alginate-based microcapsules are suffering from varying degrees of success, which is usually attributed to differences in tissue responses. This results in failure of the therapeutic cells. In the present study we show that commercial, crude alginates may contain pathogen-associated molecular patterns (PAMPs), which are recognized by the sensors of the innate immune system. Known sensors are Toll-like receptors (TLRs), NOD receptors, and C-type lectins. By using cell-lines with a non-functional adaptor molecule essential in Toll-like receptor signaling, i.e. MyD88, we were able to show that alginates signal mainly via MyD88. This was found for low-G, intermediate-G, and high-G alginates applied in calcium-beads, barium-beads as well as in alginate-PLL-alginate capsules. These alginates did stimulate TLRs 2, 5, 8, and 9 but not TLR4 (LPS receptor). Upon implantation in rats these alginates provoked a strong inflammatory response resulting in fibrosis of the capsules. Analysis demonstrated that commercial alginates contain the PAMPs peptidoglycan, lipoteichoic acid, and flagellin. By applying purification procedures, these PAMPs were largely removed. This was associated with deletion of the inflammatory tissue responses as confirmed by an implantation experiment in rats. Our data also show that alginate itself does not provoke TLR mediated responses. We were able to unravel the sensor mechanism by which contaminants in alginates may provoke inflammatory responses. PMID:24051034

Paredes-Juarez, Genaro A; de Haan, Bart J; Faas, Marijke M; de Vos, Paul

2013-12-28

209

Nanoscale patterning of a self-assembled monolayer by modification of the molecule-substrate bond.  

PubMed

The intercalation of Cu at the interface of a self-assembled monolayer (SAM) and a Au(111)/mica substrate by underpotential deposition (UPD) is studied as a means of high resolution patterning. A SAM of 2-(4'-methylbiphenyl-4-yl)ethanethiol (BP2) prepared in a structural phase that renders the Au substrate completely passive against Cu-UPD, is patterned by modification with the tip of a scanning tunneling microscope. The tip-induced defects act as nucleation sites for Cu-UPD. The lateral diffusion of the metal at the SAM-substrate interface and, thus, the pattern dimensions are controlled by the deposition time. Patterning down to the sub-20 nm range is demonstrated. The difference in strength between the S-Au and S-Cu bond is harnessed to develop the latent Cu-UPD image into a patterned binary SAM. Demonstrated by the exchange of BP2 by adamantanethiol (AdSH) this is accomplished by a sequence of reductive desorption of BP2 in Cu free areas followed by adsorption of AdSH. The appearance of Au adatom islands upon the thiol exchange suggests that the interfacial structures of BP2 and AdSH SAMs are different. PMID:24778947

Shen, Cai; Buck, Manfred

2014-01-01

210

Nanoscale patterning of a self-assembled monolayer by modification of the molecule-substrate bond  

PubMed Central

Summary The intercalation of Cu at the interface of a self-assembled monolayer (SAM) and a Au(111)/mica substrate by underpotential deposition (UPD) is studied as a means of high resolution patterning. A SAM of 2-(4'-methylbiphenyl-4-yl)ethanethiol (BP2) prepared in a structural phase that renders the Au substrate completely passive against Cu-UPD, is patterned by modification with the tip of a scanning tunneling microscope. The tip-induced defects act as nucleation sites for Cu-UPD. The lateral diffusion of the metal at the SAM–substrate interface and, thus, the pattern dimensions are controlled by the deposition time. Patterning down to the sub-20 nm range is demonstrated. The difference in strength between the S–Au and S–Cu bond is harnessed to develop the latent Cu-UPD image into a patterned binary SAM. Demonstrated by the exchange of BP2 by adamantanethiol (AdSH) this is accomplished by a sequence of reductive desorption of BP2 in Cu free areas followed by adsorption of AdSH. The appearance of Au adatom islands upon the thiol exchange suggests that the interfacial structures of BP2 and AdSH SAMs are different.

Shen, Cai

2014-01-01

211

Susceptibility Patterns and Molecular Identification of Trichosporon Species  

PubMed Central

The physiological patterns, the sequence polymorphisms of the internal transcriber spacer (ITS), and intergenic spacer regions (IGS) of the rRNA genes and the antifungal susceptibility profile were evaluated for their ability to identify Trichosporon spp. and their specificity for the identification of 49 clinical isolates of Trichosporon spp. Morphological and biochemical methodologies were unable to differentiate among the Trichosporon species. ITS sequencing was also unable to differentiate several species. However, IGS1 sequencing unambiguously identified all Trichosporon isolates. Following the results of DNA-based identification, Trichosporon asahii was the species most frequently isolated from deep sites (15 of 25 strains; 60%). In the main, other Trichosporon species were recovered from cutaneous samples. The majority of T. asahii, T. faecale, and T. coremiiforme clinical isolates exhibited resistance in vitro to amphotericin B, with geometric mean (GM) MICs >4 ?g/ml. The other species of Trichosporon did not show high MICs of amphotericin B, and GM MICs were <1 ?g/ml. Azole agents were active in vitro against the majority of clinical strains. The most potent compound in vitro was voriconazole, with a GM MIC ?0.14 ?g/ml. The sequencing of IGS correctly identified Trichosporon isolates; however, this technique is not available in many clinical laboratories, and strains should be dispatched to reference centers where these complex methods are available. Therefore, it seems to be more practical to perform antifungal susceptibility testing of all isolates belonging to Trichosporon spp., since correct identification could take several weeks, delaying the indication of an antifungal agent which exhibits activity against the infectious strain.

Rodriguez-Tudela, Juan L.; Diaz-Guerra, Teresa M.; Mellado, Emilia; Cano, Virginia; Tapia, Cecilia; Perkins, Alexander; Gomez-Lopez, Alicia; Rodero, Laura; Cuenca-Estrella, Manuel

2005-01-01

212

A comparison of neutron diffraction and molecular dynamics structures: hydroxyl group and water molecule orientations in trypsin.  

PubMed

A comparison is presented of experimentally observed hydroxyl and water hydrogen atoms in trypsin determined from neutron density maps with the results of a 140 ps molecular dynamics simulation. Experimental determination of hydrogen and deuterium atom positions in molecules as large as proteins is a unique capability of neutron diffraction. The comparison addresses the degree to which a standard force-field approach can adequately describe the local electrostatic and van der Waals forces that determine the orientations of these hydrogen atoms. The molecular dynamics simulation, based on the all-atom AMBER force-field, allowed free rotation of all hydroxyl groups and movement of water molecules making up a bath surrounding the protein. The neutron densities, derived from 2.1 A 2H2O-H2O difference Fourier maps, provide a database of 27 well-ordered hydroxyl hydrogen atoms. Virtually all of the simulated hydroxyl orientations are within a standard deviation of the experimentally observed positions, including several examples in which both the simulation and the neutron density indicate that a hydroxyl group is shifted from a "standard" rotamer. For the most highly ordered water molecules, the hydrogen distributions calculated from the trajectory were in good agreement with neutron density; simulated water molecules that displayed multiple hydrogen-bonding networks had correspondingly broadened neutron density profiles. This comparison was facilitated by development of a method to construct a pseudo 2 A density map based on the hydrogen atom distributions from the simulation. This method is particularly useful for statically disordered water molecules, in which the average location assigned from a trajectory may represent a site of relatively low occupancy. The degree of disorder of internal water molecules is shown to result primarily from the electrostatic environment surrounding that water molecule as opposed to the cavity size available to the molecule. PMID:7616573

McDowell, R S; Kossiakoff, A A

1995-07-21

213

Pattern recognition analysis in complex molecule synthesis and the preparation of iso-Diels-Alder motifs  

PubMed Central

The identification of synthesizable substructural domains within more complex structural targets is of significant value in designing a workable plan of synthesis. We term this process “pattern recognition analysis” (PRA). In this paper we continued to build on the theme of PRA as a potential resource in retrosynthetic blueprints to reach highly challenging targets. The paper operates at two levels. First, there is provided a clear sense of definitions of categories by which patterns are related to hypothetical reaction types. Although the required reaction type may for the moment not exist, we believe that this method of analysis is likely to promote innovation that identifies unmet needs and opportunities to advance the cause of complex target synthesis. In addition, we describe reductions to practice in expanding the menu of achievable patterns. It is likely that the future value of PRA will be associated with its utility in leading the way to new and exploitable chemical innovation.

Peng, Feng; Grote, Robin E.; Wilson, Rebecca M.; Danishefsky, Samuel J.

2013-01-01

214

Earle K. Plyler Prize for Molecular Spectroscopy Talk: Coherent Ultrafast Multidimensional Spectroscopy of Molecules; From NMR to X-rays  

NASA Astrophysics Data System (ADS)

Multidimensional spectroscopic techniques which originated with NMR in the 1970s have been extended over the past 15 years to the optical regime. NMR spectroscopists have developed methods for the design of pulse sequences that resolve otherwise congested spectra, enhance selected spectral features and reveal desired dynamical events. The major experimental and computational advances required for extending these ideas to study electronic and vibrational motions on the femtosecond timescale will be surveyed. The response of complex molecules and semiconductor nanostructures to sequences of optical pulses provides snapshots of their structure and dynamical processes. Two-dimensional correlation plots of the signals show characteristic cross-peak patterns which carry information about hydrogen bonding, secondary structure fluctuations of proteins and amyloid fibrils, and coherent and incoherent energy and charge transfer in photosynthetic complexes. Double quantum coherence signals that are induced by correlations among electrons or excitons allow the visualization of correlated wavefunctions. Future extensions to the attosecond regime using xray pulses will be discussed. Since core excitations are highly localized at selected atoms, such signals can monitor the motions of valence electron wavepackets in real space with atomic spatial resolution. Common principles underlying coherent spectroscopy techniques for spins, valence electrons, and core electronic excitations, spanning frequencies from radiowaves, infrared, ultraviolet all the way to hard X-rays will be discussed. [4pt] [1] "Coherent Multidimensional Optical Probes for Electronic Correlations and Exciton Dynamics; from NMR to X-rays", S. Mukamel, D. Abramavicius, L. Yang, W.Zhuang, I.V. Schweigert and D. Voronine. Acct.Chem.Res. Acct.Chem.Res. 42, 553-562 (2009). [0pt] [2] "Coherent Multidimensional Optical Spectroscopy Excitons in Molecular Aggregates; Quasiparticle vs. Supermolecule Perspectives", D. Abramavicius, B. Palmieri, D. Voronine, F. Sanda and S. Mukamel, Chem. Rev. 109, 2350-2408 (2009).

Mukamel, Shaul

2011-03-01

215

Cell patterning using molecular vapor deposition of self-assembled monolayers and lift-off technique.  

PubMed

This paper reports a precise, live cell-patterning method by means of patterning a silicon or glass substrate with alternating cytophilic and cytophobic self-assembled monolayers (SAMs) deposited via molecular vapor deposition. Specifically, a stack of hydrophobic heptadecafluoro-1,1,2,2-tetrahydrodecyltrichlorosilane SAMs and a silicon oxide adhesion layer were patterned on the substrate surface, and a hydrophilic SAM derived from 3-trimethoxysilyl propyldiethylenetriamine was coated on the remaining non-treated areas on the substrate surface to promote cell growth. The primary characteristics of the reported method include: (i) single-cell resolution; (ii) easy alignment of the patterns with the pre-existing patterns on the substrate; (iii) easy formation of nanoscale patterns (depending on the exposure equipment); (iv) long shelf life of the substrate pattern prior to cell culturing; (v) compatibility with conventional, inverted, optical microscopes for simple visualization of patterns formed on a glass wafer; and (vi) the ability to support patterned cell (osteoblast) networks for at least 2 weeks. Here, we describe the deposition technique and the characterization of the deposited layers, as well as the application of this method in the fabrication of multielectrode arrays supporting patterned neuronal networks. PMID:20934542

Jing, Gaoshan; Wang, Yu; Zhou, Tianyi; Perry, Susan F; Grimes, Michael T; Tatic-Lucic, Svetlana

2011-03-01

216

Morphology, molecular stacking, dynamics and device performance correlations of vacuum-deposited small-molecule organic solar cells.  

PubMed

The "all carbon" organic solar cells (OSCs) based on the homocyclic molecule tetraphenyldibenzoperiflanthene (DBP) as a donor and C60 as an acceptor were comprehensively characterized. The optimized planar-mixed heterojunction device with a DBP:C60 mixture ratio of DBP?:?C60 (1?:?2) exhibited a power conversion efficiency of 4.47%. To understand why DBP possesses such advantageous characteristics, the correlations of the morphology, molecular stacking, carrier dynamics and performance of DBP:fullerene-based devices have been systematically studied. First, the face-on stacked DBP molecules could enhance both the absorption of light and the charge carrier mobility. Second, DBP?:?C60 (1?:?2) thin films with optimized domain sizes and partially interconnected acceptor grains led to the most balanced carrier mobility and the lowest bimolecular recombination in devices. Finally, the DBP molecules were found to stack closely using grazing incidence wide-angle X-ray scattering measurements, with a ?-? stacking spacing of 4.58 Å, indicating an effective molecular orbital overlap in DBP. The study not only reveals the promising characteristics of DBP as a donor in OSCs but the clear correlations of the thin-film nano-morphology, molecular stacking, carrier mobility and charge recombination found here could also provide insights into the characterization methodology and optimization of the small molecule OSCs. PMID:24683598

Chen, Chang-Wen; Huang, Zheng-Yu; Lin, Yi-Min; Huang, Wei-Ching; Chen, Yi-Hong; Strzalka, Joseph; Chang, Angela Y; Schaller, Richard D; Lee, Cheng-Kuang; Pao, Chun-Wei; Lin, Hao-Wu

2014-05-21

217

Intercellular Transfer of MHC and Immunological Molecules: Molecular Mechanisms and Biological Significance  

PubMed Central

The intercellular transfer of many molecules, including the major histocompatibility complexes (MHC), both class I and II, costimulatory and adhesion molecules, extracellular matrix organization molecules as well as chemokine, viral and complement receptors, has been observed between cells of the immune system. In this review, we aim to summarize the findings of a large body of work, highlight the molecules transferred and how this is achieved, as well as the cells capable of acquiring molecules from other cells. Although a physiological role for this phenomenon has yet to be established we suggest that the exchange of molecules between cells may influence the immune system with respect to immune amplification as well as regulation and tolerance. We will discuss why this may be the case and highlight the influence intercellular transfer of MHC molecules may have on allorecognition and graft rejection.

Smyth, L. A.; Afzali, B.; Tsang, J.; Lombardi, G.; Lechler, R. I.

2013-01-01

218

Dynamical behavior of one-dimensional water molecule chains in zeolites: Nanosecond time-scale molecular dynamics simulations of bikitaite  

NASA Astrophysics Data System (ADS)

Nanosecond scale molecular dynamics simulations of the behavior of the one-dimensional water molecule chains adsorbed in the parallel nanochannels of bikitaite, a rare lithium containing zeolite, were performed at different temperatures and for the fully and partially hydrated material. New empirical potential functions have been developed for representing lithium-water interactions. The structure and the vibrational spectrum of bikitaite were in agreement both with experimental data and Car-Parrinello molecular dynamics results. Classical molecular dynamics simulations were extended to the nanosecond time scale in order to study the flip motion of water molecules around the hydrogen bonds connecting adjacent molecules in the chains, which has been observed by NMR experiments, and the dehydration mechanism at high temperature. Computed relaxation times of the flip motion follow the Arrhenius behavior found experimentally, but the activation energy of the simulated system is slightly underestimated. Based on the results of the simulations, it may be suggested that the dehydration proceeds by a defect-driven stepwise diffusion. The diffusive mechanism appears as a single-file motion: the molecules never pass one another, even at temperatures as high as about 1000 K, nor can they switch between different channels. However, the mean square displacement (MSD) of the molecules, computed with respect to the center of mass of the simulated system, shows an irregular trend from which the single-file diffusion cannot be clearly evidenced. If the MSDs are evaluated with respect to the center of mass of the molecules hosted in each channel, the expected dependence on the square root of time finally appears.

Demontis, Pierfranco; Stara, Giovanna; Suffritti, Giuseppe B.

2004-05-01

219

In situ metallization of patterned polymer brushes created by molecular transfer print and fill.  

PubMed

A chemical pattern consisting of end-grafted polystyrene brushes (20 nm lines on a 40 nm pitch) on the native oxide of silicon wafers was defined by molecular transfer printing from assembled block co-polymer films. End-grafted hydroxyl-terminated poly(2-vinyl pyridine) brushes were selectively deposited in the interspatial regions. The poly(2-vinyl pyridine) regions selectively sequester acidic HAuCl4 from solution and form arrays of small Au nanoparticles upon exposure to oxygen plasma within the confines of the macromolecular brush layer. This print and fill process to pattern polymer brushes is a generalizable strategy to create functional chemical surface patterns. PMID:23518622

Thode, Christopher J; Cook, Peter L; Jiang, Yaming; Serdar Onses, M; Ji, Shengxiang; Himpsel, Franz J; Nealey, Paul F

2013-04-19

220

In situ metallization of patterned polymer brushes created by molecular transfer print and fill  

NASA Astrophysics Data System (ADS)

A chemical pattern consisting of end-grafted polystyrene brushes (20 nm lines on a 40 nm pitch) on the native oxide of silicon wafers was defined by molecular transfer printing from assembled block co-polymer films. End-grafted hydroxyl-terminated poly(2-vinyl pyridine) brushes were selectively deposited in the interspatial regions. The poly(2-vinyl pyridine) regions selectively sequester acidic HAuCl4 from solution and form arrays of small Au nanoparticles upon exposure to oxygen plasma within the confines of the macromolecular brush layer. This print and fill process to pattern polymer brushes is a generalizable strategy to create functional chemical surface patterns.

Thode, Christopher J.; Cook, Peter L.; Jiang, Yaming; Onses, M. Serdar; Ji, Shengxiang; Himpsel, Franz J.; Nealey, Paul F.

2013-04-01

221

High-order harmonic generation in diatomic molecules: A quantum-orbit analysis of the interference patterns  

SciTech Connect

We perform a detailed analysis of high-order harmonic generation in diatomic molecules within the strong-field approximation (SFA), with emphasis on quantum-interference effects. Specifically, we investigate how the different types of electron orbits, involving one or two centers, affect the interference patterns in the spectra. We also briefly address the influence of the choice of gauge and of the initial and final electronic bound states on such patterns. For the length-gauge SFA and undressed bound states, there exist additional terms, which can be interpreted as potential energy shifts. If, on the one hand, such shifts alter the potential barriers through which the electron initially tunnels, and may lead to a questionable physical interpretation of the features encountered, on the other hand, they seem to be necessary in order to reproduce the overall maxima and minima in the spectra. Indeed, for dressed electronic bound states in the length gauge, or undressed bound states in the velocity gauge, for which such shifts are absent, there is a breakdown of the interference patterns. In order to avoid such a problem, we provide an alternative pathway for the electron to reach the continuum, by means of an additional attosecond-pulse train. A comparison of the purely monochromatic case with the situation for which the attosecond pulses are present suggests that the patterns are due to the interference between the electron orbits which finish at different centers, regardless of whether one or two centers are involved.

Figueira de Morisson Faria, C. [Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT (United Kingdom)

2007-10-15

222

Molecular and developmental contributions to divergent pigment patterns in marine and freshwater sticklebacks  

PubMed Central

SUMMARY Pigment pattern variation across species or populations offers a tractable framework in which to investigate the evolution of development. Juvenile threespine sticklebacks (Gasterosteus aculeatus) from marine and freshwater environments exhibit divergent pigment patterns that are associated with ecological differences. Juvenile marine sticklebacks have a silvery appearance, whereas sticklebacks from freshwater environments exhibit a pattern of vertical bars. We investigated both the developmental and molecular basis of this population-level variation in pigment pattern. Time course imaging during the transition from larval to juvenile stages revealed differences between marine and freshwater fish in spatial patterns of chromatophore differentiation as well as in pigment amount and dispersal. In freshwater fish, melanophores appear primarily within dark bars whereas iridophores appear within light bars. By contrast, in marine fish, these chromatophores are interspersed across the flank. In addition to spatially segregated chromatophore differentiation, pigment amount and dispersal within melanophores varies spatially across the flank of freshwater, but not marine fish. To gain insight into the molecular pathways that underlie the differences in pigment pattern development, we evaluated differential gene expression in the flanks of developing fish using high throughput cDNA sequencing (RNA-seq) and quantitative PCR. We identified several genes that were differentially expressed across dark and light bars of freshwater fish, and between freshwater and marine fish. Together, these experiments begin to shed light on the process of pigment pattern evolution in sticklebacks.

Greenwood, Anna K.; Cech, Jennifer N.; Peichel, Catherine L.

2012-01-01

223

LARGE SCALE EVALUATION OF A PATTERN RECOGNITION/EXPERT SYSTEM FOR MASS SPECTRAL MOLECULAR WEIGHT ESTIMATION  

EPA Science Inventory

A fast, personal-computer based method of estimating molecular weights of organic compounds from low resolution mass I spectra has been thoroughly evaluated. he method is based on a rule-based pattern,recognition/expert system approach which uses empirical linear corrections whic...

224

Molecular population dynamics of DNA structures in a bcl-2 promoter sequence is regulated by small molecules and the transcription factor hnRNP LL  

PubMed Central

Minute difference in free energy change of unfolding among structures in an oligonucleotide sequence can lead to a complex population equilibrium, which is rather challenging for ensemble techniques to decipher. Herein, we introduce a new method, molecular population dynamics (MPD), to describe the intricate equilibrium among non-B deoxyribonucleic acid (DNA) structures. Using mechanical unfolding in laser tweezers, we identified six DNA species in a cytosine (C)-rich bcl-2 promoter sequence. Population patterns of these species with and without a small molecule (IMC-76 or IMC-48) or the transcription factor hnRNP LL are compared to reveal the MPD of different species. With a pattern recognition algorithm, we found that IMC-48 and hnRNP LL share 80% similarity in stabilizing i-motifs with 60 s incubation. In contrast, IMC-76 demonstrates an opposite behavior, preferring flexible DNA hairpins. With 120–180 s incubation, IMC-48 and hnRNP LL destabilize i-motifs, which has been previously proposed to activate bcl-2 transcriptions. These results provide strong support, from the population equilibrium perspective, that small molecules and hnRNP LL can modulate bcl-2 transcription through interaction with i-motifs. The excellent agreement with biochemical results firmly validates the MPD analyses, which, we expect, can be widely applicable to investigate complex equilibrium of biomacromolecules.

Cui, Yunxi; Koirala, Deepak; Kang, HyunJin; Dhakal, Soma; Yangyuoru, Philip; Hurley, Laurence H.; Mao, Hanbin

2014-01-01

225

RNA:DNA hybrids are a novel molecular pattern sensed by TLR9.  

PubMed

The sensing of nucleic acids by receptors of the innate immune system is a key component of antimicrobial immunity. RNA:DNA hybrids, as essential intracellular replication intermediates generated during infection, could therefore represent a class of previously uncharacterised pathogen-associated molecular patterns sensed by pattern recognition receptors. Here we establish that RNA:DNA hybrids containing viral-derived sequences efficiently induce pro-inflammatory cytokine and antiviral type I interferon production in dendritic cells. We demonstrate that MyD88-dependent signalling is essential for this cytokine response and identify TLR9 as a specific sensor of RNA:DNA hybrids. Hybrids therefore represent a novel molecular pattern sensed by the innate immune system and so could play an important role in host response to viruses and the pathogenesis of autoimmune disease. PMID:24514026

Rigby, Rachel E; Webb, Lauren M; Mackenzie, Karen J; Li, Yue; Leitch, Andrea; Reijns, Martin A M; Lundie, Rachel J; Revuelta, Ailsa; Davidson, Donald J; Diebold, Sandra; Modis, Yorgo; MacDonald, Andrew S; Jackson, Andrew P

2014-03-18

226

Synthesis and Magnetism of High Curie Temperature Prussian Blue Analogue Molecular Nanomagnet-Chromium Cyanide Molecule Nanowire Arrays  

NASA Astrophysics Data System (ADS)

The goal to synthesize molecular nanomagnets that exhibit spontaneous magnetic ordering close to room temperature might enable one to apply them in the fields of magnetic memory devices and microelectronics. Chromium cyanide molecule nanowire arrays with diameters of about 50 nm and lengths up to 4?m have been synthesized by an electrodepositing technology based on anodizing anodic aluminum oxide films. Characterization measurements show that the oxidation state of the chromium ions in the chromium cyanide nanowires can be expressed as Cr^3+--CN--Cr^3+. Magnetic properties measurements indicate that the Curie temperature of chromium cyanide nanowire is 200 K, which is closer room temperature compared with current molecular nanomagnet systems.

Zhou, Pingheng; Xue, Desheng; Yao, Jinli

2009-03-01

227

A third-generation density-functional-theory-based method for calculating canonical molecular orbitals of large molecules.  

PubMed

We used grid-free modified Cholesky decomposition (CD) to develop a density-functional-theory (DFT)-based method for calculating the canonical molecular orbitals (CMOs) of large molecules. Our method can be used to calculate standard CMOs, analytically compute exchange-correlation terms, and maximise the capacity of next-generation supercomputers. Cholesky vectors were first analytically downscaled using low-rank pivoted CD and CD with adaptive metric (CDAM). The obtained Cholesky vectors were distributed and stored on each computer node in a parallel computer, and the Coulomb, Fock exchange, and pure exchange-correlation terms were calculated by multiplying the Cholesky vectors without evaluating molecular integrals in self-consistent field iterations. Our method enables DFT and massively distributed memory parallel computers to be used in order to very efficiently calculate the CMOs of large molecules. PMID:24622472

Hirano, Toshiyuki; Sato, Fumitoshi

2014-06-25

228

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

SciTech Connect

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.

Champion, C.; Dal Cappello, C. [Universite Paul Verlaine-Metz, Laboratoire de Physique Moleculaire et des Collisions, ICPMB (FR CNRS 2843), Institut de Physique, 57078 Metz, Cedex 3 (France); Oubaziz, D.; Aouchiche, H. [Universite M. Mammeri, Laboratoire de Mecanique, Structure et Energetique, Tizi-Ouzou 15000 (Algeria); Popov, Yu. V. [Nuclear Physics Institute, Moscow State University, Moscow 119991 (Russian Federation)

2010-03-15

229

Molecular Variation of Satellite DNA? Molecules Associated with Malvastrum yellow vein virus and Their Role in Pathogenicity? †  

PubMed Central

Previous studies have found that the diversity of begomovirus-associated DNA? satellites is related to host and geographical origin. In this study, we have cloned and sequenced 20 different isolates of DNA? molecules associated with Malvastrum yellow vein virus (MYVV) isolated from Malvastrum coromandelianum plants in different geographical locations of Yunnan Province, China. Analyses of their molecular variation indicate that the satellites are clustered together according to their geographical location but that they have only limited sequence diversity. Infectivity tests using infectious clones of MYVV and its associated DNA? molecule indicate that MYVV DNA? is indispensable for symptom induction in Nicotiana benthamiana, N. glutinosa, Petunia hybrida, and M. coromandelianum plants. Furthermore, we showed that MYVV interacts functionally with heterologous DNA? molecules in N. benthamiana plants.

