Sample records for molecular pattern molecules

  1. Algorithm for Reconstruction of 3D Molecular Structure from Diffraction Patterns of Laser-Aligned Molecules

    NASA Astrophysics Data System (ADS)

    Yang, Jie; Hensley, Christopher; Centurion, Martin

    2012-06-01

    Ultrafast electron diffraction from laser-aligned gas molecules is a promising method for the determination of 3D molecular structures. Reconstruction algorithms for diffraction patterns of perfectly aligned molecules have been widely studied theoretically. However, under experimental conditions only partial alignment can be achieved and the existing algorithms do not perform well when the alignment is not perfect. We develop a method to reconstruct the 3D structure of molecules with cylindrical symmetry from electron diffraction patterns of partially-aligned molecules. The evolutionary algorithm assumes a known angular distribution, which can be calculated numerically using existing theory for laser-alignment and verified by comparison with the data. Selecting CF3I as the cylindrically symmetric molecule, diffraction patterns from multiple alignment angles are used to reconstruct a single diffraction pattern corresponding to perfect alignment. The molecular structure can then be recovered from this pattern with no prior structural information required. Our results are in good agreement with previous models of CF3I structure.

  2. Role of extracellular damage-associated molecular pattern molecules (DAMPs) as mediators of persistent pain.

    PubMed

    Kato, Jungo; Svensson, Camilla I

    2015-01-01

    Damage-associated molecular pattern molecules (DAMPs) are endogenous molecules that are constitutively expressed and released upon tissue damage, resulting in activation of the immune system. In the absence of injury or infection, DAMPs play important intracellular roles. However, once released subsequent to cell damage or cell stress, DAMPs promote activation of innate immune cells and recruitment and activation of antigen-presenting cells engaged in host defense and tissue repair. This process involves pattern recognition receptors, such as the Toll-like receptors (TLRs) and receptor for advanced glycation end products (RAGE). Several of the TLRs and RAGE have been implicated to play key roles not only in the detection of injury but also in pain signaling. Pain-like behavior is reduced in TLR2- and TLR4-deficient mice, and after injection of TLR2-, TLR4-, and RAGE antagonists in experimental models of nerve injury, arthritis, and bone cancer pain. This suggests that the pathological processes in these models are associated with release of endogenous TLR and RAGE ligands, and further that DAMPs play an important role in persistent pain. There is now a rapidly growing list of DAMPs in the literature and here we give an overview of DAMPs that have been associated with nociceptive signaling. PMID:25744676

  3. Cell Death-Associated Molecular-Pattern Molecules: Inflammatory Signaling and Control

    PubMed Central

    Sangiuliano, Beatriz; Pérez, Nancy Marcela; Moreira, Dayson F.; Belizário, José E.

    2014-01-01

    Apoptosis, necroptosis, and pyroptosis are different cellular death programs characterized in organs and tissues as consequence of microbes infection, cell stress, injury, and chemotherapeutics exposure. Dying and death cells release a variety of self-proteins and bioactive chemicals originated from cytosol, nucleus, endoplasmic reticulum, and mitochondria. These endogenous factors are named cell death-associated molecular-pattern (CDAMP), damage-associated molecular-pattern (DAMP) molecules, and alarmins. Some of them cooperate or act as important initial or delayed inflammatory mediators upon binding to diverse membrane and cytosolic receptors coupled to signaling pathways for the activation of the inflammasome platforms and NF-?B multiprotein complexes. Current studies show that the nonprotein thiols and thiol-regulating enzymes as well as highly diffusible prooxidant reactive oxygen and nitrogen species released together in extracellular inflammatory milieu play essential role in controlling pro- and anti-inflammatory activities of CDAMP/DAMP and alarmins. Here, we provide an overview of these emerging concepts and mechanisms of triggering and maintenance of tissue inflammation under massive death of cells. PMID:25140116

  4. Molecular printboards on silicon oxide: lithographic patterning of cyclodextrin monolayers with multivalent, fluorescent guest molecules.

    PubMed

    Mulder, Alart; Onclin, Steffen; Péter, Mária; Hoogenboom, Jacob P; Beijleveld, Hans; ter Maat, Jurjen; García-Parajó, María F; Ravoo, Bart Jan; Huskens, Jurriaan; van Hulst, Niek F; Reinhoudt, David N

    2005-02-01

    Three compounds bearing multiple adamantyl guest moieties and a fluorescent dye have been synthesized for the supramolecular patterning of beta-cyclodextrin (CD) host monolayers on silicon oxide using microcontact printing and dip-pen nanolithography. Patterns created on monolayers on glass were viewed by laser scanning confocal microscopy. Semi-quantitative analysis of the patterns showed that with microcontact printing approximately a single monolayer of guest molecules is transferred. Exposure to different rinsing procedures showed the stability of the patterns to be governed by specific supramolecular multivalent interactions. Patterns of the guest molecules created at CD monolayers were stable towards thorough rinsing with water, whereas similar patterns created on poly(ethylene glycol) (PEG) reference monolayers were instantly removed. The patterns on CD monolayers displayed long-term stability when stored under N(2), whereas patterns at PEG monolayers faded within a few weeks due to the diffusion of fluorescent molecules across the surface. Assemblies at CD monolayers could be mostly removed by rinsing with a concentrated CD solution, demonstrating the reversibility of the methodology. Patterns consisting of different guest molecules were produced by microcontact printing of one guest molecule and specific adsorption of a second guest molecule from solution to non-contacted areas, giving well-defined alternating assemblies. Fluorescent features of sub-micrometer dimensions were written using supramolecular dip-pen nanolithography. PMID:17193439

  5. Cyclophilin A is a damage-associated molecular pattern molecule that mediates acetaminophen-induced liver injury.

    PubMed

    Dear, James W; Simpson, Kenneth J; Nicolai, Melianthe P J; Catterson, James H; Street, Jonathan; Huizinga, Tineke; Craig, Darren G; Dhaliwal, Kevin; Webb, Sheila; Bateman, D Nicholas; Webb, David J

    2011-09-15

    The immune system is alerted to cell death by molecules known as damage-associated molecular patterns (DAMPs). These molecules partly mediate acetaminophen-induced liver injury, an archetypal experimental model of sterile cell death and the commonest cause of acute liver failure in the western world. Cyclophilin A (CypA) is an intracellular protein that is proinflammatory when released by cells. We hypothesized that CypA is released from necrotic liver cells and acts as a DAMP to mediate acetaminophen-induced liver injury. Our data demonstrated that mice lacking CypA (Ppia(-/-)) were resistant to acetaminophen toxicity. Antagonism of the extracellular receptor for CypA (CD147) also reduced acetaminophen-induced liver injury. When injected into a wild-type mouse, necrotic liver from Ppia(-/-) mice induced less of an inflammatory response than did wild-type liver. Conversely, the host inflammatory response was increased when CypA was injected with necrotic liver. Antagonism of CD147 also reduced the inflammatory response to necrotic liver. In humans, urinary CypA concentration was significantly increased in patients with acetaminophen-induced liver injury. In summary, CypA is a DAMP that mediates acetaminophen poisoning. This mechanistic insight presents an opportunity for a new therapeutic approach to a disease that currently has inadequate treatment options. PMID:21824865

  6. Molecular biomechanics of collagen molecules

    E-print Network

    Chang, Shu-Wei

    Collagenous tissues, made of collagen molecules, such as tendon and bone, are intriguing materials that have the ability to respond to mechanical forces by altering their structures from the molecular level up, and convert ...

  7. Molecular cloning, relative expression, and structural analysis of pattern recognition molecule ?-glucan binding protein from mangrove crab Episesarma tetragonum.

    PubMed

    Sivakamavalli, Jeyachandran; Selvaraj, Chandrabose; Singh, Sanjeev Kumar; Vaseeharan, Baskaralingam

    2015-05-01

    A full-length cDNA of a ?-glucan binding protein (?-GBP) gene was identified from the mangrove crab Episesarma tetragonum. The open reading frame of the E. tetragonum ?-GBP (Epte ?-GBP) is 1,167 bp long, encoding a polypeptide of 389 amino acids. The deduced amino acid sequence of Epte ?-GBP gene has conserved a potential recognition motif for ?-1,3 linkages of polysaccharides and putative RGD (Arg-Gly-Asp) cell adhesion sites. Phylogenetic analysis of the Epte ?-GBP gene showed the similarity with ?-GBPs of other crustaceans and arthropods. Quantitative RT-PCR results showed the upregulation of Epte ?-GBP gene expression in E. tetragonum hemocytes following a 12-H challenge in response to ?-glucan (?-G). Epte ?-GBP was involved in the regulation and activation of the prophenoloxidase cascade. A three-dimensional structure of active Epte ?-GBP was modeled by homology modeling and refined with molecular dynamics simulations. A structural aspect of the protein is discussed based on experimental and theoretical results obtained. PMID:25066826

  8. Molecular spintronics using single-molecule magnets

    Microsoft Academic Search

    Lapo Bogani; Wolfgang Wernsdorfer

    2008-01-01

    A revolution in electronics is in view, with the contemporary evolution of the two novel disciplines of spintronics and molecular electronics. A fundamental link between these two fields can be established using molecular magnetic materials and, in particular, single-molecule magnets. Here, we review the first progress in the resulting field, molecular spintronics, which will enable the manipulation of spin and

  9. 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

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

    2014-01-01

    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. PMID:24391503

  10. DNA Electrophoresis on patterned Surfaces The separation of DNA molecules based on their size and mass has many applications in

    E-print Network

    Singh, Jayant K.

    DNA Electrophoresis on patterned Surfaces The separation of DNA molecules based on their size and mass has many applications in biotechnology. Traditionally gel electrophoresis and capillary electrophoresis techniques are used to separate the DNA molecules based on their molecular weight

  11. Patterns and conformations in molecularly thin films

    NASA Astrophysics Data System (ADS)

    Basnet, Prem B.

    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

  12. Molecular spintronics using noncollinear magnetic molecules

    Microsoft Academic Search

    Alessandro Soncini; Liviu F. Chibotaru

    2010-01-01

    We investigate the spin transport through strongly anisotropic noncollinear magnetic molecules and find that noncollinear magnetic quantum states act as spin-switching devices for the current. Moreover, spin currents are shown to offer a viable route to selectively prepare the molecular device in one of two degenerate noncollinear magnetic states. Spin currents can be also used to create a nonzero density

  13. Molecular-beam spectroscopy of interhalogen molecules

    SciTech Connect

    Sherrow, S.A.

    1983-08-01

    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.

  14. Rotation and anisotropic molecular orbital effect in a single H2TPP molecule transistor.

    PubMed

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

    2013-12-13

    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. PMID:24483690

  15. Molecular cloning, expression pattern, and immunocytochemical localization of a gonadotropin-releasing hormone-like molecule in the gastropod mollusk, Aplysia californica

    Microsoft Academic Search

    Lihong Zhang; Javier A. Tello; Weimin Zhang; Pei-San Tsai

    2008-01-01

    Successful reproduction in vertebrates depends upon the actions of gonadotropin-releasing hormone (GnRH). Despite the wide presence of GnRH in Phylum Chordata, GnRH has not been isolated in protostomes other than the common octopus. To provide information on the evolution of this critical hormone, we isolated the full-length cDNA of a GnRH-like molecule from the central nervous system of a gastropod

  16. Molecular Self-Assembly of Jointed Molecules on a Metallic Substrate: From Single Molecule to Monolayer**

    E-print Network

    Paris-Sud XI, Université de

    Molecular Self-Assembly of Jointed Molecules on a Metallic Substrate: From Single Molecule microscopy, molecular mechanics calculations, self-assembly. 1 hal-00080899,version1-21Jun2006 Author molecules adsorbed on metallic substrates. In this situation, self-assembled structures can be understood

  17. Controlling single-molecule junction conductance by molecular interactions

    PubMed Central

    Kitaguchi, Y.; Habuka, S.; Okuyama, H.; Hatta, S.; Aruga, T.; Frederiksen, T.; Paulsson, M.; Ueba, H.

    2015-01-01

    For the rational design of single-molecular electronic devices, it is essential to understand environmental effects on the electronic properties of a working molecule. Here we investigate the impact of molecular interactions on the single-molecule conductance by accurately positioning individual molecules on the electrode. To achieve reproducible and precise conductivity measurements, we utilize relatively weak ?-bonding between a phenoxy molecule and a STM-tip to form and cleave one contact to the molecule. The anchoring to the other electrode is kept stable using a chalcogen atom with strong bonding to a Cu(110) substrate. These non-destructive measurements permit us to investigate the variation in single-molecule conductance under different but controlled environmental conditions. Combined with density functional theory calculations, we clarify the role of the electrostatic field in the environmental effect that influences the molecular level alignment. PMID:26135251

  18. Controlling single-molecule junction conductance by molecular interactions.

    PubMed

    Kitaguchi, Y; Habuka, S; Okuyama, H; Hatta, S; Aruga, T; Frederiksen, T; Paulsson, M; Ueba, H

    2015-01-01

    For the rational design of single-molecular electronic devices, it is essential to understand environmental effects on the electronic properties of a working molecule. Here we investigate the impact of molecular interactions on the single-molecule conductance by accurately positioning individual molecules on the electrode. To achieve reproducible and precise conductivity measurements, we utilize relatively weak ?-bonding between a phenoxy molecule and a STM-tip to form and cleave one contact to the molecule. The anchoring to the other electrode is kept stable using a chalcogen atom with strong bonding to a Cu(110) substrate. These non-destructive measurements permit us to investigate the variation in single-molecule conductance under different but controlled environmental conditions. Combined with density functional theory calculations, we clarify the role of the electrostatic field in the environmental effect that influences the molecular level alignment. PMID:26135251

  19. Single Molecule Approaches Embrace Molecular Cohorts

    PubMed Central

    Ha, Taekjip

    2013-01-01

    Enormous mechanistic insight has been gained by studying the behavior of single molecules. The same approaches used to study proteins in isolation are now being leveraged to examine the changes in functional behavior that emerge when single molecules have company. PMID:23953107

  20. Ion-molecule reactions and fragmentation patterns in helium nanodroplets.

    PubMed

    Boatwright, Adrian; Jeffs, Jay; Stace, Anthony J

    2007-08-01

    A study has been made of the ion chemistry of a series of small molecules that have been embedded in helium nanodroplets. In most instances, the molecules H2O, SO2, CO2, CH3OH, C2H5OH, C3H7OH, CH3F, and CH3Cl have been allowed to form clusters, and reactivity within these has been initiated through electron impact ionization. For two of the molecules studied, CF2Cl2 and CF3I, reactivity is believed to originate from single molecules embedded in the droplets. Electron impact on the droplets is thought to first create a helium ion, and formation of molecular ions is then assumed to proceed via a charge hopping mechanism that propagates though the droplet and terminates with charge-transfer to a molecule or cluster. The chemistry exhibited by many of the cluster ions and at least one of the single molecular ions is very different from that observed for the same species in isolation. In most cases, reactivity appears to be dominated by high-energy bond breaking processes as opposed to, in the case of the clusters, ion-molecule reactions. Overall, charge-transfer from He+ does not appear to be a "soft" ionization mechanism. PMID:17585742

  1. Mechanically controlled molecular orbital alignment in single molecule junctions

    NASA Astrophysics Data System (ADS)

    Bruot, Christopher; Hihath, Joshua; Tao, Nongjian

    2012-01-01

    Research in molecular electronics often involves the demonstration of devices that are analogous to conventional semiconductor devices, such as transistors and diodes, but it is also possible to perform experiments that have no parallels in conventional electronics. For example, by applying a mechanical force to a molecule bridged between two electrodes, a device known as a molecular junction, it is possible to exploit the interplay between the electrical and mechanical properties of the molecule to control charge transport through the junction. 1,4'-Benzenedithiol is the most widely studied molecule in molecular electronics, and it was shown recently that the molecular orbitals can be gated by an applied electric field. Here, we report how the electromechanical properties of a 1,4'-benzenedithiol molecular junction change as the junction is stretched and compressed. Counterintuitively, the conductance increases by more than an order of magnitude during stretching, and then decreases again as the junction is compressed. Based on simultaneously recorded current-voltage and conductance-voltage characteristics, and inelastic electron tunnelling spectroscopy, we attribute this finding to a strain-induced shift of the highest occupied molecular orbital towards the Fermi level of the electrodes, leading to a resonant enhancement of the conductance. These results, which are in agreement with the predictions of theoretical models, also clarify the origins of the long-standing discrepancy between the calculated and measured conductance values of 1,4'-benzenedithiol, which often differ by orders of magnitude.

  2. Designed DNA molecules: principles and applications of molecular nanotechnology

    Microsoft Academic Search

    Anne Condon

    2006-01-01

    Long admired for its informational role in the cell, DNA is now emerging as an ideal molecule for molecular nanotechnology. Biologists and biochemists have discovered DNA sequences and structures with new functional properties, which are able to prevent the expression of harmful genes or detect macromolecules at low concentrations. Physical and computational scientists can design rigid DNA structures that serve

  3. Molecular Spectra of Sulfur Molecules and Solid Sulfur Allotropes

    Microsoft Academic Search

    Bodo Eckert; Ralf Steudel

    Molecular spectroscopy is one of the most important means to characterize the various species in solid, liquid and gaseous elemental sulfur. In this chapter the vibrational, UV-Vis and mass spectra of sulfur molecules with between 2 and 20 atoms are critically reviewed together with the spectra of liquid sulfur and of solid allotropes including polymeric and high-pressure phases. In particular,

  4. Molecular orbital theory of ballistic electron transport through molecules

    NASA Astrophysics Data System (ADS)

    Ernzerhof, Matthias; Rocheleau, Philippe; Goyer, Francois

    2009-03-01

    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.

  5. Molecular surface analysis by laser ionization of desorbed molecules

    SciTech Connect

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

    1992-01-01

    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.

  6. Molecular surface analysis by laser ionization of desorbed molecules

    SciTech Connect

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

    1992-07-01

    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.

  7. Discovering structural alerts for mutagenicity using stable emerging molecular patterns.

    PubMed

    Métivier, Jean-Philippe; Lepailleur, Alban; Buzmakov, Aleksey; Poezevara, Guillaume; Crémilleux, Bruno; Kuznetsov, Sergei O; Goff, Jérémie Le; Napoli, Amedeo; Bureau, Ronan; Cuissart, Bertrand

    2015-05-26

    This study is dedicated to the introduction of a novel method that automatically extracts potential structural alerts from a data set of molecules. These triggering structures can be further used for knowledge discovery and classification purposes. Computation of the structural alerts results from an implementation of a sophisticated workflow that integrates a graph mining tool guided by growth rate and stability. The growth rate is a well-established measurement of contrast between classes. Moreover, the extracted patterns correspond to formal concepts; the most robust patterns, named the stable emerging patterns (SEPs), can then be identified thanks to their stability, a new notion originating from the domain of formal concept analysis. All of these elements are explained in the paper from the point of view of computation. The method was applied to a molecular data set on mutagenicity. The experimental results demonstrate its efficiency: it automatically outputs a manageable number of structural patterns that are strongly related to mutagenicity. Moreover, a part of the resulting structures corresponds to already known structural alerts. Finally, an in-depth chemical analysis relying on these structures demonstrates how the method can initiate promising processes of chemical knowledge discovery. PMID:25871768

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

    NASA Astrophysics Data System (ADS)

    Ohishi, Masatoshi

    2008-10-01

    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.

  9. Localization of molecular orbitals: from fragments to molecule.

    PubMed

    Li, Zhendong; Li, Hongyang; Suo, Bingbing; Liu, Wenjian

    2014-09-16

    Conspectus Localized molecular orbitals (LMO) not only serve as an important bridge between chemical intuition and molecular wave functions but also can be employed to reduce the computational cost of many-body methods for electron correlation and excitation. Therefore, how to localize the usually completely delocalized canonical molecular orbitals (CMO) into confined physical spaces has long been an important topic: It has a long history but still remains active to date. While the known LMOs can be classified into (exact) orthonormal and nonorthogonal, as well as (approximate) absolutely localized MOs, the ways for achieving these can be classified into two categories, a posteriori top-down and a priori bottom-up, depending on whether they invoke the global CMOs (or equivalently the molecular density matrix). While the top-down approaches have to face heavy tasks of minimizing or maximizing a given localization functional typically of many adjacent local extrema, the bottom-up ones have to invoke some tedious procedures for first generating a local basis composed of well-defined occupied and unoccupied subsets and then maintaining or resuming the locality when solving the Hartree-Fock/Kohn-Sham (HF/KS) optimization condition. It is shown here that the good of these kinds of approaches can be combined together to form a very efficient hybrid approach that can generate the desired LMOs for any kind of gapped molecules. Specifically, a top-down localization functional, applied to individual small subsystems only, is minimized to generate an orthonormal local basis composed of functions centered on the preset chemical fragments. The familiar notion for atomic cores, lone pairs, and chemical bonds emerges here automatically. Such a local basis is then employed in the global HF/KS calculation, after which a least action is taken toward the final orthonormal localized molecular orbitals (LMO), both occupied and virtual. This last step is very cheap, implying that, after the CMOs, the LMOs can be obtained essentially for free. Because molecular fragments are taken as the basic elements, the approach is in the spirit of "from fragments to molecule". Two representatives of highly conjugated molecules, that is, C12H2 and C60, are taken as showcases for demonstrating the success of the proposed approach. The use of the so-obtained LMOs will lead naturally to low-order scaling post-HF/KS methods for electron correlation or excitation. In addition, the underlying fragment picture allows for easy and pictorial interpretations of the correlation/excitation dynamics. PMID:25019464

  10. Apparatus and method of determining molecular weight of large molecules

    SciTech Connect

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

    1998-01-01

    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.

  11. Theoretical investigation of the molecular structure of the isoquercitrin molecule

    NASA Astrophysics Data System (ADS)

    Cornard, J. P.; Boudet, A. C.; Merlin, J. C.

    1999-09-01

    Isoquercitrin is a glycosilated flavonoid that has received a great deal of attention because of its numerous biological effects. We present a theoretical study on isoquercitrin using both empirical (Molecular Mechanics (MM), with MMX force field) and quantum chemical (AM1 semiempirical method) techniques. The most stable structures of the molecule obtained by MM calculations have been used as input data for the semiempirical treatment. The position and orientation of the glucose moiety with regard to the remainder of the molecule have been investigated. The flexibility of isoquercitrin principally lies in rotations around the inter-ring bond and the sugar link. In order to know the structural modifications generated by the substitution by a sugar, geometrical parameters of quercetin (aglycon) and isoquercitrin have been compared. The good accordance between theoretical and experimental electronic spectra permits to confirm the reliability of the structural model.

  12. Patterning axonal guidance molecules using a novel strategy for microcontact printing.

    PubMed

    Oliva, Anthony A; James, Conrad D; Kingman, Caroline E; Craighead, Harold G; Banker, Gary A

    2003-11-01

    We present here a two-step strategy for micropatterning proteins on a substrate to control neurite growth in culture. First, conventional microcontact printing is used to prepare a micropattern of protein A, which binds the Fc fragment of immunoglobulins. Then, a chimeric protein, consisting of the extracellular domain of a guidance protein recombinantly linked to the Fc fragment of IgG (prepared using conventional molecular techniques), is applied from solution. The chimeric protein binds to the patterned protein A, taking on its geometric pattern. Using this method, we have micropatterned the extracellular domain of the cell adhesion molecule, L1 (as an L1-Fc chimera) and demonstrated that it retains its ability to selectively guide axonal growth. L1-Fc micropatterned on a background of poly-L-lysine resulted in selective growth of the axons on the micropattern, whereas the somata and dendrites were unresponsive. Substrates bearing simultaneous micropatterns of L1-Fc and poly-L-lysine on a background of untreated glass were also created. Using this approach, cell body position was controlled by manipulating the dimensions of the poly-L-lysine pattern, and the dendrites were constrained to the poly-L-lysine pattern, while the axons grew preferentially on L1-Fc. The two-step microcontact printing method allows preparation of substrates that contain guidance proteins in geometric patterns with resolution of approximately 1 microm. This method should be broadly applicable to many classes of proteins. PMID:14584818

  13. Molecular patterning of the mammalian dentition

    PubMed Central

    Lan, Yu; Jia, Shihai; Jiang, Rulang

    2014-01-01

    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

  14. Molecular dynamics simulation of paracetamol molecules ordering around glycogen

    NASA Astrophysics Data System (ADS)

    Lim, Wilber; Feng, Yuan Ping; Liu, X. Y.

    2005-05-01

    By the use of classical atomistic molecular dynamics simulations, we demonstrate that paracetamol molecules exist in a highly ordered phase in the presence of a glycogen substrate at 317K whereas the paracetamol fluid exists in an isotropic phase in the absence of the glycogen substrate at the same temperature. This result further validates the studies made on polysaccharide regarding its abilities to promote nucleation of paracetamol via liquid preordering. As little is known regarding liquid ordering induced by a polymeric substrate, we seek to explore the ordering mechanism from an energy perspective. This is accomplished using conformation mappings. Our analysis shows that the conformation space accessible to the paracetamol molecule at 317K in the vicinity of glycogen is smaller than the one in the absence of glycogen. An investigation on the orientation of the dipole moments of the glycogen monomers and paracetamol molecules were carried out as well. From the investigations, we show that dipolar interactions play an important role in the ordering process. These studies bear significance to the understanding of the ordering process as well as the promotion and effective control of the nucleation rate.

  15. ION AND MOLECULE SENSORS USING MOLECULAR RECOGNITION IN LUMINESCENT, CONDUCTIVE POLYMERS

    EPA Science Inventory

    This program integrates three individual, highly interactive projects that will 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 molecul...

  16. A Molecular Tuning Fork in Single-Molecule Mechanochemical Sensing.

    PubMed

    Mandal, Shankar; Koirala, Deepak; Selvam, Sangeetha; Ghimire, Chiran; Mao, Hanbin

    2015-06-22

    The separate arrangement of target recognition and signal transduction in conventional biosensors often compromises the real-time response and can introduce additional noise. To address these issues, we combined analyte recognition and signal reporting by mechanochemical coupling in a single-molecule DNA template. We incorporated a DNA hairpin as a mechanophore in the template, which, under a specific force, undergoes stochastic transitions between folded and unfolded hairpin structures (mechanoescence). Reminiscent of a tuning fork that vibrates at a fixed frequency, the device was classified as a molecular tuning fork (MTF). By monitoring the lifetime of the folded and unfolded hairpins with equal populations, we were able to differentiate between the mono- and bivalent binding modes during individual antibody-antigen binding events. We anticipate these mechanospectroscopic concepts and methods will be instrumental for the development of novel bioanalyses. PMID:25960021

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

    PubMed

    Praprotnik, Matej; Janezic, Dusanka

    2005-05-01

    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

  18. MAMP (microbe-associated molecular pattern) triggered immunity in plants

    PubMed Central

    Newman, Mari-Anne; Sundelin, Thomas; Nielsen, Jon T.; Erbs, Gitte

    2013-01-01

    Plants are sessile organisms that are under constant attack from microbes. They rely on both preformed defenses, and their innate immune system to ward of the microbial pathogens. Preformed defences include for example the cell wall and cuticle, which act as physical barriers to microbial colonization. The plant immune system is composed of surveillance systems that perceive several general microbe elicitors, which allow plants to switch from growth and development into a defense mode, rejecting most potentially harmful microbes. The elicitors are essential structures for pathogen survival and are conserved among pathogens. The conserved microbe-specific molecules, referred to as microbe- or pathogen-associated molecular patterns (MAMPs or PAMPs), are recognized by the plant innate immune systems pattern recognition receptors (PRRs). General elicitors like flagellin (Flg), elongation factor Tu (EF-Tu), peptidoglycan (PGN), lipopolysaccharides (LPS), Ax21 (Activator of XA21-mediated immunity in rice), fungal chitin, and ?-glucans from oomycetes are recognized by plant surface localized PRRs. Several of the MAMPs and their corresponding PRRs have, in recent years, been identified. This review focuses on the current knowledge regarding important MAMPs from bacteria, fungi, and oomycetes, their structure, the plant PRRs that recognizes them, and how they induce MAMP-triggered immunity (MTI) in plants. PMID:23720666

  19. Patterns of energy levels and spectra for polyatomic molecules

    SciTech Connect

    Harter, W.G.

    1983-01-01

    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.

  20. Signatures of Molecular Magnetism in Single-Molecule Transport Spectroscopy

    E-print Network

    Deshmukh, Mandar M.

    single-molecule-transistor measurements on devices incorporating magnetic molecules. By studying that sequential electron tunneling may enhance the magnetic relaxation of the magnetic molecule. Single in these molecules may affect the flow of tunneling electrons. Our experiments employ the proto- typical single

  1. A Molecular Dynamics Simulation of Adsorption of Molecules in Nanotubes Yuta Yoshino and Shigeo Maruyama

    E-print Network

    Maruyama, Shigeo

    geometrical structures of carbon materials on the physical adsorption of hydrogen and other gas moleculesA Molecular Dynamics Simulation of Adsorption of Molecules in Nanotubes Yuta Yoshino and Shigeo molecular dynamics studies of the hydrogen physical adsorption with a small bundle of SWNTs

  2. Alkoxylated dehydrobenzo[12]annulene on Au(111): from single molecules to quantum dot molecular networks.

    PubMed

    Schouteden, Koen; Ivanova, Tsveta; Li, Zhe; Iancu, Violeta; Tahara, Kazukuni; Tobe, Yoshito; Adisoejoso, Jinne; De Feyter, Steven; Van Haesendonck, Chris; Janssens, Ewald

    2015-06-23

    We demonstrate the effective confinement of surface electrons in the pores of molecular networks formed by dehydrobenzo[12]annulene (DBA) molecules with butoxy groups (DBA-OC4) on Au(111). Investigation of the network formation starting from single molecules reveals a considerable interaction of the molecules with the substrate, which is at the origin of the observed confinement. PMID:26060847

  3. Chondroitin Sulphate-Binding Molecules May Pattern Central Projections of Sensory Axons within

    E-print Network

    Golding, Jon

    Chondroitin Sulphate-Binding Molecules May Pattern Central Projections of Sensory Axons within or were washed with excess chondroitin 6-sulphate or hypertonic saline. By contrast, when trigeminal mesenchyme. Immunohistochemical analysis demonstrated chondroitin-sulphated proteoglycans throughout

  4. Molecular dynamics simulation study of the ejection of polymer molecules and generation of molecular balloons in matrix-assisted

    E-print Network

    Zhigilei, Leonid V.