Guo, Wei; Jiang, Tong; Zhang, Xian; Li, Guixin; Zhou, Xueping

2008-01-01

230

Gaussian basis sets for CO 2 molecule generated with the molecular improved generator coordinate Hartree–Fock method  

Microsoft Academic Search

The molecular improved generator coordinate Hartree–Fock (MIGCHF) method is used to generate increasing size atom-centered Gaussian basis sets for the CO2 molecule. From these basis sets total HF energies and second-order correlation energies were calculated and compared with results obtained with other approaches. Considering our largest basis set, the HF energy is in error by 98 µhartree and the second-order

M. T. Barreto; E. P. Muniz; F. E. Jorge; A. G. Cunha

2005-01-01

231

Molecular Alligator Clips for Single Molecule Electronics. Studies of Group 16 and Isonitriles Interfaced with Au Contacts  

Microsoft Academic Search

A density-functional-theory treatment has been carried out on chalcogenide- and isonitrile-containing molecular systems (alligator clips) involved at the interface of molecule\\/Au-electrode contacts. The B3PW91 functional was used with effective core potentials provided within the LANL2DZ potentials and basis set. An extended basis set, LANL-E, was implemented by combining the valence, diffuse, and polarization basis from the 6-311++G** for H, C,

Jorge M. Seminario; Angelica G. Zacarias; James M. Tour

1999-01-01

232

In vitro motility assays and single molecule analyses reveal functional structural transitions in the molecular motor myosin  

NASA Astrophysics Data System (ADS)

The molecular basis of how myosin motors work has been significantly advanced by laser trap and other single molecule studies of myosins V and VI. Myosin V moves processively by stepping arm-over-arm, walking along the 36-nm pseudo-repeat of an actin filament by swinging its long lever arms through an angle of ˜70 ^o, and hydrolyzing one ATP per step. Compared to the laser trap, we have improved time resolution to submilliseconds by tracking single gold nanoparticle-myosin V conjugates using darkfield imaging, and have directly observed the behavior of the unbound head as the motor translocates. We have also developed a technique called single-molecule high resolution co-localization (SHREC), which allows simultaneous co-localization of two chromatically differing fluorophores only 10 nm apart. We used SHREC to directly observe myosin V molecules walking hand-over-hand. Myosin VI, a considerably different myosin family member, has been the biggest challenge to the lever arm hypothesis of myosin movement. It has a very short light chain binding domain (the conventional lever arm). Nevertheless, the molecule surprisingly steps processively 36 nm along an actin filament. Furthermore, myosin VI moves in the opposite direction to that of myosin II and myosin V. We now understand how this marvelous molecular motor achieves these feats.

Spudich, James

2010-03-01

233

Single-Molecule Spectroscopy: From 2K, to Molecular Motors, to Quantum Optics  

Microsoft Academic Search

It has now been more than ten years since the first optical detection and spectroscopy of a single molecule in a solid (Phys. Rev. Lett. 62, 2535 (1989)). The interest in optical probing of individual molecules continues to expand, driven by the lifting of ensemble averaging to expose hidden heterogeneity and by the ability to acquire local information on structure

W. E. Moerner

2001-01-01

234

Resonant multiphoton ionization spectra of molecules and molecular fragments. Annual technical report, October 1987--September 1988.  

National Technical Information Service (NTIS)

The objective of the research under this contract is to carry out studies of resonant enhanced multiphoton ionization (REMPI) processes in molecules. In the (n+1)-REMPI process of interest an atom or molecule in a specific initial state absorbs n photons ...

1988-01-01

235

Ceramide and sphingosine-1-phosphate act as photodynamic therapy-elicited damage-associated molecular patterns: cell surface exposure.  

PubMed

Molecules that appear on the surface of tumor cells after their therapy treatment may have important roles either as damage-associated molecular patterns (DAMPs) or signals for phagocytes influencing the disposal of these cells. Treatment of SCCVII and CAL27 cells, models of mouse and human squamous cell carcinoma respectively, by photodynamic therapy (PDT) resulted in the presentation of ceramide and sphingosine-1-phosphate (S1P) on the cell surface. This was documented by anti-ceramide and anti-S1P antibody staining followed by flow cytometry. The exposure of these key sphingolipid molecules on PDT-treated tumor cells was PDT dose-dependent and it varied in intensity with different photosensitizers used for PDT. The above results, together with the finding that both ceramide and S1P can activate NF?B signaling in macrophages co-incubated with PDT-treated tumor cells, establish that these two sphingolipids can act as DAMPs stimulating inflammatory/immune reactions critical for tumor therapy response. PMID:24713544

Korbelik, Mladen; Banáth, Judit; Sun, Jinghai; Canals, Daniel; Hannun, Yusuf A; Separovic, Duska

2014-06-01

236

Influence of surface charge field on the electron impact fragmentation pattern of KCl molecules in the free surface vaporization of single crystals  

Microsoft Academic Search

A mass-spectrometric method was used to investigate the temperature dependence of the electron impact fragmentation pattern of KCl molecules [ion current ratio I(K+)\\/I(KCl+)] vaporizing from a free surface of a potassium chloride single crystal. In the temperature range 766–945 K a very good correlation is observed between the variation in fragmentation pattern with temperature and the pattern of the curve

M. F. Butman; A. A. Smirnov; L. S. Kudin; Z. A. Munir

2000-01-01

237

Growth and characterization of InP ringlike quantum-dot molecules grown by solid-source molecular beam epitaxy.  

PubMed

In this paper, we have studied the fabrication of InP ringlike quantum-dot molecules on GaAs(001) substrate grown by solid-source molecular beam epitaxy using droplet epitaxy technique and the effect of In deposition rate on the physical and optical properties of InP ringlike quantum-dot molecules. The In deposition rate is varied from 0.2 ML/s to 0.4, 0.8 and 1.6 ML/s. The surface morphology and cross-section were examined by ex-situ atomic force microscope and transmission electron microscope, respectively. The increasing of In deposition rate results in the decreasing of outer and inner diameters of InP ringlike quantum-dot molecules and height of InP quantum dots but increases the InP quantum dot and ringlike quantum-dot molecule densities. The photoluminescence peaks of InP ringlike quantum-dot molecules are blue-shifted and FWHM is narrower when In deposition rate is bigger. PMID:21137917

Jevasuwan, Wipakorn; Boonpeng, Poonyasiri; Panyakeow, Somsak; Ratanathammaphan, Somchai

2010-11-01

238

Molecular nanopolaritonics: cross manipulation of near-field plasmons and molecules. I. Theory and application to junction control.  

PubMed

Near-field interactions between plasmons and molecules are treated in a simple unified approach. The density matrix of a molecule is treated with linear-response random phase approximation and the plasmons are treated classically. The equations of motion for the combined system are linear, governed by a simple Liouvillian operator for the polariton (plasmon+molecule excitation) dynamics. The dynamics can be followed in time or directly in frequency space where a trace formula for the transmission is presented. A model system is studied, metal dots in a forklike arrangement, coupled to a two level system with a large transition-dipole moment. A Fano-type resonance [Phys. Rev. 103, 1202 (1956)] develops when the molecular response is narrower than the width of the absorption spectrum for the plasmons. We show that the direction of the dipole of the molecule determines the direction the polariton chooses. Further, the precise position of the molecule has a significant effect on the transfer. PMID:17949199

Neuhauser, Daniel; Lopata, Kenneth

2007-10-21

239

Density functional theory based molecular dynamics simulations of C70O3 doped with light molecules  

NASA Astrophysics Data System (ADS)

We demonstrate that light molecules such as H2, N2, H2O, NH3, BH3, CH4, and HCl can move freely inside C70 in the space roughly defined between planes of d-type carbon atoms. Contrary to that, two H2 molecules, when inserted into C70, do not cross the equatorial plane of the fullerene. The enthalpy of the ozone ring opening in C70O3 monoozonide doped with light molecules depends little on the identity of the guest. Surprisingly, two H2 molecules inside the cage modify the relative stability of the C70O3 isomer series by some 3.5 kcal mol-1.

Bil, Andrzej; Latajka, Zdzis?aw; Morrison, Carole A.

2014-01-01

240

Molecular modelling studies and the chromatographic behaviour of oxiracetam and some closely related molecules.  

PubMed

Modelling studies have been carried out on the cellulose-based chiral stationary phase used to separate the enantiomers of three simple lactams. These studies have helped in understanding differences in the chromatographic behaviour of these molecules. PMID:1795177

Camilleri, P; Murphy, J A; Saunders, M R; Thorpe, C J

1991-08-01

241

Molecular modelling studies and the chromatographic behaviour of oxiracetam and some closely related molecules  

Microsoft Academic Search

Modelling studies have been carried out on the cellulose-based chiral stationary phase used to separate the enantiomers of three simple lactams. These studies have helped in understanding differences in the chromatographic behaviour of these molecules.

Patrick Camilleri; Jose A. Murphy; Martin R. Saunders; Christopher J. Thorpe

1991-01-01

242

The Distribution of Complex Organic Molecules in the Orion KL Molecular Core  

NASA Technical Reports Server (NTRS)

We conducted high angular-resolution observations toward the massive star-forming region Orion KL at 1.3 mm using the Submillimeter Array (SMA). Spectral emission from twelve complex organic molecules was simultaneously imaged. We discuss the distinct chemical characteristics among four sub- regions in Orion KL by comparing the spatial distributions and fractional abundances of these complex molecules. These observations will allow us to test and constrain chemical models of interstellar organic synthesis.

Kuan, Yi-Jehng; Hsu, Yu-Sen; Charnley, Steven B.; Wang, Kuo-Song

2011-01-01

243

Flexible molecular-scale electronic devices composed of diarylethene photoswitching molecules.  

PubMed

The electrical properties of diarylethene photoswitching molecular devices on flexible substrates are studied. When exposed to UV or visible light, diarylethene molecular devices show two electrical states (a high and a low conductance state) with a discrepancy of an order of magnitude in the level of current between the two states. The diarylethene flexible molecular devices exhibit excellent long-time stability and reliable electrical characteristics in both conductance states when subjected to various mechanical stresses. PMID:24687399

Kim, Dongku; Jeong, Hyunhak; Lee, Hanki; Hwang, Wang-Taek; Wolf, Jannic; Scheer, Elke; Huhn, Thomas; Jeong, Heejun; Lee, Takhee

2014-06-01

244

Oligogalacturonides: plant damage-associated molecular patterns and regulators of growth and development  

PubMed Central

Oligogalacturonides (OGs) are oligomers of alpha-1,4-linked galacturonosyl residues released from plant cell walls upon partial degradation of homogalacturonan. OGs are able to elicit defense responses, including accumulation of reactive oxygen species and pathogenesis-related proteins, and protect plants against pathogen infections. Recent studies demonstrated that OGs are perceived by wall-associated kinases and share signaling components with microbe-associated molecular patterns. For this reason OGs are now considered true damage-associated molecular patterns that activate the plant innate immunity and may also be involved in the activation of responses to mechanical wounding. Furthermore, OGs appear to modulate developmental processes, likely through their ability to antagonize auxin responses. Here we review our current knowledge on the role and mode of action of this class of oligosaccharides in plant defense and development.

Ferrari, Simone; Savatin, Daniel V.; Sicilia, Francesca; Gramegna, Giovanna; Cervone, Felice; Lorenzo, Giulia De

2013-01-01

245

Noncanonical hydrogen bonding in nucleic acids. Benchmark evaluation of key base-phosphate interactions in folded RNA molecules using quantum-chemical calculations and molecular dynamics simulations.  

PubMed

RNA molecules are stabilized by a wide range of noncanonical interactions that are not present in DNA. Among them, the recently classified base-phosphate (BPh) interactions belong to the most important ones. Twelve percent of nucleotides in the ribosomal crystal structures are involved in BPh interactions. BPh interactions are highly conserved and provide major constraints on RNA sequence evolution. Here we provide assessment of the energetics of BPh interactions using MP2 computations extrapolated to the complete basis set of atomic orbitals and corrected for higher-order electron correlation effects. The reference computations are compared with DFT-D and DFT-D3 approaches, the SAPT method, and the molecular mechanics force field. The computations, besides providing the basic benchmark for the BPh interactions, allow some refinements of the original classification, including identification of some potential doubly bonded BPh patterns. The reference computations are followed by analysis of some larger RNA fragments that consider the context of the BPh interactions. The computations demonstrate the complexity of interaction patterns utilizing the BPh interactions in real RNA structures. The BPh interactions are often involved in intricate interaction networks. We studied BPh interactions of protonated adenine that can contribute to catalysis of hairpin ribozyme, the key BPh interaction in the S-turn motif of the sarcin-ricin loop, which may predetermine the S-turn topology and complex BPh patterns from the glmS riboswitch. Finally, the structural stability of BPh interactions in explicit solvent molecular dynamics simulations is assessed. The simulations well preserve key BPh interactions and allow dissection of structurally/functionally important water-meditated BPh bridges, which could not be considered in earlier bioinformatics classification of BPh interactions. PMID:21910417

Zgarbová, Marie; Jure?ka, Petr; Banáš, Pavel; Otyepka, Michal; Sponer, Judit E; Leontis, Neocles B; Zirbel, Craig L; Sponer, Ji?í

2011-10-20

246

How do molecular marker patterns of BC change at increasing age of chars?  

NASA Astrophysics Data System (ADS)

Black carbon (BC) is considered to be a relatively stable form of organic carbon. However, previous results have shown that the physical and chemical properties of BC can vary considerably with formation temperature. Thus, to understand the long-term carbon sink potential of BC there is increasing interest to gain more information about i) the conditions under which BC was formed, and ii) the resulting degradability of BC under natural conditions. In a first step, we synthesised chars from two different sources of biomass (chestnut wood, rice straw) under well-defined conditions as model substances to analyse the changes in their molecular structure at increasing formation temperature. Results are presented obtained from a set of laboratory produced char samples pyrolysed at increasing temperatures with a high resolution between 200 and 1000 °C. The chars were characterized by a molecular marker method for pyrogenic carbon quantification, which additionally provides information about the degree of condensation of chars. At temperatures between 275 and 500°C, which typically are observed during wildfires and thus are relevant for natural char formation, the molecular marker pattern of the chars remains almost constant. In a next step, we analysed changes in the molecular marker patterns of chars from a chronosequence, with BC deposited between 0 and 100 years ago. Based on the data obtained from the laboratory char series, we compare changes in the molecular marker patterns of the chars from the chronosequence over time. These results show if less condensed forms of BC are degraded preferentially and more condensed, aromatic backbone of BC becomes enriched in the soils with time of degradation. Our results provide information about the fate of BC in the environment, which has important implications in the context of carbon sequestration strategies.

Schneider, M. P. W.; Hilf, M.; Schmidt, M. W. I.

2009-04-01

247

Expression pattern of the adhesion molecule CEACAM1 (C-CAM, CD66a, BGP) in gestational trophoblastic lesions.  

PubMed

CEACAM1 (CD66a, BGP, C-CAM) is an adhesion molecule of the carcinoembryonic antigen (CEA) family which has been shown to be normally expressed at the apical pole of epithelial cells and to show a dysregulated expression pattern in tumors derived from the latter. The purpose of the present study was to investigate the expression pattern of CEACAM1 in gestational trophoblastic lesions and to compare this expression with the one observed in the normal trophoblast. For this purpose, we performed immunohistochemistry using the 4D1/C2 monoclonal antibody which specifically recognizes CEACAM1 and does not interact with other members of the CEA family. Immunohistochemistry was performed on a total of 20 cases of gestational trophoblastic lesions including complete hydatidiform moles, one placental site trophoblastic nodule (PSN), one placental site trophoblastic tumor (PSTT), and three choriocarcinomas. Immunostaining for cytokeratin, hPL, hCG, and Ki-67 was also performed. Normal placental samples served as a control. CEACAM1 was absent from villous cyto- and syncytiotrophoblast in both normal placenta and hydatidiform molar samples. It was present in the benign extravillous trophoblast, with stronger expression in the proximal extravillous trophoblast of anchoring villi, but was also observed in interstitial and endovascular intermediate trophoblast and chorionic intermediate-like trophoblast. Partial expression was observed in the trophoblast proliferating from the surface of molar villi. In choriocarcinomas, areas of weak expression could be observed along with large areas without CEACAM1 expression. In the PSN and especially in the PSTT, CEACAM1 expression was stronger and more diffuse. The specific localization to extravillous trophoblast and its expression pattern in gestational trophoblastic lesions indicate that CEACAM1 can potentially be a helpful additional diagnostic marker in the differential diagnosis of such lesions. PMID:11293162

Bamberger, A M; Sudahl, S; Wagener, C; Löning, T

2001-04-01

248

Extended molecular Ornstein-Zernike integral equation for fully anisotropic solute molecules: Formulation in a rectangular coordinate system  

NASA Astrophysics Data System (ADS)

An extended molecular Ornstein-Zernike (XMOZ) integral equation is formulated to calculate the spatial distribution of solvent around a solute of arbitrary shape and solid surfaces. The conventional MOZ theory employs spherical harmonic expansion technique to treat the molecular orientation of components of solution. Although the MOZ formalism is fully exact analytically, the truncation of the spherical harmonic expansion requires at a finite order for numerical calculation and causes the significant error for complex molecules. The XMOZ integral equation is the natural extension of the conventional MOZ theory to a rectangular coordinate system, which is free from the truncation of spherical harmonic expansion with respect to solute orientation. In order to show its applicability, we applied the XMOZ theory to several systems using the hypernetted-chain (HNC) and Kovalenko-Hirata approximations. The quality of results obtained within our theory is discussed by comparison with values from the conventional MOZ theory, molecular dynamics simulation, and three-dimensional reference interaction site model theory. The spatial distributions of water around the complex of non-charged sphere and dumbbell were calculated. Using this system, the approximation level of the XMOZ and other methods are discussed. To assess our theory, we also computed the excess chemical potentials for three realistic molecules (water, methane, and alanine dipeptide). We obtained the qualitatively reasonable results by using the XMOZ/HNC theory. The XMOZ theory covers a wide variety of applications in solution chemistry as a useful tool to calculate solvation thermodynamics.

Ishizuka, Ryosuke; Yoshida, Norio

2013-08-01

249

First Principles Study and Theoretical Analysis of a Single Molecular Diode by p-n di-block molecules  

NASA Astrophysics Data System (ADS)

The concept of a single molecular diode was first proposed by Aviram and Ratner, and there have been many studies of synthesis D-?-A or p-n di-block molecules and measurements of the current-voltage (I-V) characteristics for relating molecular junctions. Recently, the I-V measurement in a symmetric tetraphenyl junction and non-symmetric dipyrimidinyl -diphenyl diblock junction was performed, and clear rectification was found in the latter system, which resembles the p-n junction by the covalent connection between electron-deficient bypyrimidinyl and electron-rich biphenyl moieties, though an applied bias is much lower than the resonant level. In this presentation, we performed the first principles calculations of electron transport for the above tetraphenyl and dipyrimidinyl -diphenyl diblock junctions by the self-consistent nonequilibrium Green's function theory with the use of our HiRUNE program module. We carried out the systematic analysis of the rectification behavior and identified the change of electron-pathway in the bridge molecule relating to p-n junction based on the first principles data. The relation between the rectifying action and molecular conformation, particularly, the torsion of diblock, will be discussed.

Nakamura, Hisao; Asai, Yoshihiro; Hihath, Josh; Tao, Nongjian

2011-03-01

250

Extended molecular Ornstein-Zernike integral equation for fully anisotropic solute molecules: formulation in a rectangular coordinate system.  

PubMed

An extended molecular Ornstein-Zernike (XMOZ) integral equation is formulated to calculate the spatial distribution of solvent around a solute of arbitrary shape and solid surfaces. The conventional MOZ theory employs spherical harmonic expansion technique to treat the molecular orientation of components of solution. Although the MOZ formalism is fully exact analytically, the truncation of the spherical harmonic expansion requires at a finite order for numerical calculation and causes the significant error for complex molecules. The XMOZ integral equation is the natural extension of the conventional MOZ theory to a rectangular coordinate system, which is free from the truncation of spherical harmonic expansion with respect to solute orientation. In order to show its applicability, we applied the XMOZ theory to several systems using the hypernetted-chain (HNC) and Kovalenko-Hirata approximations. The quality of results obtained within our theory is discussed by comparison with values from the conventional MOZ theory, molecular dynamics simulation, and three-dimensional reference interaction site model theory. The spatial distributions of water around the complex of non-charged sphere and dumbbell were calculated. Using this system, the approximation level of the XMOZ and other methods are discussed. To assess our theory, we also computed the excess chemical potentials for three realistic molecules (water, methane, and alanine dipeptide). We obtained the qualitatively reasonable results by using the XMOZ/HNC theory. The XMOZ theory covers a wide variety of applications in solution chemistry as a useful tool to calculate solvation thermodynamics. PMID:24006986

Ishizuka, Ryosuke; Yoshida, Norio

2013-08-28

251

The inherent dynamics of a molecular liquid: Geodesic pathways through the potential energy landscape of a liquid of linear molecules  

NASA Astrophysics Data System (ADS)

Because the geodesic pathways that a liquid follows through its potential energy landscape govern its slow, diffusive motion, we suggest that these pathways are logical candidates for the title of a liquid's "inherent dynamics." Like their namesake "inherent structures," these objects are simply features of the system's potential energy surface and thus provide views of the system's structural evolution unobstructed by thermal kinetic energy. This paper shows how these geodesic pathways can be computed for a liquid of linear molecules, allowing us to see precisely how such molecular liquids mix rotational and translational degrees of freedom into their dynamics. The ratio of translational to rotational components of the geodesic path lengths, for example, is significantly larger than would be expected on equipartition grounds, with a value that scales with the molecular aspect ratio. These and other features of the geodesics are consistent with a picture in which molecular reorientation adiabatically follows translation—molecules largely thread their way through narrow channels available in the potential energy landscape.

Jacobson, Daniel; Stratt, Richard M.

2014-05-01

252

High-resolution single-molecule recognition imaging of the molecular details of ricin-aptamer interaction.  

PubMed

We studied the molecular details of DNA aptamer-ricin interactions. The toxic protein ricin molecules were immobilized on a Au(111) surface using a N-hydroxysuccinimide (NHS) ester to specifically react with lysine residues located on the ricin B chains. A single ricin molecule was visualized in situ using the AFM tip modified with an antiricin aptamer. Computer simulation was used to illustrate the protein and aptamer structures, the single-molecule ricin images on a Au(111) surface, and the binding conformations of ricin-aptamer and ricin-antibody complexes. The various ricin conformations on a Au(111) surface were caused by the different lysine residues reacting with the NHS ester. It was also observed that most of the binding sites for aptamer and antibody on the A chains of ricin molecules were not interfered by the immobilization reaction. The different locations of the ricin binding sites to aptamer and antibody were also distinguished by AFM recognition images and interpreted by simulations. PMID:22489938

Wang, Bin; Guo, Cunlan; Zhang, Mengmeng; Park, Bosoon; Xu, Bingqian

2012-05-01

253

Array Formatting of the Heat-Transfer Method (HTM) for the Detection of Small Organic Molecules by Molecularly Imprinted Polymers  

PubMed Central

In this work we present the first steps towards a molecularly imprinted polymer (MIP)-based biomimetic sensor array for the detection of small organic molecules via the heat-transfer method (HTM). HTM relies on the change in thermal resistance upon binding of the target molecule to the MIP-type receptor. A flow-through sensor cell was developed, which is segmented into four quadrants with a volume of 2.5 ?L each, allowing four measurements to be done simultaneously on a single substrate. Verification measurements were conducted, in which all quadrants received a uniform treatment and all four channels exhibited a similar response. Subsequently, measurements were performed in quadrants, which were functionalized with different MIP particles. Each of these quadrants was exposed to the same buffer solution, spiked with different molecules, according to the MIP under analysis. With the flow cell design we could discriminate between similar small organic molecules and observed no significant cross-selectivity. Therefore, the MIP array sensor platform with HTM as a readout technique, has the potential to become a low-cost analysis tool for bioanalytical applications.

Wackers, Gideon; Vandenryt, Thijs; Cornelis, Peter; Kellens, Evelien; Thoelen, Ronald; De Ceuninck, Ward; Losada-Perez, Patricia; van Grinsven, Bart; Peeters, Marloes; Wagner, Patrick

2014-01-01

254

Array Formatting of the Heat-Transfer Method (HTM) for the Detection of Small Organic Molecules by Molecularly Imprinted Polymers.  

PubMed

In this work we present the first steps towards a molecularly imprinted polymer (MIP)-based biomimetic sensor array for the detection of small organic molecules via the heat-transfer method (HTM). HTM relies on the change in thermal resistance upon binding of the target molecule to the MIP-type receptor. A flow-through sensor cell was developed, which is segmented into four quadrants with a volume of 2.5 ?L each, allowing four measurements to be done simultaneously on a single substrate. Verification measurements were conducted, in which all quadrants received a uniform treatment and all four channels exhibited a similar response. Subsequently, measurements were performed in quadrants, which were functionalized with different MIP particles. Each of these quadrants was exposed to the same buffer solution, spiked with different molecules, according to the MIP under analysis. With the flow cell design we could discriminate between similar small organic molecules and observed no significant cross-selectivity. Therefore, the MIP array sensor platform with HTM as a readout technique, has the potential to become a low-cost analysis tool for bioanalytical applications. PMID:24955945

Wackers, Gideon; Vandenryt, Thijs; Cornelis, Peter; Kellens, Evelien; Thoelen, Ronald; De Ceuninck, Ward; Losada-Pérez, Patricia; van Grinsven, Bart; Peeters, Marloes; Wagner, Patrick

2014-01-01

255

The non-covalent nature of the molecular structure of the benzene molecule.  

PubMed

The benzene molecule is one of the most emblematic systems in chemistry, with its structural features being present in numerous different compounds. We have carried out an analysis of the influence of quantum mechanical interference on the geometric features of the benzene molecule, showing that many of the characteristics of its equilibrium geometry are a consequence of non-covalent contributions to the energy. This result implies that quasi-classical reasoning should be sufficient to predict the defining aspects of the benzene structure such as its planarity and equivalence of its bond lengths. PMID:24779029

Cardozo, Thiago Messias; Fantuzzi, Felipe; Nascimento, Marco Antonio Chaer

2014-06-14

256

Ab initio and semi-empirical Molecular Dynamics simulations of chemical reactions in isolated molecules and in clusters.  