    Molecular dynamics simulation study of the ejection of polymer molecules and generation 395 McCormick Road, Charlottesville, Virginia 22904-4745 ABSTRACT Coarse-grained molecular dynamics to the complex morphologies observed in polymer films deposited by MAPLE. The effect of dynamic molecular

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

    Microsoft Academic Search

    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

    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

  6. Molecular orientational vibrations and thermodynamics in monolayers of chain molecules

    NASA Astrophysics Data System (ADS)

    Wang, Zhenghao; Gong, Changde

    1996-10-01

    We study the molecular orientational vibrations (MOVs), using analytical method, in Langmuir (Langmuir-Blodgett) monolayers. At the present stage of our study, we fix the hydrophilic heads of the amphiphilic molecules and model the hydrophobic alkane chains as rigid rods. We have considered different tilt orders in our study and self-consistently determined the tilt angle at various surface pressures and temperatures. The study of these MOVs leads us to a breakthrough in the analytical theory for monolayers, with which we are enabled to analytically investigate a wide range of thermodynamical properties, such as angular correlation functions and specific heat, and to calculate structural functions in scattering experiments. As to MOV itself, a universal frequency gap at k=0 exists (except at the upright-tilted phase transition point). This frequency gap is closely related to the upright-tilted phase transition as we explain in the text. Comparison of our results with those from previous Monte Carlo simulations is made and shows good agreement.

  7. Single Molecule Approaches to Studying Heterogeneity in Molecular Supercooled Liquids

    NASA Astrophysics Data System (ADS)

    Kaufman, Laura

    2014-03-01

    Supercooled liquids display behaviors consistent with the presence of heterogeneous dynamics. We investigate the length scales over which such heterogeneities exist and the time scales over which they persist using single molecule (SM) fluorescence microscopy. In previous work, multiple perylene diimide (PDI) probes were employed to investigate whether probe properties affected breadth of heterogeneity reported in the fragile supercooled liquid ortho-terphenyl (OTP) as well as in less fragile supercooled glycerol. In both cases, the fastest rotating probes reported the greatest breadth of heterogeneity in the host, regardless of physical probe size, suggesting slow probes were averaging over dynamic changes in the environment in time. Here, we introduce a new set of BODIPY-core based probes that are both smaller and more quickly rotating in OTP than the PDI probes. These probes show qualitatively different behavior than the PDI probes, reporting more spatial and temporal heterogeneity than previously studied probes. The newly employed probes open the door to studying the full range of consequences of dynamic heterogeneity in supercooled liquids on the molecular length scale.

  8. Molecular multipole moments of water molecules in ice Ih

    SciTech Connect

    Batista, E.R. [Department of Physics, Box 351560, University of Washington, Seattle, Washington 98195-1560 (United States)] [Department of Physics, Box 351560, University of Washington, Seattle, Washington 98195-1560 (United States); [Department of Chemistry, Box 351700, University of Washington, Seattle, Washington 98195-1700 (United States); Xantheas, S.S. [Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 906 Battelle Boulevard, PO Box 999, MS K1-96, Richland, Washington 99352 (United States)] [Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 906 Battelle Boulevard, PO Box 999, MS K1-96, Richland, Washington 99352 (United States); Jonsson, H. [Department of Chemistry, Box 351700, University of Washington, Seattle, Washington 98195-1700 (United States)] [Department of Chemistry, Box 351700, University of Washington, Seattle, Washington 98195-1700 (United States)

    1998-09-01

    We have used an induction model including dipole, dipole{endash}quadrupole, quadrupole{endash}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{percent} 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 {bold 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. {copyright} {ital 1998 American Institute of Physics.}

  9. Molecular Dynamics and the Water Molecule: An Introduction to Molecular Dynamics for Physical Chemistry Students

    NASA Astrophysics Data System (ADS)

    Saiz, Enrique; Tarazona, Maria Pilar

    1997-11-01

    A general approach to Molecular Dynamics procedures (MD), that can be included as a lesson in different parts of a physical chemistry program, is presented. The basic idea that a MD calculation consists on analyzing the evolution with time of the studied sample is presented and the difficulties arising from the amount of data to be analyzed and the computation of atomic coordinates are explained. Newton's equation of motion is integrated for a trivial system formed by just one isolated particle. Next, a system of two interacting particles is used to illustrate the leap frog algorithm employed for the integration in more realistic cases. Finally, the results obtained by performing a real MD calculation on the water molecule are presented, explained and compared with some basic ideas that we all have about this molecule.

  10. Structures of Molecules and of Molecular Systems of Informatics

    NASA Astrophysics Data System (ADS)

    W?grzyn, Stefan

    The terms contents and structure need to be discerned. For example, the molecule of water consists of one atom of oxygen and two atoms of hydrogen. But, the structure of the water molecule requires to give mutual distribution, within the three dimensional space, of the three atoms that build that molecule. In such a case, the most frequently used form is the so called structural model of a molecule. In this paper, structural models of methane and ethane are discussed in more detail. In this work, also same problems of nanotechnology and genetic engineering are discussed, which require the knowledge about the models of structures of molecules as well.

  11. Time-Resolved Molecular Frame Dynamics of Fixed-in-Space CS2 Molecules

    SciTech Connect

    Bisgaard, Christer; Clarkin, Owen; Wu, Guorong; Lee, Anthony; Gessner, Oliver; Hayden, Carl; Stolow, Albert

    2009-04-02

    Random orientation of molecules within a sample leads to blurred observationsof chemical reactions studied from the laboratory perspective. Methodsdeveloped for the dynamic imaging of molecular structures and processesstruggle with this, as measurements are optimally made in the molecular frame.Here we uselaser alignment to transiently fix CS2 molecules in space longenough to elucidate, in the molecular reference frame, details of ultrafast electronic vibrationaldynamics during a photochemical reaction. These three-dimensional photoelectron imaging results, combined with ongoing efforts in molecular alignment and orientation, presage a wide range of insights obtainable fromtime-resolved studies in the molecular frame.

  12. Chains of quantum dot molecules grown on Si surface pre-patterned by ion-assisted nanoimprint lithography

    NASA Astrophysics Data System (ADS)

    Smagina, Zh. V.; Stepina, N. P.; Zinovyev, V. A.; Novikov, P. L.; Kuchinskaya, P. A.; Dvurechenskii, A. V.

    2014-10-01

    An original approach based on the combination of nanoimprint lithography and ion irradiation through mask has been developed for fabrication of large-area periodical pattern on Si(100). Using the selective etching of regions amorphized by ion irradiation ordered structures with grooves and ridges were obtained. The shape and depth of the relief were governed by ion energy and by the number of etching stages as well. Laterally ordered chains of Ge quantum dots were fabricated by molecular beam epitaxy of Ge on the pre-patterned Si substrates. For small amount of Ge deposited chains contain separate quantum dot molecules. The increase of deposition amount leads to overlapping of quantum dot molecules with formation of dense homogeneous chains of quantum dots. It was shown that the residual irradiation-induced bulk defects underneath the grooves suppress nucleation of Ge islands at the bottom of grooves. On pre-patterned substrates with whole defect regions, etched quantum dots grow at the bottom of grooves. The observed location of Ge quantum dots is interpreted in terms of local strain-mediated surface chemical potential which controls the sites of islands nucleation. The local chemical potential is affected by additional strain formed by the residual defects. It was shown by molecular dynamics calculations that these defects form the compressive strain at the bottom of grooves.

  13. Chains of quantum dot molecules grown on Si surface pre-patterned by ion-assisted nanoimprint lithography

    SciTech Connect

    Smagina, Zh. V.; Stepina, N. P., E-mail: stepina@isp.nsc.ru; Zinovyev, V. A.; Kuchinskaya, P. A. [Rzhanov Institute of Semiconductor Physics, Siberian Branch of the Russian Academy of Sciences, Lavrenteva 13, 630090 Novosibirsk (Russian Federation); Novikov, P. L.; Dvurechenskii, A. V. [Rzhanov Institute of Semiconductor Physics, Siberian Branch of the Russian Academy of Sciences, Lavrenteva 13, 630090 Novosibirsk (Russian Federation); Novosibirsk State University, Pirogova, 2, 630090 Novosibirsk (Russian Federation)

    2014-10-13

    An original approach based on the combination of nanoimprint lithography and ion irradiation through mask has been developed for fabrication of large-area periodical pattern on Si(100). Using the selective etching of regions amorphized by ion irradiation ordered structures with grooves and ridges were obtained. The shape and depth of the relief were governed by ion energy and by the number of etching stages as well. Laterally ordered chains of Ge quantum dots were fabricated by molecular beam epitaxy of Ge on the pre-patterned Si substrates. For small amount of Ge deposited chains contain separate quantum dot molecules. The increase of deposition amount leads to overlapping of quantum dot molecules with formation of dense homogeneous chains of quantum dots. It was shown that the residual irradiation-induced bulk defects underneath the grooves suppress nucleation of Ge islands at the bottom of grooves. On pre-patterned substrates with whole defect regions, etched quantum dots grow at the bottom of grooves. The observed location of Ge quantum dots is interpreted in terms of local strain-mediated surface chemical potential which controls the sites of islands nucleation. The local chemical potential is affected by additional strain formed by the residual defects. It was shown by molecular dynamics calculations that these defects form the compressive strain at the bottom of grooves.

  14. PALM--a pattern language for molecular biology.

    PubMed

    Helgesen, C; Sibbald, P R

    1993-01-01

    This paper presents a new pattern language, PALM, for describing patterns in molecular biology sequences. The language is intended for representing knowledge about such patterns in a declarative, clear and concise way. It is also shown that its expressive power enables the definition of any regular or context free language, and also higher languages in the Chomsky hierarchy by parameter attachment, variables and procedural attachment. It is also possible to define approximate patterns. The language is rigorously defined, and several examples of its use and expressive power are given. PMID:7584333

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

    Microsoft Academic Search

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

    2008-01-01

    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

  16. Controlled Low-Temperature Molecular Manipulation of Sexiphenyl Molecules on Ag(111) Using Scanning Tunneling Microscopy

    E-print Network

    Hla, Saw-Wai

    Controlled Low-Temperature Molecular Manipulation of Sexiphenyl Molecules on Ag(111) Using Scanning; published 11 November 2004) A novel scanning tunneling microscope manipulation scheme for a controlled is constructed. The sexiphenyl manipulation signals reveal a ring flipping as the molecule moves from the hcp

  17. Molecular dynamics simulations of flexible liquid crystal molecules using a Gay-Berne/Lennard-Jones model

    E-print Network

    Wilson, Mark R.

    Molecular dynamics simulations of flexible liquid crystal molecules using a Gay for liquid crystal molecules composed of two Gay-Berne particles connected by an eight-site Lennard layers. The latter is seen through the temperature dependence of the Gay-Berne radial distribution

  18. Heteroduplex molecules cause sexing errors in a standard molecular protocol for avian sexing.

    PubMed

    Casey, Ashley E; Jones, Kenneth L; Sandercock, Brett K; Wisely, Samantha M

    2009-01-01

    Molecular methods are a necessary tool for sexing monomorphic birds. These molecular approaches are usually reliable, but sexing protocols should be evaluated carefully because biochemical interactions may lead to errors. We optimized laboratory protocols for genetic sexing of a monomorphic shorebird, the upland sandpiper (Bartramia longicauda), using two independent sets of primers, P2/P8 and 2550F/2718R, to amplify regions of the sex-linked CHD-Z and CHD-W genes. We discovered polymorphisms in the region of the CHD-Z intron amplified by the primers P2/P8 which caused four males to be misidentified as females (n = 90 mated pairs). We cloned and sequenced one CHD-W allele (370 bp) and three CHD-Z alleles in our population: Z° (335 bp), Z' (331 bp) and Z? (330 bp). Normal (Z°Z°) males showed one band in agarose gel analysis and were easily differentiated from females (Z°W), which showed two bands. However, males heterozygous for CHD-Z alleles (Z'Z?) unexpectedly showed two bands in a pattern similar to females. While the Z' and Z? fragments contained only short deletions, they annealed together during the polymerase chain reaction (PCR) process and formed heteroduplex molecules that were similar in size to the W fragment. Errors previously reported for molecular sex-assignment have usually been due to allelic dropout, causing females to be misidentified as males. Here, we report evidence that events in PCRs can lead to the opposite error, with males misidentified as females. We recommend use of multiple primer sets and large samples of known-sex birds for validation when designing protocols for molecular sex analysis. PMID:21564567

  19. Molecular Physiology of Protein Kinases (and Phosphatases): Molecules, mechanisms, medicines

    NSDL National Science Digital Library

    Michael Eck (Harvard University)

    2011-04-09

    This powerpoint presentation from the 2011 EB Refresher Course on CellPhysiology:Intracellular Signaling addressed protein kinase structure, conformational changes, molecular domains, activation, and inhibition.

  20. Molecular Physiology of Protein Kinases (and Phosphatases): Molecules, mechanisms, medicines

    NSDL National Science Digital Library

    Michael Eck (Harvard University)

    2011-04-09

    This recorded presentation from the 2011 EB Refresher Course on CellPhysiology:Intracellular Signaling addressed protein kinase structure, conformational changes, molecular domains, activation, and inhibition.

  1. Coulomb interaction in self-consistent field calculations on molecules in molecular crystals

    NASA Astrophysics Data System (ADS)

    Mestechkin, M. M.

    1997-01-01

    A method of direct calculation of Madelung sums in molecular crystals is proposed. It is based on preliminary evaluation of Coulomb interaction of two contrarily charged elements of a crystal cell translated over the whole crystal. As a result some Madelung parameters similar to Coulomb integrals enter the molecular crystal Hartree - Fock equations whose dimensionality remains the same as for the isolated molecule. As an illustration of this approach the alteration of the hyperpolarizability tensors of urea and triaminotrinitrobenzene (TATB) molecules are calculated when these molecules enter a crystal. A possible explanation of the second-harmonic generation ability by TATB is given.

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

    Microsoft Academic Search

    W. Weltner Jr.

    1980-01-01

    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

  3. Investigation of the influence factors of polyethylene molecule encapsulated into carbon nanotubes by molecular dynamics simulation

    Microsoft Academic Search

    Qun Li; Guofang He; Rengao Zhao; Yanfei Li

    2011-01-01

    In this work, the influence factors, namely chirality, temperature, radius and surface chemical modification, of the interaction energy for polyethylene (PE) molecule encapsulated into single-walled carbon nanotubes (SWNTs) had been investigated by molecular mechanics (MM) and molecular dynamics (MD) simulation. The results showed that all these factors would influence the interaction energy between PE and SWNTs. The interaction energy between

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

    PubMed

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

    2006-01-01

    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

  5. Molecular glass resist performance for nano-pattern transfer

    NASA Astrophysics Data System (ADS)

    el Otell, Ziad; Ringk, Andreas; Kolb, Tristan; Neuber, Christian; Hansel, Leander; de Marneffe, Jean-François

    2015-03-01

    The performance of novel molecular glass resists is demonstrated in this work for the purposes of performing nano-pattern transfer. In order to improve the etch durability, post apply bake (PAB) and mixing two resists platforms were investigated. These resists showed a promising etch durability for efficient pattern transfer with films as thin as 5 nm. Etch rate, surface roughness, evolution of the refractive index of these materials are presented to establish a good baseline and select appropriate candidate materials for patterning beyond-CMOS.

  6. High-order harmonic spectroscopy for molecular imaging of polyatomic molecules.

    PubMed

    Negro, M; Devetta, M; Faccialá, D; De Silvestri, S; Vozzi, C; Stagira, S

    2014-01-01

    High-order harmonic generation is a powerful and sensitive tool for probing atomic and molecular structures, combining in the same measurement an unprecedented attosecond temporal resolution with a high spatial resolution of the order of an angstrom. Imaging of the outermost molecular orbital by high-order harmonic generation has been limited for a long time to very simple molecules, like nitrogen. Recently we demonstrated a technique that overcame several of the issues that have prevented the extension of molecular orbital tomography to more complex species, showing that molecular imaging can be applied to a triatomic molecule like carbon dioxide. Here we report on the application of such a technique to nitrous oxide (N(2)O) and acetylene (C(2)H(2)). This result represents a first step towards the imaging of fragile compounds, a category which includes most of the fundamental biological molecules. PMID:25415258

  7. Molecular Polaron Formation of Acoustic Phonons in Quantum Dot Molecules

    NASA Astrophysics Data System (ADS)

    Casara, Joshua; Jacobs, Andrew; Czarnocki, Cyprian; Monteros, Alessandro; Peev, Thomas; Tin Yau Tse, Joshua; Gad, Youstina; Scheibner, Michael

    2015-03-01

    In a recent experimental study, coherent and non-dissipative behavior of optical phonons was achieved via the generation of molecular polarons in a coupled quantum dot pair. An optical transparency caused by a Fano-type resonant quantum interference between discrete interdot excitons and continuum single dot-like polaron states revealed the molecular polaron. It has been shown that the phonon-induced transparency is highly controllable by electric field, excitation energy and power. Here we review the molecular polaron formation via optical phonons and we investigate an analogous transparency induced by acoustic phonons. Photoluminescence excitation spectroscopy is used to probe the characteristics of the transparency. The study tests the molecular polaron formation as a function of the longitudinal acoustic phonon density of states in the range from 10 meV to 20 meV above the bare single dot-like neutral exciton ground state transition.

  8. Supramolecular chemistry — Scope and perspectives: Molecules — Supermolecules — Molecular devices

    Microsoft Academic Search

    Jean-Marie Lehn

    1988-01-01

    Supramolecular chemistry is the chemistry of the intermolecular bond, covering the structures and functions of the entities formed by association of two or more chemical species. Molecular recognition in the supermolecules formed by receptor-substrate binding rests on the principles of molecular complementarity, as found in spherical and tetrahedral recognition, linear recognition by co-receptors, metallo-receptors, amphilic receptors and anion coordination. Supramolecular

  9. Molecular alignment in submicron patterned polymer matrix using nanoimprint lithography

    E-print Network

    Molecular alignment in submicron patterned polymer matrix using nanoimprint lithography Jian Wang important examples are the electro-optical modulator5,6 and the frequency converter sum frequency generation or chro- mophores in a polymer matrix. Poling by electrical field5­7 or laser10 is a widely used technique

  10. A comprehensive study of extended tetrathiafulvalene cruciform molecules for molecular electronics: synthesis and electrical transport measurements.

    PubMed

    Parker, Christian R; Leary, Edmund; Frisenda, Riccardo; Wei, Zhongming; Jennum, Karsten S; Glibstrup, Emil; Abrahamsen, Peter Bæch; Santella, Marco; Christensen, Mikkel A; Della Pia, Eduardo Antonio; Li, Tao; Gonzalez, Maria Teresa; Jiang, Xingbin; Morsing, Thorbjørn J; Rubio-Bollinger, Gabino; Laursen, Bo W; Nørgaard, Kasper; van der Zant, Herre; Agrait, Nicolas; Nielsen, Mogens Brøndsted

    2014-11-26

    Cruciform-like molecules with two orthogonally placed ?-conjugated systems have in recent years attracted significant interest for their potential use as molecular wires in molecular electronics. Here we present synthetic protocols for a large selection of cruciform molecules based on oligo(phenyleneethynylene) (OPE) and tetrathiafulvalene (TTF) scaffolds, end-capped with acetyl-protected thiolates as electrode anchoring groups. The molecules were subjected to a comprehensive study of their conducting properties as well as their photophysical and electrochemical properties in solution. The complex nature of the molecules and their possible binding in different configurations in junctions called for different techniques of conductance measurements: (1) conducting-probe atomic force microscopy (CP-AFM) measurements on self-assembled monolayers (SAMs), (2) mechanically controlled break-junction (MCBJ) measurements, and (3) scanning tunneling microscopy break-junction (STM-BJ) measurements. The CP-AFM measurements showed structure-property relationships from SAMs of series of OPE3 and OPE5 cruciform molecules; the conductance of the SAM increased with the number of dithiafulvene (DTF) units (0, 1, 2) along the wire, and it increased when substituting two arylethynyl end groups of the OPE3 backbone with two DTF units. The MCBJ and STM-BJ studies on single molecules both showed that DTFs decreased the junction formation probability, but, in contrast, no significant influence on the single-molecule conductance was observed. We suggest that the origins of the difference between SAM and single-molecule measurements lie in the nature of the molecule-electrode interface as well as in effects arising from molecular packing in the SAMs. This comprehensive study shows that for complex molecules care should be taken when directly comparing single-molecule measurements and measurements of SAMs and solid-state devices thereof. PMID:25375316

  11. Molecular dynamics study on condensation/evaporation coefficients of chain molecules at liquid-vapor interface.

    PubMed

    Nagayama, Gyoko; Takematsu, Masaki; Mizuguchi, Hirotaka; Tsuruta, Takaharu

    2015-07-01

    The structure and thermodynamic properties of the liquid-vapor interface are of fundamental interest for numerous technological implications. For simple molecules, e.g., argon and water, the molecular condensation/evaporation behavior depends strongly on their translational motion and the system temperature. Existing molecular dynamics (MD) results are consistent with the theoretical predictions based on the assumption that the liquid and vapor states in the vicinity of the liquid-vapor interface are isotropic. Additionally, similar molecular condensation/evaporation characteristics have been found for long-chain molecules, e.g., dodecane. It is unclear, however, whether the isotropic assumption is valid and whether the molecular orientation or the chain length of the molecules affects the condensation/evaporation behavior at the liquid-vapor interface. In this study, MD simulations were performed to study the molecular condensation/evaporation behavior of the straight-chain alkanes, i.e., butane, octane, and dodecane, at the liquid-vapor interface, and the effects of the molecular orientation and chain length were investigated in equilibrium systems. The results showed that the condensation/evaporation behavior of chain molecules primarily depends on the molecular translational energy and the surface temperature and is independent of the molecular chain length. Furthermore, the orientation at the liquid-vapor interface was disordered when the surface temperature was sufficiently higher than the triple point and had no significant effect on the molecular condensation/evaporation behavior. The validity of the isotropic assumption was confirmed, and we conclude that the condensation/evaporation coefficients can be predicted by the liquid-to-vapor translational length ratio, even for chain molecules. PMID:26156491

  12. Paramagnetic molecule induced strong antiferromagnetic exchange coupling on a magnetic tunnel junction based molecular spintronics device.

    PubMed

    Tyagi, Pawan; Baker, Collin; D'Angelo, Christopher

    2015-07-31

    This paper reports our Monte Carlo (MC) studies aiming to explain the experimentally observed paramagnetic molecule induced antiferromagnetic coupling between ferromagnetic (FM) electrodes. Recently developed magnetic tunnel junction based molecular spintronics devices (MTJMSDs) were prepared by chemically bonding the paramagnetic molecules between the FM electrodes along the tunnel junction's perimeter. These MTJMSDs exhibited molecule-induced strong antiferromagnetic coupling. We simulated the 3D atomic model analogous to the MTJMSD and studied the effect of molecule's magnetic couplings with the two FM electrodes. Simulations show that when a molecule established ferromagnetic coupling with one electrode and antiferromagnetic coupling with the other electrode, then theoretical results effectively explained the experimental findings. Our studies suggest that in order to align MTJMSDs' electrodes antiparallel to each other, the exchange coupling strength between a molecule and FM electrodes should be ?50% of the interatomic exchange coupling for the FM electrodes. PMID:26159362

  13. Molecular multipole moments of water molecules in ice Ih

    Microsoft Academic Search

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

    1998-01-01

    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

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

    PubMed

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

    2005-01-15

    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

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

    NASA Astrophysics Data System (ADS)

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

    2014-07-01

    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.

  16. The Role of Damage-Associated Molecular Patterns in Human Diseases

    PubMed Central

    Land, Walter G.

    2015-01-01

    There is increasing interest by physicians in the impact of the innate immune system on human diseases. In particular, the role of the molecules that initiate and amplify innate immune pathways, namely damage-associated molecular patterns (DAMPs), is of interest as these molecules are involved in the pathogenesis of many human disorders. The first part of this review identifies five classes of cell stress/tissue injury-induced DAMPs that are sensed by various recognition receptor-bearing cells of the innate immune system, thereby mounting inflammation, promoting apoptosis and shaping adaptive immune responses. The DAMPs activate and orchestrate several innate immune machineries, including inflammasomes and the unfolded protein response that synergistically operates to induce inflammatory, metabolic and adaptive immune pathologies. Two examples of autoimmune diseases are discussed as they represent a typical paradigm of the intimate interplay between innate and adaptive immune responses. PMID:25685392

  17. Damage-Associated Molecular Patterns in the Course of Lung Cancer - A Review.

    PubMed

    ?agiedo, M; Sikora, J; Kaczmarek, M

    2015-08-01

    More than 20 years ago, the 'danger theory' was proposed which explains why potent immune responses with no microbial components are elicited against tissue transplants, injuries, tumours and autoimmune diseases. It states that the immune system can distinguish between dangerous and innocuous endogenous signals. In response to trauma or other types of tissue and cell damage, certain molecules that function inside the cell are released or secreted from damaged or dying cells. Such mechanisms initiate an immune response in the absence of infection. These immunostimulatory molecules were named damage-associated molecular patterns (DAMPs). In this article, we will review the available data on the influence of select DAMPs on lung cancer cells and tumour microenvironments. We will also summarize the current information regarding the interactions between lung cancer-associated DAMPs and their toll-like receptors. PMID:25966741

  18. Role of molecule flexibility on the nucleation of dislocations in molecular crystals

    NASA Astrophysics Data System (ADS)

    Munday, Lynn B.; Mitchell, Robert L.; Knap, Jaroslaw; Chung, Peter W.

    2013-10-01

    We show that a molecule's flexibility described by changes to its conformation and orientation during deformation is vital for the proper representation of dislocation nucleation in molecular crystals. This is shown for the molecular crystal hexahydro-1,3,5-trinitro-s-triazine (RDX) by comparing direct atomistic simulations to two alternate forms of a continuum dislocation nucleation model for a crack tip loaded in pure shear. The atomistic simulations show the emission of partial dislocations. These are compared to continuum dislocation nucleation models based on generalized stacking fault (GSF) energy surfaces where the molecules are allowed to be either rigid or flexible. The rigid molecules are unable to represent the partial dislocations whereas the flexible molecules agree with the direct atomistic model to within 17% of the stress intensity factor for emission of the first partial dislocation and to within 1% for the second partial. This agreement first indicates that the molecule flexibility serves a critical role in the ductile behavior of the molecular crystal and, second, the continuum dislocation nucleation model represents the correct atomistic behavior, showing two partial dislocations connected by a stacking fault, when parameterized with GSF energy surfaces that account for the molecule flexibility.

  19. Identification of the Molecule-Metal Bonding Geometries of Molecular Nanowires

    E-print Network

    Demir, Firuz

    2011-01-01

    Molecular nanowires in which a single molecule bonds chemically to two metal electrodes and forms a stable electrically conducting bridge between them have been studied intensively for more than a decade. However the experimental determination of the bonding geometry between the molecule and electrodes has remained elusive. Here we demonstrate by means of ab initio calculations that inelastic tunneling spectroscopy (IETS) can determine these geometries. We identify the bonding geometries at the gold-sulfur interfaces of propanedithiolate molecules bridging gold electrodes that give rise to the specific IETS signatures that were observed in recent experiments.

  20. Carbon Nanotube Biosensors for Space Molecule Detection and Clinical Molecular Diagnostics

    NASA Technical Reports Server (NTRS)

    Han, Jie

    2001-01-01

    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.

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

    NASA Astrophysics Data System (ADS)

    Pothoczki, Szilvia; Temleitner, László; Pusztai, László

    2010-04-01

    The method of Rey [Rey, J. Chem. Phys. 126, 164506 (2007)] for describing how molecules orient toward each other in systems with perfect tetrahedral molecules is extended to the case of distorted tetrahedral molecules of c2v symmetry by means of introducing 28 subgroups. Additionally, the original analysis developed for perfect tetrahedral molecules, based on six groups, is adapted for molecules with imperfect tetrahedral shape. Deriving orientational correlation functions have been complemented with detailed analyses of dipole-dipole correlations. This way, (up to now) the most complete structure determination can be carried out for such molecular systems. In the present work, these calculations have been applied for particle configurations resulting from reverse Monte Carlo computer modeling. These particle arrangements are fully consistent with structure factors from neutron and x-ray diffraction measurements. Here we present a complex structural study for methylene halide (chloride, bromide, and iodide) molecular liquids, as possibly the best representative examples. It has been found that the most frequent orientations of molecules are of the 2:2 type over the entire distance range in these liquids. Focusing on the short range orientation, neighboring molecules turn toward each other with there "H,Y"-"H,Y" (Y: Cl, Br, I) edges, apart from CH2Cl2 where the H,H-H,Cl arrangement is the most frequent. In general, the structure of methylene chloride appears to be different from the structure of the other two liquids.

  2. A Renaissance of Elicitors: Perception of Microbe-Associated Molecular Patterns and Danger Signals by Pattern-Recognition Receptors

    Microsoft Academic Search

    Thomas Boller; Georg Felix

    2009-01-01

    Microbe-associated molecular patterns (MAMPs) are molecular signa- tures typical of whole classes of microbes, and their recognition plays a key role in innate immunity. Endogenous elicitors are similarly recog- nized as damage-associated molecular patterns (DAMPs). This review focuses on the diversity of MAMPs\\/DAMPs and on progress to iden- tify the corresponding pattern recognition receptors (PRRs) in plants. The two best-characterized

  3. Patterning protein molecules on poly(ethylene glycol) coated Si(1 1 1)

    Microsoft Academic Search

    Yongseok Jun; Taewoon Cha; Athena Guo; X.-Y. Zhu

    2004-01-01

    We demonstrate spatially localized immobilization of protein molecules on high-density poly(ethylene glycol) (PEG) coated Si(111). Patterns of HO- and CH3O-terminated PEG regions are formed on silicon surfaces based on soft lithography techniques and an efficient reaction between alcohol functional groups and chlorine-terminated silicon. Activation of the HO-terminated PEG brush is achieved via either partial oxidation to form aldehyde groups or

  4. Molecular Magnetism: Design of High-TC Prussian Blue Molecule Based Magnets

    NASA Astrophysics Data System (ADS)

    Cartier Dit Moulin, Christophe

    Molecular magnetism is a field of rational synthesis of new systems, using the exchange interaction models between magnetic centers and the flexibility of coordination chemistry. We define first some theoretical approaches commonly used in this field and we show how they can help the building of molecule-based magnets. Orbital model combined with the Néel molecular field approach is used to increase the Curie temperature up to room temperature for Prussian blue family compounds.

  5. Decoding the Pattern of Photon Colors in Single-Molecule FRET

    PubMed Central

    Szabo, Attila

    2009-01-01

    Conformational dynamics of a single molecule can be studied using Förster resonance energy transfer (FRET) by recording a sequence of photons emitted by a donor and an acceptor dye attached to the molecule. We describe a simple and robust method to estimate the rates of transitions between different conformational states and the FRET efficiencies associated with these states. For a photon trajectory with measured interphoton times, the pattern of colors is decoded by maximizing the appropriate likelihood function. This approach can be used to analyze bursts of photons from diffusing molecules as well as photon trajectories generated by immobilized molecules. The procedure is illustrated using simulated photon trajectories corresponding to two-state and three-state molecules. The method works even when the photon colors appear to be scrambled because of high background noise, the photophysical properties of the conformers are similar, or the conformational and photon count rates are comparable. The consistency of the model with the data can be checked by recoloring the photon trajectories and comparing the predicted and observed FRET efficiency histograms. PMID:19588948

  6. Mass Spectrometric Studies of Atom–Molecule Reactions Using High-Intensity Crossed Molecular Beams

    Microsoft Academic Search

    S. N. Foner; R. L. Hudson

    1970-01-01

    Elementary gas phase reactions have been studied with high-intensity crossed molecular beams. A detailed analysis is presented on the sensitivity factors involved in mass spectrometric detection of free radicals formed in ordinary chemical reactions as contrasted to surface ionization detection of the products of alkali atom reactions. Free radicals have been observed in a number of atom–molecule reactions, including: (1)

  7. Polymers: Molecular Structure [A polymer is a very large molecule comprising hundreds or thousands of atoms,

    E-print Network

    Hall, Christopher

    1 Polymers: Molecular Structure [A polymer is a very large molecule comprising hundreds into chain or network structures|The concept of the polymer is one of the great ideas of twentieth century chemistry. It emerged in the 1920s amid prolonged controversy and its acceptance is closely associated

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

    Microsoft Academic Search

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

    2011-01-01

    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

  9. Permeation Process of Small Molecules across Lipid Membranes Studied by Molecular Dynamics Simulations

    Microsoft Academic Search

    Herman J. C. Berendsen; Siewert J. Marrink

    1996-01-01

    The transport of small molecules across a phospholipid membrane is studied by molecular dynamics simulations. The effects of size, hydrophobicity, and asphericity of the penetrants on the permeation process are investigated. For this purpose, permeability coefficients of oxygen and ammonia are computed using an inhomogeneous solubility-diffusion model and compared to the previously computed results of the permeation of water. Furthermore,

  10. Kinetics of electrons and molecules at plasma-beam discharge in molecular gases

    Microsoft Academic Search

    V. I. Karas; V. V. Mukhin; A. M. Naboka; V. E. Novikov

    1987-01-01

    Effect of molecule distribution by oscillating levels on plasma-beam discharge characteristics in molecular gases has been considered. It is shown that under conditions of gas low temperature T<< T sub v and TE sub 1E << epsilon sub 0 the higher rate of a chemical reaction can be obtained under conditions of strong nonequilibricity, i.e., when the larger stage of

  11. Local Behavior of Water Molecules on Brucite, Talc, and Halite Surfaces: A Molecular Dynamics Study

    Microsoft Academic Search

    Hiroshi Sakuma; Taku Tsuchiya; Katsuyuki Kawamura; Kenshiro Otsuki

    2004-01-01

    The structural and dynamic properties of water between brucite (0001), talc (001), and halite (100) surfaces have been calculated by classical molecular dynamics (MD) simulations at ambient conditions. The interaction potential models between water and the minerals have been developed by the energy curves obtained from the ab initio electronic state calculations. Orientational anisotropy of water molecules is almost limited

  12. Full variational molecular orbital method: Application to the positron-molecule complexes

    Microsoft Academic Search

    Masanori Tachikawa; Kazuhide Mori; Kazunari Suzuki; Kaoru Iguchi

    1998-01-01

    Optimal Gaussian-type orbital (GTO) basis sets of positron and electron in positron-molecule complexes are proposed by using the full variational treatment of molecular orbital (FVMO) method. The analytical expression for the energy gradient with respect to parameters of positronic and electronic GTO such as the orbital exponents, the orbital centers, and the linear combination of atomic orbital (LCAO) coefficients, is

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

    NASA Technical Reports Server (NTRS)

    Byer, R. L.

    1982-01-01

    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.

  14. Tris-thiourea tripodal-based molecules as chloride transmembrane transporters: insights from molecular dynamics simulations.

    PubMed

    Marques, Igor; Colaço, Ana R; Costa, Paulo J; Busschaert, Nathalie; Gale, Philip A; Félix, Vítor

    2014-05-28

    The interaction of six tripodal synthetic chloride transmembrane transporters with a POPC bilayer was investigated by means of molecular dynamics simulations using the general Amber force field (GAFF) for the transporters and the LIPID11 force field for phospholipids. These transporters are structurally simple molecules, based on the tris(2-aminoethyl)amine scaffold, containing three thiourea binding units coupled with three n-butyl (1), phenyl (2), fluorophenyl (3), pentafluorophenyl (4), trifluoromethylphenyl (5), or bis(trifluoromethyl)phenyl (6) substituents. The passive diffusion of 1-6? Cl(-) was evaluated with the complexes initially positioned either in the water phase or inside the bilayer. In the first scenario the chloride is released in the water solution before the synthetic molecules achieve the water-lipid interface and permeate the membrane. In the latter one, only when the chloride complex reaches the interface is the anion released to the water phase, with the transporter losing the initial ggg tripodal shape. Independently of the transporter used in the membrane system, the bilayer structure is preserved and the synthetic molecules interact with the POPC molecules at the phosphate headgroup level, via N-H···O hydrogen bonds. Overall, the molecular dynamics simulations' results indicate that the small tripodal molecules in this series have a low impact on the bilayer and are able to diffuse with chloride inside the lipid environment. Indeed, these are essential conditions for these molecules to promote the transmembrane transport as anion carriers, in agreement with experimental efflux data. PMID:24663079

  15. Heterogeneity of Synovial Molecular Patterns in Patients with Arthritis

    PubMed Central

    Lauwerys, Bernard R.; Hernández-Lobato, Daniel; Gramme, Pierre; Ducreux, Julie; Dessy, Adrien; Focant, Isabelle; Ambroise, Jérôme; Bearzatto, Bertrand; Nzeusseu Toukap, Adrien; Van den Eynde, Benoît J.; Elewaut, Dirk; Gala, Jean-Luc; Durez, Patrick; Houssiau, Frédéric A.; Helleputte, Thibault; Dupont, Pierre

    2015-01-01

    Objectives Early diagnosis of rheumatoid arthritis (RA) is an unmet medical need in the field of rheumatology. Previously, we performed high-density transcriptomic studies on synovial biopsies from patients with arthritis, and found that synovial gene expression profiles were significantly different according to the underlying disorder. Here, we wanted to further explore the consistency of the gene expression signals in synovial biopsies of patients with arthritis, using low-density platforms. Methods Low-density assays (cDNA microarray and microfluidics qPCR) were designed, based on the results of the high-density microarray data. Knee synovial biopsies were obtained from patients with RA, spondyloarthropathies (SA) or osteoarthritis (OA) (n = 39), and also from patients with initial undifferentiated arthritis (UA) (n = 49). Results According to high-density microarray data, several molecular pathways are differentially expressed in patients with RA, SA and OA: T and B cell activation, chromatin remodelling, RAS GTPase activation and extracellular matrix regulation. Strikingly, disease activity (DAS28-CRP) has a significant influence on gene expression patterns in RA samples. Using the low-density assays, samples from patients with OA are easily discriminated from RA and SA samples. However, overlapping molecular patterns are found, in particular between RA and SA biopsies. Therefore, prediction of the clinical diagnosis based on gene expression data results in a diagnostic accuracy of 56.8%, which is increased up to 98.6% by the addition of specific clinical symptoms in the prediction algorithm. Similar observations are made in initial UA samples, in which overlapping molecular patterns also impact the accuracy of the diagnostic algorithm. When clinical symptoms are added, the diagnostic accuracy is strongly improved. Conclusions Gene expression signatures are overall different in patients with OA, RA and SA, but overlapping molecular signatures are found in patients with these conditions. Therefore, an accurate diagnosis in patients with UA requires a combination of gene expression and clinical data. PMID:25927832

  16. Molecular Beam Scattering of Aligned Oxygen Molecules. The Nature of the Bond in the O2-O2 Dimer

    E-print Network

    Pirani, Fernando

    forces between molecules as leading to chemical-bond formation; but in exceptional cases, such as that of the O4 molecule [...] it may happen that these forces are strong enough to make it conMolecular Beam Scattering of Aligned Oxygen Molecules. The Nature of the Bond in the O2-O2 Dimer

  17. Orientation of organic molecules in a monolayer vis-à-vis their molecular orbitals and transport gap

    NASA Astrophysics Data System (ADS)

    Chakrabarti, Sudipto; Dey, Sukumar; Pal, Amlan J.

    2011-08-01

    We form a monolayer of magnetic organic molecules with its plane parallel or perpendicular to the substrate. The molecules in a monolayer are oriented with an external magnetic field followed by immobilization though an electrostatic binding. In this work, from scanning tunneling microscopy (STM) measurements, we show that conductivity, molecular orbitals, and transport gap of the molecules in a monolayer depend on its orientation. From measurements carried out with different tip-to-molecule distances, we observe that the STM tip also influences molecular orbitals and transport-gap of molecules.

  18. Rotational Spectromicroscopy: Imaging the Orbital Interaction between Molecular Hydrogen and an Adsorbed Molecule

    NASA Astrophysics Data System (ADS)

    Li, Shaowei; Yuan, Dingwang; Yu, Arthur; Czap, Gregory; Wu, Ruqian; Ho, W.

    2015-05-01

    A hydrogen molecule can diffuse freely on the surface and be trapped above an adsorbed molecule within the junction of a scanning tunneling microscope. The trapped dihydrogen exhibits the properties of a free rotor. Here we show that the intermolecular interaction between dihydrogen and Mg-porphyrin (MgP) can be visualized by imaging j =0 to 2 rotational excitation of dihydrogen. The interaction leads to a weakened H-H bond and modest electron donation from the dihydrogen to the lowest unoccupied molecular orbital of MgP, a process similarly observed for the interaction between dihydrogen and an adsorbed Au atom.

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

    PubMed Central

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

    2007-01-01

    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. PMID:17727706

  20. Tungsten polyoxometalate molecules as active nodes for dynamic carrier exchange in hybrid molecular/semiconductor capacitors

    SciTech Connect

    Balliou, A., E-mail: aballiou@imel.demokritos.gr [Institute of Nanoscience and Nanotechnology, NCSR Demokritos, Aghia Paraskevi, Athens 15310 (Greece); Department of Chemical Engineering, NTUA, Zographou Campus, Athens 15773 (Greece); Douvas, A. M.; Normand, P.; Argitis, P.; Glezos, N. [Institute of Nanoscience and Nanotechnology, NCSR Demokritos, Aghia Paraskevi, Athens 15310 (Greece); Tsikritzis, D.; Kennou, S. [Department of Chemical Engineering, University of Patras, University Campus, Patras 26504 (Greece)

    2014-10-14

    In this work we study the utilization of molecular transition metal oxides known as polyoxometalates (POMs), in particular the Keggin structure anions of the formula PW??O??³?, as active nodes for potential switching and/or fast writing memory applications. The active molecules are being integrated in hybrid Metal-Insulator/POM molecules-Semiconductor capacitors, which serve as prototypes allowing investigation of critical performance characteristics towards the design of more sophisticated devices. The charging ability as well as the electronic structure of the molecular layer is probed by means of electrical characterization, namely, capacitance-voltage and current-voltage measurements, as well as transient capacitance measurements, C (t), under step voltage polarization. It is argued that the transient current peaks observed are manifestations of dynamic carrier exchange between the gate electrode and specific molecular levels, while the transient C (t) curves under conditions of molecular charging can supply information for the rate of change of the charge that is being trapped and de-trapped within the molecular layer. Structural characterization via surface and cross sectional scanning electron microscopy as well as atomic force microscopy, spectroscopic ellipsometry, UV and Fourier-transform IR spectroscopies, UPS, and XPS contribute to the extraction of accurate electronic structure characteristics and open the path for the design of new devices with on-demand tuning of their interfacial properties via the controlled preparation of the POM layer.

  1. Molecular sieve separation of ground state HF molecules in a non-chain HF laser

    NASA Astrophysics Data System (ADS)

    Ma, Lianying; Zhou, Songqing; Huang, Chao; Cheng, Hongwei; Zhu, Feng

    2015-05-01

    A 3A molecular sieve separation device was designed and mounted in a closed-cycled non-chain HF laser to separate the ground state molecule being produced in discharge region from gas stream in order to improve the stability of laser output energy. Experiments were carried out with several different discharge voltages and gas flow velocities, and the preliminary results show that the molecular sieve separation device could dramatically decrease the decay of output energy of HF laser while improving the laser energy stability.

  2. Theoretical estimation of the electron molecular vibration coupling in several organic donor molecules

    NASA Astrophysics Data System (ADS)

    Taniguchi, M.; Misaki, Y.; Tanaka, K.

    2000-03-01

    The electron-molecular vibration (EMV) coupling constants and the accompanying vibronic energy values of five kinds of organic donor molecules (TTF +1, TTP +1, TTPY +1, TOF +1 and TSF +1) are crucial ingredients of metallic organic salts, and have been theoretically estimated in order to systematically investigate their dependencies on the molecular structures. The effect of the replacement of sulfur atoms in TTF +1 with oxygen and selenium atoms (TOF +1 and TSF +1) has been paid particular attention. It has been found that the EMV coupling constant decreases in the order of TOF +1>TTF +1>TSF +1>TTP +1>TTPY +1. That is, the smaller coupling constants appear in the larger-sized molecule with heavier atoms.

  3. Correlating Molecular Structures with Transport Dynamics in High-Efficiency Small-Molecule Organic Photovoltaics.

    PubMed

    Peng, Jiajun; Chen, Yani; Wu, Xiaohan; Zhang, Qian; Kan, Bin; Chen, Xiaoqing; Chen, Yongsheng; Huang, Jia; Liang, Ziqi

    2015-06-24

    Efficient charge transport is a key step toward high efficiency in small-molecule organic photovoltaics. Here we applied time-of-flight and organic field-effect transistor to complementarily study the influences of molecular structure, trap states, and molecular orientation on charge transport of small-molecule DRCN7T (D1) and its analogue DERHD7T (D2). It is revealed that, despite the subtle difference of the chemical structures, D1 exhibits higher charge mobility, the absence of shallow traps, and better photosensitivity than D2. Moreover, charge transport is favored in the out-of-plane structure within D1-based organic solar cells, while D2 prefers in-plane charge transport. PMID:26066398

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

    SciTech Connect

    Zhong Jun; Hector, Louis G. Jr.; Adams, James B. [School of Materials, Arizona State University, Tempe, Arizona 85287-8706 (United States); Materials and Processes Laboratory, General Motor R and D Center, Warren, Michigan 48090-9055 (United States); School of Materials, Arizona State University, Tempe, Arizona 85287-8706 (United States)

    2009-03-15

    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 deg. and 180 deg. prior to collision with Al(111)

  5. Nonadiabatic molecular high-order harmonic generation from polar molecules: Spectral redshift

    SciTech Connect

    Bian Xuebin; Bandrauk, Andre D. [Departement de Chimie, Universite de Sherbrooke, Sherbrooke, Quebec, J1K 2R1 (Canada)

    2011-04-15

    Molecular high-order harmonic generation (MHOHG) from the polar diatomic molecule HeH{sup 2+} in short intense laser fields is studied numerically. Due to the nonadiabatic response of the molecular dipole to the rapid change of laser intensity, a spectral redshift is predicted in high-intensity and ultrashort laser pulses, contrary to the blueshift observed in the harmonics generated from atoms in long laser pulses. The MHOHG temporal structures are investigated by a wavelet time-frequency analysis, which shows that the enhanced excitation of localized long lifetime excited states shifts the harmonic generation spectrum in the falling part of short laser pulses, due to the presence of a permanent dipole moment, and thus is unique to polar molecules.

  6. The functional basis of wing patterning in Heliconius butterflies: the molecules behind mimicry.

    PubMed

    Kronforst, Marcus R; Papa, Riccardo

    2015-05-01

    Wing-pattern mimicry in butterflies has provided an important example of adaptation since Charles Darwin and Alfred Russell Wallace proposed evolution by natural selection >150 years ago. The neotropical butterfly genus Heliconius played a central role in the development of mimicry theory and has since been studied extensively in the context of ecology and population biology, behavior, and mimicry genetics. Heliconius species are notable for their diverse color patterns, and previous crossing experiments revealed that much of this variation is controlled by a small number of large-effect, Mendelian switch loci. Recent comparative analyses have shown that the same switch loci control wing-pattern diversity throughout the genus, and a number of these have now been positionally cloned. Using a combination of comparative genetic mapping, association tests, and gene expression analyses, variation in red wing patterning throughout Heliconius has been traced back to the action of the transcription factor optix. Similarly, the signaling ligand WntA has been shown to control variation in melanin patterning across Heliconius and other butterflies. Our understanding of the molecular basis of Heliconius mimicry is now providing important insights into a variety of additional evolutionary phenomena, including the origin of supergenes, the interplay between constraint and evolvability, the genetic basis of convergence, the potential for introgression to facilitate adaptation, the mechanisms of hybrid speciation in animals, and the process of ecological speciation. PMID:25953905

  7. Analyzing different parameters of steered molecular dynamics for small membrane interacting molecules

    Microsoft Academic Search

    Alicia C. Lorenzo; Paulo M. Bisch

    2005-01-01

    The aim of this report is two-fold: First, to show the applicability of the Steered Molecular Dynamics (SMD) methodology for analyzing non-specific interactions governing the membrane affinity process of small biological molecules. Second, to point out a correlation between the system response and certain combinations of the SMD parameters (spring-elastic-constant and pulling-group). For these purposes, a simplified membrane model was

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

    PubMed

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

    2014-02-01

    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

  9. Solvation chemical shifts of perylenic antenna molecules from molecular dynamics simulations.

    PubMed

    Özcan, Nergiz; Mareš, Ji?í; Sundholm, Dage; Vaara, Juha

    2014-10-28

    Solvation-induced shifts in molecular properties can be realistically simulated by employing a dynamic model with explicit solvent molecules. In this work, (13)C NMR chemical shifts of various candidate antenna molecules for dye-sensitised solar cells have been studied by using density-functional theory calculations both in vacuo and by employing a dynamic solvation model. The solvent effects were investigated using instantaneous molecular dynamics snapshots containing the antenna molecule and surrounding acetonitrile solvent molecules. Such calculations take into account the main mechanisms of solvation-induced chemical shifts. We have analysed the contributions to the solvent shift due to the solvent susceptibility anisotropy, changes in the density of the virtual orbital space and the accessibility of the excited states to the pronouncedly local magnetic hyperfine operator. We present Lorentzian-broadened chemical shift stick spectra in which a comparison of the in vacuo and dynamic-solvation model results is graphically illustrated. The results show that the solvent-accessible atoms at the perimeter of the solute are influenced by the virtual states of the solvent molecules, which are visible to the hyperfine operators of the perimeter nuclei. This enables efficient coupling of the ground state of the solute to the magnetically allowed excited states, resulting in a positive chemical shift contribution of the perimeter nuclei. As a result of solvation, the chemical shift signals of perimeter nuclei are found to be displaced towards larger chemical shift values, whereas the nuclei of the inner region of the solute molecules show the opposite trend. The solvent susceptibility anisotropy is found to cause a small and practically constant contribution. PMID:25222796

  10. Mechanics and chemistry: single molecule bond rupture forces correlate with molecular backbone structure.

    PubMed

    Frei, Michael; Aradhya, Sriharsha V; Koentopp, Max; Hybertsen, Mark S; Venkataraman, L

    2011-04-13

    We simultaneously measure conductance and force across nanoscale junctions. A new, two-dimensional histogram technique is introduced to statistically extract bond rupture forces from a large data set of individual junction elongation traces. For the case of Au point contacts, we find a rupture force of 1.4 ± 0.2 nN, which is in good agreement with previous measurements. We then study systematic trends for single gold metal-molecule-metal junctions for a series of molecules terminated with amine and pyridine linkers. For all molecules studied, single molecule junctions rupture at the Au-N bond. Selective binding of the linker group allows us to correlate the N-Au bond-rupture force to the molecular backbone. We find that the rupture force ranges from 0.8 nN for 4,4' bipyridine to 0.5 nN in 1,4 diaminobenzene. These experimental results are in excellent quantitative agreement with density functional theory based adiabatic molecular junction elongation and rupture calculations. PMID:21366230

  11. Mechanics and Chemistry: Sinle Molecule Bond Rupture Forces Correlate with Molecular Backbone Structure

    SciTech Connect

    Frei, M.; Hybertsen, M.; Aradhya, S.V.; Koentopp, M.; Venkataraman, L.

    2011-03-02

    We simultaneously measure conductance and force across nanoscale junctions. A new, two-dimensional histogram technique is introduced to statistically extract bond rupture forces from a large data set of individual junction elongation traces. For the case of Au point contacts, we find a rupture force of 1.4 {+-} 0.2 nN, which is in good agreement with previous measurements. We then study systematic trends for single gold metal-molecule-metal junctions for a series of molecules terminated with amine and pyridine linkers. For all molecules studied, single molecule junctions rupture at the Au-N bond. Selective binding of the linker group allows us to correlate the N-Au bond-rupture force to the molecular backbone. We find that the rupture force ranges from 0.8 nN for 4,4' bipyridine to 0.5 nN in 1,4 diaminobenzene. These experimental results are in excellent quantitative agreement with density functional theory based adiabatic molecular junction elongation and rupture calculations.

  12. Studies of the pattern recognition molecule H-ficolin: specificity and purification.

    PubMed

    Zacho, Rikke M; Jensen, Lisbeth; Terp, Randi; Jensenius, Jens C; Thiel, Steffen

    2012-03-01

    Ficolins are pattern recognition molecules of the innate immune system. H-ficolin is found in plasma associated with mannan-binding lectin-associated serine proteases (MASPs). When H-ficolin binds to microorganisms the MASPs are activated, which in turn activate the complement system. H-ficolin is the most abundant ficolin in humans, yet its ligand binding characteristics and biological role remain obscure. We examined the binding of H-ficolin to Aerococcus viridans as well as to a more defined artificial target, i.e. acetylated bovine serum albumin. A strict dependence for calcium ions and inhibition at high NaCl concentration was found. The binding to acetylated bovine serum albumin was inhibited by acetylsalicylic acid and sodium acetate as well as by N-acetylated glucosamine and galactosamine (GlcNAc and GalNAc) and glycine (GlyNAc). The binding to A. viridans was sensitive to the same compounds, but, importantly, higher concentrations were needed for inhibition. N-Acetylated cysteine was also inhibitory, but this inhibition was parallel with reduction in the oligomerization of H-ficolin and thus represents structural changes of the molecule. Based on our findings, we developed a procedure for the purification of H-ficolin from serum, involving PEG precipitation, affinity chromatography on Sepharose derivatized with acetylated serum albumin, ion exchange chromatography, and gel permeation chromatography. The purified H-ficolin was observed to elute at 700 kDa, similar to what we find for H-ficolin in whole serum. MASP-2 was co-purified with H-ficolin, and the purified H-ficolin·MASP-2 complex could activate complement as measured by cleavage of complement factor C4. This study extends our knowledge of the specificity of this pattern recognition molecule, and the purified product will enable further studies. PMID:22238349

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

    NASA Astrophysics Data System (ADS)

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

    2013-07-01

    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.

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

    PubMed Central

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

    2013-01-01

    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. PMID:23308257

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

    PubMed Central

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

    2007-01-01

    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. PMID:17660262

  16. Molecular plasticity of beta-catenin: new insights from single-molecule measurements and MD simulation.

    PubMed

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

    2007-09-01

    The multifunctional protein, beta-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 beta-catenin underlie these two functions? Our single-molecule force spectroscopy of armadillo beta-catenin, with molecular dynamics (MD) simulation, suggests a model in which the cell generates various forms of beta-catenin, in equilibrium. We find beta-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 beta-catenin main binding site. This mechanism for the generation of the various forms offers a route to tailoring future therapeutic strategies. PMID:17660262

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

    PubMed Central

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

    2014-01-01

    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

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

    PubMed

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

    2014-06-10

    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

  19. Kinetics of Circulating Damage-Associated Molecular Patterns in Sepsis

    PubMed Central

    Miki, Takahiro; Iba, Toshiaki

    2015-01-01

    Circulating levels of conventional biomarkers and damage-associated molecular patterns were examined in 30 severe sepsis patients (20 survivors and 10 nonsurvivors). Plasma levels of interleukin 6, CRP, and procalcitonin reached their peaks on Day 0 (onset of sepsis) or Day 1 and declined rapidly thereafter despite the persistent severity. In contrast, elevated levels of histone H3, nucleosome, and high-mobility group protein Box 1 remained for longer periods of time. The peak level of histone H3 in the nonsurvivors was higher than that of the survivors (p < 0.05 on Day 7). The cutoff value of the histone H3 on Day 7 for death was 0.08?AU and the area under the receiver operating characteristic curve showed discriminative powers of 0.74. Measurement of circulating levels of the histone H3 provides additional information to that of the conventional indicators of inflammation for determining the severity of sepsis. PMID:26161427

  20. Molecular Shot Noise, Burst Size Distribution, and Single-Molecule Detection in Fluid Flow: Effects of Multiple Occupancy

    E-print Network

    Enderlein, Jörg

    Molecular Shot Noise, Burst Size Distribution, and Single-Molecule Detection in Fluid Flow: Effects of Multiple Occupancy Jo1rg Enderlein,* David L. Robbins, W. Patrick Ambrose, and Richard A. Keller CST-1, MS

  1. Distance-dependent patterns of molecular divergences in tuatara mitogenomes

    PubMed Central

    Subramanian, Sankar; Mohandesan, Elmira; Millar, Craig D.; Lambert, David M.

    2015-01-01

    Population genetic models predict that populations that are geographically close to each other are expected to be genetically more similar to each other compared to those that are widely separate. However the patterns of relationships between geographic distance and molecular divergences at neutral and constrained regions of the genome are unclear. We attempted to clarify this relationship by sequencing complete mitochondrial genomes of the relic species Tuatara (Sphenodon punctatus) from ten offshore islands of New Zealand. We observed a positive relationship that showed a proportional increase in the neutral diversity at synonymous sites (dS), with increasing geographical distance. In contrast we showed that diversity at evolutionarily constrained sites (dC) was elevated in the case of comparisons involving closely located populations. Conversely diversity was reduced in the case of comparisons between distantly located populations. These patterns were confirmed by a significant negative relationship between the ratio of dC/dS and geographic distance. The observed high dC/dS could be explained by the abundance of deleterious mutations in comparisons involving closely located populations, due to the recent population divergence times. Since distantly related populations were separated over long periods of time, deleterious mutations might have been removed by purifying selection. PMID:25731894

  2. The quantum chemical investigation of molecular complexes formed with bromine molecule of adamantylideneadamantan and its derivatives: electronic and steric effects

    Microsoft Academic Search

    R?za Abbaso?lu; Sevil Sava?kan Y?lmaz

    2002-01-01

    The strain energies and the pyramidalization parameters of adamantylideneadamantan (AD), trans-(1-methyl-2-adamantyliden)-1-methyladamantan (DMAD) and trans-(1-tert-butyl-2-adamantyliden)-1-tert-butyladamantan (DBAD) molecules were calculated by MM2 and AMBER molecular mechanic methods. The strain energy and the pyramidalization degree of the molecule are increased by increasing the volume of R groups at the allylic position of the double bond. The electron structure of the molecules were investigated

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The molecular details of DNA aptamer-ricin interactions were investigated. The toxic protein ricin molecules were immobilized on Au(111) surface using N-hydroxysuccinimide (NHS) ester to specifically react with lysine residues located on the ricin B chains. A single ricin molecule was visualized in ...

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

    PubMed Central

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

    2011-01-01

    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. PMID:22661822

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

    NASA Astrophysics Data System (ADS)

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

    2012-03-01

    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.

  6. The Molecule Calculator: A web-server for fast quantum mechanics-based estimation of molecular properties

    E-print Network

    Jensen, Jan H

    2013-01-01

    A new web-server called The Molecule Calculator (MolCalc) is presented. The entry page is a molecular editor (JSmol) for interactive molecule building. The resulting structure can then be used to estimate molecular properties such as heats of formation and other thermodynamic properties, vibrational frequencies and vibrational modes, and molecular orbitals and orbital energies. These properties are computed using the GAMESS program at either the RHF/STO-3G (orbitals and orbital energies) or PM3 level of theory (all other properties) in a matter of seconds or minutes depending on the size of the molecule. The results, though approximate, can help students develop a "chemical intuition" about how molecular structure affects molecular properties, without performing the underlying calculations by hand, a near impossible task for all but the simplest chemical systems.

  7. Molecular dynamics simulations on aqueous two-phase systems - Single PEG-molecules in solution

    PubMed Central

    2012-01-01

    Background Molecular Dynamics (MD) simulations are a promising tool to generate molecular understanding of processes related to the purification of proteins. Polyethylene glycols (PEG) of various length are commonly used in the production and purification of proteins. The molecular mechanisms behind PEG driven precipitation, aqueous two-phase formation or the effects of PEGylation are however still poorly understood. Results In this paper, we ran MD simulations of single PEG molecules of variable length in explicitly simulated water. The resulting structures are in good agreement with experimentally determined 3D structures of PEG. The increase in surface hydrophobicity of PEG of longer chain length could be explained on an atomic scale. PEG-water interactions as well as aqueous two-phase formation in the presence of PO4 were found to be correlated to PEG surface hydrophobicity. Conclusions We were able to show that the taken MD simulation approach is capable of generating both structural data as well as molecule descriptors in agreement with experimental data. Thus, we are confident of having a good in silico representation of PEG. PMID:22873343

  8. Molecular length dictates the nature of charge carriers in single-molecule junctions of oxidized oligothiophenes

    NASA Astrophysics Data System (ADS)

    Dell, Emma J.; Capozzi, Brian; Xia, Jianlong; Venkataraman, Latha; Campos, Luis M.