PubMed

Recent progress in "on-the-fly" trajectory simulations of molecular reactions, using different electronic structure methods is discussed, with analysis of the insights that such calculations can provide and of the strengths and limitations of the algorithms available. New developments in the use of both ab initio and semi-empirical electronic structure algorithms are described. The emphasis is on: (i) calculations of electronic properties along the reactive trajectories and the unique insights this can contribute to the processes; (ii) electronic structure methods recently introduced to this topic to improve accuracy, extend applicability or enhance computational efficiency. The methods are presented with examples, including new results, of reactions of both isolated molecules and of molecules in media, mostly clusters. Possible future directions for this fast growing field are suggested. PMID:24569494

Gerber, R B; Shemesh, D; Varner, M E; Kalinowski, J; Hirshberg, B

2014-06-01

257

Strigolactone analogs as molecular probes in chasing the (SLs) receptor/s: design and synthesis of fluorescent labeled molecules.  

PubMed

Originally identified as allelochemicals involved in plant-parasite interactions, more recently, Strigolactones (SLs) have been shown to play multiple key roles in the rhizosphere communication between plants and mycorrhizal fungi. Even more recent is the hormonal role ascribed to SLs which broadens the biological impact of these relatively simple molecules. In spite of the crucial and multifaceted biological role of SLs, there are no data on the receptor(s) which bind(s) such active molecules, neither in the producing plants nor in parasitic weeds or AM fungi. Information about the putative receptor of SLs can be gathered by means of structural, molecular, and genetic approaches. Our contribution on this topic is the design and synthesis of fluorescent labeled SL analogs to be used as probes for the detection in vivo of the receptor(s). Knowledge of the putative receptor structure will boost the research on analogs of the natural substrates as required for agricultural applications. PMID:23180673

Prandi, Cristina; Rosso, Helèna; Lace, Beatrice; Occhiato, Ernesto G; Oppedisano, Alberto; Tabasso, Silvia; Alberto, Gabriele; Blangetti, Marco

2013-01-01

258

Method and system of computing and rendering the nature of the chemical bond of hydrogen-type molecules and molecular ions  

US Patent & Trademark Office Database

Provided is a system of computing and rendering a nature of a chemical bond based on physical, Maxwellian solutions of charge, mass, and current density functions of hydrogen-type molecules and molecular ions. The system includes a processor for processing Maxwellian equations representing charge, mass, and current density functions of hydrogen-type molecules and molecular ions and an output device in communication with the processor for displaying the nature of the chemical bond.

2007-03-06

259

A molecular method for the delivery of small molecules and proteins across the cell wall of algae using molecular transporters  

PubMed Central

Interest in algae has significantly accelerated with the increasing recognition of their potentially unique role in medical, materials, energy, bioremediation, and synthetic biological research. However, the introduction of tools to study, control, or expand the inner-workings of algae has lagged behind. Here we describe a general molecular method based on guanidinium-rich molecular transporters (GR-MoTrs) for bringing small and large cargos into algal cells. Significantly, this method is shown to work in wild-type algae that have an intact cell wall. Developed using Chlamydomonas reinhardtii, this method is also successful with less studied algae including Neochloris oleoabundans and Scenedesmus dimorphus thus providing a new and versatile tool for algal research.

Hyman, Joel M.; Geihe, Erika I.; Trantow, Brian M.; Parvin, Bahram; Wender, Paul A.

2012-01-01

260

Patterns  

NSDL National Science Digital Library

Directions: Play the games that are listed. Do not go to another site. Be sure to take turns with your partner. First, learn to complete a pattern by playing "Which One?." Next, keep practicing patterns by playing "Pattern Mania." Finally, determine what type of pattern each set is by playing "Which pattern is it?." ...

Hinson, Mrs.

2011-10-03

261

Design and development of a field-deployable single-molecule detector (SMD) for the analysis of molecular markers†  

PubMed Central

Single-molecule detection (SMD) has demonstrated some attractive benefits for many types of biomolecular analyses including enhanced processing speed by eliminating processing steps, elimination of ensemble averaging and single-molecule sensitivity. However, it's wide spread use has been hampered by the complex instrumentation required for its implementation when using fluorescence as the readout modality. We report herein a simple and compact fluorescence single-molecule instrument that is straightforward to operate and consisted of fiber optics directly coupled to a microfluidic device. The integrated fiber optics served as waveguides to deliver the laser excitation light to the sample and collecting the resulting emission, simplifying the optical requirements associated with traditional SMD instruments by eliminating the need for optical alignment and simplification of the optical train. Additionally, the use of a vertical cavity surface emitting laser and a single photon avalanche diode serving as the excitation source and photon transducer, respectively, as well as a field programmable gate array (FPGA) integrated into the processing electronics assisted in reducing the instrument footprint. This small footprint SMD platform was tested using fluorescent microspheres and single AlexaFluor 660 molecules to determine the optimal operating parameters and system performance. As a demonstration of the utility of this instrument for biomolecular analyses, molecular beacons (MBs) were designed to probe bacterial cells for the gene encoding Gram-positive species. The ability to monitor biomarkers using this simple and portable instrument will have a number of important applications, such as strain-specific detection of pathogenic bacteria or the molecular diagnosis of diseases requiring rapid turn-around-times directly at the point-of-use.

Emory, Jason M.; Peng, Zhiyong; Young, Brandon; Hupert, Mateusz L.; Rousselet, Arnold; Patterson, Donald; Ellison, Brad; Soper, Steven A.

2012-01-01

262

'Molecules and monkeys': George Gaylord Simpson and the challenge of molecular evolution.  

PubMed

In this paper, I analyze George Gaylord Simpson's response to the molecularization of evolutionary biology from his unique perspective as a paleontologist. I do so by exploring his views on early attempts to reconstruct phylogenetic relationships among primates using molecular data. Particular attention is paid to Simpson's role in the evolutionary synthesis of the 1930s and 1940s, as well as his concerns about the rise of molecular biology as a powerful discipline and world-view in the 1960s. I argue that Simpson's belief in the supremacy of natural selection as the primary driving force of evolution, as well as his view that biology was a historical science that seeks ultimate causes and highlights contingency, prevented him from acknowledging that the study of molecular evolution was an inherently valuable part of the life sciences. PMID:15045833

Aronson, Jay D

2002-01-01

263

Templating effects in molecular growth of blended films for efficient small-molecule photovoltaics.  

PubMed

A strategy to control the molecular growth of coevaporated zinc phthalocyanine (ZnPc) and fullerene (C60) blended films for efficient organic photovoltaic (OPV) cells was demonstrated. Introduction of a 2,5-bis(4-biphenylyl)-bithiophene (BP2T) film or a ZnPc film on BP2T as nanostructured templates not only results in phase-separated domains in blended films with clear interpenetrating networks but also improves the crystallinity of ZnPc domains, both of which enhance photocurrent generation and charge carrier transport. Such morphology is strongly associated with the molecular growth of the templating layers. Roughness and adhesion of the templating layers are of great importance for the molecular growth of the blended films and in turn for cell characteristics. By carefully regulating the molecular growth of the blended films, the power conversion efficiency was improved by 125%, from 1.85 to 4.15% under 1 sun. PMID:24712371

Wang, Zhiping; Miyadera, Tetsuhiko; Yamanari, Toshihiro; Yoshida, Yuji

2014-05-14

264

Ion and molecule sensors using molecular recognition in luminescent, conductive polymers. 1998 annual progress report.  

National Technical Information Service (NTIS)

The purpose of this project is to develop sensor technology for detecting specific heavy metal ions, such as transition metals, lead, lanthanides, and actinides in waste streams. The sensing strategy uses molecular recognition of the metal ions by polymer...

K. Raymond D. E. Walt M. R. Wasielewski

1998-01-01

265

Reconciling patterns of inter-ocean molecular variance from four classes of molecular markers in blue marlin (Makaira nigricans).  

PubMed

Different classes of molecular markers occasionally yield discordant views of population structure within a species. Here, we examine the distribution of molecular variance from 14 polymorphic loci comprising four classes of molecular markers within approximately 400 blue marlin individuals (Makaira nigricans). Samples were collected from the Atlantic and Pacific Oceans over 5 years. Data from five hypervariable tetranucleotide microsatellite loci and restriction fragment length polymorphism (RFLP) analysis of whole molecule mitochondrial DNA (mtDNA) were reported and compared with previous analyses of allozyme and single-copy nuclear DNA (scnDNA) loci. Temporal variance in allele frequencies was nonsignificant in nearly all cases. Mitochondrial and microsatellite loci revealed striking phylogeographic partitioning among Atlantic and Pacific Ocean samples. A large cluster of alleles was present almost exclusively in Atlantic individuals at one microsatellite locus and for mtDNA, suggesting that, if gene flow occurs, it is likely to be unidirectional from Pacific to Atlantic oceans. Mitochondrial DNA inter-ocean divergence (FST) was almost four times greater than microsatellite or combined nuclear divergences including allozyme and scnDNA markers. Estimates of Neu varied by five orders of magnitude among marker classes. Using mathematical and computer simulation approaches, we show that substantially different distributions of FST are expected from marker classes that differ in mode of inheritance and rate of mutation, without influence of natural selection or sex-biased dispersal. Furthermore, divergent FST values can be reconciled by quantifying the balance between genetic drift, mutation and migration. These results illustrate the usefulness of a mitochondrial analysis of population history, and relative precision of nuclear estimates of gene flow based on a mean of several loci. PMID:11380876

Buonaccorsi, V P; McDowell, J R; Graves, J E

2001-05-01

266

Molecular dynamics of point mutated IA k molecules expressed on lymphocytes  

Microsoft Academic Search

We have recently reported the lateral and rotational diffusion parameters for I-Ak molecules expressing various cytoplasmic truncations (Int. Immunol. 12 (2000) 1319). We now describe the membrane dynamics of I-Ak with various mutations in the presumed contact region between ??-heterodimers in an (??)2 dimer of dimers structure. Such mutations are known to strongly affect the antigen presentation ability of these

Heidi M Munnelly; Cynthia J Brady; Guy M Hagen; Regina D Horvat; William F Wade; Deborah A Roess; B. George Barisas

2001-01-01

267

Initiating Molecular Growth in the Interstellar Medium via Dimeric Complexes of Observed Ions and Molecules.  

National Technical Information Service (NTIS)

A feasible initiation step for particle growth in the interstellar medium (ISM) is simulated by means of ab quantum chemistry methods. The systems studied are dimer ions formed by pairing nitrogen containing small molecules known to exist in the ISM with ...

M. Head-Gordon P. P. Bera T. J. Lee

2011-01-01

268

Molecular and functional characterization of granulin-like molecules of insects  

Microsoft Academic Search

Granulins are a group of highly conserved growth factors that have been described from a variety of organisms spanning the metazoa. Here, we report on the identification of two partial transcripts encoding granulin-like molecules from Aa23 embryonic cells of Aedes albopictus and primary haemocytes from Manduca sexta. Both these partial transcripts had the characteristic 12-cysteine motif that is a hallmark

Patrick C. Hanington; Lesley J. Brennan; Miodrag Belosevic; B. Andrew Keddie

2008-01-01

269

A molecular dynamics study of the structure of a model Langmuir monolayer of amphiphile molecules  

Microsoft Academic Search

We study the thermodynamics and structure of a model monomolecular film of pentadecanoic acid on water. In this model the water is treated as a uniform polarizable continuum and the pentadecanoic acid molecules as chains of 15 pseudoatom with internal bond constraints, angle bending and torsional intramolecular interactions, and Lennard-Jones atom–atom intermolecular interactions. The only low pressure phases exhibited by

Jonathan Harris; Stuart A. Rice

1988-01-01

270

Self-Assembled Chiral Superstructures Composed of Rigid Achiral Molecules and Molecular Scale Chiral Induction by Dopants  

NASA Astrophysics Data System (ADS)

We explore the phase behavior of a rigid achiral bent-core model system. Nematic and smectic phases form at higher densities, whereas micelles and columns composed of chiral clusters of these molecules self-assemble at lower densities. No nucleation mechanism requiring transient chirality is possible in the formation of these chiral superstructures due to the rigid achiral nature of the substituents. We show the chiral micelles are minima of the potential energy surface using energy minimization and parallel tempering simulations. Chiral dopants were found to induce the system to adopt a consistent chiral twist direction, the first molecular scale computer simulation of this effect.

Yan, Fangyong; Hixson, Christopher Adam; Earl, David J.

2008-10-01

271

Dynamic properties of individual water molecules in a hydrophobic pore lined with acyl chains: a molecular dynamics study.  

PubMed

Recently, a certain class of synthetic molecules has been shown to form ion channels, the pore of which is lined with hydrophobic acyl chains [M. Sokabe, in: F. Oosawa, H. Hayashi, T. Yoshioka (Eds.), Transmembrane Signaling and Sensation, JSSP/VNU Science Press BV, Tokyo, 1984, p. 119; F. Hayashi, M. Sokabe, M. Takagi, K. Hayashi, U. Kishimoto, Biochim. Biophys. Acta, 510 (1978) 305; M.J. Pregel, L. Jullien, J. Canceill, L. Lacombe, J.M. Lehn, J. Chem. Soc. Perkin Trans., 2 (1995) 417; Y. Tanaka, Y. Kobuke, M. Sokabe, Angew. Chem. Int. Ed. Engl., 34 (1995) 693; M. Sokabe, Z. Qi, K. Donowaki, H. Ishida, K. Okubo, Biophys. J., 70 (1996) A201; H. Ishida, K. Donowaki, Y. Inoue, Z. Qi, M. Sokabe, Chem. Lett. (1997) p. 953]. As an initial step towards understanding the physical mechanisms of ion permeation across such a hydrophobic pore, systematic molecular dynamics simulations were performed to investigate dynamic and energetic properties of water molecules inside the pore using a dimer of alanine-N'-acylated cyclic peptide as a channel model. Dynamic energy profiles for water molecules indicated that the energy barrier at the middle region of the pore is approximately 2-3 kcal/mol higher than that in the cap water region which was defined as a vicinity region of the channel entrance. Energetics analyses demonstrated that the mutual interactions among intrapore water molecules are the major factor to give favorable interaction (negative energy contribution) for themselves. The pore, despite being lined with acyl chains, has a favorable van der Waals interaction with intrapore water molecules. These results may help to explain why water-filled channels can be formed by the hydrophobic helices in natural channels. PMID:17027452

Qi, Z; Sokabe, M

1998-03-30

272

Modeling Molecules  

NASA Technical Reports Server (NTRS)

The molecule modeling method known as Multibody Order (N) Dynamics, or MBO(N)D, was developed by Moldyn, Inc. at Goddard Space Flight Center through funding provided by the SBIR program. The software can model the dynamics of molecules through technology which stimulates low-frequency molecular motions and properties, such as movements among a molecule's constituent parts. With MBO(N)D, a molecule is substructured into a set of interconnected rigid and flexible bodies. These bodies replace the computation burden of mapping individual atoms. Moldyn's technology cuts computation time while increasing accuracy. The MBO(N)D technology is available as Insight II 97.0 from Molecular Simulations, Inc. Currently the technology is used to account for forces on spacecraft parts and to perform molecular analyses for pharmaceutical purposes. It permits the solution of molecular dynamics problems on a moderate workstation, as opposed to on a supercomputer.

2000-01-01

273

Two distinct porcine natural killer lytic trigger molecules as PNK-E/G7 molecular complex.  

PubMed

PNK-E and G7 mAbs regulate porcine NK and ADCC activities by binding to distinct NK function-associated trigger molecules on porcine NK cells. Previous work demonstrates that PNK-E mAb binds to a 205-kDa tetrameric molecule composed of two 47-kDa peptides and two 50-kDa peptides and G7 mAb binds to a distinct 40-kDa heterodispersed monomeric peptide on porcine NK cells. The data presented herein demonstrate that all PNK-E+ PBLs are G7+ and all G7+ PBLs are PNK-E+ indicating that the PNK-E and G7 molecules are coexpressed by porcine NK cells. Bound G7 mAb blocks subsequent binding of PNK-E mAb but not the converse. Bound F(ab')2 G7 mAb abrogates the ability of whole PNK-E mAb to enhance NK activity but bound F(ab')2 PNK-E mAb has no affect on G7 mAb enhancement of NK activity. PNK-E mAb enhanced NK activity is inhibited by binding of F(ab')2 G7 mAb even though whole PNK-E mAb remains bound. However, bound F(ab')2 PNK-E mAb has no affect on G7 mAb-enhanced NK activity. When PNK-E and G7 mAbs were tested alone and together in NK assays, comparable levels of enhancement were observed. PNK-E and G7 hybridomas express surface mAb through which NK cells bind and specifically lyse these hybridomas. Lysis of PNK-E and G7 hybridomas is inhibited by pretreatment of PBLs with F(ab')2 G7 mAb. These data indicate a physical association between the PNK-E and G7 molecules on NK cells and suggest that the G7 molecule is external to the PNK-E molecule. PMID:8174170

Wierda, W G; Johnson, B D; Dato, M E; Kim, Y B

1993-02-01

274

Torsion-Inversion Tunneling Patterns in the Ch-Stretch Vibrationally Excited States of the G{_1}{_2} Molecules  

NASA Astrophysics Data System (ADS)

Torsion-inversion tunneling models have been developed for CH-stretch vibrationally excited states in G{_1}{_2} molecules, including 2-methylmalonaldehyde (2-MMA), 5-methyltropolone (5-MT), and methylamine. These models are extensions of the group theoretical approach of Hougen and the internal coordinate model of Wang and Perry in which the inversion motion is included in addition to the torsion and the small-amplitude (e.g., CH stretch) vibrations. The present models incorporate torsion-inversion tunneling parameters {_2}{_V} and {_3}{_V}, respectively and a number of low-order terms couplings to the CH-stretch vibrations. Of the three methyl CH stretch vibrations, Model I includes only the two asymmetric stretches that correlate to the E-type degenerate CH stretch in a symmetric rotor; Model II includes all three. The models yield the torsion-inversion tunneling patterns of the four symmetry species, A, B, E{_1} and E{_2}, in the CH-stretch excited states. The principal results are as follows. (i) Both models and each of the coupling terms considered yield the same tunneling patterns, which are different in the asymmetric CH stretch excited states as compared to those in the ground state. (ii) In Model I, the magnitude of the tunneling splittings in the two asymmetric CH stretch excited states is exactly half of that in the ground state. (iii) In Model II, the relative magnitude of these splittings depends on the ratio \\vert?\\vert/(\\vert{_2}{_V}\\vert+\\vert{_3}{_V}\\vert) where ? is the torsion-inversion-vibration coupling parameter. This ratio varies from 3 to 308 across the series methanol, methylamine, 2-methylmalonaldehyde and 5-methyltropolone, with a consequent variation in the magnitude of the tunneling splittings. J. T. HougenJ. Mol. Spectrosc. {207}, 60, (2001). X. Wang and D. S. PerryJ. Chem. Phys. {109}, 10795, (1998).

Dawadi, Mahesh B.; Bhatta, Ram S.; Perry, David S.

2013-06-01

275

Selectively recognizing organic semiconducting molecules on solid state molecular cages based on ZnOTCPP.  

PubMed

In this study, we constructed a novel solid state supramolecular system-the molecular cage ZnOTCPP, based on an inorganic/organic hybrid nanostructure, through the assembly of 5,10,15,20-tetra(3-carboxyphenyl)porphyrin (TCPP) onto the surfaces of ZnO nanorod (NR) arrays. The ZnOTCPP molecular cage exhibited highly selective recognition of 5,10,15,20-tetraphenylporphyrin (TPP) by optical and photoelectrical signals. The ZnOTCPP@TPP exhibited high emission efficiency, with a six-fold increase in the intensity of the emission relative to that of ZnOTCPP after the molecular cage ZnOTCPP captured TPP. The optical, electrical, and optoelectrical properties of the molecular cage ZnOTCPP could be controlled by tuning the interactions between the guest and the host's inorganic or organic moieties. Such a solid state molecular cage opens the door to controlled-delivery applications and provides an attractive platform for studying solid state supramolecular electronics and optoelectronics. PMID:24042322

Liu, Huibiao; Wang, Ke; Zhang, Liang; Qian, Xuemin; Li, Yongjun; Li, Yuliang

2014-01-14

276

Modeling Stochastic Kinetics of Molecular Machines at Multiple Levels: From Molecules to Modules  

PubMed Central

A molecular machine is either a single macromolecule or a macromolecular complex. In spite of the striking superficial similarities between these natural nanomachines and their man-made macroscopic counterparts, there are crucial differences. Molecular machines in a living cell operate stochastically in an isothermal environment far from thermodynamic equilibrium. In this mini-review we present a catalog of the molecular machines and an inventory of the essential toolbox for theoretically modeling these machines. The tool kits include 1), nonequilibrium statistical-physics techniques for modeling machines and machine-driven processes; and 2), statistical-inference methods for reverse engineering a functional machine from the empirical data. The cell is often likened to a microfactory in which the machineries are organized in modular fashion; each module consists of strongly coupled multiple machines, but different modules interact weakly with each other. This microfactory has its own automated supply chain and delivery system. Buoyed by the success achieved in modeling individual molecular machines, we advocate integration of these models in the near future to develop models of functional modules. A system-level description of the cell from the perspective of molecular machinery (the mechanome) is likely to emerge from further integrations that we envisage here.

Chowdhury, Debashish

2013-01-01

277

Phospholipid Membrane Protection by Sugar Molecules during Dehydration--Insights into Molecular Mechanisms Using Scattering Techniques  

PubMed Central

Scattering techniques have played a key role in our understanding of the structure and function of phospholipid membranes. These techniques have been applied widely to study how different molecules (e.g., cholesterol) can affect phospholipid membrane structure. However, there has been much less attention paid to the effects of molecules that remain in the aqueous phase. One important example is the role played by small solutes, particularly sugars, in protecting phospholipid membranes during drying or slow freezing. In this paper, we present new results and a general methodology, which illustrate how contrast variation small angle neutron scattering (SANS) and synchrotron-based X-ray scattering (small angle (SAXS) and wide angle (WAXS)) can be used to quantitatively understand the interactions between solutes and phospholipids. Specifically, we show the assignment of lipid phases with synchrotron SAXS and explain how SANS reveals the exclusion of sugars from the aqueous region in the particular example of hexagonal II phases formed by phospholipids.

Garvey, Christopher J.; Lenne, Thomas; Koster, Karen L.; Kent, Ben; Bryant, Gary

2013-01-01

278

Characterizing the Structure and Porosity of Organic Molecules of Intrinsic Microporosity by Molecular Simulations and Experiment  

NASA Astrophysics Data System (ADS)

Organic molecules of intrinsic microporosity (OMIMs) are amorphous, glassy solids that contain interconnected pores of sizes smaller than 2 nm. The philosophy behind OMIMs is similar to that of polymers of intrinsic microporosity (PIMs); rigid, awkwardly shaped molecules frustrate packing and form low density materials with intrinsically porous structures. Atomistic simulations were performed on OMIMs using our recently developed packing and compression procedure to study the effect of structure on packing behavior. The structure and porosity of the simulated samples were characterized, such as by surface areas and structure factors, and compared to experimental results. The presented computational procedure will further understanding of structure-property relationships and aid in the design of novel materials with high surface areas.

Abbott, Lauren J.; McDermott, Amanda G.; Del Regno, Annalaura; Msayib, Kadhum J.; Carta, Mariolino; Taylor, Rupert; McKeown, Neil B.; Siperstein, Flor R.; Runt, James; Colina, Coray M.

2011-03-01

279

Small molecule interaction with lipid bilayers: a molecular dynamics study of chlorhexidine.  

PubMed

Chlorhexidine (CHX) is an effective anti-bacterial agent whose mode of action is thought to be the disruption of the cell membrane. We tested the capability of the Slipids all atom force fields using data from neutron scattering and NMR experiments on the drug chlorhexidine in a 1,2-dimyrisoyl-3-sn-phosphatidylcholine (DMPC) membrane. Since it is not known what the charge of the CHX molecule is inside an apolar environment, a neutral, as well as a +1 and +2 charge model for the molecule were created and tested at several concentrations. This study shows that the location of CHX is minorly dependent on concentration, and dominantly reliant on the charge. The effect of adding CHX to DMPC is a thinning of the membrane, thus increasing the area per lipid. PMID:24440582

Van Oosten, Brad; Marquardt, Drew; Komljenovi?, Ivana; Bradshaw, Jeremy P; Sternin, Edward; Harroun, Thad A

2014-03-01

280

Phospholipid Membrane Protection by Sugar Molecules during Dehydration-Insights into Molecular Mechanisms Using Scattering Techniques.  

PubMed

Scattering techniques have played a key role in our understanding of the structure and function of phospholipid membranes. These techniques have been applied widely to study how different molecules (e.g., cholesterol) can affect phospholipid membrane structure. However, there has been much less attention paid to the effects of molecules that remain in the aqueous phase. One important example is the role played by small solutes, particularly sugars, in protecting phospholipid membranes during drying or slow freezing. In this paper, we present new results and a general methodology, which illustrate how contrast variation small angle neutron scattering (SANS) and synchrotron-based X-ray scattering (small angle (SAXS) and wide angle (WAXS)) can be used to quantitatively understand the interactions between solutes and phospholipids. Specifically, we show the assignment of lipid phases with synchrotron SAXS and explain how SANS reveals the exclusion of sugars from the aqueous region in the particular example of hexagonal II phases formed by phospholipids. PMID:23584028

Garvey, Christopher J; Lenné, Thomas; Koster, Karen L; Kent, Ben; Bryant, Gary

2013-01-01

281

Molecules in galaxies. IV - Molecular and atomic hydrogen in Virgo cluster galaxies  

NASA Technical Reports Server (NTRS)

If gas and dust are well mixed in a galaxy, the dust mass should be proportional to the sum of the masses of atomic and molecular gas. This assumption has been used to estimate the mean conversion ratio between the flux in the CO J = 1-0 line and the molecular gas mass of a galaxy using a set of observations of the 100 microns continuum flux density, the H I 21 cm line flux and the CO line flux for a sample of spiral galaxies in the Virgo cluster; these galaxies have a wide variation in the ratio of CO to H I line flux. The result, N(H2) = 6.3 + or - 3.5 x 10 to the 20th mol/sq cm/(K x km/s), is in agreement with values inferred from observations of the molecular interstellar medium in the Galaxy.

Knapp, G. R.; Helou, G.; Stark, A. A.

1987-01-01

282

Tissue organization by cadherin adhesion molecules: dynamic molecular and cellular mechanisms of morphogenetic regulation  

PubMed Central

This review addresses the cellular and molecular mechanisms of cadherin-based tissue morphogenesis. Tissue physiology is profoundly influenced by the distinctive organizations of cells in organs and tissues. In metazoa, adhesion receptors of the classical cadherin family play important roles in establishing and maintaining such tissue organization. Indeed, it is apparent that cadherins participate in a range of morphogenetic events that range from support of tissue integrity to dynamic cellular rearrangements. A comprehensive understanding of cadherin-based morphogenesis must then define the molecular and cellular mechanisms that support these distinct cadherin biologies. Here we focus on four key mechanistic elements: the molecular basis for adhesion through cadherin ectodomains; the regulation of cadherin expression at the cell surface; cooperation between cadherins and the actin cytoskeleton; and regulation by cell signaling. We discuss current progress and outline issues for further research in these fields.