    2015-03-01

    To develop advanced materials for electronic devices, it is of utmost importance to design organic building blocks with tunable functionality and to study their properties at the molecular level. For organic electronic and photovoltaic applications, the ability to vary the nature of charge carriers and so create either electron donors or acceptors is critical. Here we demonstrate that charge carriers in single-molecule junctions can be tuned within a family of molecules that contain electron-deficient thiophene-1,1-dioxide (TDO) building blocks. Oligomers of TDO were designed to increase electron affinity and maintain delocalized frontier orbitals while significantly decreasing the transport gap. Through thermopower measurements we show that the dominant charge carriers change from holes to electrons as the number of TDO units is increased. This results in a unique system in which the charge carrier depends on the backbone length, and provides a new means to tune p- and n-type transport in organic materials.

  9. Extracellular ATP acts as a damage-associated molecular pattern (DAMP) signal in plants

    PubMed Central

    Tanaka, Kiwamu; Choi, Jeongmin; Cao, Yangrong; Stacey, Gary

    2014-01-01

    As sessile organisms, plants have evolved effective mechanisms to protect themselves from environmental stresses. Damaged (i.e., wounded) plants recognize a variety of endogenous molecules as danger signals, referred to as damage-associated molecular patterns (DAMPs). ATP is among the molecules that are released by cell damage, and recent evidence suggests that ATP can serve as a DAMP. Although little studied in plants, extracellular ATP is well known for its signaling roles in animals, including acting as a DAMP during the inflammatory response and wound healing. If ATP acts outside the cell, then it is reasonable to expect that it is recognized by a plasma membrane-localized receptor. Recently, DORN1, a lectin receptor kinase, was shown to recognize extracellular ATP in Arabidopsis. DORN1 is the founding member of a new purinoceptor subfamily, P2K (P2 receptor kinase), which is plant-specific. P2K1 (DORN1) is required for ATP-induced cellular responses (e.g., cytosolic Ca2+ elevation, MAPK phosphorylation, and gene expression). Genetic analysis of loss-of-function mutants and overexpression lines showed that P2K1 participates in the plant wound response, consistent with the role of ATP as a DAMP. In this review, we summarize past research on the roles and mechanisms of extracellular ATP signaling in plants, and discuss the direction of future research on extracellular ATP as a DAMP signal. PMID:25232361

  10. A comparison of weak molecular adsorption of organic molecules on clean copper and platinum surfaces

    NASA Astrophysics Data System (ADS)

    Sexton, B. A.; Hughes, A. E.

    1984-05-01

    The low temperature, reversibly adsorbed states (90-300 K) of water, n-alcohols, n-ethers, acetone, acetonitrile and n-alkanes have been studied with temperature programmed desorption (TPD) and spectroscopic methods (XPS, UPS) on clean Pt(111) and Cu(100) surfaces. Each molecule forms two distinct low temperature phases at 100 K; a multilayer or condensed phase and a weakly bound monolayer or precursor phase. The monolayer state usually desorbs at a higher temperature than the multilayer and can be isolated by selective desorption. We establish several general conclusions in relation to the weakly chemisorbed monolayers: (1) In the majority of cases, spectroscopic methods (EELS, XPS and UPS) show no significant chemical shifts in the monolayer relative to the condensed phase. Structural and orientational models are therefore proposed from an analysis of the thermal desorption data. (2) Monolayer heats of adsorption were found to be comparable ( ± 5 kJ/mol) to the heats of sublimation of the multilayers for most molecules. We demonstrate, however, that all of the molecules, with the exception of alkanes are chemisorbed in the monolayer. By analysing the heat of adsorption as a function of molecular size, the contributions from the oxygen lone pair bond in alcohols and ethers, and the Van der Waals attraction of the alkane chains to the surface can be separated. A CH 2 group contributes {5-6.5 kJ}/{mol}to the heat on both metals, whereas the oxygen lone pair contributes {42 kJ}/{mol} (Pt) and {35 kJ}/{mol} (Cu), respectively. (3) Each of these weakly adsorbed monolayers may act as precursors to stronger, dissociative chemisorption as the temperature is raised. In most cases, however, the low temperature molecular phase is the only molecular state observed prior to desorption or subsequent dissociation. (4) Platinum binds weak electron donor molecules (alcohols, ethers, acetone, water) somewhat more strongly than copper. For acceptor molecules (e.g. acetonitrile), platinum back-donates electrons much more strongly than copper. These differences can be rationalized in terms of the orbital energy diagrams for the adsorbate and the band structure of the two metals, although a comprehensive bonding scheme has yet to be developed.

  11. Patterned Activity in Stratum Lacunosum Moleculare Inhibits CA1 Pyramidal Neuron Firing

    E-print Network

    Poirazi, Yiota

    Patterned Activity in Stratum Lacunosum Moleculare Inhibits CA1 Pyramidal Neuron Firing HANNAH. Patterned activ- ity in stratum lacunosum moleculare inhibits CA1 pyramidal neuron firing. J. Neurophysiol. 82: 3213­3222, 1999. CA1 pyramidal cells are the primary output neurons of the hippocampus, carrying

  12. Anomalous water molecules and mechanistic effects of water nanotube clusters confined to molecular porous crystals.

    PubMed

    Tadokoro, Makoto; Ohhara, Takashi; Ohhata, Yuhki; Suda, Takaaki; Miyasato, Yuji; Yamada, Takeshi; Kikuchi, Tatsuya; Tanaka, Ichiro; Kurihara, Kazuo; Oguni, Masaharu; Nakasuji, Kazuhiro; Yamamuro, Osamu; Ryota, Kuroki

    2010-02-18

    The movement of water molecules in the limited space present within nanoscale regions, which is different from the molecular motion of bulk water, is significantly affected by strong interfacial interactions with the surrounding outer walls. Hence, most of the water molecules that are confined to nanochannel spaces having widths less than ca. 2 nm can generally be classified together as "structural water". Since the motions of such water molecules are limited by interfacial interactions with the outer wall, the nature of structural water, which is strongly influenced by the interactions, will have different characteristics from normal water. For our investigations on the characteristics of structural water, we have developed a nanoporous crystal with a diameter of ca. 1.6 nm; it was constructed from 1-D hydrophilic channels by self-organization of the designed molecules. A tubelike three-layered water cluster, called a water nanotube (WNT), is formed in each internal channel space and is regulated by H-bonds with the outer wall. The WNT undergoes a glass transition (T(g) = 107 K) and behaves as a liquid; it freezes at 234 K and changes into an icelike nanotube cluster. In this study, the structure of the WNT is investigated through neutron structure analysis, and it is observed to stabilize by a mechanistic anchor effect of structural water. Furthermore, from neutron-scattering experiments, it is seen that a few water molecules around the center of the WNT move approximately with the same diffusion constant as those in bulk water; however, the residence time and average jump length are longer, despite the restrictions imposed by the H-bonding with structural water. The behavior of mobile water within a WNT is investigated; this can be used to elucidate the mechanism for the effect of structural water on vital functions on the cell surface. PMID:20102158

  13. NKp44 and Natural Cytotoxicity Receptors as Damage-Associated Molecular Pattern Recognition Receptors

    PubMed Central

    Horton, Nathan C.; Mathew, Porunelloor A.

    2015-01-01

    Natural killer (NK) cells are a key constituent of the innate immune system, protecting against bacteria, virally infected cells, and cancer. Recognition and protective function against such cells are dictated by activating and inhibitory receptors on the surface of the NK cell, which bind to specific ligands on the surface of target cells. Among the activating receptors is a small class of specialized receptors termed the natural cytotoxicity receptors (NCRs) comprised of NKp30, NKp46, and NKp44. The NCRs are key receptors in the recognition and termination of virally infected and tumor cells. Since their discovery over 10?years ago, ligands corresponding to the NCRs have largely remained elusive. Recent identification of the cellular ligands for NKp44 and NKp30 as exosomal proliferating cell nuclear antigen (PCNA) and HLA-B-associated transcript 3 (BAT3), respectively, implicate that NCRs may function as receptors for damage-associated molecular pattern (DAMP) molecules. In this review, we focus on NKp44, which surprisingly recognizes two distinct ligands resulting in either activation or inhibition of NK cell effector responses in response to tumor cells. The inhibitory function of NKp44 requires further study as it may play a pivotal role in placentation in addition to being exploited by tumors as a mechanism to escape NK cell killing. Finally, we suggest that the NCRs are a class of pattern recognition receptors, which recognize signals of genomic instability and cellular stress via interaction with the c-terminus of DAMP molecules localized to the surface of target cells by various co-ligands. PMID:25699048

  14. Er Effect of Low Molecular Liquid Crystal on One-Sided Patterned Electrodes

    NASA Astrophysics Data System (ADS)

    Kikuchi, Takehito; Inoue, Akio; Furusho, Junji; Kawamuki, Ryohei

    Several kinds of ER fluids (ERF) have been developed and have been applied to some mechatronics devices and processing technologies. In many conventional applications of ERFs, these devices consist of bilateral electrodes to apply electric field in ERF. However, the electric field of several kV/mm may be necessary to generate an ER effect sufficiently for practical purposes. The gap between a pair of electrodes should be, therefore, maintained narrowly and exactly for fears of short-circuit. At the same time, this electrode system also requires an interconnection on driving parts. To improve these disadvantages, we proposed "one-sided patterned electrode" (OSPE) systems in previous works. In this report, we confirmed the flow characteristics of low molecular liquid crystal (LMLC) on OSPE. Next, we also confirmed the different characteristics depending on the pattern type. Depending on results of electro-static analysis, we conclude that such a difference may results from the directors of LC molecules derived by electric field.

  15. Onset of Patterns in an Ocillated Granular Layer: Continuum and Molecular Dynamics Simulations

    E-print Network

    Texas at Austin. University of

    Onset of Patterns in an Ocillated Granular Layer: Continuum and Molecular Dynamics Simulations J of continuum equations to Navier­Stokes order and molecular dynam­ ics (MD) simulations, we find that standing for ordered standing waves is approximately 10% higher in molecular dynamics simulations than in the continuum

  16. The molecular yo-yo method: Live jump detection improves throughput of single-molecule force spectroscopy for out-of-equilibrium transitions

    E-print Network

    Regan, Lynne

    The molecular yo-yo method: Live jump detection improves throughput of single- molecule force detection and force-clamp algorithm that intelligently adjusts and maintains the force on a single molecule, 085119 (2013) The molecular yo-yo method: Live jump detection improves throughput of single-molecule

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

    SciTech Connect

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

    2012-05-01

    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.

  18. Small-molecule G-quadruplex interactions: Systematic exploration of conformational space using multiple molecular dynamics.

    PubMed

    Husby, Jarmila; Todd, Alan K; Platts, James A; Neidle, Stephen

    2013-12-01

    G-quadruplexes are higher-order four-stranded structures formed from repetitive guanine-containing tracts in nucleic acids. They comprise a core of stacked guanine-quartets linked by loops of length and sequence that vary with the context in which the quadruplex sequence occurs. Such sequences can be found in a number of genomic environments; at the telomeric ends of eukaryotic chromosomes, in promoter regions, in untranslated sequences and in open reading frames. Quadruplex formation can inhibit telomere maintenance, transcription and translation, especially when enhanced by quadruplex-binding small molecules, and quadruplex targeting is currently of considerable interest. The available experimental structural data shows that quadruplexes can have high conformational flexibility, especially in loop regions, which has hampered attempts to use high-throughput docking to find quadruplex-binding small-molecules with new scaffolds or to optimize existing ones with structure-based design methods. An approach to overcome the challenge of quadruplex conformational flexibility is presented here, which uses a combined multiple molecular dynamics and sampling approach. Two test small molecules have been used, RHPS4 and pyridostatin, which themselves have contrasting degrees of conformational flexibility. © 2013 Wiley Periodicals, Inc. Biopolymers 99: 989-1005, 2013. PMID:23828641

  19. Nanoscale patterning of organosilane molecular thin films from the gas phase and its applications: fabrication of multifunctional surfaces and large area molecular templates for site-selective material deposition.

    PubMed

    George, Antony; Knez, Mato; Hlawacek, Gregor; Hagedoorn, Daniël; Verputten, Hein H J; van Gastel, Raoul; ten Elshof, Johan E

    2012-02-01

    A simple methodology to fabricate micrometer- and nanometer-scale patterned surfaces with multiple chemical functionalities is presented. Patterns with lateral dimensions down to 110 nm were made. The fabrication process involves multistep gas-phase patterning of amine, thiol, alkyl, and fluorinated alkyl-functional organosilane molecules using PDMS molds as shadow masks. Also, a combination process of channel diffused plasma etching of organosilane molecular thin films in combination with masked gas-phase deposition to fabricate multilength scale, multifunctional surfaces is demonstrated. PMID:22229783

  20. The Hedgehog (Hh) family of signaling molecules are key agents in patterning numerous types of tissues. Mutations in Hh

    E-print Network

    Perrimon, Norbert

    503 The Hedgehog (Hh) family of signaling molecules are key agents in patterning numerous types of Hh signal transduction. Several new Sonic Hedgehog binding partners have been identified. Cholesterol and palmitic acid modifications of Hh and Sonic hedgehog have been examined in greater detail. Characterization

  1. IEEE JOURNAL OF QUANTUM ELECTRONICS, VOL. 46, NO. 12, DECEMBER 2010 1827 Patterned Quantum Dot Molecule Laser Fabricated

    E-print Network

    Li, Xiuling

    November 24, 2010. This work was supported in part by the Defense Advanced Research Projects Agency, under Molecule Laser Fabricated by Electron Beam Lithography and Wet Chemical Etching V. B. Verma, Member, IEEE of an edge-emitting semiconductor laser with a gain medium con- sisting of two layers of patterned, self

  2. Alcohol exposure alters the expression pattern of neural cell adhesion molecules during brain development.

    PubMed

    Miñana, R; Climent, E; Barettino, D; Segui, J M; Renau-Piqueras, J; Guerri, C

    2000-09-01

    Neural cell adhesion molecules (NCAMs) play critical roles during development of the nervous system. The aim of this study is to investigate the possible effect of ethanol exposure on the pattern of expression and sialylation of NCAM isoforms during postnatal rat brain development because alterations in NCAM content and distribution have been associated with defects in cell migration, synapse formation, and memory consolidation, and deficits in these processes have been observed after in utero alcohol exposure. The expression of NCAM isoforms in the developing cerebral cortex of pups from control and alcohol-fed mothers was assessed by western blotting, ribonuclease protection assay, and immunocytochemistry. The highly sialylated form of NCAM [polysialic acid (PSA)-NCAM] is mainly expressed during the neonatal period and then is down-regulated in parallel with the appearance of NCAM 180 and NCAM 140. Ethanol exposure increases PSA-NCAM levels during the neonatal period, delays the loss of PSA-NCAM, decreases the amount of NCAM 180 and NCAM 140 isoforms, and reduces sialyltransferase activity during postnatal brain development. Neuraminidase treatment of ethanol-exposed neonatal brains leads to more intense band degradation products, suggesting a higher content of NCAM polypeptides carrying PSA in these samples. However, NCAM mRNA levels are not changed by ethanol. Immunocytochemical analysis demonstrates that ethanol triggers an increase in PSA-NCAM immunolabeling in the cytoplasm of astroglial cells, accompanied by a decrease in immunogold particles over the plasma membrane. These findings indicate that ethanol exposure during brain development alters the pattern of NCAM expression and suggest that modification of NCAM could affect neuronal-glial interactions that might contribute to the brain defects observed after in utero alcohol exposure. PMID:10936176

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

    PubMed

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

    2014-05-01

    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

  4. Structure of the F-Spondin Domain of Mindin, an Integrin Ligand and Pattern Recognition Molecule

    SciTech Connect

    Li, Y.; Cao, C; Jia, W; Yu, L; Mo, M; Wang, Q; Huang, Y; Lim, J; Ishihara, M; et. al.

    2009-01-01

    Mindin (spondin-2) is an extracellular matrix protein of unknown structure that is required for efficient T-cell priming by dendritic cells. Additionally, mindin functions as a pattern recognition molecule for initiating innate immune responses. These dual functions are mediated by interactions with integrins and microbial pathogens, respectively. Mindin comprises an N-terminal F-spondin (FS) domain and C-terminal thrombospondin type 1 repeat (TSR). We determined the structure of the FS domain at 1.8-A resolution. The structure revealed an eight-stranded antiparallel ?-sandwich motif resembling that of membrane-targeting C2 domains, including a bound calcium ion. We demonstrated that the FS domain mediates integrin binding and identified the binding site by mutagenesis. The mindin FS domain therefore represents a new integrin ligand. We further showed that mindin recognizes lipopolysaccharide (LPS) through its TSR domain, and obtained evidence that C-mannosylation of the TSR influences LPS binding. Through these dual interactions, the FS and TSR domains of mindin promote activation of both adaptive and innate immune responses.

  5. Structure of the F-spondin Domain of Mindin an Integrin Ligand and Pattern Recognition Molecule

    SciTech Connect

    Y Li; C Cao; W Jia; L Yu; M Mo; Q Wang; Y Huang; J Lim; M Ishihara; et. al.

    2011-12-31

    Mindin (spondin-2) is an extracellular matrix protein of unknown structure that is required for efficient T-cell priming by dendritic cells. Additionally, mindin functions as a pattern recognition molecule for initiating innate immune responses. These dual functions are mediated by interactions with integrins and microbial pathogens, respectively. Mindin comprises an N-terminal F-spondin (FS) domain and C-terminal thrombospondin type 1 repeat (TSR). We determined the structure of the FS domain at 1.8-A resolution. The structure revealed an eight-stranded antiparallel beta-sandwich motif resembling that of membrane-targeting C2 domains, including a bound calcium ion. We demonstrated that the FS domain mediates integrin binding and identified the binding site by mutagenesis. The mindin FS domain therefore represents a new integrin ligand. We further showed that mindin recognizes lipopolysaccharide (LPS) through its TSR domain, and obtained evidence that C-mannosylation of the TSR influences LPS binding. Through these dual interactions, the FS and TSR domains of mindin promote activation of both adaptive and innate immune responses.

  6. Periodic arrays of epitaxial self-assembled SiGe quantum dot molecules grown on patterned Si substrates

    SciTech Connect

    Gray, J. L.; Hull, R.; Floro, J. A. [Department of Materials Science and Engineering, University of Pittsburgh, 848 Benedum Hall, Pittsburgh, Pennsylvania 15261 (United States); Sandia National Laboratories, Albuquerque, New Mexico 87185-1415 (United States)

    2006-10-15

    Ex situ focused ion-beam (FIB) patterning of arrays of holes on Si (001) substrates results in the subsequent formation of SiGe quantum dot molecules at each of the patterned sites during heteroepitaxial growth under kinetically limited growth conditions where island formation is constrained. These quantum dot molecules are fourfold self-assembled island nanostructures bound by a central pit. During growth, material is ejected from the patterned sites forming the pits that in turn provide favorable sites for the cooperative nucleation of (105) faceted islands. The degree of order and quality of the resulting structures depend on many factors including growth temperature, ion-beam milling depth, Si buffer thickness, and spacings between FIB exposed sites. This technique provides a method for controlling the lateral placement of semiconductor nanostructures, which could be used in applications such as complex nanoelectronic architectures.

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

    SciTech Connect

    Chu, P.M.Y.

    1991-10-01

    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.

  8. Cryogenic micro-calorimeters for mass spectrometric identification of neutral molecules and molecular fragments

    E-print Network

    Novotný, O; Enss, C; Fleischmann, A; Gamer, L; Hengstler, D; Kempf, S; Krantz, C; Pabinger, A; Pies, C; Savin, D W; Schwalm, D; Wolf, A

    2015-01-01

    We have systematically investigated the energy resolution of a magnetic micro-calorimeter (MMC) for atomic and molecular projectiles at impact energies ranging from $E\\approx13$ to 150~keV. For atoms we obtained absolute energy resolutions down to $\\Delta E \\approx 120$~eV and relative energy resolutions down to $\\Delta E/E\\approx10^{-3}$. We also studied in detail the MMC energy-response function to molecular projectiles of up to mass 56~u. We have demonstrated the capability of identifying neutral fragmentation products of these molecules by calorimetric mass spectrometry. We have modeled the MMC energy-response function for molecular projectiles and conclude that backscattering is the dominant source of the energy spread at the impact energies investigated. We have successfully demonstrated the use of a detector absorber coating to suppress such spreads. We briefly outline the use of MMC detectors in experiments on gas-phase collision reactions with neutral products. Our findings are of general interest fo...

  9. Nanomechanical recognition measurements of individual DNA molecules reveal epigenetic methylation patterns

    Microsoft Academic Search

    Rong Zhu; Stefan Howorka; Johannes Pröll; Ferry Kienberger; Johannes Preiner; Jan Hesse; Andreas Ebner; Vassili Ph. Pastushenko; Hermann J. Gruber; Peter Hinterdorfer

    2010-01-01

    Atomic force microscopy (AFM) is a powerful tool for analysing the shapes of individual molecules and the forces acting on them. AFM-based force spectroscopy provides insights into the structural and energetic dynamics of biomolecules by probing the interactions within individual molecules, or between a surface-bound molecule and a cantilever that carries a complementary binding partner. Here, we show that an

  10. Density wave patterns for fermionic dipolar molecules on a square optical lattice: mean field theory analysis

    Microsoft Academic Search

    Karlis Mikelsons; Jim Freericks

    2011-01-01

    We model a system of ultra cold 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 planes, we approximate these molecules as spinless fermions with long range repulsive dipolar interactions. We use mean field theory to obtain the phase

  11. The serum mannose-binding protein and the macrophage mannose receptor are pattern recognition molecules that link innate and adaptive immunity

    Microsoft Academic Search

    Iain P Fraser; Henry Koziel; R. Alan B Ezekowitz

    1998-01-01

    The innate immune system evolved to protect the host in the early phases of an infectious challenge. The soluble mannose binding protein, and the cell surface mannose receptor are two key pattern recognition molecules of innate immunity. The ligand binding specificity of these molecules enables them to differentiate ‘self’ from ‘non-self’. These pattern recognition capabilities are coupled to effector functions,

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

    PubMed Central

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

    2014-01-01

    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. PMID:24618531

  13. Comparative study of complex N- and O-bearing molecules in hot molecular cores

    E-print Network

    F. Fontani; I. Pascucci; P. Caselli; F. Wyrowski; R. Cesaroni; C. M. Walmsley

    2007-05-11

    We have observed several emission lines of two Nitrogen-bearing (C2H5CN and C2H3CN) and two Oxygen-bearing (CH3OCH3 and HCOOCH3) molecules towards a sample of well-known hot molecular cores (HMCs) in order to check whether the chemical differentiation seen in the Orion-HMC and W3(H_2O) between O- and N-bearing molecules is a general property of HMCs. With the IRAM-30m telescope we have observed 12 HMCs in 21 bands, centered at frequencies from 86250 to 258280 MHz. The rotational temperatures obtained range from ~100 to ~150 K in these HMCs. Single Gaussian fits performed to unblended lines show a marginal difference in the line peak velocities of the C2H5CN and CH3OCH3 lines, indicating a possible spatial separation between the region traced by the two molecules. On the other hand, neither the linewidths nor the rotational temperatures and column densities confirm such a result. By comparing the abundance ratio of the pair C2H5CN/C2H3CN with the predictions of theoretical models, we derive that the age of our cores ranges between 3.7 and 5.9x10^{4} yrs. The abundances of C2H5CN and C2H3CN are strongly correlated, as expected from theory which predicts that C2H3CN is formed through gas phase reactions involving C2H5CN. A correlation is also found between the abundances of C2H3CN and CH3OCH3, and C2H5CN and CH3OCH3. In all tracers the fractional abundances increase with the H_2 column density while they are not correlated with the gas temperature.

  14. [Molecular motility of a fluorescent probe in binding sites of albumin molecules].

    PubMed

    Dobretsov, G E; Syre?shchikov, T I; Smolina, N V

    2011-01-01

    The molecular mobility of the fluorescent probe, N-(carboxymethyl)imide of 4-(dimethylamino)naphthalic acid (K-35) in three types of binding sites on a human serum albumin (HSA) molecule has been studied. The time-resolved decay of K-35 polarized fluorescence in HSA has been studied and it has been shown that probe molecules bound to different sites have different fluorescence decay time, which poses problems in the interpretation of polarization decay. However, it has been found that, in the case of rather slow thermal rotation of the probe, the decay of each of vertical and horizontal polarized fluorescence components can be approximated by three exponentials corresponding to three types of binding sites. The mobility of the probe in different sites was estimated. The mobility was different but hindered by tens of times in all sites as compared with the rotation of K-35 in water. The slowest motion occurred in the sites of the first type localized in the region of the well known first drug-binding site: here the rotational correlation was close to 72 ns or more. In the sites of the second type, the time was about 40 ns, and in the sites of the third type, the time was about 10 ns. It was found that the higher the rotation rate, the higher the fluorescence quenching rate. Probably, it is this motion that is responsible for different fluorescence decay times in different HSA sites. PMID:21786694

  15. Molecular dynamics simulations of nucleation from vapor to solid composed of Lennard-Jones molecules.

    PubMed

    Tanaka, Kyoko K; Tanaka, Hidekazu; Yamamoto, Tetsuo; Kawamura, Katsuyuki

    2011-05-28

    We performed molecular dynamics (MD) simulations of nucleation from vapor at temperatures below the triple point for systems consisting of 10(4)-10(5) Lennard-Jones (L-J) type molecules in order to test nucleation theories at relatively low temperatures. Simulations are performed for a wide range of initial supersaturation ratio (S(0) ? 10-10(8)) and temperature (kT = 0.2-0.6?), where ? and k are the depth of the L-J potential and the Boltzmann constant, respectively. Clusters are nucleated as supercooled liquid droplets because of their small size. Crystallization of the supercooled liquid nuclei is observed after their growth slows. The classical nucleation theory (CNT) significantly underestimates the nucleation rates (or the number density of critical clusters) in the low-T region. The semi-phenomenological (SP) model, which corrects the CNT prediction of the formation energy of clusters using the second virial coefficient of a vapor, reproduces the nucleation rate and the cluster size distributions with good accuracy in the low-T region, as well as in the higher-T cases considered in our previous study. The sticking probability of vapor molecules onto the clusters is also obtained in the present MD simulations. Using the obtained values of sticking probability in the SP model, we can further refine the accuracy of the SP model. PMID:21639446

  16. Molecular patterns and sequence polymorphisms in the red and green visual pigment genes of Japanese men

    Microsoft Academic Search

    Samir S. Deeb; Angeles Alvarez; Mari Malkki; Arno G. Motulsky

    1995-01-01

    The red-green pigment gene arrays of 203 (101 from a previous study and 102 from this study) randomly selected men of Japanese ancestry from the Seattle area were screened for the abnormal molecular patterns (deletions and red\\/green or green\\/red hybrid genes) that are usually associated with defective color vision. Such molecular patterns were found in approximately 5% of these individuals,

  17. Characterization of phospholipid molecular species and peptide molecules in wheat sprout hydroalcoholic extract.

    PubMed

    Lucci, Paolo; Pacetti, Deborah; Calzuola, Isabella; Marsili, Valeria; Perni, Stefano; Giavarini, Flavio; Frega, Natale Giuseppe; Gianfranceschi, Gian Luigi

    2013-11-27

    The phospholipid molecular species and the main peptide molecules of wheat sprout hydroalcoholic extract have been fully characterized by normal-phase high performance liquid chromatography coupled online with positive electrospray ionization tandem mass spectrometry. The extract that resulted was rich in phospholipid molecular species formed by the combination of the two essential fatty acids (?-linoleic and ?-linolenic). These species accounted for 51.7% of total phosphatidic acid, 47.3% of total phosphatidylethanolamine, 37.7% of total phosphatidylcholine, and 14.1% of total phosphatidylinositol. The last one showed the highest amounts of species containing palmitic acid, thus representing the most saturated phospholipid class. The extract was also shown to contain several peptide sequences with both potential antioxidant domains and interaction sites for phospholipids (i.e., H-Ala-Gly-Ser-Met-Met-Cys-NH2, H-Tyr-Met-Thr-Val-Val-Ala-Cys-NH2, etc.); this latter finding can have a highly positive impact on the poor peptides bioavailability. Because of the presence of essential fatty acids-rich phospholipids and bioactive peptides, wheat sprout hydroalcoholic extract can be considered a potential functional food ingredient. PMID:24156493

  18. Patterns of molecular genetic variation among African elephant populations

    Microsoft Academic Search

    Kenine E. Comstock; Nicholas Georgiadis; Jill Pecon-Slattery; Alfred L. Roca; Elaine A. Ostrander; Stephen J. O'Brien; Samuel K. Wasser

    2002-01-01

    The highly threatened African elephants have recently been subdivided into two species, Loxodonta africana (savannah or bush elephant) and L. cyclotis (forest elephant) based on morphological and molecular studies. A molecular genetic assessment of 16 microsatellite loci across 20 populations (189 individuals) affirms species level genetic differentiation and provides robust genotypic assessment of species affiliation. Savannah elephant popula- tions show

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

    PubMed Central

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

    2013-01-01

    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

  20. Functional Hydrogel Surfaces: Binding Kinesin-Based Molecular Motor Proteins to Selected Patterned Sites**

    E-print Network

    Wang, Michelle

    Functional Hydrogel Surfaces: Binding Kinesin-Based Molecular Motor Proteins to Selected Patterned cellular movements, such as muscle contraction, vesicle transport, cell division, and gene expression.[1 translocation on long biological polymers, such as kinesin, which may be thought of as ªtracksº for molecular

  1. Waldmann-Snider collision integrals and nonspherical molecular interaction. II - DWBA-scattering amplitude and cross sections for linear molecules

    Microsoft Academic Search

    W. E. Koehler

    1975-01-01

    The binary scattering amplitude matrix is derived from the general interaction potential between linear molecules. The first-order distorted wave Born approximation (DWBA) is used which is applicable for small nonsphericity of the interaction. The molecular cross sections determining the most important Waldmann-Snider collision integrals are calculated. In particular, the scattering cross section, the orientation cross sections for vector- and tensor

  2. Observation of Bose-Einstein Condensation of Molecules Molecular condensates could lead to a host of new scientific explorations. These

    E-print Network

    of new scientific explorations. These include quantum gases with anisotropic dipolar interactions, testsObservation of Bose-Einstein Condensation of Molecules Molecular condensates could lead to a host and vibrational energy transfer processes, and coherent chemistry, where reactants and products are in coherent

  3. Identification and molecular characterization of a complement C3 molecule in a lophotrochozoan, the Hawaiian bobtail squid Euprymna scolopes

    E-print Network

    Ruby, Edward G.

    Identification and molecular characterization of a complement C3 molecule in a lophotrochozoan The complement system is a group of serum and membrane- associated proteins that plays an essential role in innate immune defenses. In vertebrates, the complement system not only serves as a bridge between

  4. Kiloelectronvolt Particle-Induced Emission and Fragmentation of Polystyrene Molecules Adsorbed on Silver: Insights from Molecular Dynamics

    E-print Network

    on Silver: Insights from Molecular Dynamics A. Delcorte, X. Vanden Eynde, P. Bertrand, J. C. Vickerman the emission of many silver atoms and organic molecules in a single high action event. 1. Introduction of interactions which results in the sputtering (or desorption) of fragment, parent, and cluster ions or neutral

  5. Molecular-scale quantitative charge density measurement of biological molecule by frequency modulation atomic force microscopy in aqueous solutions

    NASA Astrophysics Data System (ADS)

    Umeda, Kenichi; Kobayashi, Kei; Oyabu, Noriaki; Matsushige, Kazumi; Yamada, Hirofumi

    2015-07-01

    Surface charge distributions on biological molecules in aqueous solutions are essential for the interactions between biomolecules, such as DNA condensation, antibody–antigen interactions, and enzyme reactions. There has been a significant demand for a molecular-scale charge density measurement technique for better understanding such interactions. In this paper, we present the local electric double layer (EDL) force measurements on DNA molecules in aqueous solutions using frequency modulation atomic force microscopy (FM-AFM) with a three-dimensional force mapping technique. The EDL forces measured in a 100 mM KCl solution well agreed with the theoretical EDL forces calculated using reasonable parameters, suggesting that FM-AFM can be used for molecular-scale quantitative charge density measurements on biological molecules especially in a highly concentrated electrolyte.

  6. Molecular-scale quantitative charge density measurement of biological molecule by frequency modulation atomic force microscopy in aqueous solutions.

    PubMed

    Umeda, Kenichi; Kobayashi, Kei; Oyabu, Noriaki; Matsushige, Kazumi; Yamada, Hirofumi

    2015-07-17

    Surface charge distributions on biological molecules in aqueous solutions are essential for the interactions between biomolecules, such as DNA condensation, antibody-antigen interactions, and enzyme reactions. There has been a significant demand for a molecular-scale charge density measurement technique for better understanding such interactions. In this paper, we present the local electric double layer (EDL) force measurements on DNA molecules in aqueous solutions using frequency modulation atomic force microscopy (FM-AFM) with a three-dimensional force mapping technique. The EDL forces measured in a 100 mM KCl solution well agreed with the theoretical EDL forces calculated using reasonable parameters, suggesting that FM-AFM can be used for molecular-scale quantitative charge density measurements on biological molecules especially in a highly concentrated electrolyte. PMID:26120025

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

    SciTech Connect

    Wasielewski, M.R.

    1997-01-01

    '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.'

  8. Geometrical and algebraic approach to central molecular chirality: a chirality index and an Aufbau description of tetrahedral molecules.

    PubMed

    Capozziello, Salvatore; Lattanzi, Alessandra

    2006-08-01

    On the basis of empirical Fischer projections, we develop an algebraic approach to the central molecular chirality of tetrahedral molecules. The elements of such an algebra are obtained from the 24 projections which a single chiral tetrahedron can generate in S and R absolute configurations. They constitute a matrix representation of the O4 orthogonal group. According to this representation, given a molecule with n chiral centres, it is possible to define an "index of chirality chi identical with {n, p}", where n is the number of stereogenic centres of the molecule and p the number of permutations observed under rotations and superimpositions of the tetrahedral molecule to its mirror image. The chirality index not only assigns the global chirality of a given tetrahedral chain, but indicates also a way to predict the same property for new compounds, which can be built up consistently. PMID:16612801

  9. Biomimicry issues: the quest for sensing molecules at the origin of life using molecularly imprinter polymer

    NASA Astrophysics Data System (ADS)

    Carbonnier, Benjamin; Chehimi, Mohamed M.; Bakas, Idriss; Salmi, Zakaria; Mazerie, Isabelle; Floner, Didier; Geneste, Florence; Guerrouache, Mohamed

    The use of real time sensing analysis is becoming very popular in many applications and research areas such as, environment and agriculture for in situ monitoring of contaminants and food safety analysis, fundamental biology for studying for example protein-membrane interactions or drug discovery, health research for clinical diagnosis.[1] More recently, chip technology involving antibody-based detection system has been envisioned to search for life outside the Earth with a specific focus on Mars. [2] Sensors using such natural receptors are usually costly and suffer from the unstability of the surface-immobilized receptors. In this respect, the use of synthetic receptors appears as a very promising approach. Molecularly imprinting is undoubtedly one of the most promising approaches for designing biomimetic materials. In this respect, sensing microdevices based on molecularly imprinted polymers (MIPs) have attracted a great deal of interest over the recent years given their ability to recognize specifically and selectively molecules, proteins and even microorganisms, with excellent detection limits. MIPs can be prepared as powders, colloids and ultrathin films. The latter option is particularly interesting because it limits diffusion of the analytes to the artificial receptor sites within the sensing layers [3] and facilitates the making of nanostructured MIP grafts [4]. In addition, MIP sensing ultrathin layers are amenable to the detection of the analytes with varied transducing methods among which electrochemistry, a simple, versatile and easy to implement technique is very appealing to detect analytes concentrations in the picomolar or sub-picomolar range [5]. In this contribution, the important parameters in obtaining molecularly imprinted polymer layers grafted on gold working electrodes and exhibiting high sensitivity towards acid and base molecules are addressed. Square wave voltammetry is demonstrated to be a very powerful electroanalytical while the limit of detection of analytes can be decreased down to sub-nanomolar by controlling the MIP layers thickness. Finally, it is shown that such an approach offers potentials and opportunities for miniaturization to fulfill workspace constraints inherent to space exploration. Indeed, electrode arrays grafted with MIPs are prepared for portable sensor devices design. This work undoubtedly highlights molecularly imprinting in tandem with electrochemical detection as a very promising approach for sensing organic matter in a fast, highly sensitive and specific way. MIP-based biomimetic materials and their applications of as recognition layers within sensors are increasingly considered and it is expected that MIP will become a generic sensing technology This work is funded by the French National Research Agency (ANR) References: [1] C. Ayela, F. Roquet, L. Valera, C. Granier, L. Nicu, M. Pugnière, M. Biosensors and Bioelectronics 22 (2007) 3113. [2] M.A. Sephton, M.R. Sims, R.W. Court, D. Luong, D.C. Cullen, Planetary and Space Science 86 (2013) 66. [3] S. Lepinay, K. Khémara, M.-C. Millot, B. Carbonnier, Chem. Pap. 66 (2012) 340. [4] Y. Fuchs, O. Soppera, K. Haupt, Anal. Chim. Acta, 717 (2012) 7. [5] C. Malitesta, E. Mazzotta, R. A. Picca, A. Poma, I. Chianella, S. A. Piletsky, Anal. Bioanal. Chem. 402 (2012) 1827

  10. Photoisomerization dynamics of a rhodopsin-based molecule (potential molecular switch) with high quantum yields

    NASA Astrophysics Data System (ADS)

    Allen, Roland; Jiang, Chen-Wei; Zhang, Xiu-Xing; Fang, Ai-Ping; Li, Hong-Rong; Xie, Rui-Hua; Li, Fu-Li

    2015-03-01

    It is worthwhile to explore the detailed reaction dynamics of various candidates for molecular switches, in order to understand, e.g., the differences in quantum yields and switching times. Here we report density-functional-based simulations for the rhodopsin-based molecule 4-[4-Methylbenzylidene]-5-p-tolyl-3,4-dihydro-2H-pyrrole (MDP), synthesized by Sampedro et al. We find that the photoisomerization quantum yields are remarkably high: 82% for cis-to-trans, and 68% for trans-to-cis. The lifetimes of the S1 excited state in cis-MDP in our calculations are in the range of 900-1800 fs, with a mean value of 1270 fs, while the range of times required for full cis-to-trans isomerization are 1100-2000 fs, with a mean value of 1530 fs. In trans-MDP, the calculated S1 excited state lifetimes are 860-2140 fs, with a mean value of 1330 fs, and with the full trans-to-cis isomerization completed about 200 fs later. In both cases, the dominant reaction mechanism is rotation around the central C =C bond (connected to the pyrroline ring), and de-excitation occurs at an avoided crossing between the ground state and the lowest singlet state, near the midpoint of the rotational pathway. Research Fund for the Doctoral Program of Higher Education of China; Fundamental Research Funds for the Central Universities; Robert A. Welch Foundation; National Natural Science Foundation of China.

  11. Small molecule kinase inhibitors alleviate different molecular features of myotonic dystrophy type 1

    PubMed Central

    Wojciechowska, Marzena; Taylor, Katarzyna; Sobczak, Krzysztof; Napierala, Marek; Krzyzosiak, Wlodzimierz J

    2014-01-01

    Expandable (CTG)n repeats in the 3? UTR of the DMPK gene are a cause of myotonic dystrophy type 1 (DM1), which leads to a toxic RNA gain-of-function disease. Mutant RNAs with expanded CUG repeats are retained in the nucleus and aggregate in discrete inclusions. These foci sequester splicing factors of the MBNL family and trigger upregulation of the CUGBP family of proteins resulting in the mis-splicing of their target transcripts. To date, many efforts to develop novel therapeutic strategies have been focused on disrupting the toxic nuclear foci and correcting aberrant alternative splicing via targeting mutant CUG repeats RNA; however, no effective treatment for DM1 is currently available. Herein, we present results of culturing of human DM1 myoblasts and fibroblasts with two small-molecule ATP-binding site-specific kinase inhibitors, C16 and C51, which resulted in the alleviation of the dominant-negative effects of CUG repeat expansion. Reversal of the DM1 molecular phenotype includes a reduction of the size and number of foci containing expanded CUG repeat transcripts, decreased steady-state levels of CUGBP1 protein, and consequent improvement of the aberrant alternative splicing of several pre-mRNAs misregulated in DM1. PMID:24824895

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

    PubMed

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

    2014-05-01

    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. PMID:24609386

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

    NASA Astrophysics Data System (ADS)

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

    2004-05-01

    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.

  14. Estimation of synthetic accessibility score of drug-like molecules based on molecular complexity and fragment contributions

    PubMed Central

    2009-01-01

    Background A method to estimate ease of synthesis (synthetic accessibility) of drug-like molecules is needed in many areas of the drug discovery process. The development and validation of such a method that is able to characterize molecule synthetic accessibility as a score between 1 (easy to make) and 10 (very difficult to make) is described in this article. Results The method for estimation of the synthetic accessibility score (SAscore) described here is based on a combination of fragment contributions and a complexity penalty. Fragment contributions have been calculated based on the analysis of one million representative molecules from PubChem and therefore one can say that they capture historical synthetic knowledge stored in this database. The molecular complexity score takes into account the presence of non-standard structural features, such as large rings, non-standard ring fusions, stereocomplexity and molecule size. The method has been validated by comparing calculated SAscores with ease of synthesis as estimated by experienced medicinal chemists for a set of 40 molecules. The agreement between calculated and manually estimated synthetic accessibility is very good with r2 = 0.89. Conclusion A novel method to estimate synthetic accessibility of molecules has been developed. This method uses historical synthetic knowledge obtained by analyzing information from millions of already synthesized chemicals and considers also molecule complexity. The method is sufficiently fast and provides results consistent with estimation of ease of synthesis by experienced medicinal chemists. The calculated SAscore may be used to support various drug discovery processes where a large number of molecules needs to be ranked based on their synthetic accessibility, for example when purchasing samples for screening, selecting hits from high-throughput screening for follow-up, or ranking molecules generated by various de novo design approaches. PMID:20298526

  15. Dual-molecule spectroscopy: molecular rulers for the study of biological macromolecules

    Microsoft Academic Search

    T. Ha; Th. Enderle; D. S. Chemla; S. Weiss

    1996-01-01

    Single-molecule detection and spectroscopy by laser induced fluorescence offer many applications to life sciences. We review recent techniques and experiments based on the detection and spectroscopy of two near-by molecules. The spectroscopic signature of the light emitted from the two molecules can be used to measure the distance, orientation and relative dynamics between biological macromolecules

  16. Single-molecule imaging of organic semiconductors: Toward nanoscale insights into photophysics and molecular packing

    NASA Astrophysics Data System (ADS)

    Shepherd, W. E. B.; Grollman, R.; Robertson, A.; Paudel, K.; Hallani, R.; Loth, M. A.; Anthony, J. E.; Ostroverkhova, O.

    2015-06-01

    Photophysical properties of functionalized anthradithiophene (ADT) and pentacene (Pn) derivatives, as well as energy and charge transfer properties of donor-acceptor (D/A) pairs of these derivatives, are presented. The molecules studied were imaged on the single-molecule level in a polymeric and in a functionalized benzothiophene (BTBTB) crystalline host using room-temperature wide-field epifluorescence microscopy. The BTBTB host imposed orientational constraints on the guest molecules, depending on their functionalization. Flexibility of functionalization of both guest (ADT, Pn) and host (BTBTB) molecules can be used for systematic studies of nanoscale morphology and photophysics of D/A organic semiconductor bulk heterojunctions using single-molecule fluorescence microscopy.

  17. Monitoring patterned enzymatic polymerization on DNA origami at single-molecule level.

    PubMed

    Okholm, A H; Aslan, H; Besenbacher, F; Dong, M; Kjems, J

    2015-07-01

    DNA origami has been used to orchestrate reactions with nano-precision using a variety of biomolecules. Here, the dynamics of albumin-assisted, localized single-molecule DNA polymerization by terminal deoxynucleotidyl transferase on a 2D DNA origami are monitored using AFM in liquid. Direct visualization of the surface activity revealed the mechanics of growth. PMID:26061114

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

    PubMed Central

    Goulopoulou, Styliani; Wenceslau, Camilla F.; Spitler, Kathryn; Matsumoto, Takayuki; Webb, R. Clinton

    2013-01-01

    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

  19. Molecular processes studied at a single-molecule level using DNA origami nanostructures and atomic force microscopy.

    PubMed

    Bald, Ilko; Keller, Adrian

    2014-01-01

    DNA origami nanostructures allow for the arrangement of different functionalities such as proteins, specific DNA structures, nanoparticles, and various chemical modifications with unprecedented precision. The arranged functional entities can be visualized by atomic force microscopy (AFM) which enables the study of molecular processes at a single-molecular level. Examples comprise the investigation of chemical reactions, electron-induced bond breaking, enzymatic binding and cleavage events, and conformational transitions in DNA. In this paper, we provide an overview of the advances achieved in the field of single-molecule investigations by applying atomic force microscopy to functionalized DNA origami substrates. PMID:25191873

  20. Towards redistribution laser cooling of molecular gases: Production of candidate molecules SrH by laser ablation

    E-print Network

    Simon, Philipp; Weller, Lars; Sass, Anne; Weitz, Martin; 10.1117/12.2002379

    2013-01-01

    Laser cooling by collisional redistribution of radiation has been successfully applied in the past for cooling dense atomic gases. Here we report on progress of work aiming at the demonstration of redistribution laser cooling in a molecular gas. The candidate molecule strontium monohydride is produced by laser ablation of strontium dihydride in a pressurized noble gas atmosphere. The composition of the ablation plasma plume is analyzed by measuring its emission spectrum. The dynamics of SrH molecular density following the ablation laser pulse is studied as a function of the buffer gas pressure and the laser intensity.

  1. H2 Molecular Clusters with Embedded Molecules and Atoms as the Source of the Diffuse Interstellar Bands

    NASA Astrophysics Data System (ADS)

    Bernstein, L. S.; Clark, F. O.; Lynch, D. K.

    2013-05-01

    We suggest that the diffuse interstellar bands (DIBs) arise from absorption lines of electronic transitions in molecular clusters primarily composed of a single molecule, atom, or ion ("seed"), embedded in a single-layer shell of H2 molecules. Less abundant variants of the cluster, including two seed molecules and/or a two-layer shell of H2 molecules, may also occur. The lines are broadened, blended, and wavelength-shifted by interactions between the seed and surrounding H2 shell. We refer to these clusters as contaminated H2 clusters (CHCs). We show that CHC spectroscopy matches the diversity of observed DIB spectral profiles and provides good fits to several DIB profiles based on a rotational temperature of 10 K. CHCs arise from ~centimeter-sized, dirty H2 ice balls, called contaminated H2 ice macro-particles (CHIMPs), formed in cold, dense, giant molecular clouds (GMCs), and later released into the interstellar medium (ISM) upon GMC disruption. Attractive interactions, arising from Van der Waals and ion-induced dipole potentials, between the seeds and H2 molecules enable CHIMPs to attain centimeter-sized dimensions. When an ultraviolet (UV) photon is absorbed in the outer layer of a CHIMP, it heats the icy matrix and expels CHCs into the ISM. While CHCs are quickly destroyed by absorbing UV photons, they are replenished by the slowly eroding CHIMPs. Since CHCs require UV photons for their release, they are most abundant at, but not limited to, the edges of UV-opaque molecular clouds, consistent with the observed, preferred location of DIBs. An inherent property of CHCs, which can be characterized as nanometer size, spinning, dipolar dust grains, is that they emit in the radio-frequency region. We also show that the CHCs offer a natural explanation for the anomalous microwave emission feature in the ~10-100 GHz spectral region.

  2. Bench-to-bedside review: Damage-associated molecular patterns in the onset of ventilator-induced lung injury

    PubMed Central

    2011-01-01

    Mechanical ventilation (MV) has the potential to worsen pre-existing lung injury or even to initiate lung injury. Moreover, it is thought that injurious MV contributes to the overwhelming inflammatory response seen in patients with acute lung injury or acute respiratory distress syndrome. Ventilator-induced lung injury (VILI) is characterized by increased endothelial and epithelial permeability and pulmonary inflammation, in which the innate immune system plays a key role. A growing body of evidence indicates that endogenous danger molecules, also termed damage-associated molecular patterns (DAMPs), are released upon tissue injury and modulate the inflammatory response. DAMPs activate pattern recognition receptors, may induce the release of proinflammatory cytokines and chemokines, and have been shown to initiate or propagate inflammation in non-infectious conditions. Experimental and clinical studies demonstrate the presence of DAMPs in bronchoalveolar lavage fluid in patients with VILI and the upregulation of pattern recognition receptors in lung tissue by MV. The objective of the present article is to review research in the area of DAMPs, their recognition by the innate immune system, their role in VILI, and the potential utility of blocking DAMP signaling pathways to reduce VILI in the critically ill. PMID:22216838

  3. A study of adsorption and molecular dynamics of spin-labeled molecules on the surface of silica nanoparticles

    Microsoft Academic Search

    V. A. Livshits; I. V. Demisheva; B. B. Meshkov; V. P. Tsybyshev; M. V. Alfimov

    2009-01-01

    Stable nitroxyl radicals of different structures, hydrophobicities, and electric charges were used as spin probes for studying\\u000a the adsorption and molecular dynamics of the adsorbed molecules on the surface of LEVASIL silica nanoparticles. Neutral hydrophobic\\u000a probes, namely, spin labeled derivatives of indole, are not adsorbed on the nanoparticles; however, the microviscosity and\\u000a hydrophobicity of their environment differ from those in

  4. Evolution of Surface Morphology of Patterned GaAs(100) during Molecular Beam Epitaxial Growth

    Microsoft Academic Search

    Hung-Chih Kan; Sonam Shah; Tabassom Tadayyon-Eslami; Raymond Phaneuf

    2003-01-01

    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

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

    NASA Astrophysics Data System (ADS)

    Spudich, James

    2010-03-01

    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.

  6. Monitoring patterned enzymatic polymerization on DNA origami at single-molecule level

    NASA Astrophysics Data System (ADS)

    Okholm, A. H.; Aslan, H.; Besenbacher, F.; Dong, M.; Kjems, J.

    2015-06-01

    DNA origami has been used to orchestrate reactions with nano-precision using a variety of biomolecules. Here, the dynamics of albumin-assisted, localized single-molecule DNA polymerization by terminal deoxynucleotidyl transferase on a 2D DNA origami are monitored using AFM in liquid. Direct visualization of the surface activity revealed the mechanics of growth.DNA origami has been used to orchestrate reactions with nano-precision using a variety of biomolecules. Here, the dynamics of albumin-assisted, localized single-molecule DNA polymerization by terminal deoxynucleotidyl transferase on a 2D DNA origami are monitored using AFM in liquid. Direct visualization of the surface activity revealed the mechanics of growth. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr01945a

  7. Onset of Patterns in an Ocillated Granular Layer: Continuum and Molecular Dynamics Simulations

    E-print Network

    J. Bougie; J. Kreft; J. B. Swift; Harry L. Swinney

    2009-09-15

    We study the onset of patterns in vertically oscillated layers of frictionless dissipative particles. Using both numerical solutions of continuum equations to Navier-Stokes order and molecular dynamics (MD) simulations, we find that standing waves form stripe patterns above a critical acceleration of the cell. Changing the frequency of oscillation of the cell changes the wavelength of the resulting pattern; MD and continuum simulations both yield wavelengths in accord with previous experimental results. The value of the critical acceleration for ordered standing waves is approximately 10% higher in molecular dynamics simulations than in the continuum simulations, and the amplitude of the waves differs significantly between the models. The delay in the onset of order in molecular dynamics simulations and the amplitude of noise below this onset are consistent with the presence of fluctuations which are absent in the continuum theory. The strength of the noise obtained by fit to Swift-Hohenberg theory is orders of magnitude larger than the thermal noise in fluid convection experiments, and is comparable to the noise found in experiments with oscillated granular layers and in recent fluid experiments on fluids near the critical point. Good agreement is found between the mean field value of onset from the Swift-Hohenberg fit and the onset in continuum simulations. Patterns are compared in cells oscillated at two different frequencies in MD; the layer with larger wavelength patterns has less noise than the layer with smaller wavelength patterns.

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

    PubMed

    Shen, Cai; Buck, Manfred

    2014-01-01

    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

  9. Molecular Ions and Other Exotic Molecules in Space: A Coordinated Astronomical, Laboratory, and Theoretical Study

    NASA Astrophysics Data System (ADS)

    McCarthy, Michael

    This proposal request funds to continue a laboratory program in close coordination with radio astronomical observations dedicated to the study of highly reactive molecular ions, radicals, and metastable isomers that are thought to be key intermediates in rich interstellar and circumstellar sources. Determining the carriers of strong unidentified lines, such as U617.6 which has recently been observed with the Herschel space satellite, is the type of problem in laboratory astrophysics that our group is particularly adept at, and will be also emphasized in the upcoming grant period. Most new molecular species will be detected using microwave cavity rotational spectroscopy, followed either by microwave/millimeter-wave double resonance or millimeter/THz absorption to better characterize the rotational spectra in bands where Herschel and SOFIA operate. Using this combined approach, the rotational spectra of a number of ions of astronomical interest such as the cis- and trans isomers of HOSO+, H2NCO+, HNCOH+, H2CCHCNH+, C3N-, and NCO- have recently been detected in our laboratory, as have metastable isomers or derivatives of isocyanic acid, HNCO. As a result of this work, HOCN, HSCN, TiO2, and several molecular anions have been identified for the first time in space in the span of only a few years. Emphasis in the upcoming grant period will be placed on the detection of diatomic and small polyatomic ions such as SiH+, SiN-, CN+, NCS-, etc., other prototypical ions, including protonated benzene C6H7+, and silicon- and phosphorus-bearing species of astronomical interest. On the assumption that U617.6 is the fundamental b-type transition of a small polyatomic molecule, systematic searches for species of the form XOH, where X is likely either an atom or diatomic, will be given high priority because slightly bent species with this functional group (e.g., NNOH+, SiOH, etc.) possess an A rotational constants of about the right magnitude. Instrumental refinement will also be emphasized in the next three years, including experimentation with other discharge sources and the use of an electrical discharge in combination with laser ablation to increase the production of metal-bearing species. A mass spectrometer may allow in situ optimization and monitoring of ion abundances. Another important objective of the proposed work are studies of abundant interstellar or circumstellar species, motivated by recent spectral line surveys in sources such as IRC+10216 and VY CMa that indicate the presence of many new unidentified lines. Interferometric observations suggest that a substantial fraction of these lines originate in the inner circumstellar envelope and have high excitation temperatures. Measurements of the rotational spectra of several metal oxides such as ScO, ZrO, and YO are needed now that TiO and TiO2 have been found, as are rotational satellite transitions from vibrationally excited states of species like SiCC. The research proposed here should have an impact on a number of areas of astronomical research. Our broad laboratory program is well aligned with NASA's overall mission because we seek to understand the role of the chemical bond on a cosmic scale and to provide a firm chemical foundation by which more complicated questions of biological origins can be addressed. The work here also provides much basic information to aid subsequent astronomical searches, particularly in the infrared. Finally, our research program is an excellent vehicle for integrating research and education. It provides exposure to quite diverse areas of science in a setting which encourages student initiative and independent investigation.

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

    PubMed Central

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

    2013-01-01

    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. PMID:23784777

  11. The molecular Zeeman effect in diamagnetic molecules and the determination of molecular magnetic moments (g values), magnetic susceptibilities, and molecular quadrupole moments

    Microsoft Academic Search

    W. H. Flygare; R. C. Benson

    1971-01-01

    The experimental and theoretical literature on the molecular Zeeman effect is surveyed. The observation of the linear (H) and quadratic (H ) Zeeman effect leads to a direct determination of the molecular g values, magnetic susceptibility anisotropies and molecular quadrupole moments. The recent results are discussed and the available molecular g values, magnetic susceptibility anisotropies, and molecular quadrupole moments are

  12. Molecular Mechanics of Single Protein Molecules Measured with the Atomic Force Microscope

    Microsoft Academic Search

    Paul K. Hansma

    2000-01-01

    After a short history of AFM development in our lab, including recent developments with small cantilevers, this talk will focus on 1) pulling single protein molecules to explore the forces involved in unfolding and 2) watching single protein molecules in action to learn how they function mechanically. 1) Pulling experiments on proteins used as marine adhesives in abalone shells and

  13. Dynamics of Single-Molecule Rotations on Surfaces that Depend on Symmetry, Interactions, and Molecular Sizes

    E-print Network

    . The sulfur atom is strongly bound to the gold surface, and alkyl branches can rotate around it. Using STM on gold surfaces suggest that the size of the molecules, their flexibility, and steric repulsions as dialkylsulfides, are linear molecules with the sulfur atom in the middle connected to two symmetric alkyl chains

  14. Enhancing the molecular signature in molecule-nanoparticle networks via inelastic cotunneling.

    PubMed

    Dayen, Jean-Francois; Devid, Edwin; Kamalakar, Mutta Venkata; Golubev, Dmitry; Guédon, Constant; Faramarzi, Vina; Doudin, Bernard; van der Molen, Sense Jan

    2013-01-18

    Charge transport in networks of nanoparticles linked by molecular spacers is investigated. Remarkably, in the regime where cotunneling dominates, the molecular signature of a device is strongly enhanced. We demonstrate that the resistance ratio of identical networks with different molecular spacers increases dramatically, from an initial value of 50 up to 10(5) , upon entering the cotunneling regime. Our work shows that intrinsic molecular properties can be amplified through nanoscale engineering. PMID:22936462

  15. Patterning a hydrogen-bonded molecular monolayer with a hand-controlled scanning probe microscope.

    PubMed

    Green, Matthew F B; Esat, Taner; Wagner, Christian; Leinen, Philipp; Grötsch, Alexander; Tautz, F Stefan; Temirov, Ruslan

    2014-01-01

    One of the paramount goals in nanotechnology is molecular-scale functional design, which includes arranging molecules into complex structures at will. The first steps towards this goal were made through the invention of the scanning probe microscope (SPM), which put single-atom and single-molecule manipulation into practice for the first time. Extending the controlled manipulation to larger molecules is expected to multiply the potential of engineered nanostructures. Here we report an enhancement of the SPM technique that makes the manipulation of large molecular adsorbates much more effective. By using a commercial motion tracking system, we couple the movements of an operator's hand to the sub-angstrom precise positioning of an SPM tip. Literally moving the tip by hand we write a nanoscale structure in a monolayer of large molecules, thereby showing that our method allows for the successful execution of complex manipulation protocols even when the potential energy surface that governs the interaction behaviour of the manipulated nanoscale object(s) is largely unknown. PMID:25383304

  16. Patterning a hydrogen-bonded molecular monolayer with a hand-controlled scanning probe microscope

    PubMed Central

    Green, Matthew F B; Esat, Taner; Wagner, Christian; Leinen, Philipp; Grötsch, Alexander; Tautz, F Stefan

    2014-01-01

    Summary One of the paramount goals in nanotechnology is molecular-scale functional design, which includes arranging molecules into complex structures at will. The first steps towards this goal were made through the invention of the scanning probe microscope (SPM), which put single-atom and single-molecule manipulation into practice for the first time. Extending the controlled manipulation to larger molecules is expected to multiply the potential of engineered nanostructures. Here we report an enhancement of the SPM technique that makes the manipulation of large molecular adsorbates much more effective. By using a commercial motion tracking system, we couple the movements of an operator's hand to the sub-angstrom precise positioning of an SPM tip. Literally moving the tip by hand we write a nanoscale structure in a monolayer of large molecules, thereby showing that our method allows for the successful execution of complex manipulation protocols even when the potential energy surface that governs the interaction behaviour of the manipulated nanoscale object(s) is largely unknown. PMID:25383304

  17. Patterns of molecular evolution and diversification in a biodiversity hotspot: the California Floristic Province

    Microsoft Academic Search

    Ryan Calsbeek; John N. Thompson; James E. Richardson

    2003-01-01

    The California Floristic Province harbours more endemic plant and animal taxa and more identifiable subspecies than any other area of comparable size in North America. We present evidence that physical historical processes have resulted in congruent patterns of genetic diversity over the past 2—10 million years. Using a molecular clock approach we show that diversification and establishment of spatial genetic

  18. Periodic orbit analysis of molecular vibrational spectra: Spectral patterns and dynamical bifurcations in Fermi resonant systems

    E-print Network

    Periodic orbit analysis of molecular vibrational spectra: Spectral patterns and dynamical University, Ithaca, New York 14853 Received 28 August 1995; accepted 27 September 1995 Semiclassical periodic Hamiltonians describing stretch/bend modes with and without 2:1 Fermi resonant coupling. Periods of classical

  19. INTEGR. COMP. BIOL., 45:377385 (2005) Biodiversity, molecular ecology and phylogeography of marine sponges: patterns,

    E-print Network

    Solé-Cava, Antonio M.