Niessen, Carien M.; Leckband, Deborah; Yap, Alpha S.

2013-01-01

283

Structural and electronic features of the ubiquinone and ubiquinol molecules: molecular dynamics and quantum chemical treatments  

Microsoft Academic Search

The coenzyme Q (CoQ) molecule plays a critical role in the biochemical generation of energy in the form of adenosine triphosphate. Various types of CoQ can be classified according to their number of isoprenoid units in the tail. In human beings, CoQ10 is produced and is necessary for the basic functioning of cells. CoQ10 exists in two forms, as ubiquinone

E. D. Tekin; S. Erkoc

2010-01-01

284

DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases  

Microsoft Academic Search

Abstract In this paper we describe the search strategies developed for docking flexible molecules to macomolecular,sites that are incorporated into the widely distributed DOCK software, version 4.0. The search strategies include incremental construction and random,conformation,search and utilize the existing Coulombic and Lennard-Jones grid-based scoring function. The incremental construction strategy is tested with a panel of 15 crystallographic testcases, created from

Todd J. A. Ewing; Shingo Makino; A. Geoffrey Skillman; Irwin D. Kuntz

2001-01-01

285

DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases  

Microsoft Academic Search

In this paper we describe the search strategies developed for docking flexible molecules to macomolecular sites that are incorporated into the widely distributed DOCK software, version 4.0. The search strategies include incremental construction and random conformation search and utilize the existing Coulombic and Lennard-Jones grid-based scoring function. The incremental construction strategy is tested with a panel of 15 crystallographic testcases,

Todd J. A. Ewing; Shingo Makino; A. Geoffrey Skillman; Irwin D. Kuntz

2001-01-01

286

ATOMIC AND MOLECULAR PHYSICS: A Time-Dependent Wavepacket Method for Photodissociation Dynamics of Triatomic Molecule  

NASA Astrophysics Data System (ADS)

We report a time-dependent quantum wavepacket theory employed to interpret the photoabsorption spectrum of the N2O molecule in terms of the nuclear motion on the upper 21A? and 11A? potential energy surfaces. The N2-O bond breaks upon excitation leading to dissociation. The total angular momentum is treated correctly taking into account the vector property of the electric field of the exciting radiation.

Mohammad Noh, Daud; Gabriel, Balint-Kurti G.

2009-07-01

287

Pseudolocal modes of guest molecules in mixed molecular crystals: Photon echo experiments and computer simulations  

Microsoft Academic Search

The temperature-dependent optical dephasing of anthracene, 9-methylanthracene, and 2-methylanthracene monomers in phenanthrene host crystals has been measured using photon echo experiments. Despite large linear electron–acoustic phonon coupling, all three systems dephase because of coupling to pseudolocal modes (local motions of the guest molecule). Computer simulations of the three systems calculate the pseudolocal mode eigenvalues and eigenvectors. In contrast to previous

R. W. Olson; Jeffrey S. Meth; C. D. Marshall; Vincent J. Newell; M. D. Fayer

1990-01-01

288

Detection of deep traps for gas molecules in the diffusion processes in low-molecular glasses  

NASA Astrophysics Data System (ADS)

The kinetics of the diffusion-controlled radical oxidation in galssy alcohol matrices of n-butanol- d10 and isopentanol has been studied at various concentrations of oxygen and nitrogen in the samples. The influences of matrix annealing and gas concentrations on the kinetics have been analyzed. A conclusion on the existence of deep traps for gas molecules in n-butanol- d10 and isoamyl alcohol is drawn.

Vasenkov, S. V.; Tolkatchev, V. A.; Bazhin, N. M.

1993-05-01

289

Initiating Molecular Growth in the Interstellar Medium via Dimeric Complexes of Observed Ions and Molecules  

NASA Technical Reports Server (NTRS)

A feasible initiation step for particle growth in the interstellar medium (ISM) is simulated by means of ab quantum chemistry methods. The systems studied are dimer ions formed by pairing nitrogen containing small molecules known to exist in the ISM with ions of unsaturated hydrocarbons or vice versa. Complexation energies, structures of ensuing complexes and electronic excitation spectra of the encounter complexes are estimated using various quantum chemistry methods. Moller-Plesset perturbation theory (MP2, Z-averaged perturbation theory (ZAP2), coupled cluster singles and doubles with perturbative triples corrections (CCSD(T)), and density functional theory (DFT) methods (B3LYP) were employed along with the correlation consistent cc-pVTZ and aug-cc-pVTZ basis sets. Two types of complexes are predicted. One type of complex has electrostatic binding with moderate (7-20 kcal per mol) binding energies, that are nonetheless significantly stronger than typical van der Waals interactions between molecules of this size. The other type of complex develops strong covalent bonds between the fragments. Cyclic isomers of the nitrogen containing complexes are produced very easily by ion-molecule reactions. Some of these complexes show intense ultraviolet visible spectra for electronic transitions with large oscillator strengths at the B3LYP, omegaB97, and equations of motion coupled cluster (EOM-CCSD) levels. The open shell nitrogen containing carbonaceous complexes especially exhibit a large oscillator strength electronic transition in the visible region of the electromagnetic spectrum.

Bera, Partha P.; Head-Gordon, Martin; Lee, Timothy J.

2011-01-01

290

Molecular targeting of inhibitor of apoptosis proteins based on small molecule mimics of natural binding partners.  

PubMed

An assay based on a solvent-sensitive fluorogenic dye molecule, badan, is used to test the binding affinity of a library of tetrapeptide molecules for the BIR3 (baculovirus IAP repeat) domain of XIAP (X-linked inhibitor of apoptosis protein). The fluorophore is attached to a tetrapeptide, Ala-Val-Pro-Cys-NH(2), through a thiol linkage and, upon binding to XIAP, undergoes a solvatochromic shift in fluorescence emission. When a molecule (e.g., a natural protein known to bind to XIAP or a tetrapeptide mimic) displaces the dye, the emission shifts back to the spectrum observed in water. As emission intensity is related to the binding of the tetrapeptide, the intensity can be used to determine the equilibrium constant, K, for the displacement of the dye by the tetrapeptide. The results permit residue-specific analysis of the interaction. Furthermore, we show that hydrophobic effects in the fourth position are general and can effectively increase overall affinity. PMID:12044166

Kipp, Rachael A; Case, Martin A; Wist, Aislyn D; Cresson, Catherine M; Carrell, Maria; Griner, Erin; Wiita, Arun; Albiniak, Philip A; Chai, Jijie; Shi, Yigong; Semmelhack, Martin F; McLendon, George L

2002-06-11

291

Scanning tunneling microscopy characterization of potential molecules for implementing molecular-quantum-dot cellular automata  

NASA Astrophysics Data System (ADS)

Quantum-dot cellular automata (QCA) which is a transistorless paradigm for fabricating computational hardware has gained considerable attention since cells, wires, and majority gates (made using metal dots connected by tunnel junctions) have all been experimentally demonstrated. To explore the additional advantages of the QCA paradigm, a molecular scale implementation is pursued. Two viable candidates (Si-phthalocyanine and ruthenium complexes) for the molecular QCA approach have been examined carefully using UHV-scanning tunneling microscopy and spectroscopy. These results as well as data obtained by ellipsometry, x-ray photoelectron spectroscopy, and cyclic voltammetry will be discussed in this talk.

Peiris, Frank; Snider, Gregory; Li, Zhiyong; Chellamma, Sudha; Varughese, Bindhu; Lieberman, Marya

2001-03-01

292

Single Molecules  

NSDL National Science Digital Library

A new molecular science journal, Single Molecules, from Wiley Interscience, "will provide researchers with a broad overview of current methods and techniques, recent applications and shortcomings of present techniques in the field of single molecules." With temporary free access, the journal's latest issue contains a few full-text articles, with more articles being regularly added. This journal is currently calling for papers.

293

The humoral pattern recognition molecule PTX3 is a key component of innate immunity against urinary tract infection.  

PubMed

Immunity in the urinary tract has distinct and poorly understood pathophysiological characteristics and urinary tract infections (UTIs) are important causes of morbidity and mortality. We investigated the role of the soluble pattern recognition molecule pentraxin 3 (PTX3), a key component of the humoral arm of innate immunity, in UTIs. PTX3-deficient mice showed defective control of UTIs and exacerbated inflammation. Expression of PTX3 was induced in uroepithelial cells by uropathogenic Escherichia coli (UPEC) in a Toll-like receptor 4 (TLR4)- and MyD88-dependent manner. PTX3 enhanced UPEC phagocytosis and phagosome maturation by neutrophils. PTX3 was detected in urine of UTI patients and amounts correlated with disease severity. In cohorts of UTI-prone patients, PTX3 gene polymorphisms correlated with susceptibility to acute pyelonephritis and cystitis. These results suggest that PTX3 is an essential component of innate resistance against UTIs. Thus, the cellular and humoral arms of innate immunity exert complementary functions in mediating resistance against UTIs. PMID:24745336

Jaillon, Sébastien; Moalli, Federica; Ragnarsdottir, Bryndis; Bonavita, Eduardo; Puthia, Manoj; Riva, Federica; Barbati, Elisa; Nebuloni, Manuela; Cvetko Krajinovic, Lidija; Markotic, Alemka; Valentino, Sonia; Doni, Andrea; Tartari, Silvia; Graziani, Giorgio; Montanelli, Alessandro; Delneste, Yves; Svanborg, Catharina; Garlanda, Cecilia; Mantovani, Alberto

2014-04-17

294

THE PEPTIDE-RECEPTIVE TRANSITION STATE OF MHC-I MOLECULES: INSIGHT FROM STRUCTURE AND MOLECULAR DYNAMICS  

PubMed Central

MHC-I proteins of the adaptive immune system require antigenic peptides for maintenance of mature conformation and immune function via specific recognition by MHC-I-restricted CD8+ T lymphocytes. New MHC-I molecules in the endoplasmic reticulum are held by chaperones in a peptide-receptive (PR) transition state pending release by tightly binding peptides. We show, by crystallographic, docking, and molecular dynamics methods, dramatic movement of a hinged unit containing a conserved 310 helix, that flips from an exposed “open” position in the PR transition state, to a “closed” position with buried hydrophobic side chains in the peptide-loaded (PL) mature molecule. Crystallography of hinged unit residues 46-53 of murine H-2Ld MHC-I heavy chain, complexed with mAb 64-3-7 demonstrates solvent exposure of these residues in the PR conformation. Docking and molecular dynamics predict how this segment moves to help form the A and B pockets crucial for the tight peptide binding needed for stability of the mature PL conformation, chaperone dissociation, and antigen presentation.

Mage, Michael G.; Dolan, Michael A.; Wang, Rui; Boyd, Lisa F.; Revilleza, Maria Jamela; Robinson, Howard; Natarajan, Kannan; Myers, Nancy B.; Hansen, Ted H.; Margulies, David H.

2012-01-01

295

Resonance enhanced multiphoton and single-photon ionization of molecules and molecular fragments. Final report, May 1993--April 1997  

SciTech Connect

Resonance enhanced multiphoton ionization (REMPI) utilizes pulsed laser radiation to prepare a molecule in an excited state via absorption of one or more photons and to subsequently ionize that level before it decays. A remarkable feature of REMPI is that the very narrow bandwidth of laser radiation makes it possible to select a specific rotational level in the initial (ground) state and to prepare the excited state of interest in a single rotational level. Thus, by suitable choice of the excitation step, it is possible to selectively ionize a species that may be present. The key objective of the effort is to carry out quantitative studies of REMPI of molecules and molecular fragments, as well as of single-photon ionization of these species by coherent VUV radiation, in order to provide a robust description of significant spectral features of interest in related experiments and needed insight into the underlying dynamics of these spectra. A major focus of the effort is joint theoretical and experimental studies of these ion rotational distributions which are being widely studied by the zero-kinetic-energy (ZEKE) technique. This technique, which is based on the detection of photoelectrons resulting from pulsed-field ionization of very high Rydberg states lying just below an ion threshold, makes it possible to obtain cation distributions with subwavenumber resolution. The unprecedented resolution of this ZEKE technique is opening up entirely new vistas in studies of photoionization dynamics, ion spectroscopy, and state-selected ion-molecule reactions. Emerging applications built on the ultra-high resolution of this technique include its use for accurate determination of thermochemically important ionization energies, for characterization of ion rovibrational level structure of large organic molecules, of elemental clusters, and of weakly bound molecular complexes, for probing reactive fragments, and for pump-probe photoelectron studies of wavepacket dynamics. This surge of experimental activity in ultra-high resolution studies of molecular photoelectron spectra continues to raise new theoretical challenges and has provided the stimulus for several of the collaborations with experimental groups in North America and Europe.

McKoy, V.

1998-09-01

296

Crossed molecular beams study of O({sup 1}D) reactions with H{sub 2} molecules  

SciTech Connect

Reaction dynamics of O({sup 1}D) atoms with H{sub 2} molecules was reinvestigated using the crossed molecular beams technique with pulsed beams. The O({sup 1}D) beam was generated by photodissociating O{sub 3} molecules at 248 nm. Time-of-flight spectra and the laboratory angular distribution of the OH products were measured. The derived OH product center-of-mass flux-velocity contour diagram shows more backward scattered intensity with respect to the O({sup 1}D) beam. In contrast to previous studies which show that the insertion mechanism is the dominant process, our results indicate that the contribution from the collinear approach of the O({sup 1}D) atom to the H{sub 2} molecule on the first excited state potential energy surface is significant and the energy barrier for the collinear approach is therefore minimal. Despite the increased time resolution in this experiment, no vibrational structure in the OH product time-of-flight spectra was resolved. This is in agreement with LIF studies, which have shown that the rotational distributions of the OH products in all vibrational states are broad and highly inverted.

Miau, T.T.

1995-05-01

297

Mechanical operation and intersubunit coordination of ring-shaped molecular motors: insights from single-molecule studies.  

PubMed

Ring NTPases represent a large and diverse group of proteins that couple their nucleotide hydrolysis activity to a mechanical task involving force generation and some type of transport process in the cell. Because of their shape, these enzymes often operate as gates that separate distinct cellular compartments to control and regulate the passage of chemical species across them. In this manner, ions and small molecules are moved across membranes, biopolymer substrates are segregated between cells or moved into confined spaces, double-stranded nucleic acids are separated into single strands to provide access to the genetic information, and polypeptides are unfolded and processed for recycling. Here we review the recent advances in the characterization of these motors using single-molecule manipulation and detection approaches. We describe the various mechanisms by which ring motors convert chemical energy to mechanical force or torque and coordinate the activities of individual subunits that constitute the ring. We also examine how single-molecule studies have contributed to a better understanding of the structural elements involved in motor-substrate interaction, mechanochemical coupling, and intersubunit coordination. Finally, we discuss how these molecular motors tailor their operation-often through regulation by other cofactors-to suit their unique biological functions. PMID:24806916

Liu, Shixin; Chistol, Gheorghe; Bustamante, Carlos

2014-05-01

298

Lubrication by physisorbed molecules in equilibrium with vapor at ambient condition: effects of molecular structure and substrate chemistry.  

PubMed

The effects of physisorbed organic vapor molecules on friction and wear were studied for various materials with different surface chemistries (metals, ceramics, glasses, carbons, polymers) and adsorbed species with distinct functional groups (short linear-chain, branched, and fluorinated alcohols with alkyl chain lengths up to five carbons as well as acetone and n-decane). Friction test results of stainless steel under equilibrium vapor adsorption conditions indicated that the longer chain length of the adsorbed alcohols results in lower friction and that n-pentanol gives the lowest friction and wear among the molecules investigated. The adsorption isotherm measurements revealed that the functional groups of the adsorbed molecules appear to play important roles in lubrication. Friction coefficients that ranged from 0.02 to 0.9 for the various materials in dry and humid environments converged to ?0.15 for the inorganic solid materials tested in n-pentanol. These findings indicate that the molecular lubrication by the physisorbed species dominates the tribological behaviors of the inorganic solid materials, regardless of bulk mechanical properties. Tribotests using polymeric materials did not show the same lubricating effects for n-pentanol vapor. The failure of n-pentanol to lubricate polymeric materials may be due to vapor ingress into the polymer and the absence of an adsorbed surface layer. PMID:24827583

Barthel, Anthony J; Kim, Seong H

2014-06-10

299

Red Fluorescent Line Emission from Hydrogen Molecules in Diffuse Molecular Clouds  

NASA Technical Reports Server (NTRS)

We have modeled the fluorescent pumping of electronic and vibrational emissions of molecular hydrogen (H2) within diffuse molecular clouds that are illuminated by ultraviolet continuum radiation. Fluorescent line intensities are predicted for transitions at ultraviolet, infrared, and red visible wavelengths as functions of the gas density, the visual extinction through the cloud, and the intensity of the incident UV continuum radiation. The observed intensity in each fluorescent transition is roughly proportional to the integrated rate of H2 photodissociation along the line of sight. Although the most luminous fluorescent emissions detectable from ground-based observatories lie at near-infrared wavelengths, we argue that the lower sky brightness at visible wavelengths makes the red fluorescent transitions a particularly sensitive probe. Fabry-Perot spectrographs of the type that have been designed to observe very faint diffuse Ha emissions are soon expected to yield sensitivities that will be adequate to detect H2 vibrational emissions from molecular clouds that are exposed to ultraviolet radiation no stronger than the mean radiation field within the Galaxy. Observations of red H2 fluorescent emission together with cospatial 21 cm H I observations could serve as a valuable probe of the gas density in diffuse molecular clouds.

Neufeld, David A.; Spaans, Marco

1996-01-01

300

Autler-Townes Splitting in Molecular Lithium: Prospects for All-Optical Alignment of Nonpolar Molecules  

Microsoft Academic Search

We demonstrate Autler-Townes (AT) splitting in molecular lithium using cw triple resonance spectroscopy. The pump and tunable probe lasers create sub-Doppler double resonance excitation of an upper rovibrational level. The line shape is split in the presence of a third, coupling laser. The AT line shape consists of the superposition of several narrower twin peaks, one for each \\\\|MJ\\\\|. The

Jianbing Qi; Guenadiy Lazarov; Xuejun Wang; Li Li; Lorenzo M. Narducci; A. Marjatta Lyyra; Frank C. Spano

1999-01-01

301

Friction and energy dissipation mechanisms in adsorbed molecules and molecularly thin films  

Microsoft Academic Search

This review provides an overview of recent advances that have been achieved in understanding the basic physics of friction and energy dissipation in molecularly thin adsorbed films and the associated impact on friction at microscopic and macroscopic length scales. Topics covered include a historical overview of the fundamental understanding of macroscopic friction, theoretical treatments of phononic and electronic energy dissipation

Jacqueline Krim

2012-01-01

302

Molecularly imprinted nanoparticles as tailor-made sensors for small fluorescent molecules.  

PubMed

Water-soluble nanoparticles molecularly imprinted against naphthyl derivatives could bind the templates with high affinity and excellent selectivity among structural analogues in aqueous solution. Fluorescent dansyl groups installed during template polymerization allowed these nanoparticles to detect the presence of the target analytes by Förster resonance energy transfer. PMID:24752667

Awino, Joseph K; Zhao, Yan

2014-06-01

303

Meet the Molecules in Chocolate: Informal Opportunities for Building Thematic Molecular Models with Children  

ERIC Educational Resources Information Center

We describe the development and use of a molecular model building activity with a chocolate theme, suitable for a public presentation of chemistry through interaction with visitors to science festivals and museums, and as a special classroom activity during science weeks, and so forth. (Contains 3 figures.)

Amey, Jennifer R.; Fletcher, Matthew D.; Fletcher, Rachael V.; Jones, Alison; Roberts, Erica W.; Roberts, Ieuan O.

2008-01-01

304

Macrophage migration inhibitory factor: molecular, cellular and genetic aspects of a key neuroendocrine molecule  

Microsoft Academic Search

The immunological and neuroendocrine properties of macrophage migration inhibitory factor (MIF) are diverse. In this article we review the known cellular, molecular and genetic properties of MIF that place it as a key regulatory cytokine, acting within both the innate and adaptive immune responses. The unexpected and paradoxical induction of MIF secretion by low concentrations of glucocorticoids is explored. The

R P Donn; D W Ray

2004-01-01

305

Molecular basis of natural variation and environmental control of trichome patterning  

PubMed Central

Trichomes are differentiated epidermal cells on above ground organs of nearly all land plants. They play important protective roles as structural defenses upon biotic attacks such as herbivory, oviposition and fungal infections, and against abiotic stressors such as drought, heat, freezing, excess of light, and UV radiation. The pattern and density of trichomes is highly variable within natural population suggesting tradeoffs between traits positively affecting fitness such as resistance and the costs of trichome production. The spatial distribution of trichomes is regulated through a combination of endogenous developmental programs and external signals. This review summarizes the current understanding on the molecular basis of the natural variation and the role of phytohormones and environmental stimuli on trichome patterning.

Hauser, Marie-Theres

2014-01-01

306

Molecular phylogenetics reveals a pattern of biome conservatism in New World anchovies (family Engraulidae).  

PubMed

Evolutionary transitions between marine and freshwater biomes are relatively rare events, yielding a widespread pattern of biome conservatism among aquatic organisms. We investigated biome transitions in anchovies (Engraulidae), a globally distributed clade of economically important fishes. Most anchovy species are near-shore marine fishes, but several exclusively freshwater species are known from tropical rivers of South America and were previously thought to be the product of six or more independent freshwater invasions. We generated a comprehensive molecular phylogeny for Engraulidae, including representatives from 15 of 17 currently recognized genera. Our data support previous hypotheses of higher-level relationships within Engraulidae, but show that most New World genera are not monophyletic and in need of revision. Ancestral character reconstruction reveals that New World freshwater anchovies are the product of a single marine to freshwater transition, supporting a pattern of biome conservatism. We argue that competition is the principal mechanism that regulates aquatic biome transitions on a continental scale. PMID:22300535

Bloom, Devin D; Lovejoy, N R

2012-04-01

307

A unique feature of chiral transition of a difluorobenzo[c]phenanthrene molecule confined in a boron-nitride nanotube based on molecular dynamics simulations  

NASA Astrophysics Data System (ADS)

Reliable structural information of extremal points in a reaction is important but difficult to achieve in molecular chiral transitions under confinement due to the complex molecular interactions. In this Letter, based on statistical results of a number of classical molecular dynamics simulations, we found that a complete chiral transition process of a difluorobenzo[c]phenanthrene molecule (C18H12F2, called D molecule) within a single-walled boron-nitride nanotube involves at least five extremal point structures, showing a unique feature of chiral transition in the confined environment and suggesting an alternative to conventional first-principles calculations to determine the complex potential energy surface of intermolecular interactions.

Meng, Yan; Xiu, Peng; Huang, Bolong; Wang, Zhigang; Zhang, Rui-Qin; Zhou, Ruhong

2014-01-01

308

Redox-derived damage-associated molecular patterns: Ligand function of lipid peroxidation adducts.  

PubMed

Endogenous electrophiles, such as ?,?-unsaturated aldehydes and ketones generated during lipid peroxidation, exhibit a facile reactivity with proteins, generating a variety of intra and intermolecular covalent adducts. It has been postulated that these host-derived, modified proteins with electrophiles, which constitute the products of diverse classes of oxidative reactions, represent damage-associated molecular patterns (DAMPs). The DAMPs, that occur in vivo, can be a ligand of multiple proteins, which in turn, may lead to the profound innate and adaptive immune responses and mediate homeostatic functions consequent to inflammation and cell death. PMID:24024141

Uchida, Koji

2013-01-01

309

Redox-derived damage-associated molecular patterns: Ligand function of lipid peroxidation adducts?  

PubMed Central

Endogenous electrophiles, such as ?,?-unsaturated aldehydes and ketones generated during lipid peroxidation, exhibit a facile reactivity with proteins, generating a variety of intra and intermolecular covalent adducts. It has been postulated that these host-derived, modified proteins with electrophiles, which constitute the products of diverse classes of oxidative reactions, represent damage-associated molecular patterns (DAMPs). The DAMPs, that occur in vivo, can be a ligand of multiple proteins, which in turn, may lead to the profound innate and adaptive immune responses and mediate homeostatic functions consequent to inflammation and cell death.

Uchida, Koji

2013-01-01

310

Nonequilibrium molecular dynamics of the rheological and structural properties of linear and branched molecules. Simple shear and poiseuille flows; instabilities and slip.  

PubMed

Nonequilibrium molecular-dynamics simulations are performed for linear and branched chain molecules to study their rheological and structural properties under simple shear and Poiseuille flows. Molecules are described by a spring-monomer model with a given intermolecular potential. The equations of motion are solved for shear and Poiseuille flows with Lees and Edward's [A. W. Lees and S. F. Edwards, J. Phys. C 5, 1921 (1972)] periodic boundary conditions. A multiple time-scale algorithm extended to nonequilibrium situations is used as the integration method, and the simulations are performed at constant temperature using Nose-Hoover [S. Nose, J. Chem. Phys. 81, 511 (1984)] dynamics. In simple shear, molecules with flow-induced ellipsoidal shape, having significant segment concentrations along the gradient and neutral directions, exhibit substantial flow resistance. Linear molecules have larger zero-shear-rate viscosity than that of branched molecules, however, this behavior reverses as the shear rate is increased. The relaxation time of the molecules is associated with segment concentrations directed along the gradient and neutral directions, and hence it depends on structure and molecular weight. The results of this study are in qualitative agreement with other simulation studies and with experimental data. The pressure (Poiseuille) flow is induced by an external force F(e) simulated by confining the molecules in the region between surfaces which have attractive forces. Conditions at the boundary strongly influence the type of the slip flow predicted. A parabolic velocity profile with apparent slip on the wall is predicted under weakly attractive wall conditions, independent of molecular structure. In the case of strongly attractive walls, a layer of adhered molecules to the wall produces an abrupt distortion of the velocity profile which leads to slip between fluid layers with magnitude that depends on the molecular structure. Finally, the molecular deformation under flow depends on the attractive force of the wall, in such a way that molecules are highly deformed in the case of strong attracting walls. PMID:16108693

Castillo-Tejas, Jorge; Alvarado, Juan F J; González-Alatorre, Guillermo; Luna-Bárcenas, Gabriel; Sanchez, Isaac C; Macias-Salinas, Ricardo; Manero, Octavio

2005-08-01

311

Guided Cell Patterning On Gold-Silicon Dioxide Substrates by Surface Molecular Engineering  

SciTech Connect

We report an effective approach to patterning cells on a gold-silicon substrate with high precision, selectivity, stability, and reproducibility. This technique is based on photolithography and surface molecular engineering and does not involve a cell positioning or delivery device, thus reducing potential damage to cells. Cell patterning is achieved by activating the gold regions with functionalized thiols that covalently bind proteins to guide the subsequent cell adhesion and passivating the silicon regions with polyethylene glycol (PEG) to resist cell adhesion. Time-of-light secondary ion mass spectrometry (TOF-SIMS), a powerful surface chemical state imaging technique that allows simultaneous chemical and spatial characterization, was used to characterize the chemistry of the cell-adhesive and cell-resistant regions of the surface at key stages in the device fabrication. Fourier transform infrared (FTIR) reflectance spectroscopy was used to verify the immobilization of proteins on model surfaces. Proteins were tagged with Rhodamine fluorescent probes to characterize patterned surfaces by fluorescence microscopy. Finally, the ability of the engineered surfaces to guide cell adhesion was illustrated by differential interference contrast (DIC) reflectance microscopy. The cell patterning technique introduced in this study is compatible with micro- and photo- electronics, and may have numerous medical, environmental, and defense applications.