    2005-01-01

    377 INTEGR. COMP. BIOL., 45:377­385 (2005) Biodiversity, molecular ecology and phylogeography Rio de Janeiro, Ilha do Funda~o, 21941-490-Rio de Janeiro, Brazil Queensland Centre for Biodiversity biogeographic affinities and biodiversity patterns is rudimentary, and there are still few data about genetic

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

    Microsoft Academic Search

    John Christoffersen Pearson

    1995-01-01

    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

  1. CERAMIDE AND SPHINGOSINE-1-PHOSPHATE ACT AS PHOTODYNAMIC THERAPY-ELICITED DAMAGE-ASSOCIATED MOLECULAR PATTERNS: CELL SURFACE EXPOSURE

    PubMed Central

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

    2014-01-01

    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-phposphate (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

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

    PubMed Central

    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

    2014-01-01

    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

  3. In situ formation and photo patterning of emissive quantum dots in small organic molecules

    NASA Astrophysics Data System (ADS)

    Bansal, Ashu K.; Sajjad, Muhammad T.; Antolini, Francesco; Stroea, Lenuta; Ge?ys, Paulius; Raciukaitis, Gediminas; André, Pascal; Hirzer, Andreas; Schmidt, Volker; Ortolani, Luca; Toffanin, Stefano; Allard, Sybille; Scherf, Ullrich; Samuel, Ifor D. W.

    2015-06-01

    Nanostructured composites of inorganic and organic materials are attracting extensive interest for electronic and optoelectronic device applications. Here we report a novel method for the fabrication and patterning of metal selenide nanoparticles in organic semiconductor films that is compatible with solution processable large area device manufacturing. Our approach is based upon the controlled in situ decomposition of a cadmium selenide precursor complex in a film of the electron transporting material 1,3,5-tris(N-phenyl-benzimidazol-2-yl)-benzene (TPBI) by thermal and optical methods. In particular, we show that the photoluminescence quantum yield (PLQY) of the thermally converted CdSe quantum dots (QDs) in the TPBI film is up to 15%. We also show that laser illumination can form the QDs from the precursor. This is an important result as it enables direct laser patterning (DLP) of the QDs. DLP was performed on these nanocomposites using a picosecond laser. Confocal microscopy shows the formation of emissive QDs after laser irradiation. The optical and structural properties of the QDs were also analysed by means of UV-Vis, PL spectroscopy and transmission electron microscopy (TEM). The results show that the QDs are well distributed across the film and their emission can be tuned over a wide range by varying the temperature or irradiated laser power on the blend films. Our findings provide a route to the low cost patterning of hybrid electroluminescent devices.

  4. In situ formation and photo patterning of emissive quantum dots in small organic molecules.

    PubMed

    Bansal, Ashu K; Sajjad, Muhammad T; Antolini, Francesco; Stroea, Lenuta; Ge?ys, Paulius; Raciukaitis, Gediminas; André, Pascal; Hirzer, Andreas; Schmidt, Volker; Ortolani, Luca; Toffanin, Stefano; Allard, Sybille; Scherf, Ullrich; Samuel, Ifor D W

    2015-06-18

    Nanostructured composites of inorganic and organic materials are attracting extensive interest for electronic and optoelectronic device applications. Here we report a novel method for the fabrication and patterning of metal selenide nanoparticles in organic semiconductor films that is compatible with solution processable large area device manufacturing. Our approach is based upon the controlled in situ decomposition of a cadmium selenide precursor complex in a film of the electron transporting material 1,3,5-tris(N-phenyl-benzimidazol-2-yl)-benzene (TPBI) by thermal and optical methods. In particular, we show that the photoluminescence quantum yield (PLQY) of the thermally converted CdSe quantum dots (QDs) in the TPBI film is up to 15%. We also show that laser illumination can form the QDs from the precursor. This is an important result as it enables direct laser patterning (DLP) of the QDs. DLP was performed on these nanocomposites using a picosecond laser. Confocal microscopy shows the formation of emissive QDs after laser irradiation. The optical and structural properties of the QDs were also analysed by means of UV-Vis, PL spectroscopy and transmission electron microscopy (TEM). The results show that the QDs are well distributed across the film and their emission can be tuned over a wide range by varying the temperature or irradiated laser power on the blend films. Our findings provide a route to the low cost patterning of hybrid electroluminescent devices. PMID:26062105

  5. Analysis of Bonding Patterns in the Valence Isoelectronic series O-3, S-3, SO2 and OS2 in Terms of Oriented Quasi-Atomic Molecular Orbitals

    SciTech Connect

    Glezakou, Vassiliki Alexandra; Elbert, Stephen T.; Xantheas, Sotiris S.; Ruedenberg, Klaus

    2010-08-26

    A novel analysis of the chemical bonding pattern in the valence isoelectronic series of triatomic molecules O3, S3, SO2 and OS2 is reported. The analysis is based on examining the bond order matrix elements between the Oriented Localized Molecular Orbitals (OLMOs) that are localized on the three individual left (L), center (C) and right (R) atoms. The analysis indicates that there is a (L-C) and (C-R) ?-bonding interaction and a (L-R) ??antibonding interaction. This finding supports the previously proposed "partial biradical" interpretation of these triatomic systems, which had recently been challenged.

  6. Pulsed molecular beam scattering of a planar-shaped organic molecule on regularly stepped surfaces of hydrogen-terminated Si(111)

    SciTech Connect

    Shimada, Toshihiro; Ichikawa, Hisashi; Saiki, Koichiro [Department of Chemistry, University of Tokyo, Bunkyo-ku, Tokyo 113-0033 (Japan); Department of Chemistry, University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan and Department of Complexity Science and Engineering, University of Tokyo, Kashiwa, Chiba 277-8561 (Japan)

    2006-10-02

    Strong dependence of surface residence time of a planar organic molecule (hydrogen phthalocyanine) on vicinal surfaces of hydrogen-terminated Si(111) was observed in pulsed molecular beam scattering experiments. These results can be explained by the difference in the microscopic contact area of the molecules on the surface, which determines the binding force between the migrating molecules and the surface. The relationship between the observed behavior and the organic thin film growth is discussed.

  7. Modeling Molecules

    NASA Technical Reports Server (NTRS)

    2000-01-01

    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.

  8. A recombinant horseshoe crab plasma lectin recognizes specific pathogen-associated molecular patterns of bacteria through rhamnose.

    PubMed

    Ng, Sim-Kun; Huang, Yu-Tsyr; Lee, Yuan-Chuan; Low, Ee-Ling; Chiu, Cheng-Hsun; Chen, Shiu-Ling; Mao, Liang-Chi; Chang, Margaret Dah-Tsyr

    2014-01-01

    Horseshoe crab is an ancient marine arthropod that, in the absence of a vertebrate-like immune system, relies solely on innate immune responses by defense molecules found in hemolymph plasma and granular hemocytes for host defense. A plasma lectin isolated from the hemolymph of Taiwanese Tachypleus tridentatus recognizes bacteria and lipopolysaccharides (LPSs), yet its structure and mechanism of action remain unclear, largely because of limited availability of horseshoe crabs and the lack of a heterogeneous expression system. In this study, we have successfully expressed and purified a soluble and functional recombinant horseshoe crab plasma lectin (rHPL) in an Escherichia coli system. Interestingly, rHPL bound not only to bacteria and LPSs like the native HPL but also to selective medically important pathogens isolated from clinical specimens, such as Gram-negative Pseudomonas aeruginosa and Klebsiella pneumoniae and Gram-positive Streptococcus pneumoniae serotypes. The binding was demonstrated to occur through a specific molecular interaction with rhamnose in pathogen-associated molecular patterns (PAMPs) on the bacterial surface. Additionally, rHPL inhibited the growth of P. aeruginosa PAO1 in a concentration-dependent manner. The results suggest that a specific protein-glycan interaction between rHPL and rhamnosyl residue may further facilitate development of novel diagnostic and therapeutic strategies for microbial pathogens. PMID:25541995

  9. A Recombinant Horseshoe Crab Plasma Lectin Recognizes Specific Pathogen-Associated Molecular Patterns of Bacteria through Rhamnose

    PubMed Central

    Ng, Sim-Kun; Huang, Yu-Tsyr; Lee, Yuan-Chuan; Low, Ee-Ling; Chiu, Cheng-Hsun; Chen, Shiu-Ling; Mao, Liang-Chi; Chang, Margaret Dah-Tsyr

    2014-01-01

    Horseshoe crab is an ancient marine arthropod that, in the absence of a vertebrate-like immune system, relies solely on innate immune responses by defense molecules found in hemolymph plasma and granular hemocytes for host defense. A plasma lectin isolated from the hemolymph of Taiwanese Tachypleus tridentatus recognizes bacteria and lipopolysaccharides (LPSs), yet its structure and mechanism of action remain unclear, largely because of limited availability of horseshoe crabs and the lack of a heterogeneous expression system. In this study, we have successfully expressed and purified a soluble and functional recombinant horseshoe crab plasma lectin (rHPL) in an Escherichia coli system. Interestingly, rHPL bound not only to bacteria and LPSs like the native HPL but also to selective medically important pathogens isolated from clinical specimens, such as Gram-negative Pseudomonas aeruginosa and Klebsiella pneumoniae and Gram-positive Streptococcus pneumoniae serotypes. The binding was demonstrated to occur through a specific molecular interaction with rhamnose in pathogen-associated molecular patterns (PAMPs) on the bacterial surface. Additionally, rHPL inhibited the growth of P. aeruginosa PAO1 in a concentration-dependent manner. The results suggest that a specific protein-glycan interaction between rHPL and rhamnosyl residue may further facilitate development of novel diagnostic and therapeutic strategies for microbial pathogens. PMID:25541995

  10. Imaging molecular structure through femtosecond photoelectron diffraction on aligned and oriented gas-phase molecules.

    PubMed

    Boll, Rebecca; Rouzée, Arnaud; Adolph, Marcus; Anielski, Denis; Aquila, Andrew; Bari, Sadia; Bomme, Cédric; Bostedt, Christoph; Bozek, John D; Chapman, Henry N; Christensen, Lauge; Coffee, Ryan; Coppola, Niccola; De, Sankar; Decleva, Piero; Epp, Sascha W; Erk, Benjamin; Filsinger, Frank; Foucar, Lutz; Gorkhover, Tais; Gumprecht, Lars; Hömke, André; Holmegaard, Lotte; Johnsson, Per; Kienitz, Jens S; Kierspel, Thomas; Krasniqi, Faton; Kühnel, Kai-Uwe; Maurer, Jochen; Messerschmidt, Marc; Moshammer, Robert; Müller, Nele L M; Rudek, Benedikt; Savelyev, Evgeny; Schlichting, Ilme; Schmidt, Carlo; Scholz, Frank; Schorb, Sebastian; Schulz, Joachim; Seltmann, Jörn; Stener, Mauro; Stern, Stephan; Techert, Simone; Thøgersen, Jan; Trippel, Sebastian; Viefhaus, Jens; Vrakking, Marc; Stapelfeldt, Henrik; Küpper, Jochen; Ullrich, Joachim; Rudenko, Artem; Rolles, Daniel

    2014-01-01

    This paper gives an account of our progress towards performing femtosecond time-resolved photoelectron diffraction on gas-phase molecules in a pump-probe setup combining optical lasers and an X-ray free-electron laser. We present results of two experiments aimed at measuring photoelectron angular distributions of laser-aligned 1-ethynyl-4-fluorobenzene (C(8)H(5)F) and dissociating, laser-aligned 1,4-dibromobenzene (C(6)H(4)Br(2)) molecules and discuss them in the larger context of photoelectron diffraction on gas-phase molecules. We also show how the strong nanosecond laser pulse used for adiabatically laser-aligning the molecules influences the measured electron and ion spectra and angular distributions, and discuss how this may affect the outcome of future time-resolved photoelectron diffraction experiments. PMID:25290160

  11. Effect of an improved molecular potential on strong-field tunneling ionization of molecules

    SciTech Connect

    Zhao Songfeng; Jin Cheng [J. R. Macdonald Laboratory, Physics Department, Kansas State University, Manhattan, Kansas 66506-2604 (United States); College of Physics and Electronic Engineering, Northwest Normal University, Lanzhou, Gansu 730070 (China); Le, Anh-Thu; Lin, C. D. [J. R. Macdonald Laboratory, Physics Department, Kansas State University, Manhattan, Kansas 66506-2604 (United States)

    2010-09-15

    We study the effect of one-electron model potentials on the tunneling ionization rates of molecules in strong fields. By including electron correlation using the modified Leeuwen-Baerends (LB {alpha}) model, the binding energies of outer shells of molecules are significantly improved. However, we show that the tunneling ionization rates from the LB {alpha} do not differ much from the earlier calculations [Phys. Rev. A 81, 033423 (2010)], in which the local correlation potential was neglected.

  12. A kinetic Monte Carlo simulation of surface microfluidic patterning organic molecules based on anisotropic wetting

    NASA Astrophysics Data System (ADS)

    Liu, Gang; Zhang, Heng; Wang, Wenchong; Yuan, Shiling

    2015-05-01

    In this Letter, the kinetic Monte Carlo simulations are employed to study the microscopic mechanisms of patterning molten organic particles based on liquid behavior on templated surfaces. The simulated results show that the binding energy difference between the organic particle and templated surface plays a key role in the anisotropic wetting of organic particles. And the square root of time law between the spreading distance and simulated time on different temperatures is well consistent with experimental observation. We also note that the geometry effect of channel edge has very significant effect on the dependence of spreading velocity on template dimensions.

  13. Interstellar molecules

    NASA Technical Reports Server (NTRS)

    Townes, C. H.

    1976-01-01

    Progress in the discovery and study of interstellar molecules is summarized. The 36 molecular species thus far identified in interstellar space are listed in several groups which include simple hydrides, oxides, and sulfides, various derivatives of ammonia, molecules involving linear carbon chains, cyanides, and molecules related in structure to formaldehyde, alcohols, or ethers. Several free radicals are described, the discovery of molecules in external galaxies is discussed, and possible mechanisms for molecular formation are noted. Methods for examining relative isotopic abundances by measuring molecules in interstellar clouds are outlined, mechanisms for the excitation of interstellar molecules are reviewed, and values are presented for the C-12/C-13 abundance ratio in a number of interstellar clouds. The detection of interstellar masers is discussed along with pumping mechanisms and masing transitions in H2CO, CH, OH, and SiO. The nature of dense interstellar clouds is examined in terms of several simple and complex cloud models, with emphasis on multiple condensation models.

  14. Extracting physics of life at the molecular level: A review of single-molecule data analyses

    NASA Astrophysics Data System (ADS)

    Colomb, Warren; Sarkar, Susanta K.

    2015-06-01

    Studying individual biomolecules at the single-molecule level has proved very insightful recently. Single-molecule experiments allow us to probe both the equilibrium and nonequilibrium properties as well as make quantitative connections with ensemble experiments and equilibrium thermodynamics. However, it is important to be careful about the analysis of single-molecule data because of the noise present and the lack of theoretical framework for processes far away from equilibrium. Biomolecular motion, whether it is free in solution, on a substrate, or under force, involves thermal fluctuations in varying degrees, which makes the motion noisy. In addition, the noise from the experimental setup makes it even more complex. The details of biologically relevant interactions, conformational dynamics, and activities are hidden in the noisy single-molecule data. As such, extracting biological insights from noisy data is still an active area of research. In this review, we will focus on analyzing both fluorescence-based and force-based single-molecule experiments and gaining biological insights at the single-molecule level. Inherently nonequilibrium nature of biological processes will be highlighted. Simulated trajectories of biomolecular diffusion will be used to compare and validate various analysis techniques.

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

    NASA Astrophysics Data System (ADS)

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

    2011-03-01

    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.

  16. Why is the crystal shape of TATB is so similar to its molecular shape? Understanding by only its root molecule.

    PubMed

    Zhang, Chaoyang; Kang, Bin; Cao, Xia; Xiang, Bin

    2012-05-01

    We present an understanding of the quasi-regular or regular hexagonal enlargement of 1,3,5-triamino-2,4,6 (TATB) from its root molecule to its bulk crystal, by only its root molecule. That is, the mechanism of regular hexagonal TATB molecules stacking to a quasi-regular or regular hexagonal TATB crystal was discussed using a combined method of a density functional theory BLYP and Dreiding forcefield, and a series of static scanning calculations. As a result, we found that there are two styles of forming the most energetically favored TATB dimers: a hydrogen bonding along the molecular plane and an offset ?-stacking vertical to the plane, just leading to the outspread and the thickening of the regular hexagon during the crystal growth, respectively. At the same time, it was found that the rotation of one TATB layer in any parallel stacked double-layer should overcome a very high energy barrier. It suggests that the TATB molecules or layers are arranged on the crystal face always along the special orientation of a regular hexagon and other orientations are strongly thermodynamically forbidden, resulting in a hexagonal crystal bulk. PMID:21965034

  17. Between molecules and experience: role of early patterns of coordinated activity for the development of cortical maps and sensory abilities.

    PubMed

    Hanganu-Opatz, Ileana L

    2010-09-01

    Sensory systems processing information from the environment rely on precisely formed and refined neuronal networks that build maps of sensory receptor epithelia at different subcortical and cortical levels. These sensory maps share similar principles of function and emerge according to developmental processes common in visual, somatosensory and auditory systems. Whereas molecular cues set the coarse organization of cortico-subcortical topography, its refinement is known to succeed under the influence of experience-dependent electrical activity during critical periods. However, coordinated patterns of activity synchronize the cortico-subcortical networks long before the meaningful impact of environmental inputs on sensory maps. Recent studies elucidated the cellular and network mechanisms underlying the generation of these early patterns of activity and highlighted their similarities across species. Moreover, the experience-independent activity appears to act as a functional template for the maturation of sensory networks and cortico-subcortical maps. A major goal for future research will be to analyze how this early activity interacts with the molecular cues and to determine whether it is permissive or rather supporting for the establishment of sensory topography. PMID:20381527

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

    PubMed

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

    2014-06-01

    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

  19. 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.

  20. H{sub 2} MOLECULAR CLUSTERS WITH EMBEDDED MOLECULES AND ATOMS AS THE SOURCE OF THE DIFFUSE INTERSTELLAR BANDS

    SciTech Connect

    Bernstein, L. S.; Clark, F. O. [Spectral Sciences, Inc., 4 Fourth Avenue, Burlington, MA 01803 (United States); Lynch, D. K., E-mail: larry@spectral.com, E-mail: dave@thulescientific.com [Thule Scientific, P.O. Box 953, Topanga, CA 90290 (United States)

    2013-05-01

    We suggest that the diffuse interstellar bands (DIBs) arise from absorption lines of electronic transitions in molecular clusters primarily composed of a single molecule, atom, or ion ({sup s}eed{sup )}, embedded in a single-layer shell of H{sub 2} molecules. Less abundant variants of the cluster, including two seed molecules and/or a two-layer shell of H{sub 2} molecules, may also occur. The lines are broadened, blended, and wavelength-shifted by interactions between the seed and surrounding H{sub 2} shell. We refer to these clusters as contaminated H{sub 2} clusters (CHCs). We show that CHC spectroscopy matches the diversity of observed DIB spectral profiles and provides good fits to several DIB profiles based on a rotational temperature of 10 K. CHCs arise from {approx}centimeter-sized, dirty H{sub 2} ice balls, called contaminated H{sub 2} ice macro-particles (CHIMPs), formed in cold, dense, giant molecular clouds (GMCs), and later released into the interstellar medium (ISM) upon GMC disruption. Attractive interactions, arising from Van der Waals and ion-induced dipole potentials, between the seeds and H{sub 2} molecules enable CHIMPs to attain centimeter-sized dimensions. When an ultraviolet (UV) photon is absorbed in the outer layer of a CHIMP, it heats the icy matrix and expels CHCs into the ISM. While CHCs are quickly destroyed by absorbing UV photons, they are replenished by the slowly eroding CHIMPs. Since CHCs require UV photons for their release, they are most abundant at, but not limited to, the edges of UV-opaque molecular clouds, consistent with the observed, preferred location of DIBs. An inherent property of CHCs, which can be characterized as nanometer size, spinning, dipolar dust grains, is that they emit in the radio-frequency region. We also show that the CHCs offer a natural explanation for the anomalous microwave emission feature in the {approx}10-100 GHz spectral region.

  1. Probing molecular frame photoelectron angular distributions via high-order harmonic generation from aligned molecules

    E-print Network

    Lin, Chii-Dong

    OF PHYSICS B: ATOMIC, MOLECULAR AND OPTICAL PHYSICS J. Phys. B: At. Mol. Opt. Phys. 45 (2012) 194010 (9ppProbing molecular frame photoelectron angular distributions via high-order harmonic generation from that terms and conditions apply. View the table of contents for this issue, or go to the journal homepage

  2. Coulomb interaction in self-consistent field calculations on molecules in molecular crystals

    Microsoft Academic Search

    M. M. Mestechkin

    1997-01-01

    A method of direct calculation of Madelung sums in molecular crystals is proposed. It is based on preliminary evaluation of Coulomb interaction of two contrarily charged elements of a crystal cell translated over the whole crystal. As a result some Madelung parameters similar to Coulomb integrals enter the molecular crystal Hartree - Fock equations whose dimensionality remains the same as

  3. Calculating Structures and Free Energies of Complex Molecules:  Combining Molecular Mechanics and Continuum Models

    Microsoft Academic Search

    Peter A. Kollman; Irina Massova; Carolina Reyes; Bernd Kuhn; Shuanghong Huo; Lillian Chong; Matthew Lee; Taisung Lee; Yong Duan; Wei Wang; Oreola Donini; Piotr Cieplak; Jaysharee Srinivasan; David A. Case; Thomas E. Cheatham

    2000-01-01

    A historical perspective on the application of molecular dynamics (MD) to biological macromolecules is presented. Recent develop- ments combining state-of-the-art force fields with continuum solvation calculations have allowed us to reach the fourth era of MD applications in which one can often derive both accurate structure and accurate relative free energies from molecular dynam- ics trajectories. We illustrate such applications

  4. Molecular analogs of the hemihelix: A computational study of chain molecules containing left- and right-handed helices

    NASA Astrophysics Data System (ADS)

    Pichierri, Fabio

    2014-08-01

    Using density functional theory (DFT) we design two novel chain molecules containing a left-handed (thia)helicene unit connected to a right-handed (thia)helicene unit via a phosphoroussbnd phosphorous (Psbnd P) bond. These chains represent the molecular analogs of the novel hemihelix structure recently discovered by a group of Harvard University scientists. The HOMO and LUMO levels of the heterochiral chains, termed hemihelicenes, are localized on the left- and right-handed blocks, respectively. In contrast, the frontier orbitals of the chains containing homochiral (thia)helicenes connected by a Psbnd P bond are delocalized all over the chain.

  5. ATOMIC AND MOLECULAR PHYSICS: Lie Algebraic Approach to Energy Transfer for Collinear Collision of Two Anharmonic Diatomic Molecules

    NASA Astrophysics Data System (ADS)

    Wang, Xiao-Yan; Wang, Peng-Cheng; Qiu, Jian-Feng; Wang, Jin-Xi; Hou, Li-Xia; Xie, Jin-Dong Ding, Shi-Liang

    2010-02-01

    An anharmonic oscillator algebra model is used to study the collinear collisions of two diatomic molecules. The transition probability for vibration-vibration energy transfer is presented. For an application of the method, we talk about the collision of N2+CO, N2+O2, and N2+N2. Through long time averaging, the transition probability changes to the function of total energy of the system. Comparing the results with the quantum results, we can see that the dynamical Lie algebraic method is useful for describing the anharmonic diatomic molecular collision.

  6. Sulphur-bearing molecules in diffuse molecular clouds: new results from SOFIA/GREAT and the IRAM 30 m telescope

    NASA Astrophysics Data System (ADS)

    Neufeld, D. A.; Godard, B.; Gerin, M.; Pineau des Forêts, G.; Bernier, C.; Falgarone, E.; Graf, U. U.; Güsten, R.; Herbst, E.; Lesaffre, P.; Schilke, P.; Sonnentrucker, P.; Wiesemeyer, H.

    2015-05-01

    We have observed five sulphur-bearing molecules in foreground diffuse molecular clouds lying along the sight-lines to five bright continuum sources. We have used the GREAT instrument on SOFIA to observe the SH 1383 GHz 2?3/2 J = 5/2 ? 3/2 lambda doublet toward the star-forming regions W31C, G29.96-0.02, G34.3+0.1, W49N and W51, detecting foreground absorption towards all five sources; and the EMIR receivers on the IRAM 30 m telescope at Pico Veleta to detect the H2S 110-101 (169 GHz), CS J = 2-1 (98 GHz) and SO 32-21 (99 GHz) transitions. Upper limits on the H3S+10-00 (293 GHz) transition were also obtained at the IRAM 30 m. In nine foreground absorption components detected towards these sources, the inferred column densities of the four detected molecules showed relatively constant ratios, with N(SH) /N(H2S) in the range 1.1-3.0, N(CS) /N(H2S) in the range 0.32-0.61, and N(SO) /N(H2S) in the range 0.08-0.30. The column densities of the sulphur-bearing molecules are very well correlated amongst themselves, moderately well correlated with CH (a surrogate tracer for H2), and poorly correlated with atomic hydrogen. The observed SH/H2 ratios - in the range 5 to 26 × 10-9 - indicate that SH (and other sulphur-bearing molecules) account for ? 1% of the gas-phase sulphur nuclei. The observed abundances of sulphur-bearing molecules, however, greatly exceed those predicted by standard models of cold diffuse molecular clouds, providing further evidence for the enhancement of endothermic reaction rates by elevated temperatures or ion-neutral drift. We have considered the observed abundance ratios in the context of shock and turbulent dissipation region (TDR) models. Using the TDR model, we find that the turbulent energy available at large scale in the diffuse ISM is sufficient to explain the observed column densities of SH and CS. Standard shock and TDR models, however, fail to reproduce the column densities of H2S and SO by a factor of about 10; more elaborate shock models - in which account is taken of the velocity drift, relative to H2, of SH molecules produced by the dissociative recombination of H3S+ - reduce this discrepancy to a factor ~3. Appendices are available in electronic form at http://www.aanda.org

  7. Dimeric and trimeric triazole based molecules as a new class of Hsp90 molecular chaperone inhibitors.

    PubMed

    Terracciano, Stefania; Chini, Maria Giovanna; Piaz, Fabrizio Dal; Vassallo, Antonio; Riccio, Raffaele; Bruno, Ines; Bifulco, Giuseppe

    2013-07-01

    In the last decade Hsp90 inhibitors have emerged as attractive candidates for the development of new potent anticancer therapeutics. In order to identify novel agents able to block the chaperone activity, following a structure-based approach, we used in silico screening to direct the synthesis of potential inhibitors bearing the triazole scaffold, a widespread motif in drug-like molecules. Docking results, performed on a larger collection of dimeric and trimeric triazole derivatives, suggested the synthesis of some molecules showing different calculated binding energies and modes. Surface Plasmon Resonance Binding assay, performed on the synthesized compounds, allow to identify a series of molecules able to potently interact with the target enzyme and to disclose an interesting hit: compound 2b showed to interact with the ATP binding site in the N-terminus domain of Hsp90 and to efficiently inhibit the chaperone activity. PMID:23770448

  8. Interaction between water molecules and zinc sulfide nanoparticles studied by temperature-programmed desorption and molecular dynamics simulations.

    PubMed

    Zhang, Hengzhong; Rustad, James R; Banfield, Jillian F

    2007-06-14

    We have investigated the bonding of water molecules to the surfaces of ZnS nanoparticles (approximately 2-3 nm sphalerite) using temperature-programmed desorption (TPD). The activation energy for water desorption was derived as a function of the surface coverage through kinetic modeling of the experimental TPD curves. The binding energy of water equals the activation energy of desorption if it is assumed that the activation energy for adsorption is nearly zero. Molecular dynamics (MD) simulations of water adsorption on 3 and 5 nm sphalerite nanoparticles provided insights into the adsorption process and water binding at the atomic level. Water binds with the ZnS nanoparticle surface mainly via formation of Zn-O bonds. As compared with bulk ZnS crystals, ZnS nanoparticles can adsorb more water molecules per unit surface area due to the greatly increased curvature, which increases the distance between adjacent adsorbed molecules. Results from both TPD and MD show that the water binding energy increases with decreasing the water surface coverage. We attribute the increase in binding energy with decreasing surface water coverage to the increasing degree of surface under-coordination as removal of water molecules proceeds. MD also suggests that the water binding energy increases with decreasing particle size due to the further distance and hence lower interaction between adsorbed water molecules on highly curved smaller particle surfaces. Results also show that the binding energy, and thus the strength of interaction of water, is highest in isolated nanoparticles, lower in nanoparticle aggregates, and lowest in bulk crystals. Given that water binding is driven by surface energy reduction, we attribute the decreased binding energy for aggregated as compared to isolated particles to the decrease in surface energy that occurs as the result of inter-particle interactions. PMID:17518448

  9. Investigating the molecular and aggregated states of a drug molecule rutaecarpine using spectroscopy, microscopy, crystallography and computational studies.