Veiseh, Mandana; Wickes, Bronwyn; Castner, David G.; Zhang, Miqin

2004-07-01

312

Proton Donor/acceptor Propensities of Ammonia: Rotational Studies of its Molecular Complexes with Organic Molecules  

NASA Astrophysics Data System (ADS)

We studied the rotational spectra of the adducts of ammonia with several organic molecules, namely tert-butanol, glycidol, ethyl alcohol, anisol and 1,4-difluorobenzene. The adducts with glycidol and ethanol have been observed for both conformers of the substrate molecule. Based on the rotational and ^{14}N quadrupole coupling constants of the various complexes, we found a considerably different behaviour of ammonia, with respect to water, in its proton donor/acceptor double role. In the interaction with the three alcohol molecules, NH_{3} acts as a proton acceptor and the OH groups as a proton donor. However, in the case of glycidol-NH_{3}, a secundary N-H\\cdotsO interaction occurrs between ammonia and the ether oxygen. This interaction generates a sizable V_{3} barrier to the internal rotation of the NH_{3} moiety, while NH_{3} undergoes a free rotation in tert-butanol-NH_{3} and in ethanol-NH_{3}. As to the anisole-NH_{3} and 1,4-difluorobenzene-NH_{3} complexes, the NH_{3} group explicits its double proton donor/acceptor role, although through two weak (C_{Me}-H\\cdotsN and N-H\\cdots?) H-bonds. There is, however, an important difference between the two complexes, because in the first one NH_{3} lies out of the aromatic plane, while in the second one it is in the plane of the aromatic ring. B. M. Giuliano, M. C. Castrovilli, A. Maris, S. Melandri, W. Caminati and E. A. Cohen, Chem.Phys.Lett., 2008, 463, 330 B. M. Giuliano, S. Melandri, A. Maris, L. B. Favero and W. Caminati, Angew.Chem.Int.Ed., 2009, 48, 1102

Giuliano, Barbara M.; Maris, Assimo; Melandri, Sonia; Favero, Laura B.; Evangelisti, Luca; Caminati, Walther

2009-06-01

313

Initiating molecular growth in the interstellar medium via dimeric complexes of observed ions and molecules  

NASA Astrophysics Data System (ADS)

A feasible initiation step for particle growth in the interstellar medium (ISM) is simulated by means of ab initio quantum chemistry methods. The systems studied are dimer ions formed by pairing nitrogen containing small molecules known to exist in the ISM with ions of unsaturated hydrocarbons or vice versa. Complexation energies, structures of ensuing complexes and electronic excitation spectra of the encounter complexes are estimated using various quantum chemistry methods. Møller-Plesset perturbation theory (MP2), Z-averaged perturbation theory (ZAPT2), coupled cluster singles and doubles with perturbative triples corrections (CCSD(T)), and density functional theory (DFT) methods (B3LYP) were employed along with the correlation consistent cc-pVTZ and aug-cc-pVTZ basis sets. Two types of complexes are predicted. One type of complex has electrostatic binding with moderate (7-20 kcal mol-1) binding energies, that are nonetheless significantly stronger than typical van der Waals interactions between molecules of this size. The other type of complex develops strong covalent bonds between the fragments. Cyclic isomers of the nitrogen containing complexes are produced very easily by ion-molecule reactions. Some of these complexes show intense ultraviolet-visible spectra for electronic transitions with large oscillator strengths at the B3LYP, ?B97, and equations of motion coupled cluster (EOM-CCSD) levels. The open shell nitrogen containing carbonaceous complexes especially exhibit a large oscillator strength electronic transition in the visible region of the electromagnetic spectrum. Appendix A is available in electronic form at http://www.aanda.org

Bera, Partha P.; Head-Gordon, Martin; Lee, Timothy J.

2011-11-01

314

The expression pattern of small nucleolar and small Cajal body-specific RNAs characterizes distinct molecular subtypes of multiple myeloma  

PubMed Central

Small nucleolar RNAs (snoRNAs) and small Cajal body-specific RNAs (scaRNAs) are non-coding RNAs involved in the maturation of other RNA molecules and generally located in the introns of host genes. It is now emerging that altered sno/scaRNAs expression may have a pathological role in cancer. This study elucidates the patterns of sno/scaRNAs expression in multiple myeloma (MM) by profiling purified malignant plasma cells from 55 MMs, 8 secondary plasma cell leukemias (sPCLs) and 4 normal controls. Overall, a global sno/scaRNAs downregulation was found in MMs and, even more, in sPCLs compared with normal plasma cells. Whereas SCARNA22 resulted the only sno/scaRNA characterizing the translocation/cyclin D4 (TC4) MM, TC2 group displayed a distinct sno/scaRNA signature overexpressing members of SNORD115 and SNORD116 families located in a region finely regulated by an imprinting center at 15q11, which, however, resulted overall hypomethylated in MMs independently of the SNORD115 and SNORD116 expression levels. Finally, integrative analyses with available gene expression and genome-wide data revealed the occurrence of significant sno/scaRNAs/host genes co-expression and the putative influence of allelic imbalances on specific snoRNAs expression. Our data extend the current view of sno/scaRNAs deregulation in cancer and add novel information to the bio-molecular complexity of plasma cell dyscrasias.

Ronchetti, D; Todoerti, K; Tuana, G; Agnelli, L; Mosca, L; Lionetti, M; Fabris, S; Colapietro, P; Miozzo, M; Ferrarini, M; Tassone, P; Neri, A

2012-01-01

315

Universal scaling behavior of molecular electronic stopping cross section for protons colliding with small molecules and nucleobases  

NASA Astrophysics Data System (ADS)

The electronic stopping cross section and mean excitation energy for molecules and 5 nucleobases have been calculated within the first Born approximation in terms of an orbital decomposition to take into account the molecular structure. The harmonic oscillator (HO) description of the stopping cross section together with a Floating Spherical Gaussian Orbital (FSGO) model is implemented to account for the chemical composition of the target. This approach allows us to use bonds, cores, and lone pairs as HO basis to describe the ground state molecular structure. In the HO model, the orbital angular frequency is the only parameter that connects naturally with the mean excitation energy. As a result, we obtain a simple expression for the equivalent mean excitation energy in terms of the orbital radius parameter, as well as an analytical expression of the stopping cross section. For gas phase molecular targets, we provide HO based orbital mean excitation energies to describe any molecule containing C, N, O, H, and P atoms. We present results for protons colliding with H2, N2, O2, H2O, CO2, propylene (C3H6), methane (CH4), ethylene (C2H4) and the nucleobases - guanine (C5H5N5O), cytosine (C4H5N2O2), thymine (C5H6N2O2), adenine (C5H5N5) and uracil (C4H4N2O2). The results for the stopping cross section are compared with available experimental and theoretical data showing good to excellent agreement in the region of validity of the model. The HO approach allows us to obtain a universal stopping cross section formula to describe a universal scaling behavior for the energy loss process. The universal scaled curve is confirmed by the experimental data.

Trujillo-López, L. N.; Martínez-Flores, C.; Cabrera-Trujillo, R.

2013-10-01

316

Airborne molecular contamination control in the micromirror SLM-based deep ultraviolet DUV SIGMA7300 laser pattern generator  

Microsoft Academic Search

Airborne molecular contamination (AMC) in the form of bases, acids and condensable organic and inorganic substances threaten both costly and sensitive optics and mask pattern formation in the chemically amplified resists (CAR) used for both E-beam and laser lithography. This is particularly so for mask pattern generators due to the relatively long writing times. In the development work of the

Mats Ekberg; Hans A. Fosshaug; Thomas Ostrom; Peter Bjornangen; Thomas Utterback; Per-Uno Skotte; John Higley; David Ruede; Oleg P. Kishkovich

2004-01-01

317

Small molecule penetrant diffusion in aromatic polyesters: a molecular dynamics simulation study  

Microsoft Academic Search

Molecular dynamics (MD) simulations have been used to study diffusion of methane in three highly impermeable aromatic polyesters that are good barrier materials. These are amorphous poly(ethylene terephthalate) (PET) and poly(ethylene 2,6-naphthalene dicarboxylate) (PEN), and the nematic mesophase of the thermotropic liquid crystalline copolyester (LCP) of p-hydroxy benzoic acid (HBA) and 2,6 hydroxy naphthoic acid (HNA). Diffusion coefficients were determined

Rishikesh K. Bharadwaj; Richard H. Boyd

1999-01-01

318

Molecular understanding of atmospheric particle formation from sulfuric acid and large oxidized organic molecules  

PubMed Central

Atmospheric aerosols formed by nucleation of vapors affect radiative forcing and therefore climate. However, the underlying mechanisms of nucleation remain unclear, particularly the involvement of organic compounds. Here, we present high-resolution mass spectra of ion clusters observed during new particle formation experiments performed at the Cosmics Leaving Outdoor Droplets chamber at the European Organization for Nuclear Research. The experiments involved sulfuric acid vapor and different stabilizing species, including ammonia and dimethylamine, as well as oxidation products of pinanediol, a surrogate for organic vapors formed from monoterpenes. A striking resemblance is revealed between the mass spectra from the chamber experiments with oxidized organics and ambient data obtained during new particle formation events at the Hyytiälä boreal forest research station. We observe that large oxidized organic compounds, arising from the oxidation of monoterpenes, cluster directly with single sulfuric acid molecules and then form growing clusters of one to three sulfuric acid molecules plus one to four oxidized organics. Most of these organic compounds retain 10 carbon atoms, and some of them are remarkably highly oxidized (oxygen-to-carbon ratios up to 1.2). The average degree of oxygenation of the organic compounds decreases while the clusters are growing. Our measurements therefore connect oxidized organics directly, and in detail, with the very first steps of new particle formation and their growth between 1 and 2 nm in a controlled environment. Thus, they confirm that oxidized organics are involved in both the formation and growth of particles under ambient conditions.

Schobesberger, Siegfried; Junninen, Heikki; Bianchi, Federico; Lonn, Gustaf; Ehn, Mikael; Lehtipalo, Katrianne; Dommen, Josef; Ehrhart, Sebastian; Ortega, Ismael K.; Franchin, Alessandro; Nieminen, Tuomo; Riccobono, Francesco; Hutterli, Manuel; Duplissy, Jonathan; Almeida, Joao; Amorim, Antonio; Breitenlechner, Martin; Downard, Andrew J.; Dunne, Eimear M.; Flagan, Richard C.; Kajos, Maija; Keskinen, Helmi; Kirkby, Jasper; Kupc, Agnieszka; Kurten, Andreas; Kurten, Theo; Laaksonen, Ari; Mathot, Serge; Onnela, Antti; Praplan, Arnaud P.; Rondo, Linda; Santos, Filipe D.; Schallhart, Simon; Schnitzhofer, Ralf; Sipila, Mikko; Tome, Antonio; Tsagkogeorgas, Georgios; Vehkamaki, Hanna; Wimmer, Daniela; Baltensperger, Urs; Carslaw, Kenneth S.; Curtius, Joachim; Hansel, Armin; Petaja, Tuukka; Kulmala, Markku; Donahue, Neil M.; Worsnop, Douglas R.

2013-01-01

319

Explicit ion, implicit water solvation for molecular dynamics of nucleic acids and highly charged molecules.  

PubMed

An explicit ion, implicit water solvent model for molecular dynamics was developed and tested with DNA and RNA simulations. The implicit water model uses the finite difference Poisson (FDP) model with the smooth permittivity method implemented in the OpenEye ZAP libraries. Explicit counter-ions, co-ions, and nucleic acid were treated with a Langevin dynamics molecular dynamics algorithm. Ion electrostatics is treated within the FDP model when close to the solute, and by the Coulombic model when far from the solute. The two zone model reduces computation time, but retains an accurate treatment of the ion atmosphere electrostatics near the solute. Ion compositions can be set to reproduce specific ionic strengths. The entire ion/water treatment is interfaced with the molecular dynamics package CHARMM. Using the CHARMM-ZAPI software combination, the implicit solvent model was tested on A and B form duplex DNA, and tetraloop RNA, producing stable simulations with structures remaining close to experiment. The model also reproduced the A to B duplex DNA transition. The effect of ionic strength, and the structure of the counterion atmosphere around B form duplex DNA were also examined. PMID:18074338

Prabhu, Ninad V; Panda, Manoranjan; Yang, Qingyi; Sharp, Kim A

2008-05-01

320

Molecular cloning of POEM: a novel adhesion molecule that interacts with alpha8beta1 integrin.  

PubMed

Cell adhesion molecules are involved in a number of biological functions, such as cell survival, cell differentiation, tissue repair, and development. A novel molecule, POEM (preosteoblast epidermal growth factor-like repeat protein with meprin, A5 protein, and receptor protein-tyrosine phosphatase mu domain), was isolated by reverse transcription-polymerase chain reaction using a set of degenerate primers designed after other known epidermal growth factor (EGF)-like motifs. From its structure, POEM was suggested to be a novel adhesion molecule with five EGF-like domains, an Arg-Gly-Asp (RGD) cell binding motif, and a meprin, A5 protein, and receptor protein-tyrosine phosphatase mu (MAM) domain. By in situ hybridization using embryonic day 16.5 (E16.5) mouse embryos, strong expression of POEM mRNA was observed in developing kidney renal tubules, parathyroid and thyroid glands, developing bone, tooth germ, and endocrine organs of the brain. The inner ear, skeletal muscle, smooth muscle (except for the vascular system), and skin were also positive for POEM expression. Bacterial recombinant POEM protein containing the RGD sequence and MAM domain showed strong cell adhesion, spreading, and survival-promoting activities. By mutating the RGD sequence to RGE, the cell spreading and survival activities were significantly decreased, but the MAM domain was shown to contribute only to cell adhesion and not to cell spreading and survival-promoting activities. The distribution of POEM in several tissues was close to that of alpha(8)beta(1) integrin. Therefore, we conducted cell adhesion assays using KA8 cells, a K562 leukemia clone stably expressing alpha(8) integrin. Parental K562 cells, which expressed alpha(5)beta(1) integrin, bound to fibronectin but not to POEM. On the other hand, KA8 cells showed strong binding and spreading on both fibronectin and POEM. These results suggest that POEM is a novel ligand for alpha(8)beta(1) integrin and that POEM may be involved in the development and function of various tissues, such as kidney, bone, muscles, and endocrine organs. PMID:11546798

Morimura, N; Tezuka, Y; Watanabe, N; Yasuda, M; Miyatani, S; Hozumi, N; Tezuka Ki, K

2001-11-01

321

Highly consistent patterns for inherited human diseases at the molecular level.  

PubMed

Over 1600 mammalian genes are known to cause an inherited disorder, when subjected to one or more mutations. These disease genes represent a unique resource for the identification and quantification of relationships between phenotypic attributes of a disease and the molecular features of the associated disease genes, including their ascribed annotated functional classes and expression patterns. Such analyses can provide a more global perspective and a deeper understanding of the probable causes underlying human hereditary diseases. In this perspective and critical view of disease genomics, we present a comparative analysis of genes reported to cause inherited diseases in humans in terms of their causative effects on physiology, their genetics and inheritance modes, the functional processes they are involved in and their expression profiles across a wide spectrum of tissues. Our analysis reveals that there are more extensive correlations between these attributes of genetic disease genes than previously appreciated. For instance, the functional pattern of genes causing dominant and recessive diseases is markedly different. Also, the function of the genes and their expression correlate with the type of disease they cause when mutated. The results further indicate that a comparative genomics approach for the analysis of genes linked to human genetic diseases will facilitate the elucidation of the underlying molecular and cellular mechanisms. PMID:16287936

López-Bigas, Núria; Blencowe, Benjamin J; Ouzounis, Christos A

2006-02-01

322

Cyclic enterobacterial common antigens from Escherichia coli O157 as microbe-associated molecular patterns.  

PubMed

In a previous study, we described 2 forms of cyclic enterobacterial common antigen (ECACYC), a tetramer and a pentamer, from Escherichia coli O157. ECACYC is present in several representatives of the Enterobacteriaceae. To date, functional studies on ECACYC are sparse. Cyclic oligosaccharides in other bacteria, like the cyclic ?-glucans in Rhizobiaceae, represent microbe-associated molecular patterns involved in host-bacteria interaction. This observation determined the aim of the present study: to test whether the tetrameric and pentameric ECACYC from E. coli O157 can be recognised by host humoral and cellular mechanisms. ELISA tests designed to compare the 2 ECACYC with the O157 lipopolysaccharide showed that both ECACYC were not recognised by polyclonal anti-O157 serum but were good ligands for mannan-binding lectin. The lectin had a higher affinity for the tetramer than the pentamer. ECACYC deposited more C3b than did the lipopolysaccharide. To examine the interactions with human circulating neutrophils, the antigens were loaded onto fluorescent latex beads and applied in a phagocytosis experiment. Spheres coated with the 2 ECACYC occasionally adhered to phagocyte surfaces but, unlike O157-loaded spheres, failed to induce free-radical release. The results show that the 2 ECACYC represent microbe-associated molecular patterns recognised by host humoral non-self-recognition mechanisms. PMID:24588391

Paunova-Krasteva, Tsvetelina S; Pavlova, Velichka A; De Castro, Cristina; Ivanova, Radka M; Molinaro, Antonio; Nikolova, Elena B; Stoitsova, Stoyanka R

2014-03-01

323

A theoretical study on the molecular and electronic structure of heteroaromatic bowl-shaped molecules  

NASA Astrophysics Data System (ADS)

Geometries, inversion barriers, local aromaticities and vertical excitation energies of four heteroaromatic coronenes including (triphenylenotri)-pyrrole, (-)-furan, (-)-phosphole and (-)-thiophene were computed using MO and DFT methods, and compared with those of coronene and corannulene. The barriers to bowl-to-bowl inversion amount to 297, 183 and 8 kJ/mol for O-, N- and S-forms, respectively, thus the recently synthetized thiophene derivative is a floppy bowl-shaped species. The P-derivative exhibits an almost planar form. NICS values point out that the bowl-shaped molecules have similar local aromaticity in the six-membered rings but differ in those of the five membered rings. The excitation energies were evaluated using the DFT-RPA method.

Delaere, David; Tho Nguyen, Minh; Vanquickenborne, Luc G.

2001-01-01

324

Agent-based modeling for the 2D molecular self-organization of realistic molecules.  

PubMed

We extend our previously developed agent-based (AB) algorithm to the study of the self-assembly of a fully atomistic model of experimental interest. We study the 2D self-assembly of a rigid organic molecule (1,4-benzene-dicarboxylic acid or TPA), comparing the AB results with Monte Carlo (MC) and MC simulated annealing, a technique traditionally used to solve the global minimization problem. The AB algorithm gives a lower energy configuration in the same simulation time than both of the MC simulation techniques. We also show how the AB algorithm can be used as a part of the protocol to calculate the phase diagram with less computational effort than standard techniques. PMID:20684638

Fortuna, Sara; Troisi, Alessandro

2010-08-12

325

Molecular frame photoemission in multiphoton ionization of small molecules induced by linearly and circularly polarized light  

NASA Astrophysics Data System (ADS)

We report results for one-color multiphoton dissociative ionization (MPDI) of NO2 induced by linearly (P) and circularly (k, ê) polarized femtosecond (fs) pulses centered at 400 nm. The experiments were performed by combining the use of 1 kHz femtosecond laser sources (SLIC, Saclay) and the electron-ion vector correlation method. The recoil frame photoelectron angular distributions (RFPADs), derived from the analysis of the (Ve, VNO+) velocity vector correlation, are analyzed using a new formalism. It generalizes the expression of the MFPADs for one-photon photoionization of linear molecules, and models the reaction as n-1 bound-to-bound transitions and ionization induced by the nth photon. The polar and azimuthal angle dependences of the RFPAD are characterized. We illustrate the discussion by the RFPADs measured for a MPDI process induced by five-photon absorption.

Lucchese, R. R.; Elkharrat, C.; Picard, Y.; Billaud, P.; Dowek, D.

2009-11-01

326

Molecular Collision Cross Section of the CHF3 Molecule Due to Higher Order Interactions  

NASA Astrophysics Data System (ADS)

The foreign-gas broadening parameters for fluoroform molecules interacting with spherical (He, Ne, Ar, Kr, Xe, CH4, CCl4) perturbers have been measured. The results are pressure broadening coefficients (in kHz/Pa) for J=1?0 transition of CHF3: Cw(He)=23.8±0.4, Cw(Ne)=16.4±0.5, Cw(Ar)=18.5±0.4, Cw(Kr)=19.7±0.6, Cw(Xe)=21.7±0.5, Cw(CH4)=26.3±0.7, Cw(CCl4)=34.7±0.7. Experimental linewidth parameters are interpreted using Anderson-Tsao-Curnutte as well as Murphy-Boggs theories for the mixed - interactions case. The first-order London dispersion forces, induction forces and exchange forces were taken into account.

Gierszal, S.; Galica, J.; Mi?-Ku?mi?ska, E.

327

Molecular Collision Cross Section of the CHF3 Molecule Due to Higher Order Interactions  

Microsoft Academic Search

The foreign-gas broadening parameters for fluoroform molecules interacting with spherical (He, Ne, Ar, Kr, Xe, CH4, CCl4) perturbers have been measured. The results are pressure broadening coefficients (in kHz\\/Pa) for J=1<--0 transition of CHF3: Cw(He)=23.8±0.4, Cw(Ne)=16.4±0.5, Cw(Ar)=18.5±0.4, Cw(Kr)=19.7±0.6, Cw(Xe)=21.7±0.5, Cw(CH4)=26.3±0.7, Cw(CCl4)=34.7±0.7. Experimental linewidth parameters are interpreted using Anderson-Tsao-Curnutte as well as Murphy-Boggs theories for the mixed - interactions case. The

S. Gierszal; J. Galica; E. Mis-Kuzminska

2000-01-01

328

Complex temporal patterns in molecular dynamics: a direct measure of the phase-space exploration by the trajectory at macroscopic time scales.  

PubMed

Computer simulated trajectories of bulk water molecules form complex spatiotemporal structures at the picosecond time scale. This intrinsic complexity, which underlies the formation of molecular structures at longer time scales, has been quantified using a measure of statistical complexity. The method estimates the information contained in the molecular trajectory by detecting and quantifying temporal patterns present in the simulated data (velocity time series). Two types of temporal patterns are found. The first, defined by the short-time correlations corresponding to the velocity autocorrelation decay times (< or = 0.1 ps), remains asymptotically stable for time intervals longer than several tens of nanoseconds. The second is caused by previously unknown longer-time correlations (found at longer than the nanoseconds time scales) leading to a value of statistical complexity that slowly increases with time. A direct measure based on the notion of statistical complexity that describes how the trajectory explores the phase space and independent from the particular molecular signal used as the observed time series is introduced. PMID:18517503

Nerukh, Dmitry; Ryabov, Vladimir; Glen, Robert C

2008-03-01

329

Determination of the sticking coefficient of energetic hydrocarbon molecules by molecular dynamics  

NASA Astrophysics Data System (ADS)

The sticking coefficient of hydrocarbon species is a key quantity that influences the growth process of amorphous hydrocarbon layers. To extend the very limited database for low impact energies, classical molecular dynamics simulations were performed, determining the sticking coefficients of CH x ( x = 0 … 4) with kinetic energies between 5 and 100 eV. Similar simulations are performed with hydrogen substituted by deuterium. Additionally, analytical formulas are presented that fit the data very well and can be used to interpolate the simulation results.

Tichmann, Klaus; von Toussaint, Udo; Jacob, Wolfgang

2012-01-01

330

CONDORR--CONstrained Dynamics of Rigid Residues: a molecular dynamics program for constrained molecules.  

PubMed

A computer program CONDORR (CONstrained Dynamics of Rigid Residues) was developed for molecular dynamics simulations of large and/or constrained molecular systems, particularly carbohydrates. CONDORR efficiently calculates molecular trajectories on the basis of 2D or 3D potential energy maps, and can generate such maps based on a simple force field. The simulations involve three translational and three rotational degrees of freedom for each rigid, asymmetrical residue in the model. Total energy and angular momentum are conserved when no stochastic or external forces are applied to the model, if the time step is kept sufficiently short. Application of Langevin dynamics allows longer time steps, providing efficient exploration of conformational space. The utility of CONDORR was demonstrated by application to a constrained polysaccharide model and to the calculation of residual dipolar couplings for a disaccharide. [Figure: see text]. Molecular models (bottom) are created by cloning rigid residue archetypes (top) and joining them together. As defined here, the archetypes AX, HM and BG respectively correspond to an alpha-D-Xyl p residue, a hydroxymethyl group, and a beta-D-Glc p residue lacking O6, H6a and H6b. Each archetype contains atoms (indicated by boxes) that can be shared with other archetypes to form a linked structure. For example, the glycosidic link between the two D-Glc p residues is established by specifying that O1 of the nonreducing beta-D-Glc p (BG) residue (2) is identical to O4 of the reducing Glc p (BG) residue (1). The coordinates of the two residues are adjusted so as to superimpose these two (nominally distinct) atoms. Flexible hydroxymethyl (HM) groups (3 and 4) are treated as separate residues, and the torsional angles (normally indicated by the symbol omega) that define their geometric relationships to the pyranosyl rings of the BG residues are specified as psi3 and psi4, respectively. The torsional angles phi3 and phi4, defined solely to maintain the orientation of the geminal H-atoms of the hydroxymethyl group, are not shown. (See text.). The illustrated trisaccharide is thus specified as a collection of 5 residues which are represented by 3 archetypes. Models of the disaccharide cellobiose (beta-D-Glc p-(1-->4)-D-Glc p) must include residues 1 and 2, but the hydroxymethyl groups (residues 3 and 4) can also be explicitly included in this model PMID:15322949

York, William S; Yi, Xiaobing

2004-08-01

331

Molecular Dynamics of 8-oxoguanine Lesioned B-DNA Molecule - Structure and Energy Analysis  

NASA Astrophysics Data System (ADS)

The molecular dynamics (MD) simulation of DNA mutagenic oxidative lesion - 7,8-dihydro-8-oxoguanine (8-oxoG), complexed with the repair enzyme - human oxoguanine glycosylase 1 (hOGG1) was performed for 1 nanosecond (ns) in order to describe the dynamical process of DNA-enzyme complex formation. After 900 picoseconds of MD the lesioned DNA and enzyme formed a complex that lasted until the end of the simulation at 1 ns. The amino group of arginine 324 was located close to the phosphodiester bond of nucleotide with 8-oxoG enabling chemical reactions between amino acid and lesion. Phosphodiester bond at C5' of 8-oxoG was displaced to the position close to the amino group of arginine 324. In the background simulation of the identical molecular system with the native DNA, neither the complex nor the water mediated hydrogen bond network were observed. The electrostatic energy is supposed to be significant factor causing the disruption of DNA base stacking in DNA duplex and may also to serve as a signal toward the repair enzyme informing on the presence of the lesion.

Pinak, M.; O'Neill, P.; Fujimoto, H.; Nemoto, T.

2004-04-01

332

Light scattering study of natural DNAs over a wide range of molecular weights: Evidence for compaction of the large molecules.  

PubMed

This work reports light scattering measurements on DNA in aqueous solutions (100mM NaCl, 1mM EDTA and 10mM Tris-HCl buffer, pH 7.8) over a wide range of molecular weights (10(2)-10(5) base pairs) and shows that, in the above standard solvent, shorter chains (<10(4) base pairs) behave as a "wormlike chain" and their diffusion coefficients as obtained by dynamic light scattering measurements, confirm the prediction of standard wormlike model, whilst longer chains (>10(4) base pairs) behave in a different manner. Dynamic and static light scattering and SEM analysis indicate that DNA molecules 10(5) base pairs long, condense into compact structures in our solvent conditions. Calculations done using a wormlike model are also presented and discussed in comparison both to our experimental data and to other data reported in the literature. PMID:19482041

Zimbone, Massimo; Baeri, Pietro; Barcellona, Maria Luisa; Li Volti, Giovanni; Bonaventura, Gabriele; Viscuso, Orazio

2009-10-01

333

Molecule-level imaging of Pax6 mRNA distribution in mouse embryonic neocortex by molecular interaction force microscopy  

PubMed Central

Detection of the cellular and tissue distributions of RNA species is critical in our understanding of the regulatory mechanisms underlying cellular and tissue differentiation. Here, we show that an atomic force microscope tip modified with 27-acid dendron, a cone shaped molecule with 27 monomeric units forming its base, can be successfully used to map the spatial distribution of mouse Pax6 mRNA on sectioned tissues of the mouse embryonic neocortex. Scanning of the sectioned tissue with a 30-mer DNA probe attached to the apex of the dendron resulted in detection of the target mRNA on the tissue section, permitting mapping of the mRNA distribution at nanometer resolution. The unprecedented sensitivity and resolution of this process should be applicable to identification of molecular level distribution of various RNAs in a cell.

Jung, Yu Jin; Park, Yu Shin; Yoon, Ki-Jun; Kong, Young-Yun; Park, Joon Won; Nam, Hong Gil

2009-01-01

334

Features in the electronic structure and photoemission spectra of organic molecular semiconductors: The molecules of metal-phthalocyanines and PTCDA  

NASA Astrophysics Data System (ADS)

The role of many-electron effects in the formation of electronic quasiparticle spectra in organic molecular semiconductors (OMS) is analyzed. Many-body perturbation theory, ab initio calculations of metal phthalocyanines and PTCDA molecules, and experimental photoemission spectra are applied to this analysis. It is shown that density functional theory (DFT) poorly reproduces the electronic spectra of OMS. The use of a hybrid functional method (HFM) provides precise reproduction of both valence and conducting bands, while the HOMO-LUMO gap remains underestimated. The correct gap width is obtained in both DFT and HFM, when it is calculated through ionization and affinity energies. It is shown that such an approach gives a formula for gap correction due to electron correlations, which is close to an expression derived from the GW approximation.

Tikhonov, E. V.; Uspenskii, Yu. A.; Khokhlov, D. R.

2013-09-01

335

Diffusion coefficients of small gas molecules in amorphous cis-1,4-polybutadiene estimated by molecular dynamics simulations  

NASA Astrophysics Data System (ADS)

Molecular dynamics (MD) simulations were employed to estimate the diffusion coefficients of small gas molecules (Ar, O2, N2, CO2, and CH4) in amorphous cis-1,4-polybutadiene in the temperature range of 250-400 K. The VT diagram and solubility parameter of the amorphous polymer have been successfully reproduced using a full atomistic potential. Diffusion coefficients were calculated from long NPT MD runs (up to 3 ns) at temperature ranging from 250 up to 400 K. Calculated diffusion coefficients compare well with experimental data as well as previous published work, though a systematic overestimation is found due to the finite-size effect of the model. The influence of various physical and computational parameters on the results is discussed. The diffusion mechanism is examined at the different temperatures of study.

Meunier, M.

2005-10-01

336

Organic molecules in the atmosphere of Jupiter. [low molecular weight hydrocarbons  

NASA Technical Reports Server (NTRS)

Organic synthesis in the primitive solar system was simulated by Fischer Tropsch type experiments. Particular attention was given to the formation of lower molecular weight hydrocarbons. In a gas flow experiment, a gas mixture of H2 and CO was introduced into a heated reaction tube at a constant flow rate and passed through a catalyst (powdered Canyon Diablo). The products that emerged were directly analyzed by gas chromatography. The results of 21 runs under various gas mixing rations, reaction temperatures, and gas-catalyst contact times showed the predominance of the saturated hydrocarbon formation at C sub 4 and C sub 5 over the unsaturated ones. Saturate/unsaturate ratios were mostly less than 0.4 and none showed over 0.7.

Ponnamperuma, C. A.

1978-01-01

337

Bulk and Single-Molecule Characterization of an Improved Molecular Beacon Utilizing H-Dimer Excitonic Behavior  

PubMed Central

Pairs of fluorophores in close proximity often show self-quenching of fluorescence by the well-known H-dimer mechanism. We use a pair of fluorophores in the new dicyanomethylenedihydrofuran (DCDHF) dye family in the design and characterization of a new fluorescent probe for nucleic acid detection, which we refer to as a self-quenched intramolecular dimer (SQuID) molecular beacon (MB). We obtain a quenching efficiency of 97.2%, higher than the only other reported value for a MB employing fluorophore self-quenching by H-dimer formation. Furthermore, the excellent single-molecule (SM) emitter characteristics of the DCDHF dyes allow observation of individual SQuID MB—target complexes immobilized on a surface, where the doubled SM emission intensity of our target-bound beacon ensures a higher signal-to-background ratio than conventional fluorophore-quencher MBs. Additional advantages of the SQuID MB are single-pot labeling, visible colorimetric detection of the target, and intrinsic single-molecule two-step photobleaching behavior, which offers a specific means of discriminating between functional MBs and spurious fluorescence.

Conley, Nicholas R.; Pomerantz, Andrea Kurtz; Wang, Hui; Twieg, Robert J.; Moerner, W. E.

2009-01-01

338

Bulk and single-molecule characterization of an improved molecular beacon utilizing H-dimer excitonic behavior.  

PubMed

Pairs of fluorophores in close proximity often show self-quenching of fluorescence by the well-known H-dimer mechanism. We use a pair of fluorophores in the new dicyanomethylenedihydrofuran (DCDHF) dye family in the design and characterization of a new fluorescent probe for nucleic acid detection, which we refer to as a self-quenched intramolecular dimer (SQuID) molecular beacon (MB). We obtain a quenching efficiency of 97.2%, higher than the only other reported value for a MB employing fluorophore self-quenching by H-dimer formation. Furthermore, the excellent single-molecule (SM) emitter characteristics of the DCDHF dyes allow observation of individual SQuID MB-target complexes immobilized on a surface, where the doubled SM emission intensity of our target-bound beacon ensures a higher signal-to-background ratio than conventional fluorophore-quencher MBs. Additional advantages of the SQuID MB are single-pot labeling, visible colorimetric detection of the target, and intrinsic single-molecule two-step photobleaching behavior, which offers a specific means of discriminating between functional MBs and spurious fluorescence. PMID:17583944

Conley, Nicholas R; Pomerantz, Andrea Kurtz; Wang, Hui; Twieg, Robert J; Moerner, W E

2007-07-19

339

Effects of magnesium ions and water molecules on the structure of amorphous calcium carbonate: a molecular dynamics study.  

PubMed

Molecular dynamics simulations were conducted to elucidate the effects of Mg(2+) and H2O additives on the structure of amorphous calcium carbonate (ACC). New potential parameters for Mg(2+) ions were developed. The distribution function of the angle formed by three nearest-neighbor atoms was introduced to analyze the short-range local structure of ACC. The simulation indicated that ACC had a weakly ordered local structure resembling the local structure of a CaCO3 crystal. The local structure of pure ACC resembled that of vaterite. The formation of the vaterite-like local structure was hindered by Mg(2+) ions, whereas H2O molecules did not significantly influence the structure of ACC when the fraction of H2O molecules was low. However, when the fraction of H2O was high, the formation of a monohydrocalcite-like local structure was promoted. The effects of the additives on the structure of ACC were verified using the size of the additives and the interaction between the additives and CaCO3. The simulated structure of ACC was compared with the structure of CaCO3 crystals nucleated through the formation of ACC particles in real systems. PMID:24188003

Tomono, Hidekazu; Nada, Hiroki; Zhu, Fangjie; Sakamoto, Takeshi; Nishimura, Tatsuya; Kato, Takashi

2013-11-27

340

Molecular dynamics of DNA quadruplex molecules containing inosine, 6-thioguanine and 6-thiopurine.  

PubMed Central

The ability of the four-stranded guanine (G)-DNA motif to incorporate nonstandard guanine analogue bases 6-oxopurine (inosine, I), 6-thioguanine (tG), and 6-thiopurine (tI) has been investigated using large-scale molecular dynamics simulations. The simulations suggest that a G-DNA stem can incorporate inosines without any marked effect on its structure and dynamics. The all-inosine quadruplex stem d(IIII)(4) shows identical dynamical properties as d(GGGG)(4) on the nanosecond time scale, with both molecular assemblies being stabilized by monovalent cations residing in the channel of the stem. However, simulations carried out in the absence of these cations show dramatic differences in the behavior of d(GGGG)(4) and d(IIII)(4). Whereas vacant d(GGGG)(4) shows large fluctuations but does not disintegrate, vacant d(IIII)(4) is completely disrupted within the first nanosecond. This is a consequence of the lack of the H-bonds involving the N2 amino group that is not present in inosine. This indicates that formation of the inosine quadruplex could involve entirely different intermediate structures than formation of the guanosine quadruplex, and early association of cations in this process appears to be inevitable. In the simulations, the incorporation of 6-thioguanine and 6-thiopurine sharply destabilizes four-stranded G-DNA structures, in close agreement with experimental data. The main reason is the size of the thiogroup leading to considerable steric conflicts and expelling the cations out of the channel of the quadruplex stem. The G-DNA stem can accommodate a single thioguanine base with minor perturbations. Incorporation of a thioguanine quartet layer is associated with a large destabilization of the G-DNA stem whereas the all-thioguanine quadruplex immediately collapses.

Stefl, R; Spackova, N; Berger, I; Koca, J; Sponer, J

2001-01-01

341

Manipulating photogenerated radical ion pair lifetimes in wirelike molecules using microwave pulses: molecular spintronic gates.  

PubMed

We have studied spin-dependent charge transfer dynamics in wirelike donor-bridge-acceptor (D-B-A) molecules comprising a phenothiazine (PTZ) donor, an oligo(2,7-fluorene) (FL(n)) bridge, and a perylene-3,4:9,10-bis(dicarboximide) (PDI) acceptor, PTZ-FL(3)-PDI (1) and PTZ-FL(4)-PDI (2), dissolved in the magnetic field-aligned nematic phase of 4-cyano-4'-n-pentylbiphenyl (5CB) at 295 K. Time-resolved EPR spectroscopy using both continuous wave and pulsed microwaves shows that the photogenerated radical pairs (RPs), PTZ(+•)-FL(3)-PDI(-•) and PTZ(+•)-FL(4)-PDI(-•), recombine much faster from the singlet RP manifold than the triplet RP manifold. When a strong resonant microwave ? pulse is applied following RP photogeneration in 1 and 2, the RP lifetimes increase about 50-fold as indicated by electron spin-echo detection. This result shows that the RP lifetime can be greatly extended by rapidly switching off fast triplet RP recombination. PMID:21319821

Miura, Tomoaki; Wasielewski, Michael R

2011-03-01

342

Reconciling molecular regulatory mechanisms with noise patterns of bacterial metabolic promoters in induced and repressed states  

PubMed Central

Assessing gene expression noise in order to obtain mechanistic insights requires accurate quantification of gene expression on many individual cells over a large dynamic range. We used a unique method based on 2-photon fluorescence fluctuation microscopy to measure directly, at the single cell level and with single-molecule sensitivity, the absolute concentration of fluorescent proteins produced from the two Bacillus subtilis promoters that control the switch between glycolysis and gluconeogenesis. We quantified cell-to-cell variations in GFP concentrations in reporter strains grown on glucose or malate, including very weakly transcribed genes under strong catabolite repression. Results revealed strong transcriptional bursting, particularly for the glycolytic promoter. Noise pattern parameters of the two antagonistic promoters controlling the nutrient switch were differentially affected on glycolytic and gluconeogenic carbon sources, discriminating between the different mechanisms that control their activity. Our stochastic model for the transcription events reproduced the observed noise patterns and identified the critical parameters responsible for the differences in expression profiles of the promoters. The model also resolved apparent contradictions between in vitro operator affinity and in vivo repressor activity at these promoters. Finally, our results demonstrate that negative feedback is not noise-reducing in the case of strong transcriptional bursting.

Ferguson, Matthew L.; Le Coq, Dominique; Jules, Matthieu; Aymerich, Stephane; Radulescu, Ovidiu; Declerck, Nathalie; Royer, Catherine A.

2012-01-01

343

Reconciling molecular regulatory mechanisms with noise patterns of bacterial metabolic promoters in induced and repressed states.  

PubMed

Assessing gene expression noise in order to obtain mechanistic insights requires accurate quantification of gene expression on many individual cells over a large dynamic range. We used a unique method based on 2-photon fluorescence fluctuation microscopy to measure directly, at the single cell level and with single-molecule sensitivity, the absolute concentration of fluorescent proteins produced from the two Bacillus subtilis promoters that control the switch between glycolysis and gluconeogenesis. We quantified cell-to-cell variations in GFP concentrations in reporter strains grown on glucose or malate, including very weakly transcribed genes under strong catabolite repression. Results revealed strong transcriptional bursting, particularly for the glycolytic promoter. Noise pattern parameters of the two antagonistic promoters controlling the nutrient switch were differentially affected on glycolytic and gluconeogenic carbon sources, discriminating between the different mechanisms that control their activity. Our stochastic model for the transcription events reproduced the observed noise patterns and identified the critical parameters responsible for the differences in expression profiles of the promoters. The model also resolved apparent contradictions between in vitro operator affinity and in vivo repressor activity at these promoters. Finally, our results demonstrate that negative feedback is not noise-reducing in the case of strong transcriptional bursting. PMID:22190493

Ferguson, Matthew L; Le Coq, Dominique; Jules, Matthieu; Aymerich, Stéphane; Radulescu, Ovidiu; Declerck, Nathalie; Royer, Catherine A

2012-01-01

344

Molecular and biochemical characterization of human galactokinase and its small molecule inhibitors.  

PubMed

Human galactokinase (GALK) is the first enzyme in the Leloir pathway, converting ?-d-galactose into galactose-1-phosphate (Gal-1-P). Recently, there is increasing interest in targeting GALK as a novel therapy to ameliorate the disease manifestations in patients with Classic Galactosemia as it would, in combination with (ga-)lactose restriction reduce accumulation of Gal-1-P, a cytotoxic agent. Previously, we identified 34 small molecule compounds that inhibited GALK in vitro using experimental high-throughput screening. In order to isolate useful lead compounds, we characterized these hits with regards to their kinase selectivity profiles, potency and capability to reduce Gal-1-P accumulation in patient cell lines, and their modes of action. We found that the majority of these compounds had IC(50)s ranging from 0.7?M to 33.3?M. When tested against other members of the GHMP kinase family, three compounds (1, 4, and 24) selectively inhibited GALK with high potency. Through alignment of GALK and mevalonate kinase (MVK) crystal structures, we identified that eight amino acid residues and an L1 loop were different within the ATP-binding pockets of these two closely related kinases. By site-directed mutagenesis experiments, we identified one amino acid residue required for the inhibitory function of two of the three selective compounds. Based on these results, we generated binding models of these two compounds using a high-precision docking program. Compounds 4 and 24 inhibited GALK in a mixed model, while compound 1 exhibited parabolic competitive inhibition. Most importantly, using cells from galactosemic patients we found that selected compounds lowered Gal-1-P concentrations. PMID:20696150

Tang, M; Wierenga, K; Elsas, L J; Lai, K

2010-12-01

345

A molecular beam study of the interaction of CO molecules with a Pt(111) surface using pulse shape analysis  

NASA Astrophysics Data System (ADS)

CO adsorption/desorption on a clean Pt(111) surface has been studied using molecular beam relaxation spectroscopy (MBRS). In contrast to conventional MBRS experiments, lock-in tecniques (or Fourier analysis) have been used here only for a qualitative survey. Pulse shape analysis, which allows the deduction of more detailed information from the experimental data, is discussed in detail, compared to conventional Fourier analysis and used for the results presented here. Detailed analysis of the shape of the MBRS pulse waveform has been used to determine the rate constant for CO desorption, the fraction of scattered signal attributable to chemisorption and the time-of-flight distribution of the non-chemisorbed fraction. The rate constant for CO desorption was measured with MBRS in the temperature range 530-650 K. Complementary measurements under quasi-equilibrium conditions using thermal energy atom (helium) scattering (TEAS) were also performed to extend the desorption rate constant determination down to 430 K, allowing accurate determinations of k over six orders of magnitude. On the clean surface (coverage < 1%), the rate constant for CO desorption obtained was k = 1.5 × 10 5T3sexp(-28.8/ RTs) s-1 (or in Arrhenius form, k = 4.3 × 10 14exp(-32.0/ RTs) s-1), with R in {kcal}/{mol}. The MBRS measurements have also afforded identification of three distinct interactions of CO molecules with the clean Pt(111) surface: chemisorption, direct scattering and a third interaction showing all characteristics which are expected for physisorption. Approximately 3% of the molecules incident at zero coverage desorb from this state independently of temperature in the range 530-650 K. The angular distribution of the directly scattered molecules shows a peak with its maximum shifted away from the specular direction toward the surface normal. The time-of-flight distribution of the directly scattered molecules is similar to that of the incident beam, though somewhat broadened. Both the shift away from the specular direction and the broadening are ascribed to inelastic effects. Measurements of the relative intensities of the chemisorbed and physisorbed signals as a function of surface temperature provide no support to the assignment of the clean surface physisorption state as a precursor to chemisorption.

Verheij, Laurens K.; Lux, Joachim; Anton, A. Brad; Poelsema, Bene; Comsa, George

1987-04-01

346

Metalorganic molecular beam epitaxy growth of GaAs on patterned GaAs substrates  

NASA Astrophysics Data System (ADS)

GaAs layers were grown on etch-patterned (100) GaAs substrates by MOMBE (metalorganic molecular beam epitaxy) using TEGa (triethylgallium) and thermally cracked TEAs (triethylarsine). Morphology and orientation dependencies of the grown facets on the growth temperature (400-630°C) and V/III ratio (2-4) are investigated. Good morphology of grown layers was obtained on (111)A side facets at a low V/III ratio of 3 and low growth temperatures of 450-500°C. We also found strong evidence that the formation of facets is not only governed by the migration of Ga precursors and/or Ga atoms, but also by a preferential catalytic decomposition of Ga precursors on the facet edges.

Marx, D.; Asahi, H.; Liu, X. F.; Okuno, Y.; Inoue, K.; Gonda, S.; Shimomura, S.; Hiyamizu, S.

1994-03-01

347

Identification of a small molecule inhibitor of serine 276 phosphorylation of the p65 subunit of NF-?B using in silico molecular docking  

PubMed Central

NF-?B is activated in many types of cancer. Phosphorylation of p65 at serine 276 is required for the expression of a subset of NF-?B regulated genes, including vascular cell adhesion molecule-1 (VCAM-1) and interleukin-8 (IL-8). Thus, inhibition of serine 276 phosphorylation may prevent metastasis and angiogenesis in certain tumor types. Using in silico molecular docking, small molecules that are predicted to bind to a structural pocket near serine 276 were identified. One compound, NSC-127102, hinders serine 276 phosphorylation and the expression of IL-8 and VCAM-1. Small molecules such as NSC-127102 may be optimized for the future treatment of cancer.

Law, Mary; Corsino, Patrick; Parker, Nicole Teoh; Law, Brian K.

2009-01-01

348

The design, synthesis, and evaluation of molecules that enable or enhance cellular uptake: Peptoid molecular transporters  

PubMed Central

Certain proteins contain subunits that enable their active translocation across the plasma membrane into cells. In the specific case of HIV-1, this subunit is the basic domain Tat49–57 (RKKRRQRRR). To establish the optimal structural requirements for this translocation process, and thereby to develop improved molecular transporters that could deliver agents into cells, a series of analogues of Tat49–57 were prepared and their cellular uptake into Jurkat cells was determined by flow cytometry. All truncated and alanine-substituted analogues exhibited diminished cellular uptake, suggesting that the cationic residues of Tat49–57 play a principal role in its uptake. Charge alone, however, is insufficient for transport as oligomers of several cationic amino acids (histidine, lysine, and ornithine) are less effective than Tat49–57 in cellular uptake. In contrast, a 9-mer of l-arginine (R9) was 20-fold more efficient than Tat49–57 at cellular uptake as determined by Michaelis–Menton kinetic analysis. The d-arginine oligomer (r9) exhibited an even greater uptake rate enhancement (>100-fold). Collectively, these studies suggest that the guanidinium groups of Tat49–57 play a greater role in facilitating cellular uptake than either charge or backbone structure. Based on this analysis, we designed and synthesized a class of polyguanidine peptoid derivatives. Remarkably, the subset of peptoid analogues containing a six-methylene spacer between the guanidine head group and backbone (N-hxg), exhibited significantly enhanced cellular uptake compared to Tat49–57 and even to r9. Overall, a transporter has been developed that is superior to Tat49–57, protease resistent, and more readily and economically prepared.

Wender, Paul A.; Mitchell, Dennis J.; Pattabiraman, Kanaka; Pelkey, Erin T.; Steinman, Lawrence; Rothbard, Jonathan B.

2000-01-01

349

Interstellar molecules  

NASA Astrophysics Data System (ADS)

Some 70 different molecular species have so far been detected variously in diffuse interstellar clouds, dense interstellar clouds, and circumstellar shells. Only simple (diatomic and triatomic) species exist in diffuse clouds because of the penetration of destructive UV radiations, whereas more complex (polyatomic) molecules survive in dense clouds as a result of the shielding against this UV radiation provided by dust grains. A current list of interstellar molecules is given together with a few other molecular species that have so far been detected only in circumstellar shells. Also listed are those interstellar species that contain rare isotopes of several elements. The gas phase ion chemistry is outlined via which the observed molecules are synthesized, and the process by which enrichment of the rare isotopes occurs in some interstellar molecules is described.

Smith, D.

1987-09-01

350

Molecular phylogeny of echiuran worms (Phylum: Annelida) reveals evolutionary pattern of feeding mode and sexual dimorphism.  

PubMed

The Echiura, or spoon worms, are a group of marine worms, most of which live in burrows in soft sediments. This annelid-like animal group was once considered as a separate phylum because of the absence of segmentation, although recent molecular analyses have placed it within the annelids. In this study, we elucidate the interfamily relationships of echiuran worms and their evolutionary pattern of feeding mode and sexual dimorphism, by performing molecular phylogenetic analyses using four genes (18S, 28S, H3, and COI) of representatives of all extant echiuran families. Our results suggest that Echiura is monophyletic and comprises two unexpected groups: [Echiuridae+Urechidae+Thalassematidae] and [Bonelliidae+Ikedidae]. This grouping agrees with the presence/absence of marked sexual dimorphism involving dwarf males and the paired/non-paired configuration of the gonoducts (genital sacs). Furthermore, the data supports the sister group relationship of Echiuridae and Urechidae. These two families share the character of having anal chaetae rings around the posterior trunk as a synapomorphy. The analyses also suggest that deposit feeding is a basal feeding mode in echiurans and that filter feeding originated once in the common ancestor of Urechidae. Overall, our results contradict the currently accepted order-level classification, especially in that Echiuroinea is polyphyletic, and provide novel insights into the evolution of echiuran worms. PMID:23457618

Goto, Ryutaro; Okamoto, Tomoko; Ishikawa, Hiroshi; Hamamura, Yoichi; Kato, Makoto

2013-01-01

351

Molecular layer deposition of functional thin films for advanced lithographic patterning.  

PubMed

Photoresist materials comprise one of the main challenges faced by lithography to meet the requirements of electronic device size scaling. Here we report for the first time the use of molecular layer deposition (MLD) to produce photoresist materials with controllable placement of functional moieties. Polyurea resists films are deposited by MLD using urea coupling reactions between 1,4-phenylene diisocyanate (PDIC) and ethylenediamine (ED) or 2,2'-(propane-2,2-diylbis(oxy))diethanamine (PDDE) monomers in a layer-by-layer fashion with a linear growth rate, allowing acid-labile groups to be incorporated into the film at well-controlled positions. The films are deposited with stoichiometric compositions and have highly uniform surface morphology as investigated using atomic force microscopy. We show that acid treatment can cleave the backbone of the polyurea film at positions where the acid-labile groups are embedded. We further show that after soaking the polyurea film with photoacid generator (PAG), it acts as a photoresist material and we present several UV patterning demonstrations. This approach presents a new way to make molecularly designed resist films for lithography. PMID:21302918

Zhou, Han; Bent, Stacey F

2011-02-01

352

Density-wave patterns for fermionic dipolar molecules on a square optical lattice: Mean-field-theory analysis  

SciTech Connect

We model a system of ultracold fermionic dipolar molecules on a two-dimensional square lattice. Assuming that the molecules are in their nondegenerate hyperfine ground state, and that the dipole moment is polarized perpendicular to the plane (as in the recent experiments on {sup 40}K-{sup 87}Rb molecules), we approximate these molecules as spinless fermions with long-range repulsive dipolar interactions. We use mean-field theory to obtain the restricted phase diagram as a function of the filling, the strength of interaction, and the temperature. We find a number of ordered density-wave phases in the system, as well as phase separation between these phases. A Monte Carlo analysis shows that the higher-period phases are usually suppressed in the exact solution.