    PubMed

    Dandpat, Shiba Sundar; Sarkar, Moloy

    2015-06-01

    The photophysical properties of a potential drug molecule rutaecarpine have been investigated in molecular as well as aggregated states. All systems have been characterized by various spectroscopic, microscopic and dynamic light scattering (DLS) techniques. The investigation has been carried out by keeping the fact in mind that hydrophobic organic molecules have a strong tendency to form aggregates in aqueous solution. A blue shift in the absorption spectrum of rutaecarpine has been observed for aggregates (compared to molecular solution) indicating the formation of H-type aggregates. The intermolecular interactions responsible for such aggregation have been further investigated through crystallographic and computational studies. It has been observed that ?-? stacking interactions among the monomer units play an important role in the formation of H-type aggregates. Quantum mechanical calculations also substantiate the blue shift in the absorption that has been observed for aggregates. In the present case, enhanced emission for aggregates as compared to the molecular solution of rutaecarpine has also been observed. The observed enhanced emission upon aggregation is attributed to the decrease of the non-radiative rate constant (knr) upon aggregation. The effect of a surface active ionic liquid (SAIL), 1-dodecyl-3-methylimidazolium bromide ([C12mim]Br), on the aggregation of rutaecarpine has been investigated. Interestingly, in addition to the decrease in the particle size, a change in the morphology of the aggregates has also been observed with gradual addition of [C12mim]Br to the colloidal solution of rutaecarpine. The present study demonstrates that a SAIL can effectively be used as a medium for dissociation of colloidal aggregates and encapsulation of molecular species, which in turn would be helpful in influencing the drug activity. PMID:25948504

  10. Direct observation of molecularly-aligned molecules in the second physisorbed layer-CO/Ag(110)

    SciTech Connect

    Lee, J.-G. (Chevron Science Center, Pittsburgh, PA); Hong, S.-H. (Chevron Science Center, Pittsburgh, PA); Ahner, J. (Chevron Science Center, Pittsburgh, PA); Zhao, X. (Univ. of Pittsburgh, PA); Chen, L.; Johnson, J.K.; Yates, J.T., Jr. (Chevron Science Center, Pittsburgh, PA)

    2006-01-25

    We report the direct observation of oriented second-layer physisorbed molecules on a single crystal surface by electron stimulated desorption. Experiments and simulations show that the orientation of the second-layer physisorbed CO molecules on Ag(110) is the result of both electrostatic and dispersion forces from the underlying chemisorbed CO and Ag atoms. At 25 K, the physisorbed C-O bond is tilted and azimuthally oriented with the C-O bond axis inclined in an azimuthal plane at 45° to the principal Ag( 110) azimuthal crystallographic directions. The O atom in CO is directed outward, giving an O+ beam at 43° to the normal.

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

    PubMed Central

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

    2013-01-01

    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. PMID:23493833

  12. Quasi- and inelastic neutron scattering to investigate the molecular dynamics of discotic molecules in the bulk

    NASA Astrophysics Data System (ADS)

    Krause, Christina; Zorn, Reiner; Frick, Bernhard; Schönhals, Andreas

    2015-01-01

    In- and quasielastic neutron scattering is employed to investigate both the vibrational density of states and the molecular dynamics of two homologous discotic liquid crystals (DLC) with different length of the alkyl side chain based on a triphenylene derivate. For both compounds characteristic low frequency excess contributions to the vibrational density of states are found. Therefore it is concluded that these liquid crystals show a glass-like behaviour. Elastic scans further show that in these materials a rich molecular dynamics takes place.

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

    PubMed Central

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

    2012-01-01

    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. PMID:22847404

  14. Water-inducing molecular self-assembly of amphiphilic molecules into nanofibers

    SciTech Connect

    Zhang, Weiguang [Jiangsu Key Laboratory for Chemistry of Low-Dimensional Materials, Huaiyin Normal University, Huaian, Jiangsu 223300 (China)] [Jiangsu Key Laboratory for Chemistry of Low-Dimensional Materials, Huaiyin Normal University, Huaian, Jiangsu 223300 (China); Zhao, Pusu, E-mail: zhaopusu@qust.edu.cn [Jiangsu Key Laboratory for Chemistry of Low-Dimensional Materials, Huaiyin Normal University, Huaian, Jiangsu 223300 (China)] [Jiangsu Key Laboratory for Chemistry of Low-Dimensional Materials, Huaiyin Normal University, Huaian, Jiangsu 223300 (China); Song, Jie, E-mail: songjiesj@163.com [Jiangsu Key Laboratory for Chemistry of Low-Dimensional Materials, Huaiyin Normal University, Huaian, Jiangsu 223300 (China) [Jiangsu Key Laboratory for Chemistry of Low-Dimensional Materials, Huaiyin Normal University, Huaian, Jiangsu 223300 (China); Materials Chemistry Laboratory, Nanjing University of Science and Technology, Nanjing, Jiangsu 210094 (China)

    2011-12-15

    Graphical abstract: TPDP nanofibers with smooth surfaces can be obtained by reprecipitation method using ethanol as good solvent and water as poor solvent. In the self-assembly process, during the water adding to the amphiphilic molecules' saturated solution, the amphiphilic molecules firstly assembled into needle-like small rods. With an increase in the self-assembled time, a large number of the nanofibers are produced. The assembly behavior was revealed in the course of direct in situ monitoring of its growth with optical microscopy. Highlights: Black-Right-Pointing-Pointer 2,3,6,7-Tetramethoxy-9,10-di(4-pyridyl)-9,10-dihydroanthracen (TPDP) was synthesized. Black-Right-Pointing-Pointer TPDP nanofibers can be obtained by reprecipitation method. Black-Right-Pointing-Pointer The assembly behavior was revealed in situ monitoring with optical microscopy. -- Abstract: We present investigations on the microcosmic self-assembly process of new synthesized amphiphilic TPDP molecules. It can be seen that pure TPDP nanofibers with smooth surfaces can be obtained by reprecipitation method using ethanol as good solvent and water as poor solvent. In the self-assembly process, during the water adding to the amphiphilic molecules' saturated solution, the amphiphilic molecules firstly assembled into needle-like small rods. With an increase in the self-assembled time, a large number of the nanofibers are produced. The assembly behavior was revealed in the course of direct in situ monitoring of its growth with optical microscopy. Field emission scanning electron microscopy was adopted to characterize the morphologies of the products.

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

    SciTech Connect

    McKoy, V.

    1998-09-01

    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.

  16. Sulphur-bearing molecules in diffuse molecular clouds: new results from SOFIA/GREAT and the IRAM 30 m telescope

    E-print Network

    Neufeld, D A; Gerin, M; Forêts, G Pineau des; Bernier, C; Falgarone, E; Graf, U U; Güsten, R; Herbst, E; Lesaffre, P; Schilke, P; Sonnentrucker, P; Wiesemeyer, H

    2015-01-01

    We have observed five sulphur-bearing molecules in foreground diffuse molecular clouds lying along the sight-lines to five bright continuum sources. We have used the GREAT instrument on SOFIA to observe the 1383 GHz $^2\\Pi_{3/2} J=5/2-3/2$ transitions of SH towards the star-forming regions W31C, G29.96-0.02, G34.3+0.1, W49N and W51, detecting foreground absorption towards all five sources; and the EMIR receivers on the IRAM 30m telescope at Pico Veleta to detect the H$_2$S 1(10)-1(01), CS J=2-1 and SO 3(2)-2(1) transitions. In nine foreground absorption components detected towards these sources, the inferred column densities of the four detected molecules showed relatively constant ratios, with N(SH)/N(H$_2$S) in the range 1.1 - 3.0, N(CS)/N(H$_2$S) in the range 0.32 - 0.61, and N(SO)/N(H$_2$S) in the range 0.08 - 0.30. The observed SH/H$_2$ ratios - in the range (0.5-2.6) $\\times 10^{-8}$ - indicate that SH (and other sulphur-bearing molecules) account for << 1% of the gas-phase sulphur nuclei. The obs...

  17. Dissociation of molecular iodine in a flow tube in the presence of O2(1?) molecules.

    PubMed

    Zagidullin, Marsel V; Khvatov, Nickolay A; Malyshev, Michael S; Svistun, Michael I

    2012-10-18

    Molecular iodine dissociates in the presence of O(2)((1)?) and O(2)((1)?) molecules, but the mechanism of this process is not completely understood. In this paper, using flow tube experiments, we studied the initiation stage of iodine dissociation. Absolute spectral irradiance measurements were employed for measurements of concentrations of electronically excited particles. It was found that under the present experimental conditions initiation of iodine dissociation is mainly caused by reaction O(2)((1)?) + I(2) ? O(2)((3)?) + 2I with a rate constant of (9.3 ± 2.0) × 10(-11) cm(3) s(-1). An appreciable role of the O(2)((1)?) molecule as the dissociation initiator has not been observed. It was observed that the growth rate of iodine atoms sharply accelerated when the concentration of I((2)P(1/2)) atoms approached 2 × 10(-4) of O(2)((1)?) concentration or when production rates of O(2)((1)?) molecules in reactions O(2)((1)?) + I((2)P(1/2)) and O(2)((1)?) + O(2)((1)?) became equal. PMID:23009345

  18. The hydrogen molecule and the H+2 molecular ion inside padded prolate spheroidal cavities with arbitrary nuclear positions

    NASA Astrophysics Data System (ADS)

    Colín-Rodríguez, R.; Díaz-García, C.; Cruz, S. A.

    2011-12-01

    A generalization of previous theoretical studies of molecular confinement based on the molecule-in-a-box model for the H+2 and H2 systems whereby the confining cavity is assumed to be prolate spheroidal in shape is presented. A finite height for the confining barrier potential is introduced and the independent variation of the nuclear positions from the cavity size and shape is allowed. Within this scheme, the non-separable Schrödinger problem for the confined H+2 and H2 molecules in their ground states is treated variationally. In both cases, an important dependence of the equilibrium bond length and total energy on the confining barrier height is observed for fixed cavity sizes and shapes. It is also shown that—given a barrier height—as the cavity size is reduced, the limit of stability of the confined molecule is attained for a critical size. The results of this work suggest the adequacy of the proposed method for more realistic studies of electronic and vibrational properties of confined one- and two-electron diatomics for proper comparison with experiment.

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

    SciTech Connect

    Miau, T.T.

    1995-05-01

    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.

  20. Interaction between Water Molecules and Zinc Sulfide Nanoparticles Studied by Temperature-Programmed Desorption and Molecular Dynamics Simulations.

    SciTech Connect

    Zhang, Hengzon; Rustad, James R.; Banfield, Jillian F.

    2007-05-23

    The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. We have investigated the bonding of water molecules to the surfaces of ZnS nanoparticles (2-3 nm sphalerite) using temperature-programmed desorption (TPD). The activation energy for water desorption was derived as a function of the surface coverage through kinetic modeling of the experimental TPD curves. The binding energy of water equals the activation energy of desorption if it is assumed that the activation energy for adsorption is nearly zero. Molecular dynamics (MD) simulations of water adsorption on 3 and 5 nm sphalerite nanoparticles provided insights into the adsorption process and water binding at the atomic level. Water binds with the ZnS nanoparticle surface mainly via formation of Zn-O bonds. As compared with bulk ZnS crystals, ZnS nanoparticles can adsorb more water molecules per unit surface area due to the greatly increased curvature, which increases the distance between adjacent adsorbed molecules. Results from both TPD and MD show that the water binding energy increases with decreasing the water surface coverage. We attribute the increase in binding energy with decreasing surface water coverage to the increasing degree of surface under-coordination as removal of water molecules proceeds. MD also suggests that the water binding energy increases with decreasing particle size due to the further distance and hence lower interaction between adsorbed water molecules on highly curved smaller particle surfaces. Results also show that the binding energy, and thus the strength of interaction of water, is highest in isolated nanoparticles, lower in nanoparticle aggregates, and lowest in bulk crystals. Given that water binding is driven by surface energy reduction, we attribute the decreased binding energy for aggregated as compared to isolated particles to the decrease in surface energy that occurs as the result of inter-particle interactions.

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

    PubMed Central

    Chowdhury, Debashish

    2013-01-01

    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. PMID:23746505

  2. Atomically wired molecular junctions: Connecting a single organic molecule by chains of metal atoms

    E-print Network

    Yelin, Tamar; Kuritz, Natalia; Korytár, Richard; Bagrets, Alexei; Evers, Ferdinand; Kronik, Leeor; Tal, Oren

    2015-01-01

    Using a break junction technique, we find a clear signature for the formation of conducting hybrid junctions composed of a single organic molecule (benzene, naphthalene or anthracene) connected to chains of platinum atoms. The hybrid junctions exhibit metallic-like conductance (~0.1-1G0), which is rather insensitive to further elongation by additional atoms. At low bias voltage the hybrid junctions can be elongated significantly beyond the length of the bare atomic chains. Ab initio calculations reveal that benzene based hybrid junctions have a significant binding energy and high structural flexibility that may contribute to the survival of the hybrid junction during the elongation process. The fabrication of hybrid junctions opens the way for combining the different properties of atomic chains and organic molecules to realize a new class of atomic scale interfaces.

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

    PubMed Central

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

    2013-01-01

    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

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

    NASA Astrophysics Data System (ADS)

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

    2009-07-01

    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.

  5. Molecular Dynamics Simulation of Dextran Extension by Constant Force in Single Molecule AFM

    Microsoft Academic Search

    Igor M. Neelov; David B. Adolf; Tom C. B. McLeish; Emanuele Paci

    2006-01-01

    The extension of 1–6 polysaccharides has been studied in a series of recent single molecule AFM experiments. For dextran, a key finding was the existence of a plateau in the force-extension curve at forces between 700 and 1000pN. We studied the extension of the dextran 10-mer under constant force using atomistic simulation with various force fields. All the force fields

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

    NASA Astrophysics Data System (ADS)

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

    2013-10-01

    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.

  7. Fundamental molecular mechanism for the cellular uptake of guanidinium-rich molecules.

    PubMed

    Herce, Henry D; Garcia, Angel E; Cardoso, M Cristina

    2014-12-17

    Guanidinium-rich molecules, such as cell-penetrating peptides, efficiently enter living cells in a non-endocytic energy-independent manner and transport a wide range of cargos, including drugs and biomarkers. The mechanism by which these highly cationic molecules efficiently cross the hydrophobic barrier imposed by the plasma membrane remains a fundamental open question. Here, a combination of computational results and in vitro and live-cell experimental evidence reveals an efficient energy-independent translocation mechanism for arginine-rich molecules. This mechanism unveils the essential role of guanidinium groups and two universal cell components: fatty acids and the cell membrane pH gradient. Deprotonated fatty acids in contact with the cell exterior interact with guanidinium groups, leading to a transient membrane channel that facilitates the transport of arginine-rich peptides toward the cell interior. On the cytosolic side, the fatty acids become protonated, releasing the peptides and resealing the channel. This fundamental mechanism appears to be universal across cells from different species and kingdoms. PMID:25405895

  8. Molecular entomology: analyzing tiny molecules to answer big questions about disease vectors and their biology

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The entomologists at the Arthropod-Borne Animal Diseases Research Unit at USDA-Agricultural Research Service are tasked with protecting the nation’s livestock from domestic, foreign and emerging vector-borne diseases. To accomplish this task, a vast array of molecular techniques are being used in pr...

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

    PubMed

    Awino, Joseph K; Zhao, Yan

    2014-06-01

    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

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

    ERIC Educational Resources Information Center

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

    2008-01-01

    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.)

  11. A Novel Approach for Characterizing Protein Ligand Complexes: Molecular Basis for Specificity of Small-Molecule

    E-print Network

    in Biophysics, HarVard UniVersity, Cambridge, Massachusetts 02138, Department of Biochemistry and Molecular Pharmacology, HarVard Medical School, 240 Longwood AVenue, Boston, Massachusetts 02115, and Department of Cell Biology, HarVard Medical School, 240 Longwood AVenue, Boston, Massachusetts 02115 Received May 21, 2001

  12. Recognizing molecular patterns by machine learning: an agnostic structural definition of the hydrogen bond.

    PubMed

    Gasparotto, Piero; Ceriotti, Michele

    2014-11-01

    The concept of chemical bonding can ultimately be seen as a rationalization of the recurring structural patterns observed in molecules and solids. Chemical intuition is nothing but the ability to recognize and predict such patterns, and how they transform into one another. Here, we discuss how to use a computer to identify atomic patterns automatically, so as to provide an algorithmic definition of a bond based solely on structural information. We concentrate in particular on hydrogen bonding--a central concept to our understanding of the physical chemistry of water, biological systems, and many technologically important materials. Since the hydrogen bond is a somewhat fuzzy entity that covers a broad range of energies and distances, many different criteria have been proposed and used over the years, based either on sophisticate electronic structure calculations followed by an energy decomposition analysis, or on somewhat arbitrary choices of a range of structural parameters that is deemed to correspond to a hydrogen-bonded configuration. We introduce here a definition that is univocal, unbiased, and adaptive, based on our machine-learning analysis of an atomistic simulation. The strategy we propose could be easily adapted to similar scenarios, where one has to recognize or classify structural patterns in a material or chemical compound. PMID:25381505

  13. Molecular patterns of X chromosome-linked color vision genes among 134 menof European ancestry

    SciTech Connect

    Drummond-Borg, M.; Deeb, S.S.; Motulsky, A.G. (Univ. of Washington, Seattle (USA))

    1989-02-01

    The authors used Southern blot hybridization to study X chromosome-linked color vision genes encoding the apoproteins of red and green visual pigments in 134 unselected Caucasian men. One hundred and thirteen individuals (84.3%) had a normal arrangement of their color vision pigment genes. All had one red pigment gene; the number of green pigment genes ranged from one to five with a mode of two. The frequency of molecular genotypes indicative of normal color vision (84.3%) was significantly lower than had been observed in previous studies of color vision phenotypes. Color vision defects can be due to deletions of red or green pigment genes or due to formation of hybrid genes comprising portions of both red and green pigment genes. Characteristic anomalous patterns were seen in 15 (11.2%) individuals: 7 (5.2%) had patterns characteristic of deuteranomaly, 2 (1.5%) had patterns characteristic of deuteranopia, and 6 (4.5%) had protan patterns. Previously undescribed hybrid gene patterns consisting of both green and red pigment gene fragments in addition to normal red and green genes were observed in another 6 individuals (4.5%). Thus, DNA testing detected anomalous color vision pigment genes at a higher frequency than expected from phenotypic color vision tests.

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

    NASA Astrophysics Data System (ADS)

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

    2009-06-01

    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

  15. The RCSB PDB "Molecule of the Month": Inspiring a Molecular View of Biology.

    PubMed

    Goodsell, David S; Dutta, Shuchismita; Zardecki, Christine; Voigt, Maria; Berman, Helen M; Burley, Stephen K

    2015-05-01

    The Research Collaboratory for Structural Bioinformatics (RCSB) Molecule of the Month series provides a curated introduction to the 3-D biomolecular structures available in the Protein Data Bank archive and the tools that are available at the RCSB website for accessing and exploring them. A variety of educational materials, such as articles, videos, posters, hands-on activities, lesson plans, and curricula, build on this series for use in a variety of educational settings as a general introduction to key topics, such as enzyme action, protein synthesis, and viruses. The series and associated educational materials are freely available at www.rcsb.org. PMID:25942442

  16. The RCSB PDB “Molecule of the Month”: Inspiring a Molecular View of Biology

    PubMed Central

    Goodsell, David S.; Dutta, Shuchismita; Zardecki, Christine; Voigt, Maria; Berman, Helen M.; Burley, Stephen K.

    2015-01-01

    The Research Collaboratory for Structural Bioinformatics (RCSB) Molecule of the Month series provides a curated introduction to the 3-D biomolecular structures available in the Protein Data Bank archive and the tools that are available at the RCSB website for accessing and exploring them. A variety of educational materials, such as articles, videos, posters, hands-on activities, lesson plans, and curricula, build on this series for use in a variety of educational settings as a general introduction to key topics, such as enzyme action, protein synthesis, and viruses. The series and associated educational materials are freely available at www.rcsb.org. PMID:25942442

  17. Liquid crystal polymer networks: preparation, properties, and applications of films with patterned molecular alignment.

    PubMed

    Liu, Danqing; Broer, Dirk J

    2014-11-18

    Monolithically ordered liquid crystal polymer networks are formed by the photoinitiated polymerization of multifunctional liquid crystal monomers. This paper describes the relevant principles and methods, the basic structure-property relationships in terms of mesogenic properties of the monomers, and the mechanical and optical properties of the polymers. Strategies are discussed to control the molecular orientation by various means and in all three dimensions. The versatility of the process is demonstrated by two examples of films with a patterned molecular order. It is shown that patterned retarders can be made by a two-step polymerization process which is successfully employed in a transflective display principle. A transflective display is a liquid crystal display that operates in both a reflective mode using ambient light and a transmissive mode with light coming from a backlight system. Furthermore, a method is discussed to create a patterned film in a single polymerization process. This film has alternating planar chiral nematic areas next to perpendicularly oriented (so-called homeotropic) areas. When applied as a coating to a substrate, the film changes its surface texture. During exposure to UV light, it switches from a flat to a corrugated state. PMID:24707811

  18. Molecular Framework of a Regulatory Circuit Initiating Two-Dimensional Spatial Patterning of Stomatal Lineage

    PubMed Central

    Rychel, Amanda L.; Garrick, Jacqueline M.; Kawaguchi, Masayoshi; Peterson, Kylee M.; Torii, Keiko U.

    2015-01-01

    Stomata, valves on the plant epidermis, are critical for plant growth and survival, and the presence of stomata impacts the global water and carbon cycle. Although transcription factors and cell-cell signaling components regulating stomatal development have been identified, it remains unclear as to how their regulatory interactions are translated into two-dimensional patterns of stomatal initial cells. Using molecular genetics, imaging, and mathematical simulation, we report a regulatory circuit that initiates the stomatal cell-lineage. The circuit includes a positive feedback loop constituting self-activation of SCREAMs that requires SPEECHLESS. This transcription factor module directly binds to the promoters and activates a secreted signal, EPIDERMAL PATTERNING FACTOR2, and the receptor modifier TOO MANY MOUTHS, while the receptor ERECTA lies outside of this module. This in turn inhibits SPCH, and hence SCRMs, thus constituting a negative feedback loop. Our mathematical model accurately predicts all known stomatal phenotypes with the inclusion of two additional components to the circuit: an EPF2-independent negative-feedback loop and a signal that lies outside of the SPCH•SCRM module. Our work reveals the intricate molecular framework governing self-organizing two-dimensional patterning in the plant epidermis. PMID:26203655

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

    PubMed Central

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

    2013-01-01

    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. PMID:24101502

  20. Plk1-Targeted Small Molecule Inhibitors: Molecular Basis for Their Potency and Specificity

    PubMed Central

    N. Murugan, Ravichandran; Park, Jung-Eun; Kim, Eun-Hee; Shin, Song Yub; Cheong, Chaejoon; Lee, Kyung S; Bang, Jeong Kyu

    2011-01-01

    Members of polo-like kinases (collectively, Plks) have been identified in various eukaryotic organisms and play pivotal roles in cell proliferation. They are characterized by the presence of a distinct region of homology in the C-terminal noncatalytic domain, called polo-box domain (PBD). Among them, Plk1 and its functional homologs in other organisms have been best characterized because of its strong association with tumorigenesis. Plk1 is overexpressed in a wide spectrum of cancers in humans, and is thought to be an attractive anti-cancer drug target. Plk1 offers, within one molecule, two functionally different drug targets with distinct properties-the N-terminal catalytic domain and the C-terminal PBD essential for targeting the catalytic activity of Plk1 to specific subcellular locations. In this review, we focused on discussing the recent development of small-molecule and phosphopeptide inhibitors for their potency and specificity against Plk1. Our effort in understanding the binding mode of various inhibitors to Plk1 PBD are also presented. PMID:21809214

  1. Identification of DNA adduct formation of small molecules by molecular descriptors and machine learning methods

    Microsoft Academic Search

    Hanbing Rao; Xianyin Zeng; Yanying Wang; Hua He; Feng Zhu; Zerong Li; Yuzong Chen

    2012-01-01

    In this study, we developed new computational DNA adduct prediction models by using significantly more diverse training data-set of 217 DNA adducts and 1024 non-DNA adducts, and applying five machine learning methods which include support vector machine (SVM), k-nearest neighbour, artificial neural networks, logistic regression and continuous kernel discrimination. The molecular descriptors used for DNA adduct prediction were selected from

  2. Identification of DNA adduct formation of small molecules by molecular descriptors and machine learning methods

    Microsoft Academic Search

    Hanbing Rao; Xianyin Zeng; Yanying Wang; Hua He; Feng Zhu; Zerong Li; Yuzong Chen

    2011-01-01

    In this study, we developed new computational DNA adduct prediction models by using significantly more diverse training data-set of 217 DNA adducts and 1024 non-DNA adducts, and applying five machine learning methods which include support vector machine (SVM), k-nearest neighbour, artificial neural networks, logistic regression and continuous kernel discrimination. The molecular descriptors used for DNA adduct prediction were selected from

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

    Microsoft Academic Search

    Rishikesh K. Bharadwaj; Richard H. Boyd

    1999-01-01

    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

  4. Characterization of skin penetration processes of organic molecules using molecular similarity and QSAR analysis.

    PubMed

    Santos-Filho, Osvaldo A; Hopfinger, A J; Zheng, Tao

    2004-01-01

    Molecular similarity and QSAR analyses have been used to develop compact, robust, and definitive models for skin penetration by organic compounds. The QSAR models have been sought to provide an interpretation and characterization of plausible molecular mechanisms of skin penetration. A training set of 40 structurally diverse compounds were selected to be representative of a parent set of 152 compounds in terms of both structural diversity and range in measured skin penetration. The subset of 40 compounds was used in a series of QSAR analyses in the search for the most significant, compact, and straightforward skin penetration QSAR models. Molecular dynamics simulations were employed to determine a set of MI (membrane-interaction) descriptors for each test compound (solute) interacting with a model DMPC monolayer membrane model. The MI-QSAR models may capture features of cellular membrane lateral transverse transport involved in the overall skin penetration process by organic compounds. An additional set of intramolecular solute descriptors, the non-MI-QSAR descriptors, were computed and added to the trial pool of descriptors for building QSAR models. All QSAR models were constructed using multidimensional linear regression fitting and a genetic algorithm optimization function. QSAR models were constructed using only non-MI-QSAR descriptors and using a combination of both these descriptor sets. It was found that a combination of non-MI-QSAR and MI-QSAR descriptors yielded the optimum models, not only with respect to the statistical measures of fit but also regarding model predictivity. PMID:16028358

  5. Intracellular patterns of sialophorin expression define a new molecular classification of breast cancer and represent new targets for therapy

    PubMed Central

    Fu, Q; Cash, S E; Andersen, J J; Kennedy, C R; Madadi, A R; Raghavendra, M; Dietrich, L L; Agger, W A; Shelley, C S

    2014-01-01

    Background: Sialophorin is a transmembrane sialoglycoprotein. Normally, the molecule is only produced by white blood cells where it regulates functions such as intercellular adhesion, intracellular signalling, apoptosis, migration and proliferation. Methods: Normal breast tissue and primary breast tumours were analysed by immunohistochemistry for sialophorin expression. The sialophorin-positive breast cancer cell line MCF7 was engineered to stably express either non-targeted or sialophorin-targeted small interfering RNA (siRNA). Assays were then performed in vitro to assess apoptosis, intracellular adhesion, transendothelial migration and cytotoxicity. An orthotopic mouse model assayed ability to produce tumours in vivo. Results: Normal breast epithelial cells exhibit expression of the N-terminal domain of sialophorin in the cytoplasm but not the nucleus. The majority of these normal cells are also negative for expression of the C-terminal domain. In contrast, malignant breast epithelial cells exhibit N-terminal expression both in the cytoplasm and nucleus and the majority express the C-terminus in the nucleus. Using differential patterns of intracellular expression of the N and C termini of sialophorin, we define six subtypes of breast cancer that are independent of histological and receptor status classification. Targeting sialophorin with siRNA resulted in the MCF7 breast cancer cell line exhibiting increased homotypic adhesion, decreased transendothelial migration, increased susceptibility to apoptosis, increased vulnerability to lysis by natural killer cells and decreased ability to produce tumours in mice. Conclusion: Our results indicate that intracellular patterns of sialophorin expression define a new molecular classification of breast cancer and that sialophorin represents a novel therapeutic target. PMID:24281005

  6. Single-molecule analysis reveals the molecular bearing mechanism of DNA strand exchange by a serine recombinase.

    PubMed

    Bai, Hua; Sun, Mingxuan; Ghosh, Pallavi; Hatfull, Graham F; Grindley, Nigel D F; Marko, John F

    2011-05-01

    Structural and topological data suggest that serine site-specific DNA recombinases exchange duplex DNAs by rigid-body relative rotation of the two halves of the synapse, mediated by a flat protein-protein interaction surface. We present evidence for this rotational motion for a simple serine recombinase, the Bxb1 phage integrase, from a single-DNA-based supercoil-release assay that allows us to follow crossover site cleavage, rotation, religation, and product release in real time. We have also used a two-DNA braiding-relaxation experiment to observe the effect of synapse rotation in reactions on two long molecules. Relaxation and unbraiding are rapid (averaging 54 and 70 turns/s, respectively) and complete, with no discernible pauses. Nevertheless, the molecular friction associated with rotation is larger than that of type-I topoisomerases in a similar assay. Surprisingly we find that the synapse can stay rotationally "open" for many minutes. PMID:21502527

  7. Simulation of electron paramagnetic resonance spectra of spin-labeled molecules from replica-exchange molecular dynamics.