Mikelsons, K.; Freericks, J. K. [Department of Physics, Georgetown University, Washington, DC, 20057 (United States)

2011-04-15

353

Tuning of EAG K+ channel inactivation: Molecular determinants of amplification by mutations and a small molecule  

PubMed Central

Ether-à-go-go (EAG) and EAG-related gene (ERG) K+ channels are close homologues but differ markedly in their gating properties. ERG1 channels are characterized by rapid and extensive C-type inactivation, whereas mammalian EAG1 channels were previously considered noninactivating. Here, we show that human EAG1 channels exhibit an intrinsic voltage-dependent slow inactivation that is markedly enhanced in rate and extent by 1–10 µM 3-nitro-N-(4-phenoxyphenyl) benzamide, or ICA105574 (ICA). This compound was previously reported to have the opposite effect on ERG1 channels, causing an increase in current magnitude by inhibition of C-type inactivation. The voltage dependence of 2 µM ICA-induced inhibition of EAG1 current was half-maximal at ?73 mV, 62 mV negative to the half-point for channel activation. This finding suggests that current inhibition by the drug is mediated by enhanced inactivation and not open-channel block, where the voltage half-points for current inhibition and channel activation are predicted to overlap, as we demonstrate for clofilium and astemizole. The mutation Y464A in the S6 segment also induced inactivation of EAG1, with a time course and voltage dependence similar to that caused by 2 µM ICA. Several Markov models were investigated to describe gating effects induced by multiple concentrations of the drug and the Y464A mutation. Models with the smallest fit error required both closed- and open-state inactivation. Unlike typical C-type inactivation, the rate of Y464A- and ICA-induced inactivation was not decreased by external tetraethylammonium or elevated [K+]e. EAG1 channel inactivation introduced by Y464A was prevented by additional mutation of a nearby residue located in the S5 segment (F359A) or pore helix (L434A), suggesting a tripartite molecular model where interactions between single residues in S5, S6, and the pore helix modulate inactivation of EAG1 channels.

Garg, Vivek; Sachse, Frank B.

2012-01-01

354

Evolution of Surface Morphology of Patterned GaAs(100) during Molecular Beam Epitaxial Growth  

NASA Astrophysics Data System (ADS)

We report the results of an investigation of the evolution of the surface morphology during molecular beam epitaxial growth on a patterned GaAs(100) surface. The initial GaAs(100) surfaces were patterned lithographically with arrays of cylindrical pits whose diameters and center-to-center distances are varied in a combinatorial manner. Using atomic force microscopy (AFM), we characterized the evolution of the corrugation throughout the growth. We compare the measured height profiles with simulations from various continuum models[1]. This comparison allows us to discriminate between various continuum modes of growth. * Work supported by the Minta-Martin Foundation, the Laboratory for Physical Sciences, and an NSF-MRSEC, DMR 00-8008. Reference 1 Mehran Kardar, Giorgio Parisi, and Yi-Cheng Zhang, Physical Review Letters 56 (9), 889 (1986); Tao Sun, Hong Guo, and Martin Grant, Physical Review A 40 (11), 6763 (1989); Z.-W. Lai and S. Das Sarma, Physical Review Letters 66 (18), 2348 (1991); M. D. Johnson, C. Orme, A. W. Hunt et al., Physical Review Letters 72 (1), 116 (1994).

Kan, Hung-Chih; Shah, Sonam; Tadayyon-Eslami, Tabassom; Phaneuf, Raymond

2003-03-01

355

Molecular fingerprinting of lacustrian cyanobacterial communities: regional patterns in summer diversity.  

PubMed

The assessment of lacustrian water quality is necessary to comply with environmental regulations. At the regional scale, difficulties reside in the selection of representative lakes. Given the risks towards water quality associated with phytoplankton blooms, a mesoscale survey was carried out in Irish lakes to identify patterns in the distribution and diversity of planktonic cyanobacteria. A stratified sampling strategy was carried out via geographic information systems (GIS) analysis of river catchment attributes due to the range of hydrogeomorphological features and the high number of lakes within the study area. 16S rRNA gene denaturing gradient gel electrophoresis analysis showed variation between the cyanobacterial communities sampled, with lower occurrence of cyanobacteria in August concomitant to increased wind and precipitation regimes. Multivariate analysis delineated three ecoregions based on land cover typology and revealed significant patterns in the distribution of cyanobacterial diversity. A majority of filamentous cyanobacteria genotypes occurred in larger lakes contained river catchments with substantial forest cover. In contrast, higher diversity of spherical cyanobacteria genotypes was observed in lakes of lesser trophic state. In the context of aquatic resource management, the combined use of GIS-based sampling strategy and molecular methods offers promising prospects for assessing microbial community structure at varying scales of space and time. PMID:23802655

Touzet, Nicolas; McCarthy, David; Fleming, Gerard T A

2013-12-01

356

Morphologic and molecular evaluation of Chlamydia trachomatis growth in human endocervix reveals distinct growth patterns  

PubMed Central

In vitro models of Chlamydia trachomatis growth have long been studied to predict growth in vivo. Alternative or persistent growth modes in vitro have been shown to occur under the influence of numerous stressors but have not been studied in vivo. Here, we report the development of methods for sampling human infections from the endocervix in a manner that permits a multifaceted analysis of the bacteria, host and the endocervical environment. Our approach permits evaluating total bacterial load, transcriptional patterns, morphology by immunofluorescence and electron microscopy, and levels of cytokines and nutrients in the infection microenvironment. By applying this approach to two pilot patients with disparate infections, we have determined that their contrasting growth patterns correlate with strikingly distinct transcriptional biomarkers, and are associated with differences in local levels of IFN?. Our multifaceted approach will be useful to dissect infections in the human host and be useful in identifying patients at risk for chronic disease. Importantly, the molecular and morphological analyses described here indicate that persistent growth forms can be isolated from the human endocervix when the infection microenvironment resembles the in vitro model of IFN?-induced persistence.

Lewis, Maria E.; Belland, Robert J.; AbdelRahman, Yasser M.; Beatty, Wandy L.; Aiyar, Ashok A.; Zea, Arnold H.; Greene, Sheila J.; Marrero, Luis; Buckner, Lyndsey R.; Tate, David J.; McGowin, Chris L.; Kozlowski, Pamela A.; O'Brien, Michelle; Lillis, Rebecca A.; Martin, David H.; Quayle, Alison J.

2014-01-01

357

Self-organized density patterns of molecular motors in arrays of cytoskeletal filaments.  

PubMed

The stationary states of systems with many molecular motors are studied theoretically for uniaxial and centered (asterlike) arrangements of cytoskeletal filaments using Monte Carlo simulations and a two-state model. Mutual exclusion of motors from binding sites of the filaments is taken into account. For small overall motor concentration, the density profiles are exponential and algebraic in uniaxial and centered filament systems, respectively. For uniaxial systems, exclusion leads to the coexistence of regions of high and low densities of bound motors corresponding to motor traffic jams, which grow upon increasing the overall motor concentration. These jams are insensitive to the motor behavior at the end of the filament. In centered systems, traffic jams remain small and an increase in the motor concentration leads to a flattening of the profile if the motors move inwards, and to the buildup of a concentration maximum in the center of the aster if motors move outwards. In addition to motor density patterns, we also determine the corresponding patterns of the motor current. PMID:15855661

Klumpp, Stefan; Nieuwenhuizen, Theo M; Lipowsky, Reinhard

2005-05-01

358

Molecular insights into the origin of the Hox-TALE patterning system.  

PubMed

Despite tremendous body form diversity in nature, bilaterian animals share common sets of developmental genes that display conserved expression patterns in the embryo. Among them are the Hox genes, which define different identities along the anterior-posterior axis. Hox proteins exert their function by interaction with TALE transcription factors. Hox and TALE members are also present in some but not all non-bilaterian phyla, raising the question of how Hox-TALE interactions evolved to provide positional information. By using proteins from unicellular and multicellular lineages, we showed that these networks emerged from an ancestral generic motif present in Hox and other related protein families. Interestingly, Hox-TALE networks experienced additional and extensive molecular innovations that were likely crucial for differentiating Hox functions along body plans. Together our results highlight how homeobox gene families evolved during eukaryote evolution to eventually constitute a major patterning system in Eumetazoans. DOI: http://dx.doi.org/10.7554/eLife.01939.001. PMID:24642410

Hudry, Bruno; Thomas-Chollier, Morgane; Volovik, Yael; Duffraisse, Marilyne; Dard, Amélie; Frank, Dale; Technau, Ulrich; Merabet, Samir

2014-01-01

359

The Relation between Recombination Rate and Patterns of Molecular Evolution and Variation in Drosophila melanogaster  

PubMed Central

Genetic recombination associated with sexual reproduction increases the efficiency of natural selection by reducing the strength of Hill–Robertson interference. Such interference can be caused either by selective sweeps of positively selected alleles or by background selection (BGS) against deleterious mutations. Its consequences can be studied by comparing patterns of molecular evolution and variation in genomic regions with different rates of crossing over. We carried out a comprehensive study of the benefits of recombination in Drosophila melanogaster, both by contrasting five independent genomic regions that lack crossing over with the rest of the genome and by comparing regions with different rates of crossing over, using data on DNA sequence polymorphisms from an African population that is geographically close to the putatively ancestral population for the species, and on sequence divergence from a related species. We observed reductions in sequence diversity in noncrossover (NC) regions that are inconsistent with the effects of hard selective sweeps in the absence of recombination. Overall, the observed patterns suggest that the recombination rate experienced by a gene is positively related to an increase in the efficiency of both positive and purifying selection. The results are consistent with a BGS model with interference among selected sites in NC regions, and joint effects of BGS, selective sweeps, and a past population expansion on variability in regions of the genome that experience crossing over. In such crossover regions, the X chromosome exhibits a higher rate of adaptive protein sequence evolution than the autosomes, implying a Faster-X effect.

Campos, Jose L.; Halligan, Daniel L.; Haddrill, Penelope R.; Charlesworth, Brian

2014-01-01

360

Analysis of molecular expression patterns and integration with other knowledge bases using probabilistic Bayesian network models  

SciTech Connect

How can molecular expression experiments be interpreted with greater than ten to the fourth measurements per chip? How can one get the most quantitative information possible from the experimental data with good confidence? These are important questions whose solutions require an interdisciplinary combination of molecular and cellular biology, computer science, statistics, and complex systems analysis. The explosion of data from microarray techniques present the problem of interpreting the experiments. The availability of large-scale knowledge bases provide the opportunity to maximize the information extracted from these experiments. We have developed new methods of discovering biological function, metabolic pathways, and regulatory networks from these data and knowledge bases. These techniques are applicable to analyses for biomedical engineering, clinical, and fundamental cell and molecular biology studies. Our approach uses probabilistic, computational methods that give quantitative interpretations of data in a biological context. We have selected Bayesian statistical models with graphical network representations as a framework for our methods. As a first step, we use a nave Bayesian classifier to identify statistically significant patterns in gene expression data. We have developed methods which allow us to (a) characterize which genes or experiments distinguish each class from the others, (b) cross-index the resulting classes with other databases to assess biological meaning of the classes, and (c) display a gross overview of cellular dynamics. We have developed a number of visualization tools to convey the results. We report here our methods of classification and our first attempts at integrating the data and other knowledge bases together with new visualization tools. We demonstrate the utility of these methods and tools by analysis of a series of yeast cDNA microarray data and to a set of cancerous/normal sample data from colon cancer patients. We discuss extending our methods to inferring biological pathways and networks using more complex dynamic Bayesian networks.

Moler, Edward J.; Mian, I.S.

2000-03-01

361

Contribution of damage-associated molecular patterns to transfusion-related acute lung injury in cardiac surgery  

PubMed Central

Background The incidence of transfusion-related acute lung injury (TRALI) in cardiac surgery patients is high and this condition contributes to an adverse outcome. Damage-associated molecular pattern (DAMP) molecules, HMGB1 and S100A12, are thought to mediate inflammatory changes in acute respiratory distress syndrome. We aimed to determine whether DAMP are involved in the pathogenesis of TRALI in cardiac surgery patients. Materials and methods This was a secondary analysis of a prospective observational trial in cardiac surgery patients admitted to the Intensive Care Unit of a university hospital in the Netherlands. Fourteen TRALI cases were randomly matched with 32 transfused and non-transfused controls. Pulmonary levels of HMGB1, S100A12 and inflammatory cytokines (interleukins-1?, -6, and -8 and tumour necrosis factor-?) were determined when TRALI evolved. In addition, systemic and pulmonary levels of soluble receptor for advanced glycation end products (sRAGE) were determined. Results HMGB1 expression and levels of sRAGE in TRALI patients did not differ from those in controls. There was a trend towards higher S100A12 levels in TRALI patients compared to the controls. Furthermore, S100A12 levels were associated with increased levels of markers of pulmonary inflammation, prolonged cardiopulmonary bypass, hypoxemia and duration of mechanical ventilation. Conclusion No evidence was found that HMGB1 and sRAGE contribute to the development of TRALI. S100A12 is associated with duration of cardiopulmonary bypass, pulmonary inflammation, hypoxia and prolonged mechanical ventilation and may contribute to acute lung injury in cardiac surgery patients.

Muller, Marcella C.A.; Tuinman, Pieter R.; Vlaar, Alexander P.; Tuip, Anita M.; Maijoor, Kelly; Achouiti, Achmed; van t Veer, Cornelis; Vroom, Margreeth B.; Juffermans, Nicole P.

2014-01-01

362

Macromolecular effect on crystal pattern formation in ultra-thin films: Molecular segregation in a binary blend of PEO fractions  

Microsoft Academic Search

In this work we report our investigation on the crystal patterns of a 50\\/50 blend of two polyethylene oxide (PEO) fractions with different molecular weights (M¯w=5040 and 35000 g\\/mol) in ultra-thin films. Using AFM with a hot stage the samples on the surface of silicon wafer were isothermally crystallized at 20.0?Tc?60.0°C. The crystal patterns are different from those of the two pure fractions.

Liuxin Jin; Guoliang Zhang; Xuemei Zhai; Zhenpeng Ma; Ping Zheng; Wei Wang

2009-01-01

363

Quantum-Interference-Controlled Three-Terminal Molecular Transistors Based on a Single Ring-Shaped Molecule Connected to Graphene Nanoribbon Electrodes  

Microsoft Academic Search

We study molecular transistors where graphene nanoribbons act as three metallic electrodes connected to a ring-shaped 18-annulene molecule. Using the nonequilibrium Green function formalism combined with density functional theory, recently extended to multiterminal devices, we show that these nanostructures exhibit exponentially small transmission when the source and drain electrodes are attached in a configuration with destructive interference of electron paths

Kamal K. Saha; Branislav K. Nikolic; Vincent Meunier; Wenchang Lu; J. Bernholc

2010-01-01

364

Synthesis of "Porphyrin-linker-Thiol" molecules with diverse linkers for studies of molecular-based information storage  

PubMed

The attachment of redox-active molecules such as porphyrins to an electroactive surface provides an attractive approach for electrically addressable molecular-based information storage. Porphyrins are readily attached to a gold surface via thiol linkers. The rate of electron transfer between the electroactive surface and the porphyrin is one of the key factors that dictates suitability for molecular-based memory storage. This rate depends on the type and length of the linker connecting the thiol unit to the porphyrin. We have developed different routes for the preparation of thiol-derivatized porphyrins with eight different linkers. Two sets of linkers explore the effects of linker length and conjugation, with one set comprising phenylethyne units and one set comprising alkyl units. One electron-deficient linker has four fluorine atoms attached directly to a thiophenyl unit. To facilitate the synthesis of the porphyrins, convenient routes have been developed to a wide range of aldehydes possessing a protected S-acetylthio group. An efficient synthesis of 1-(S-acetylthio)-4-iodobenzene also has been developed. A set of porphyrins, each bearing one S-acetyl-derivatized linker at one meso position and mesityl moieties at the three remaining meso positions, has been synthesized. Altogether seven new aldehydes, eight free base porphyrins and eight zinc porphyrins have been prepared. The zinc porphyrins bearing the different linkers all form self-assembled monolayers (SAMs) on gold via in situ cleavage of the S-acetyl protecting group. The SAM of each porphyrin is electrochemically robust and exhibits two reversible oxidation waves. PMID:11076590

Gryko; Clausen; Roth; Dontha; Bocian; Kuhr; Lindsey

2000-11-01

365

Molecular orientation of vapor-deposited films of long-chain molecules observed with atomic force microscopy  

NASA Astrophysics Data System (ADS)

Surface structures of the vapor-grown thin films of a long-chain fatty acid, behenic acid, were observed with atomic force microscopy (AFM). The thin films were grown on two substrates, KCl and mica. The present study gave the same conclusion as those obtained with transmission electron microscopy using a replica method: the films on mica revealed island-like growth hillocks with normal orientation of the long chain axis with respect to the substrate. The averaged thickness of the film was 6 nm which corresponds to the length of one dimer of behenic acid. In contrast, the films on KCl showed long-needle morphology with lateral orientation, whose averaged thickness was 3-4 nm. To our best knowledge, the present study is the first AFM observation of the normally oriented growth hillocks of long-chain molecules prepared by physical vapor deposition. The molecular resolution of the methyl end packing of the normal growth film revealed a rectangular lattice (orthorhombic perpendicular subcell) with a two-dimensional lattice diameters at 0.909 and 0.526 nm.

Takiguchi, H.; Izawa, M.; Yase, K.; Ueno, S.; Yoshimura, M.; Yao, T.; Sato, K.

1995-01-01

366

Structure and energetics of model amphiphilic molecules at the water liquid-vapor interface - A molecular dynamics study  

NASA Technical Reports Server (NTRS)

A molecular dynamics study of adsorption of p-n-pentylphenol at infinite dilution at the water liquid-vapor interface is reported. The calculated free energy of adsorption is -8.8 +/- 0.7 kcal/mol, in good agreement with the experimental value of -7.3 kcal/mol. The transition between the interfacial region and the bulk solution is sharp and well-defined by energetic, conformational, and orientational criteria. At the water surface, the phenol head group is mostly immersed in aqueous solvent. The most frequent orientation of the hydrocarbon tail is parallel to the interface, due to dispersion interactions with the water surface. This arrangement of the phenol ring and the alkyl chain requires that the chain exhibits a kink. As the polar head group is being moved into the solvent, the chain length increases and the tail becomes increasingly aligned toward the surface normal, such that the nonpolar part of the molecule exposed to water is minimized. The same effect was achieved when phenol was replaced by a more polar head group, phenolate.

Pohorille, Andrew; Benjamin, Ilan

1993-01-01

367

The pattern recognition molecule ficolin-1 exhibits differential binding to lymphocyte subsets, providing a novel link between innate and adaptive immunity.  

PubMed

Ficolin-1 is a soluble pattern recognition molecule synthesized by myeloid cells and capable of activating the lectin pathway of complement on the surface of pathogens. It is tethered to the membranes of monocytes and granulocytes; however, the biological significance of cell-associated ficolin-1 is unknown. Recognition of healthy host cells by a pattern recognition molecule constitutes a potential hazard to self cells and tissues, emphasizing the importance of further elucidating the reported self-recognition. In the current study we investigated the potential recognition of lymphocytes by ficolin-1 and demonstrated that CD56(dim) NK-cells and both CD4(+) and CD8(+) subsets of activated T-cells were recognized by ficolin-1. In contrast we did not detect binding of ficolin-1 to CD56(bright) NK-cells, NKT-cells, resting T-cells or B-cells. Furthermore, we showed that the protein-lymphocyte interaction occurred via the pathogen-recognition domain of ficolin-1 to sialic acid on the cell surface. Thus, the differential binding of ficolin-1 to lymphocyte subsets suggests ficolin-1 as a novel link between innate and adaptive immunity. Our results provide new insight about the recognition properties of ficolin-1 and point toward additional immune modulating functions of the molecule besides its role in pathogen recognition. PMID:24161415

Genster, Ninette; Ma, Ying Jie; Munthe-Fog, Lea; Garred, Peter

2014-02-01

368

Versatile piezoelectric pulsed molecular beam source for gaseous compounds and organic molecules with femtomole accuracy for UHV and surface science applications  

SciTech Connect

This note describes the construction of a piezoelectric pulsed molecular beam source based upon a design presented in an earlier work [D. Proch and T. Trickl, Rev. Sci. Instrum. 60, 713 (1988)]. The design features significant modifications that permit the determination of the number of molecules in a beam pulse with an accuracy of 1x10{sup 11} molecules per pulse. The 21 cm long plunger-nozzle setup allows the molecules to be brought to any point of the UHV chamber with very high intensity. Furthermore, besides typical gaseous compounds, also smaller organic molecules with a vapor pressure higher than 0.1 mbar at room temperature may serve as feed material. This makes the new design suitable for various applications in chemical and surface science studies.

Schiesser, Alexander; Schaefer, Rolf [Eduard-Zintl-Institut fuer Anorganische und Physikalische Chemie, Technische Universitaet Darmstadt, Petersenstrasse 20, 64287 Darmstadt (Germany)

2009-08-15

369

Comparison of the Singer method and the constraints method for molecular dynamics with linear molecules on the vector computer CYBER 205  

NASA Astrophysics Data System (ADS)

The vectorization of FORTRAN programmes for the computation of the forces in molecular dynamics (MD) calculations are described. For systems containing linear molecules, two equivalent MD methods can be used: the Singer method and the constraints method. The FORTRAN vector code is presented and discussed for both methods. A comparison of computational times on the CYBER 205 is presented. For the two-centre Lennard-Jones potential, the constraints algorithm becomes increasingly less efficient than the Singer algorithm when executed on the CYBER 205. The reason for this is the difference in the neighbour-list which is made for the centre of each molecule in the Singer method and for each site in the molecule in the constraints method. Both programmes run about a factor of 15 faster on the Cyber 205 than on the conventional computer Cyber 175, for 108 or 256 linear molecules.

Hoheisel, C.; Vogelsang, R.; Schoen, M.

1987-01-01

370

The Plant Actin Cytoskeleton Responds to Signals from Microbe-Associated Molecular Patterns  

PubMed Central

Plants are constantly exposed to a large and diverse array of microbes; however, most plants are immune to the majority of potential invaders and susceptible to only a small subset of pathogens. The cytoskeleton comprises a dynamic intracellular framework that responds rapidly to biotic stresses and supports numerous fundamental cellular processes including vesicle trafficking, endocytosis and the spatial distribution of organelles and protein complexes. For years, the actin cytoskeleton has been assumed to play a role in plant innate immunity against fungi and oomycetes, based largely on static images and pharmacological studies. To date, however, there is little evidence that the host-cell actin cytoskeleton participates in responses to phytopathogenic bacteria. Here, we quantified the spatiotemporal changes in host-cell cytoskeletal architecture during the immune response to pathogenic and non-pathogenic strains of Pseudomonas syringae pv. tomato DC3000. Two distinct changes to host cytoskeletal arrays were observed that correspond to distinct phases of plant-bacterial interactions i.e. the perception of microbe-associated molecular patterns (MAMPs) during pattern-triggered immunity (PTI) and perturbations by effector proteins during effector-triggered susceptibility (ETS). We demonstrate that an immediate increase in actin filament abundance is a conserved and novel component of PTI. Notably, treatment of leaves with a MAMP peptide mimic was sufficient to elicit a rapid change in actin organization in epidermal cells, and this actin response required the host-cell MAMP receptor kinase complex, including FLS2, BAK1 and BIK1. Finally, we found that actin polymerization is necessary for the increase in actin filament density and that blocking this increase with the actin-disrupting drug latrunculin B leads to enhanced susceptibility of host plants to pathogenic and non-pathogenic bacteria.

Henty-Ridilla, Jessica L.; Shimono, Masaki; Li, Jiejie; Chang, Jeff H.; Day, Brad; Staiger, Christopher J.

2013-01-01

371

Changes in holothurian coelomocyte populations following immune stimulation with different molecular patterns  

PubMed Central

Echinoderms possess a variety of cells populating the coelomic fluid; these cells are responsible for mounting defense against foreign agents. In the sea cucumber Holothuria glaberrima, four different coelomocyte types were readily distinguished using morphological, histochemical and physiological (phagocytic activity) parameters: lymphocytes, phagocytes, spherulocytes and “giant” cells (listed in order of abundance). Monoclonal antibodies generated against sea cucumber tissues and one polyclonal against sea urchin mayor yolk protein (MYP) were also used to characterize these cell populations. The effects of several pathogen-associated molecular patterns (PAMPs): Lipopolysaccharides from E. coli (LPS), heat-killed Staphylococcus aureus (SA) and a synthetic dsRNA were studied on coelomocyte cell populations. PAMPs increased the phagocytic activity of the holothurian coelomocytes, and were able to induce selective immune responses in several of these populations, demonstrating the ability of the sea cucumber to respond to a different variety of immune challenges. Overall, these results show the variety of cells that populate the coelomic fluid of the holothurian and demonstrate their involvement in immune reactions. These animals represent an untapped resource for new findings into the evolution and development of the immune response not only in invertebrates but also in phylogenetically shared reactions with vertebrates.

Ramirez-Gomez, Francisco; Aponte-Rivera, Francisco; Mendez-Castaner, Lumen; Garcia-Arraras, Jose E.

2010-01-01

372

Viral Capsid Is a Pathogen-Associated Molecular Pattern in Adenovirus Keratitis  

PubMed Central

Human adenovirus (HAdV) infection of the human eye, in particular serotypes 8, 19 and 37, induces the formation of corneal subepithelial leukocytic infiltrates. Using a unique mouse model of adenovirus keratitis, we studied the role of various virus-associated molecular patterns in subsequent innate immune responses of resident corneal cells to HAdV-37 infection. We found that neither viral DNA, viral gene expression, or viral replication was necessary for the development of keratitis. In contrast, empty viral capsid induced keratitis and a chemokine profile similar to intact virus. Transfected viral DNA did not induce leukocyte infiltration despite CCL2 expression similar to levels in virus infected corneas. Mice without toll-like receptor 9 (Tlr9) signaling developed clinical keratitis upon HAdV-37 infection similar to wild type mice, although the absolute numbers of activated monocytes in the cornea were less in Tlr9?/? mice. Virus induced leukocytic infiltrates and chemokine expression in mouse cornea could be blocked by treatment with a peptide containing arginine glycine aspartic acid (RGD). These results demonstrate that adenovirus infection of the cornea induces chemokine expression and subsequent infiltration by leukocytes principally through RGD contact between viral capsid and the host cell, possibly through direct interaction between the viral capsid penton base and host cell integrins.

Chintakuntlawar, Ashish V.; Zhou, Xiaohong; Rajaiya, Jaya; Chodosh, James

2010-01-01

373

TLR activation regulates damage-associated molecular pattern isoforms released during pyroptosis  

PubMed Central

Infection of macrophages by bacterial pathogens can trigger Toll-like receptor (TLR) activation as well as Nod-like receptors (NLRs) leading to inflammasome formation and cell death dependent on caspase-1 (pyroptosis). Complicating the study of inflammasome activation is priming. Here, we develop a priming-free NLRC4 inflammasome activation system to address the necessity and role of priming in pyroptotic cell death and damage-associated molecular pattern (DAMP) release. We find pyroptosis is not dependent on priming and when priming is re-introduced pyroptosis is unaffected. Cells undergoing unprimed pyroptosis appear to be independent of mitochondrial involvement and do not produce inflammatory cytokines, nitrous oxide (NO), or reactive oxygen species (ROS). Nevertheless, they undergo an explosive cell death releasing a chemotactic isoform of the DAMP high mobility group protein box 1 (HMGB1). Importantly, priming through surface TLRs but not endosomal TLRs during pyroptosis leads to the release of a new TLR4-agonist cysteine redox isoform of HMGB1. These results show that pyroptosis is dominant to priming signals and indicates that metabolic changes triggered by priming can affect how cell death is perceived by the immune system.

Nystrom, Sanna; Antoine, Daniel J; Lundback, Peter; Lock, John G; Nita, Andreia F; Hogstrand, Kari; Grandien, Alf; Erlandsson-Harris, Helena; Andersson, Ulf; Applequist, Steven E

2013-01-01

374

Multielectron effects in high harmonic generation in N2 and benzene: Simulation using a non-adiabatic quantum molecular dynamics approach for laser-molecule interactions  

NASA Astrophysics Data System (ADS)

A mixed quantum-classical approach is introduced which allows the dynamical response of molecules driven far from equilibrium to be modeled. This method is applied to the interaction of molecules with intense, short-duration laser pulses. The electronic response of the molecule is described using time-dependent density functional theory (TDDFT) and the resulting Kohn-Sham equations are solved numerically using finite difference techniques in conjunction with local and global adaptations of an underlying grid in curvilinear coordinates. Using this approach, simulations can be carried out for a wide range of molecules and both all-electron and pseudopotential calculations are possible. The approach is applied to the study of high harmonic generation in N2 and benzene using linearly polarized laser pulses and, to the best of our knowledge, the results for benzene represent the first TDDFT calculations of high harmonic generation in benzene using linearly polarized laser pulses. For N2 an enhancement of the cut-off harmonics is observed whenever the laser polarization is aligned perpendicular to the molecular axis. This enhancement is attributed to the symmetry properties of the Kohn-Sham orbital that responds predominantly to the pulse. In benzene we predict that a suppression in the cut-off harmonics occurs whenever the laser polarization is aligned parallel to the molecular plane. We attribute this suppression to the symmetry-induced response of the highest-occupied molecular orbital.

Dundas, Daniel

2012-05-01

375

Patterns of integration of DNA microinjected into cultured mammalian cells: Evidence for homologous recombination between injected plasmid DNA molecules  

SciTech Connect

The authors examined the fate of DNA microinjected into nuclei of cultured mammalian cells. The sequence composition and the physical form of the vector carrying the selectable gene affected the efficiency of DNA-mediated transformation. Introduction of sequences near the simian virus 40 origin of DNA replication or in the long terminal repeat of avian sarcoma provirus into a recombinant plasmid containing the herpes simplex virus thymidine kinase gene (pBR322/HSV-tk) enhanced the frequency of transformation of LMtk/sup -/ and RAT-2tk/sup -/ cells to the TK/sup +/ phenotype 20- to 40-fold. In cells receiving injections of only a few plasmid DNA molecules, the transformation frequency was 40-fold higher after injection of linear molecules than after injection of supercoiled molecules. By controlling the number of gene copies injected into a recipient cell, we could obtain transformants containing a single copy or as many as 50 to 100 copies of the selectable gene. By analyzing transformants obtained by coinjecting two vectors which were identical except that in one a portion of the vector was inverted, the authors were able to conclude that the head-to-tail concatemers were generated predominantly by homologous recombination. Surprisingly, these head-to-tail concatemers were found in transformants obtained by injecting either supercoiled or linear plasmid DNA.

Folger, K.R.; Wong, E.A.; Wahl, G.; Capecchi, M.R.

1982-11-01

376

Nanopolaritonics with a continuum of molecules: simulations of molecular-induced selectivity in plasmonics transport through a continuous Y-shape.  

PubMed

Using the recent NF (near-field) formulation for electrodynamics on the nanoscale, we simulate transport in a Y-shape gold nanostructure in the presence of 2-level molecules. NF is shown to be easily integrated with the Liouville equation, producing a simple and efficient nanopolaritons (plasmons-excitons) solver, with a large time step. Two cases are considered: coating of the gold structure with molecular layers thinner than the structure, and filling space with aligned molecules. In both cases significant effects on the radiation transport are obtained even for low molecular densities. At low densities the effects are primarily an overall reduction of the plasmonics peak, but at higher densities there is a significant selectivity control by the molecules. A redshift is predicted, especially for the space-filling case. The combined nanopolariton shows qualitative hybridization, and the spectral peaks separate with increasing coupling, i.e., with increasing molecular densities. The results open the way to "control of light by light," i.e., controlling plasmonic light transport by inducing a change in the direction of the guiding molecular dipoles through radiation or other means. PMID:22128933

Neuhauser, Daniel

2011-11-28

377

Molecular dynamics simulation of the dynamical behaviors of an aromatic carboxylic acid molecule with different conformations on a Au (111) surface  

NASA Astrophysics Data System (ADS)

In this study, the behavior of a single tricarboxylic acid derivative, 1,3,5-tris(carboxymethoxy) benzene [TCMB, C6H3(OCH2COOH)3] on a Au (111) substrate at 50 K has been investigated by molecular dynamics simulation. Four possible conformations of the TCMB molecule adsorbed on the Au (111) substrate are found and which display different trajectories of movement and dynamical behaviors. The lock-and-key geometry between the TCMB molecule of different conformations and atomic arrangement of the Au (111) surface was also observed.

Ju, Shin-Pon; Lee, Wen-Jay; Chen, Hui-Chuan; Chang, Jee-Gong

2007-04-01

378

Simulation of single DNA molecule stretching and immobilization in a de-wetting two-phase flow over micropillar-patterned surface  

PubMed Central

We investigate single DNA stretching dynamics in a de-wetting flow over micropillars using Brownian dynamics simulation. The Brownian dynamics simulation is coupled with transient flow field computation through a numerical particle tracking algorithm. The droplet formation on the top of the micropillar during the de-wetting process creates a flow pattern that allows DNA to stretch across the micropillars. It is found that DNA nanowire forms if DNA molecules could extend across the stagnation point inside the connecting water filament before its breakup. It also shows that DNA locates closer to the top wall of the micropillar has higher chance to enter the flow pattern of droplet formation and thus has higher chance to be stretched across the micropillars. Our simulation tool has the potential to become a design tool for DNA manipulation in complex biomicrofluidic devices.

Liao, Wei-Ching; Hu, Xin; Wang, Weixiong; James Lee, L.

2013-01-01

379

Simulation of single DNA molecule stretching and immobilization in a de-wetting two-phase flow over micropillar-patterned surface.  

PubMed

We investigate single DNA stretching dynamics in a de-wetting flow over micropillars using Brownian dynamics simulation. The Brownian dynamics simulation is coupled with transient flow field computation through a numerical particle tracking algorithm. The droplet formation on the top of the micropillar during the de-wetting process creates a flow pattern that allows DNA to stretch across the micropillars. It is found that DNA nanowire forms if DNA molecules could extend across the stagnation point inside the connecting water filament before its breakup. It also shows that DNA locates closer to the top wall of the micropillar has higher chance to enter the flow pattern of droplet formation and thus has higher chance to be stretched across the micropillars. Our simulation tool has the potential to become a design tool for DNA manipulation in complex biomicrofluidic devices. PMID:24404023

Liao, Wei-Ching; Hu, Xin; Wang, Weixiong; James Lee, L

2013-01-01

380

Beyond the molecular orbital conception of electronically excited states through the quantum theory of atoms in molecules.  

PubMed

We show that the use of the quantum theory of atoms in molecules (QTAIM) in electronically excited states allows expanding the knowledge that the molecular orbital (MO) framework provides about electronic rearrangements. Despite that historical prejudice seemed to preclude the use of QTAIM beyond the electronic ground state, this paper evidences that QTAIM is versatile enough to deal with excited states. As an example, the paradigmatic n ? ?* electronic transition of formaldehyde is analyzed. Using QTAIM, an energy partition of excited state energies into atomic and diatomic energies is carried out for the first time. This partition shows that upon electronic excitation the atoms of the CO bond experience a stabilization in their net energies, accompanied by a destabilization in their interaction, a fact which is in accordance with the idea of populating an antibonding ?* MO. The associated C-O bond elongation in the n?* state does not involve a change in the ? atomic populations - as one would expect from a ?* orbital - but in the ? ones. Moreover, it is also found that the n?* state is characterized by a weaker C-O interaction energy in comparison to that in the electronic ground state. In order to strengthen this interaction, the electron-electron repulsion between C and O is reduced via a symmetry-breaking of the electron density, causing the C pyramidalization. A topological analysis based on the Laplacian of the electron density and on the electron localization function (ELF) reveals that the n ? ?* transition can be visualized as a rotation of 90° of the oxygen lone pairs. PMID:24709865

Ferro-Costas, David; Pendás, Angel Martín; González, Leticia; Mosquera, Ricardo A

2014-04-23

381

Airborne molecular contamination control in the micromirror SLM-based deep ultraviolet DUV SIGMA7300 laser pattern generator  

NASA Astrophysics Data System (ADS)

Airborne molecular contamination (AMC) in the form of bases, acids and condensable organic and inorganic substances threaten both costly and sensitive optics and mask pattern formation in the chemically amplified resists (CAR) used for both E-beam and laser lithography. This is particularly so for mask pattern generators due to the relatively long writing times. In the development work of the SLM-based DUV-laser mask pattern generator Sigma7300, AMC aspects have been taken into consideration from an early stage. That includes e.g. analysis and selection of construction materials and development of handling methods as well as application of chemical filtering systems. Tool manufacturer and filter supplier have together specified and designed efficient hybrid filtration systems for use in Sigma7300. This paper describes AMC aspects specific for mask pattern generators, the successful design actions of the Sigma7300 and verifying analyses of the processes.

Ekberg, Mats; Fosshaug, Hans A.; Ostrom, Thomas; Bjornangen, Peter; Utterback, Thomas; Skotte, Per-Uno; Higley, John; Ruede, David; Kishkovich, Oleg P.

2004-05-01

382

Tuning stamp surface energy for soft lithography of polar molecules to fabricate bioactive small-molecule microarrays.  

PubMed

Soft-lithography-based techniques are widely used to fabricate microarrays. Here, the use of microcontact insertion printing is described, a soft-lithography method specifically developed for patterning at the dilute scales necessary for highly selective biorecognition. By carefully tuning the polar surface energy of polymeric stamps, problems associated with patterning hydrophilic tether molecules inserted into hydrophilic host self-assembled monolayers (SAMs) are surmounted. Both prefunctionalized tethers and on-chip functionalization of SAMs patterned by microcontact insertion printing enable the fabrication of small-molecule microarrays. Substrates patterned with the neurotransmitter precursor 5-hydroxytryptophan selectively capture a number of different types of membrane-associated receptor proteins, which are native binding partners evolved to recognize free serotonin. These advances provide new avenues for chemically patterning small molecules and fabricating small molecule microarrays with highly specific molecular recognition capabilities. PMID:21538866

Vaish, Amit; Shuster, Mitchell J; Cheunkar, Sarawut; Weiss, Paul S; Andrews, Anne M

2011-05-23

383

Photoelectron diffraction mapping: Molecules illuminated fromwithin  

SciTech Connect

We demonstrate the use of a multiparticle coincidencetechnique to image the diffraction of an electronwave whose source isplaced at a specific site in a free molecule. Core-level photoelectronsare usedto illuminate the molecule from within. By measuring the vectormomenta of two molecular fragmentsand the photoelectron, a richlystructured electron diffraction pattern is obtained in a body-fixed frameof the randomly oriented molecule in the gas phase. We illustrate thistechnique for CO, creating aphotoelectron from the C1s shell and scanningits energy from zero to 30 eV.

Landers, A.; Weber, Th.; Ali, I.; Cassimi, A.; Hattass, M.; Jagutzki, O.; Nauert, A.; Osipov, T.; Staudte, A.; Prior, M.H.; Schmidt-Bocking, H.; Cocke, C.L.; Dorner, R.

2001-07-02

384

The first vitellogenin receptor from a Lepidopteran insect: molecular characterization, expression patterns and RNA interference analysis.  

PubMed

The vitellogenin receptor (VgR) belongs to the low-density lipoprotein receptor (LDLR) superfamily, and is an important carrier for the uptake of vitellogenin (Vg) into developing oocytes of all oviparous species. The first full-length message for a VgR from a Lepidopteran insect was cloned and sequenced from the ovary of Spodoptera litura Fabricius (GenBank accession no. GU983858). The coding region consisted of 5370 bp flanked by a 49 bp 5'-untranslated region (UTR) and a 177 bp 3'-UTR, which encoded a 1798-residue protein with a predicted molecular weight (MW) of 201.69 kDa. S. litura VgR (SlVgR)comprised two ligand binding sites with four LDLR class A repeats in the first domain and seven in the second domain, an epidermal growth factor-like domain containing an LDLR class B repeat and a YWXD motif, a transmembrane domain and a cytoplasmic domain. A phylogenetic relationship placed SlVgR as a separate group from the other insects. SlVgR messenger RNA (mRNA) was specifically expressed in the ovarian tissues. The developmental expression patterns showed that VgR mRNA was first transcribed in 6(th) day female pupae and the maximum level of VgR mRNA appeared in 36-h-old adults. Immunoblot analysis detected an ovary-specific VgR protein with a MW of ?200 kDa, whose development profiles were consistent with VgR mRNA expression patterns. RNA inteference (RNAi) specifically disrupted the VgR gene by injection of 3 or 5 µg VgR double-stranded RNA per insect in 4(th) or 6(th) day pupae. RNAi of SlVgR led to a phenotype characterized by high Vg accumulation in the haemolymph, low Vg deposition in the ovary and the failure of insect spawning. These results mean that VgR is critical for binding Vg and transporting it into the oocytes of the insect ovary, thus playing an important role in insect reproduction. PMID:20955241

Shu, Y H; Wang, J W; Lu, K; Zhou, J L; Zhou, Q; Zhang, G R

2011-02-01

385

Diverse redox-active molecules bearing O-, S-, or Se-terminated tethers for attachment to silicon in studies of molecular information storage.  

PubMed

A molecular approach to information storage employs redox-active molecules tethered to an electroactive surface. Attachment of the molecules to electroactive surfaces requires control over the nature of the tether (linker and surface attachment group). We have synthesized a collection of redox-active molecules bearing different linkers and surface anchor groups in free or protected form (hydroxy, mercapto, S-acetylthio, and Se-acetylseleno) for attachment to surfaces such as silicon, germanium, and gold. The molecules exhibit a number of cationic oxidation states, including one (ferrocene), two [zinc(II)porphyrin], three [cobalt(II)porphyrin], or four (lanthanide triple-decker sandwich compound). Electrochemical studies of monolayers of a variety of the redox-active molecules attached to Si(100) electrodes indicate that molecules exhibit a regular mode of attachment (via a Si-X bond, X = O, S, or Se), relatively homogeneous surface organization, and robust reversible electrochemical behavior. The acetyl protecting group undergoes cleavage during the surface deposition process, enabling attachment to silicon via thio or seleno groups without handling free thiols or selenols. PMID:14986994

Balakumar, Arumugham; Lysenko, Andrey B; Carcel, Carole; Malinovskii, Vladimir L; Gryko, Daniel T; Schweikart, Karl-Heinz; Loewe, Robert S; Yasseri, Amir A; Liu, Zhiming; Bocian, David F; Lindsey, Jonathan S

2004-03-01

386

Microbe associated molecular patterns from rhizosphere bacteria trigger germination and Papaver somniferum metabolism under greenhouse conditions.  

PubMed

Ten PGPR from different backgrounds were assayed on Papaver somniferum var. Madrigal to evaluate their potential as biotic elicitors to increase alkaloid content under the rationale that some microbe associated molecular patterns (MAMPs) are able to trigger plant metabolism. First, the 10 strains and their culture media at two different concentrations were tested for their ability to trigger seed germination. Then, the best three strains were tested for their ability to increase seedling growth and alkaloid levels under greenhouse conditions. Only three strains and their culture media enhanced germination. Then, germination enhancing capacity of these best three strains, N5.18 Stenotrophomonas maltophilia, Aur9 Chryseobacterium balustinum and N21.4 Pseudomonas fluorescens was evaluated in soil. Finally, the three strains were applied on seedlings at two time points, by soil drench or by foliar spray. Photosynthesis was measured, plant height was recorded, capsules were weighted and alkaloids analyzed by HPLC. Only N5.18 delivered by foliar spray significantly increased plant height coupled to an increase in total alkaloids and a significant increase in opium poppy straw dry weight; these increases were supported by a better photosynthetic efficiency. The relative contents of morphine, thebaine, codeine and oripavine were affected by this treatment causing a significant increase in morphine coupled to a decrease in thebaine, demonstrating the effectivity of MAMPs from N5.18 in this plant species. Considering the increase in capsule biomass and alkaloids together with the acceleration of germination, strain N5.18 appears as a good candidate to elicit plant metabolism and consequently, to increase productivity of Papaver somniferum. PMID:24296249

Bonilla, A; Sarria, A L F; Algar, E; Muñoz Ledesma, F J; Ramos Solano, B; Fernandes, J B; Gutierrez Mañero, F J

2014-01-01

387

Temporal Patterns of Soluble Adhesion Molecules in Cerebrospinal Fluid and Plasma in Patients with the Acute Brain Infraction  

PubMed Central

The aim of this study was to define concentration changes of soluble adhesion molecules (sICAM-1, sVCAM-1 and sE-Selectin) in cerebrospinal fluid and plasma, as well as, number of peripheral blood leukocytes and the albumin coefficient in the patients with the acute brain infarction. We also, analyzed the correlation between the measured levels, the infarct volume and the degree of neurological and the functional deficit. The study included 50 patients with the acute cerebral infarction and the control group consisted of 16 patients, age and sex matched. Obtained results showed significant increase in number of leukocytes, the albumin coefficient and the level of soluble adhesion molecules within the first seven days in patients. The highest values of measured parameters were noted within the third and the fourth day after the insult, which is the suggested period of maximal intensity of inflammatory reactions. Significant correlation was found between measured parameters and the infarct volume, the degree of neurological and the functional deficit. The results suggest that investigated parameters in CSF and blood represent a dynamic index of inflammatory events as one of the fundametal mechanisms responsible for neuron damage during acute phase of brain infarction.

Selakovic, Vesna; Raicevic, Ranko; Radenovic, Lidija

2009-01-01

388

Investigation of multi-state charge-storage properties of redox-active organic molecules in silicon-molecular hybrid devices for DRAM and Flash applications  

NASA Astrophysics Data System (ADS)

Molecular electronics has recently spawned a considerable amount of interest with several molecules possessing charge-conduction and charge-storage properties proposed for use in electronic devices. Hybrid silicon-molecular technology has the promise of augmenting the current silicon technology and provide for a transitional path to future molecule-only technology. The focus of this dissertation work has been on developing a class of hybrid silicon-molecular electronic devices for DRAM and Flash memory applications utilizing redox-active molecules. This work exploits the ability of molecules to store charges with single-electron precision at room temperature. The hybrid devices are fabricated by forming self-assembled monolayers of redox-active molecules on Si and oxide (SiO2 and HfO2) surfaces via formation of covalent linkages. The molecules possess discrete quantum states from which electrons can tunnel to the Si substrate at discrete applied voltages (oxidation process, cell write), leaving behind a positively charged layer of molecules. The reduction (erase) process, which is the process of electrons tunneling back from Si to the molecules, neutralizes the positively charged molecular monolayer. Hybrid silicon-molecular capacitor test structures were electrically characterized with an electrolyte gate using cyclic voltammetry (CyV) and impedance spectroscopy (CV) techniques. The redox voltages, kinetics (write/erase speeds) and charge-retention characteristics were found to be strongly dependent on the Si doping type and densities, and ambient light. It was also determined that the redox energy states in the molecules communicate with the valence band of the Si substrate. This allows tuning of write and read states by modulating minority carriers in n- and p-Si substrates. Ultra-thin dielectric tunnel barriers (SiO2, HfO2) were placed between the molecules and the Si substrate to augment charge-retention for Flash memory applications. The redox response was studied as a function of tunnel oxide thickness, dielectric permittivity and energy barrier, and modified Butler-Volmer expressions were postulated to describe the redox kinetics. The speed vs. retention performance of the devices was improved via asymmetric layered tunnel barriers. The properties of molecules can be tailored by molecular design and synthetic chemistry. In this work, it was demonstrated that an alternate route to tune/enhance the properties of the hybrid device is to engineer the substrate (silicon) component. The molecules were attached to diode surfaces to tune redox voltages and improve charge-retention characteristics. N+ pockets embedded in P-Si well were utilized to obtain multiple states from a two-state molecule. The structure was also employed as a characterization tool in investigating the intrinsic properties of the molecules such as lateral conductivity within the monolayer. Redox molecules were also incorporated on an ultra thin gate-oxide of Si MOSFETs with the intent of studying the interaction of redox states with Si MOSFETs. The discrete molecular states were manifested in the drain current and threshold voltage characteristics of the device. This work demonstrates the multi-state modulation of Si-MOSFETs' drain current via redox-active molecular monolayers. Polymeric films of redox-active molecules were incorporated to improve the charge-density (ON/OFF ratio) and these structures may be employed for multi-state, low-voltage Flash memory applications. The most critical aspect of this research effort is to build a reliable and high density solid state memory technology. To this end, efforts were directed towards replacement of the electrolytic gate, which forms an extremely thin insulating double layer (˜10 nm) at the electrolyte-molecule interface, with a combination of an ultra-thin high-K dielectric layer and a metal gate. Several interesting observations were made in the research approaches towards integration and provided valuable insights into the electrolyte-redox systems. In summary, this work provides fundamental insigh

Gowda, Srivardhan Shivappa

389

Study of Rayleigh-Benard convection by pattern of water molecular flow observation as function of temperature difference  

NASA Astrophysics Data System (ADS)

An observation set up of Rayleigh Benard Convection (RBC) phenomenon has been developed. Observation set up made from glass box limited by two reservoirs, i.e. bottom and top reservoirs. The bottom reservoir is hotter than the top reservoir which has function to heat horizontal layers of fluid from below. The used media to observe fluid dynamics is water which mixed by teak saw dust as representation of water molecular. The observation show that increasing of temperature difference (?T) between two reservoirs causes the pattern of water molecular flow was different i.e. laminar and turbulent.

Poluakan, Cosmas; Yusuf, Yusril; Tiwow, Vistarani Arini

2012-06-01

390

MAp44, a human protein associated with pattern recognition molecules of the complement system and regulating the lectin pathway of complement activation.  

PubMed

Essential effector functions of innate immunity are mediated by complement activation initiated by soluble pattern recognition molecules: mannan-binding lectin (MBL) and the ficolins. We present a novel, phylogenetically conserved protein, MAp44, which is found in human serum at 1.4 microg/ml in Ca(2+)-dependent complexes with the soluble pattern recognition molecules. The affinity for MBL is in the nanomolar range (K(D) = 0.6 nM) as determined by surface plasmon resonance. The first eight exons of the gene for MAp44 encode four domains shared with MBL-associated serine protease (MASP)-1 and MASP-3 (CUB1-EGF-CUB2-CCP1), and a ninth exon encodes C-terminal 17 aa unique to MAp44. mRNA profiling in human tissues shows high expression in the heart. MAp44 competes with MASP-2 for binding to MBL and ficolins, resulting in inhibition of complement activation. Our results add a novel mechanism to those known to control the innate immune system. PMID:19917686

Degn, Søren E; Hansen, Annette G; Steffensen, Rudi; Jacobsen, Christian; Jensenius, Jens C; Thiel, Steffen

2009-12-01

391

EXPRESSION OF PATTERN IN PLANTS: COMBINING MOLECULAR AND CALCULUS-BASED BIOPHYSICAL PARADIGMS1  

Microsoft Academic Search

Pattern formation in plant meristems occurs across a broad scale. At the topographical level (large scale), tissue folding in the meristem is responsible for the initiation of new organs in specific phyllotactic patterns and also determines organ shape. At the cellular level (small scale), oriented cell division and microtubule-based cellulose reinforcement control cell pattern and growth direction. I argue here

PAUL B. GREEN

392

Cyclodextrin-supported organic matrix for application of MALDI-MS for forensics. Soft-ionization to obtain protonated molecules of low molecular weight compounds  

NASA Astrophysics Data System (ADS)

A mass measurement technique for detecting low-molecular-weight drugs with a cyclodextrin-supported organic matrix was investigated. By using cyclodextrin-supported 2,4,6-trihydroxyacetophenone (THAP), the matrix-related peaks of drugs were suppressed. The peaks of protonated molecules of the sample and THAP were mainly observed, and small fragments were detected in a few cases. Despite the Na+ and K+ peaks were observed in the spectrum, Na+ or K+ adduct sample molecules were undetected, owing to the sugar units of cyclodextrin. The advantages of MALDI-MS with cyclodextrin-supported matrices as an analytical tool for forensic samples are discussed. The suppression of alkali adducted molecules and desorption process are also discussed.

Yonezawa, Tetsu; Asano, Takashi; Fujino, Tatsuya; Nishihara, Hiroshi

2013-06-01

393

Direct Molecular Simulation of Gradient-Driven Diffusion of Large Molecules using Constant Pressure;Journal of Chemical Physics.  

National Technical Information Service (NTIS)

Dual control volume grand canonical molecular dynamics (DCV-GCMD) is a boundary-driven non-equilibrium molecular dynamics technique for simulating gradient driven diffusion in multi-component systems. Two control volumes are established at opposite ends o...

G. S. Heffelfinger A. P. Thompson

1998-01-01

394

MCL and Mincle: C-Type Lectin Receptors That Sense Damaged Self and Pathogen-Associated Molecular Patterns  

PubMed Central

Macrophage C-type lectin (MCL) and macrophage inducible C-type lectin (Mincle) comprise part of an extensive repertoire of pattern recognition receptors with the ability to sense damage-associated and pathogen-associated molecular patterns. In this review, we cover the discovery and molecular characterization of these C-type lectin receptors, and highlight recent advances in the understanding of their roles in orchestrating the response of the immune system to bacterial and fungal infection, and damaged self. We also discuss the identification and structure–activity relationships of activating ligands, particularly trehalose dimycolate and related mycobacterial glycolipids, which have significant potential in the development of TH1/TH17 vaccination strategies.

Richardson, Mark B.; Williams, Spencer J.

2014-01-01

395

Spectroscopic and Theoretical Study on the Structures and Dynamics of Functional Molecules - Towards AN Understanding of the Molecular Recognition for Encapsulation Complexes  

NASA Astrophysics Data System (ADS)

Functional molecules, such as crown ethers and calixarenes, can act as hosts for encapsulating guest species through non-covalent interactions. Applications of crown ethers and calixarenes as