    PubMed

    Tyrrell, S; Oganesyan, V S

    2013-10-01

    We report a general approach for the simulation of the electron paramagnetic resonance (EPR) spectra of spin labels attached to peptides and proteins directly from replica-exchange molecular dynamics (REMD) trajectories. Conventional MD trajectories are generally inadequate for the prediction of EPR line shapes since the label can become trapped in one or more of a set of rotameric states, thus preventing both conformational sampling and accurate estimates of the exchange rates between different rotamers. The advantage of using REMD is its ability to provide both efficient conformational sampling and kinetic information for spin-label dynamics. Our approach is illustrated with spin-labeled peptide. This approach to REMD-EPR simulation paves the way for the wider application of MD modeling to the simulation and interpretation of EPR spectra of spin-labeled molecules. PMID:24229207

  8. I. Molecular magnetism and single-molecule magnets The research in the area of molecular magnetism is focused on molecular assemblies containing a

    E-print Network

    Vardi, Amichay

    and double exchange in metal clusters Development of the microscopic electronic theory of mixed valency (MV. 3. Cooperative and photochromic phenomena in molecule based systems Mixed MV crystals: charge from the Fe2+ ion to the * orbitals of the NO-ligand as well as the vibronic mixing of three

  9. Symbolic computation engines and molecular modeling templates: Maple-assisted point group analysis of the vibrational activity of molecules

    NASA Astrophysics Data System (ADS)

    Vail, Benjamin; Aris, Damian; Scarlete, Mihai

    The present study proposes an algorithm for point-group analysis (PGA) of the vibrational activity of molecules, adapted for the efficient utilization of the linear packages incorporated into currently available symbolic computation engines (SCE), such as Maple, Mathcad, or Mathematica. By the creation of this algorithm, we have addressed the need for a numerically friendly environment, outside the "locked" procedures within molecular modeling packages, which will preserve its flexibility, transparency, and maneuverability, regardless of the complexity of the calculation. The format of the character tables of the point groups significant to chemical species has been adapted to ensure automatic numerization, and consistent input of the alphanumeric data from the existent character tables into the SCE templates designed to perform the PGA. The two proposed templates address two complementary objectives: (i) a totally transparent and interactive file has been designed to allow access to all intermediate results at all levels of the procedure for easy implementation of potential additional modules of special interest 1-5, and (ii) for fast output and routine calculations of the IR/Raman vibrational activity of molecules based on their point groups, a totally automatic file with a highly simplified input interface has been designed. The numerical interface conveniently replaces the usual graphic user interface that is common to most commercial molecular modeling software packages, requiring minimum input determination. The structure for both templates is based on the use of the digitized forms for the character tables, for the symmetry operations, and for symmetry elements, all saved in dedicated libraries uploaded to the numerical database of the SCE.

  10. Electron, proton and ion induced molecular synthesis and VUV spectroscopy of interstellar molecules in the ice phase

    NASA Astrophysics Data System (ADS)

    Sivaraman, Bhalamurugan; Jheeta, Sohan; Mason, Nigel; Hunniford, Adam; Merrigan, Tony; McCullough, Bob; Fulvio, Daniele; Palumbo, Maria Elisabetta; Moore, Marla

    2008-10-01

    Planets and their moons are constantly subjected to irradiation from both their respective planetary magnetospheres and the solar wind. Energetic particles (electrons, protons and ions) in such radiation may induce complex chemistry within the icy mantles of such bodies, producing many organic compounds. Such processes can be simulated in laboratory experiments. In this report we present recent results from experiments exploring both molecular synthesis and the morphology of such ices. The morphology of any ice may be characterised by IR and Vacuum Ultra-Violet (VUV) spectroscopy. The latter is particularly useful for studying ices in which infrared inactive molecules like oxygen (O2) are common. We have shown that oxygen forms dimers in typical planetary ices and that, in contrast to previous analysis, many of the chemical reactions within the ice involve such dimer (and larger cluster) chemistry. We also present the results of a series of experiments that explore electron, proton and ion irradiation on Solar System relevant ices such as carbon dioxide (CO2) at different temperatures. Infrared spectra recorded before and after irradiation are used to identify and quantify molecules formed in such irradiation, e. g. ozone. These experiments show that the morphology of the ice plays a critical role in the chemistry.

  11. Effects of magnesium ions and water molecules on the structure of amorphous calcium carbonate: a molecular dynamics study.

    PubMed

    Tomono, Hidekazu; Nada, Hiroki; Zhu, Fangjie; Sakamoto, Takeshi; Nishimura, Tatsuya; Kato, Takashi

    2013-11-27

    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

  12. Molecular cloning and adhesive properties of murine platelet/endothelial cell adhesion molecule 1.

    PubMed Central

    Xie, Y; Muller, W A

    1993-01-01

    We describe the isolation and characterization of a functional murine platelet/endothelial cell adhesion molecule (PECAM) 1 cDNA clone from a mouse lung library. At the nucleotide level, the coding sequence of murine PECAM-1 is 73% identical to human PECAM-1, and at the amino acid level, the sequence is 79% homologous to its human counterpart. Southern hybridization reveals that one copy of the gene exists in the mouse genome; Northern hybridization reveals a single mRNA species in mouse lung tissue. COS-7 and mouse L cells transfected with murine PECAM-1 expressed a 130-kDa glycoprotein on their surfaces that reacted with anti-murine PECAM-1 monoclonal antibody and comigrated on SDS/PAGE with human PECAM-1. Stable L-cell transfectants aggregate with each other in a PECAM-dependent, homophilic manner. Images Fig. 3 Fig. 6 PMID:8516303

  13. ATOMIC AND MOLECULAR PHYSICS: Interference of dissociating wave packets in the I2 molecule driven by femtosecond laser pulses

    NASA Astrophysics Data System (ADS)

    Han, Yong-Chang; Hu, Wen-Hui; Yu, Jie; Cong, Shu-Lm

    2009-11-01

    The interference between two dissociating wave packets of the I2 molecule driven by femtosecond laser pulses is theoretically studied by using the time-dependent quantum wave packet method. Both the internuclear distance- and velocity-dependent density functions are calculated and discussed. It is demonstrated that the interference pattern is determined by the phase difference and the delay time between two pump pulses. With two identical pulses with a delay time of 305 fs and a FWHM of 20 fs, more interference fringes can be observed, while with two pump pulses with a delay time of 80 fs and a FWHM of 20 fs, only a few interference fringes can be observed.

  14. Molecular basis of natural variation and environmental control of trichome patterning

    PubMed Central

    Hauser, Marie-Theres

    2014-01-01

    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. PMID:25071803

  15. Major histocompatibility complex class IIA and IIB genes of Nile tilapia Oreochromis niloticus: genomic structure, molecular polymorphism and expression patterns.

    PubMed

    Pang, Ji-cai; Gao, Feng-ying; Lu, Mai-xin; Ye, Xing; Zhu, Hua-ping; Ke, Xiao-li

    2013-02-01

    Major histocompatibility complex (MHC) is a large genomic region characterized by extremely high polymorphism, and it plays an important role in the immune response of vertebrates. In the present study, we isolated MHC class II genes from Nile tilapia in order to investigate the immune mechanism in tilapia and develop better strategies for disease prevention. Moreover, we cloned the full-length cDNA sequences of MHC IIA and IIB from Nile tilapia by the RACE approach. In addition, the genomic structure, molecular polymorphism and expression patterns of MHC II genes in Nile tilapia were also examined. Compared with that of other teleosts, Nile tilapia MHC class IIA contained four exons and three introns. The deduced amino acid sequence of the MHC IIA molecule shared 25.4-64.5% similarity with those of other teleosts and mammals. Six exons and five introns were identified from Nile tilapia MHC IIB, and the deduced amino acid sequence shared 26.9-74.7% similarity with those of other teleosts and mammals. All the characteristic features of MHC class II chain structure could be identified in the deduced sequences of MHC IIA and IIB molecules, including the leader peptide, ?1/?1 and ?2/?2 domains, connecting peptide and transmembrane and cytoplasmic regions, as well as conserved cysteines and N-glycosylation site. A total of 12 MHC IIA alleles were identified from six individuals. Four alleles originating from a single individual suggested that at least four MHC IIA loci existed. Moreover, 10 MHC IIB alleles were identified, among which four were detected in a single individual, suggesting that at least four MHC IIB loci existed. The expression of MHC IIA and IIB at the mRNA level in 10 types of normal tissues was determined using quantitative real-time PCR analysis. The highest expression level was detected in stomach and gill, whereas the lowest expression was detected in muscle and brain. Furthermore, MHC IIA and IIB were probably two candidate immune molecules involved in the resistance against streptococcosis, because their expression was significantly up-regulated in gill, kidney, intestine and spleen after the intraperitoneal injection of Streptococcus agalactiae. PMID:23261509

  16. Electrospray laser desorption ionization (ELDI) mass spectrometry for molecular imaging of small molecules on tissues.

    PubMed

    Huang, Min-Zong; Jhang, Siou-Sian; Shiea, Jentaie

    2015-01-01

    The use of an ambient ionization mass spectrometry technique known as electrospray laser desorption ionization mass spectrometry (ELDI/MS) for molecular imaging is described in this section. The technique requires little or no sample pretreatment and the application of matrix on sample surfaces is unnecessary. In addition, the technique is highly suitable for the analysis of hard and thick tissues compared to other molecular imaging methods because it does not require production of thin tissue slices via microtomes, which greatly simplifies the overall sample preparation procedure and prevents the redistribution of analytes during matrix desorption. In this section, the ELDI/MS technique was applied to the profiling and imaging of chemical compounds on the surfaces of dry plant slices. Analyte distribution on plant slices was obtained by moving the sample relative to a pulsed laser and an ESI capillary for analyte desorption and post-ionization, respectively. Images of specific ions on sample surfaces with resolutions of 250 ?m were typically created within 4.2 h for tissues with sizes of approximately 57 mm?×?10 mm. PMID:25361671

  17. Splitting molecular oxygen en route to a stable molecule containing diphosphorus tetroxide.

    PubMed

    Wang, Yuzhong; Xie, Yaoming; Wei, Pingrong; Schaefer, Henry F; Schleyer, Paul von R; Robinson, Gregory H

    2013-12-26

    In contrast to stable phosphorus oxides such as P4O6 and P4O10 that possess iconic adamantane-like cage structures, highly reactive phosphorus oxides such as PO, PO2, and P2Ox (x = 1-5) only have been studied in the gas phase or by matrix isolation techniques. Elusive diphosphorus tetroxide, the long sought phosphorus analogue of N2O4, is particularly noteworthy. Computations predict that the oxo-bridged O2POPO form of P2O4 is energetically more favored than the P-P bonded O2P-PO2 isomer. Herein, we report the experimental realization of diphosphorus tetroxide-in its energetically disfavored O2P-PO2 form-via carbene-stabilization. The synthesis of the title compound involves the splitting of molecular oxygen by carbene-stabilized diphosphorus. PMID:24299493

  18. Si-bearing molecules towards IRC+10216: ALMA unveils the molecular envelope of CWLeo

    E-print Network

    Prieto, L Velilla; Quintana-Lacaci, G; Agúndez, M; Castro-Carrizo, A; Fonfría, J P; Marcelino, N; Zúñiga, J; Requena, A; Bastida, A; Lique, F; Guélin, M

    2015-01-01

    We report the detection during the ALMA Cycle 0 of SiS rotational lines in high-vibrational states as well as SiO and SiC$_2$ lines in their ground vibrational state, towards IRC+10216. The spatial distribution of these molecules shows compact emission for SiS and a more extended emission for SiO and SiC$_2$ , and also proves the existence of an increase in the SiC$_2$ emission at the outer shells of the circumstellar envelope. We analyze the excitation conditions of the vibrationally excited SiS using the population diagram technique and we used a large velocity gradient model to compare with the observations. We found moderate discrepancies between the observations and the models that could be explained if SiS lines detected are optically thick. Additionally, the line profiles of the detected rotational lines in the high energy vibrational states show a decreasing linewidth with increasing energy levels. This may evidence that these lines could be excited only in the inner shells, i.e. the densest and hotte...

  19. Si-bearing Molecules Toward IRC+10216: ALMA Unveils the Molecular Envelope of CWLeo

    NASA Astrophysics Data System (ADS)

    Velilla Prieto, L.; Cernicharo, J.; Quintana-Lacaci, G.; Agúndez, M.; Castro-Carrizo, A.; Fonfría, J. P.; Marcelino, N.; Zúñiga, J.; Requena, A.; Bastida, A.; Lique, F.; Guélin, M.

    2015-06-01

    We report the detection of SiS rotational lines in high-vibrational states as well as SiO and SiC2 lines in their ground vibrational state toward IRC+10216 during the Atacama Large Millimeter Array Cycle 0. The spatial distribution of these molecules shows compact emission for SiS and a more extended emission for SiO and SiC2 and also proves the existence of an increase in the SiC2 emission at the outer shells of the circumstellar envelope (CSE). We analyze the excitation conditions of the vibrationally excited SiS using the population diagram technique, and we use a large velocity gradient model to compare with the observations. We found moderate discrepancies between the observations and the models that could be explained if SiS lines detected are optically thick. Additionally, the line profiles of the detected rotational lines in the high-energy vibrational states show a decreasing linewidth with increasing energy levels. This may be evidence that these lines could be excited only in the inner shells, i.e., the densest and hottest, of the CSE of IRC+10216.

  20. SPARCoC: A New Framework for Molecular Pattern Discovery and Cancer Gene Identification

    PubMed Central

    Ma, Shiqian; Johnson, Daniel; Ashby, Cody; Xiong, Donghai; Cramer, Carole L.; Moore, Jason H.; Zhang, Shuzhong; Huang, Xiuzhen

    2015-01-01

    It is challenging to cluster cancer patients of a certain histopathological type into molecular subtypes of clinical importance and identify gene signatures directly relevant to the subtypes. Current clustering approaches have inherent limitations, which prevent them from gauging the subtle heterogeneity of the molecular subtypes. In this paper we present a new framework: SPARCoC (Sparse-CoClust), which is based on a novel Common-background and Sparse-foreground Decomposition (CSD) model and the Maximum Block Improvement (MBI) co-clustering technique. SPARCoC has clear advantages compared with widely-used alternative approaches: hierarchical clustering (Hclust) and nonnegative matrix factorization (NMF). We apply SPARCoC to the study of lung adenocarcinoma (ADCA), an extremely heterogeneous histological type, and a significant challenge for molecular subtyping. For testing and verification, we use high quality gene expression profiling data of lung ADCA patients, and identify prognostic gene signatures which could cluster patients into subgroups that are significantly different in their overall survival (with p-values < 0.05). Our results are only based on gene expression profiling data analysis, without incorporating any other feature selection or clinical information; we are able to replicate our findings with completely independent datasets. SPARCoC is broadly applicable to large-scale genomic data to empower pattern discovery and cancer gene identification. PMID:25768286

  1. Imaging superatomic molecular orbitals in a C60 molecule through four 800-nm photons

    NASA Astrophysics Data System (ADS)

    Zhang, G. P.; Zhu, H. P.; Bai, Y. H.; Bonacum, J.; Wu, X. S.; George, Thomas F.

    2015-05-01

    Superatomic molecular orbitals (SAMOs) in C60 are ideal building blocks for functional nanostructures. However, imaging them spatially in the gas phase has been unsuccessful. It is found experimentally that if C60 is excited by an 800-nm laser, the photoelectron casts an anisotropic velocity image, but the image becomes isotropic if excited at a 400-nm wavelength. This diffuse image difference has been attributed to electron thermal ionization, but more recent experiments (800 nm) reveal a clear nondiffuse image superimposed on the diffuse image, whose origin remains a mystery. Here we show that the nondiffuse anisotropic image is the precursor of the f SAMOs. We predict that four 800-nm photons can directly access the 1f SAMO, and with one more photon, can image the orbital, with the photoelectron angular distribution having two maxima at 0° and 180° and two humps separated by 56.5°. Since two 400-nm photons only resonantly excite the spherical 1s SAMO and four 800-nm photons excite the anisotropic 1f SAMO, our finding gives a natural explanation of the nondiffuse image difference, complementing the thermal scenario.

  2. From a single molecule to a membrane of structured ionic polymers: A molecular dynamic simulation study

    NASA Astrophysics Data System (ADS)

    Aryal, Dipak; Perahia, Dvora; Grest, Gary S.

    2012-02-01

    The association of an A-B-C-B-A co-polymer with an ionizable center and a bulky end block has been investigated using molecular dynamic simulations. The center block consists of a randomly sulfonated polystyrene connected to a flexible poly (ethylene-r-propylene) bridge and end caped with poly (t-butyl styrene). Tailoring the nature of individual segments within a block co-polymer is a potential design tool to form membranes with desired properties. The association mode and the dynamics of the segments control the overall characteristics. The membranes with three sulfonation level for the center block were made by evaporating a common solvent for all blocks. The local structure including size and distribution of the ionic blocks and the continuity of the styrene phase as well as long range correlations were identified at 300 and 500K. The initial membrane structure is affected by the structure in solution. Studies on changes that take place above the glass transition temperature for each of the blocks will also be presented.

  3. Novel Strategy for Biofilm Inhibition by Using Small Molecules Targeting Molecular Chaperone DnaK

    PubMed Central

    Arita-Morioka, Ken-ichi; Yamanaka, Kunitoshi; Mizunoe, Yoshimitsu; Ogura, Teru

    2014-01-01

    Biofilms are complex communities of microorganisms that attach to surfaces and are embedded in a self-produced extracellular matrix. Since these cells acquire increased tolerance against antimicrobial agents and host immune systems, biofilm-associated infectious diseases tend to become chronic. We show here that the molecular chaperone DnaK is important for biofilm formation and that chemical inhibition of DnaK cellular functions is effective in preventing biofilm development. Genetic, microbial, and microscopic analyses revealed that deletion of the dnaK gene markedly reduced the production of the extracellular functional amyloid curli, which contributes to the robustness of Escherichia coli biofilms. We tested the ability of DnaK inhibitors myricetin (Myr), telmisartan, pancuronium bromide, and zafirlukast to prevent biofilm formation of E. coli. Only Myr, a flavonol widely distributed in plants, inhibited biofilm formation in a concentration-dependent manner (50% inhibitory concentration [IC50] = 46.2 ?M); however, it did not affect growth. Transmission electron microscopy demonstrated that Myr inhibited the production of curli. Phenotypic analyses of thermosensitivity, cell division, intracellular level of RNA polymerase sigma factor RpoH, and vulnerability to vancomycin revealed that Myr altered the phenotype of E. coli wild-type cells to make them resemble those of the isogenic dnaK deletion mutant, indicating that Myr inhibits cellular functions of DnaK. These findings provide insights into the significance of DnaK in curli-dependent biofilm formation and indicate that DnaK is an ideal target for antibiofilm drugs. PMID:25403660

  4. Molecule Polarity

    NSDL National Science Digital Library

    The PhET project at the University of Colorado creates "fun, interactive, research-based simulations of physical phenomena." This particular one deals with molecular polarity. When is a molecule polar? Change the electronegativity of atoms in a molecule to see how it affects polarity. This simulation will allow visitors to see how molecules behave in an electric field, and change the bond angle to see how shape affects polarity for real molecules in 3D. The simulation is also paired with teaching tips and user-contirubed Teaching Ideas, lessons using the simulation in context, that can be found near the bottom of the page. The simulation is also available in multiple languages.

  5. Density-wave patterns for fermionic dipolar molecules on a square optical lattice: Mean-field-theory analysis

    SciTech Connect

    Mikelsons, K.; Freericks, J. K. [Department of Physics, Georgetown University, Washington, DC, 20057 (United States)

    2011-04-15

    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.

  6. Surface anchoring of rodlike molecules on corrugated substrates

    NASA Astrophysics Data System (ADS)

    Kiyohara, Kenji; Asaka, Kinji; Monobe, Hirosato; Terasawa, Naohiro; Shimizu, Yo

    2006-01-01

    We studied the mechanism of surface anchoring of rodlike molecules on substrates with the surfaces corrugated at molecular scale by molecular-dynamics simulation. We constructed a model for substrates that can have anisotoropic topographical patterns such as corrugation. The structural and thermodynamic properties of rodlike molecules on the corrugated surfaces, including the elastic and anchoring properties, were calculated and the influence of the surface structure on the anchoring was discussed. We found that the rodlike molecules are aligned along the grooves of the corrugated surfaces guided by the anisotropic molecular interaction between the molecules and the corrugated surface. The strength of anchoring was found to be increased when the period of corrugation is decreased at molecular level.

  7. Nitric Oxide-Enhanced Molecular Imaging of Atheroma using Vascular Cellular Adhesion Molecule 1-Targeted Echogenic Immunoliposomes.

    PubMed

    Kim, Hyunggun; Kee, Patrick H; Rim, Yonghoon; Moody, Melanie R; Klegerman, Melvin E; Vela, Deborah; Huang, Shao-Ling; McPherson, David D; Laing, Susan T

    2015-06-01

    The aim of this study was to determine whether pre-treatment with nitric oxide-loaded echogenic liposomes (NO-ELIP) plus ultrasound can improve highlighting by molecularly targeted (anti-vascular cell adhesion molecule 1 [VCAM-1]) ELIP of atheroma components. Atherosclerotic animals were treated with anti-VCAM-1-ELIP or immunoglobulin (IgG)-ELIP. Each group was selected at random to receive pre-treatment with standard ELIP plus ultrasound, NO-ELIP without ultrasound and NO-ELIP plus ultrasound. Intravascular ultrasound highlighting data for the same arterial segments were collected before and after treatment. Pre-treatment with NO-ELIP plus ultrasound resulted in a significant increase in acoustic enhancement by anti-VCAM-1-ELIP (21.3 ± 1.5% for gray-scale value, 53.9 ± 3.1% for radiofrequency data; p < 0.001 vs. IgG-ELIP, p < 0.05 vs. pre-treatment with standard ELIP plus ultrasound or NO-ELIP without ultrasound). NO-ELIP plus ultrasound can improve highlighting of atheroma by anti-VCAM-1 ELIP. This NO pre-treatment strategy may be useful in optimizing contrast agent delivery to the vascular wall for both diagnostic and therapeutic applications. PMID:25819469

  8. Molecular Characterization and Clinical Implications of Spindle Cells in Nasopharyngeal Carcinoma: A Novel Molecule-Morphology Model of Tumor Progression Proposed

    PubMed Central

    Luo, Weiren; Yao, Kaitai

    2013-01-01

    Up to now, the precise molecular and morphological changes underlying the invasive and metastatic properties of nasopharyngeal carcinoma (NPC) remain largely unresolved. We speculate that neoplastic spindle cells, which are prominently found in the invasive tumor front and the surrounding stroma, might be responsible for the aggressive patterns. Expression profiling of various biomarkers relevant to cancer stem cells (CSCs) and epithelial-mesenchymal transition (EMT) was performed by tissue microarray-based immunohistochemistry in NPC samples. The expression of EBER and LMP1 was detected by in situ hybridization and immunohistochemistry, respectively. We found that overexpression of CSCs-related markers (ALDH1, Nanog and ABCG2) and up-regulation of EMT markers (Fibronectin, MMP-2, Periostin, SPARC, Snail and Slug), together with E- to N-cadherin switching, occurred preferentially in tumors containing a large proportion of spindle-shaped malignant cells. Furthermore, CSCs-like properties were highly present in spindle cells compared with non-spindle cells of tumors, and correlated strongly with EMT features. In addition, EBV-related factors EBER and LMP1 were highly expressed and correlated strongly with CSCs and EMT characteristics in neoplastic spindle cells. Importantly, high proportion of spindle cells (?20%) correlated significantly with various aggressive aspects including lymph node metastasis (P = 0.031) and local recurrence (P = 0.014). Patients with high proportion of spindle cells had poor survival (P = 0.004), though it was not an independent value. In conclusion, we demonstrate that spindle cells could be valuable morphological indicators of tumor progression and unfavorable prognosis of NPC. An integrated molecule-morphology model of NPC firstly constructed may shed significant light on the metastatic cascade and clinical relevance of patients. PMID:24349446

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

    NASA Astrophysics Data System (ADS)

    Mukamel, Shaul

    2011-03-01

    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.

  10. Intensity enhancement and selective detection of proximate solvent molecules by molecular near-field effect in resonance hyper-Raman scattering

    NASA Astrophysics Data System (ADS)

    Shimada, Rintaro; Kano, Hideaki; Hamaguchi, Hiro-o.

    2008-07-01

    A new molecular phenomenon associated with resonance hyper-Raman (HR) scattering in solution has been discovered. Resonance HR spectra of all-trans-?-carotene and all-trans-lycopene in various solvents exhibited several extra bands that were not assignable to the solute but were unequivocally assigned to the solvents. Neat solvents did not show detectable HR signals under the same experimental conditions. Similar experiments with all-trans-retinal did not exhibit such enhancement either. All-trans-?-carotene and all-trans-lycopene have thus been shown to induce enhanced HR scattering of solvent molecules through a novel molecular effect that is not associated with all-trans-retinal. We call this new effect the "molecular near-field effect." In order to explain this newly found effect, an extended vibronic theory of resonance HR scattering is developed where the vibronic interaction including the proximate solvent molecule (intermolecular vibronic coupling) is explicitly introduced in the solute hyperpolarizability tensor. The potential of "molecular near-field HR spectroscopy," which selectively detects molecules existing in the close vicinity of a HR probe in complex chemical or biological systems, is discussed.

  11. Inorganic Molecules; A Visual Database

    NSDL National Science Digital Library

    Inorganic Molecules: A Visual Data Base contains text and graphics describing 66 molecules and ions commonly used as examples in general chemistry courses. For each molecule, fifteen molecular properties are presented visually by eight or nine different molecular models created by the CAChe Scientific Molecular Modeling program.

  12. Electrical readouts of single and few molecule systems in metal-molecule-metal device structures.

    PubMed

    Mahapatro, Ajit K; Janes, David B

    2007-06-01

    Electrical conduction through molecular junctions are measured in different local environments through two test beds that are ideal for single/few molecule and molecular monolayer systems. A technique has been developed to realize Au films with approximately 1.5 A surface roughness comparable to the best available techniques and suitable for formation of patterned device structures. The technique utilizes room temperature e-beam evaporated Au films over oxidized Si substrates silanized with (3-mercaptopropyl)trimethoxysilane (MPTMS). The lateral (single/few molecule) and vertical (many molecules) device structures are both enabled by the process for realizing ultraflat Au layer. Lateral metal-molecule-metal (M-M-M) device structures are fabricated by forming pairs of Au electrodes with nanometer separation (nano-gap) through an electromigration-induced break-junction (EIBJ) technique at room temperature and conductivity measurements are carried out for dithiol functionalized single molecules. We have used the flat Au layer (using the current technique) as the bottom contact in vertical M-M-M device structures. Here, molecular self-assembly are formed on the Au surface, and patterned (20 x 20 microm2) top Au contacts were successfully transferred on to the device using a stamping technique (where the Au is deposited on a polydimethylsiloxane (PDMS) pad and following a physical contact on the thiolated Au layer). The single molecular property of XYL, a highly conductive molecule and many molecular property of HS-C9-SH, an insulating molecule in its molecular monolayer form are measured. Observation of enhanced conduction following molecular deposition, and comparison of conductance-voltage characteristics to those predicted theoretically, confirms the success of trapping single/few molecules in the nano-gap. The observed approximately 10(2) less conductance through the molecular monolayer of HS-C9-SH compared to the estimation of a linear sum of single molecule conductances over large area indicate that either all the molecules are not in physical contact with the top stamping electrode or electrode-molecule coupling has a less broadening in presence of it own environment or both. PMID:17655006

  13. Time dependent chemistry in dense molecular clouds. III - Infrared band cross sections of molecules in the solid state at 10 K

    NASA Technical Reports Server (NTRS)

    Dhendecourt, L. B.; Allamandola, L. J.

    1986-01-01

    Thin film transmission infrared spectra and a list of integrated absorbance values (band strengths) of bands in the 2.5 to 20 micron range of various molecular solids deposited on a CsI window cooled to 10 K are presented. These solids include molecules known or suspected to be present on interstellar grains such as H2O, CO, NH3 and CH4 and mixtures of these molecules as well as various hydrocarbons. The method is described by which the absorbance values derived can be used to estimate column densities of species adsorbed on interstellar grains and other solids associated with celestial IR sources.

  14. Characterization of currently marketed heparin products: analysis of molecular weight and heparinase-I digest patterns.

    PubMed

    Sommers, Cynthia D; Ye, Hongping; Kolinski, Richard E; Nasr, Moheb; Buhse, Lucinda F; Al-Hakim, Ali; Keire, David A

    2011-11-01

    We evaluated polyacrylamide gel electrophoresis (PAGE) and size exclusion chromatography coupled with multi-angle laser light scattering (SEC-MALLS) approaches to determine weight-average molecular weight (M(w)) and polydispersity (PD) of heparins. A set of unfractionated heparin sodium (UFH) and low-molecular-weight heparin (LMWH) samples obtained from nine manufacturers which supply the US market were assessed. For SEC-MALLS, we measured values for water content, refractive index increment (dn/dc), and the second virial coefficient (A(2)) for each sample prior to molecular weight assessment. For UFH, a mean ± standard deviation value for M(w) of 16,773 ± 797 was observed with a range of 15,620 to 18,363 (n = 20, run in triplicate). For LMWHs by SEC-MALLS, we measured mean M(w) values for dalteparin, tinzaparin, and enoxaparin of 6,717 ± 71 (n = 4), 6,670 ± 417 (n = 3), and 3,959 ± 145 (n = 3), respectively. PAGE analysis of the same UFH, dalteparin, tinzaparin, and enoxaparin samples showed values of 16,135 ± 643 (n = 20), 5,845 ± 45 (n = 4), 6,049 ± 95 (n = 3), and 4,772 ± 69 (n = 3), respectively. These orthogonal measurements are the first M(w) results obtained with a large heparin sample set on product being marketed after the heparin crisis of 2008 changed the level of scrutiny of this drug class. In this study, we compare our new data set to samples analyzed over 10 years earlier. In addition, we found that the PAGE analysis of heparinase digested UFH and neat LMWH samples yield characteristic patterns that provide a facile approach for identification and assessment of drug quality and uniformity. PMID:21901459

  15. Analysis of molecular expression patterns and integration with other knowledge bases using probabilistic Bayesian network models

    SciTech Connect

    Moler, Edward J.; Mian, I.S.

    2000-03-01

    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.

  16. Molecular insights into the origin of the Hox-TALE patterning system

    PubMed Central

    Hudry, Bruno; Thomas-Chollier, Morgane; Volovik, Yael; Duffraisse, Marilyne; Dard, Amélie; Frank, Dale; Technau, Ulrich; Merabet, Samir

    2014-01-01

    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

  17. Pathogen associated molecular pattern (PAMP)-triggered immunity is compromised under C-limited growth.

    PubMed

    Park, Hyeong Cheol; Lee, Shinyoung; Park, Bokyung; Choi, Wonkyun; Kim, Chanmin; Lee, Sanghun; Chung, Woo Sik; Lee, Sang Yeol; Sabir, Jamal; Bressan, Ray A; Bohnert, Hans J; Mengiste, Tesfaye; Yun, Dae-Jin

    2015-01-31

    In the interaction between plants and pathogens, carbon (C) resources provide energy and C skeletons to maintain, among many functions, the plant immune system. However, variations in C availability on pathogen associated molecular pattern (PAMP) triggered immunity (PTI) have not been systematically examined. Here, three types of starch mutants with enhanced susceptibility to Pseudomonas syringae pv. tomato DC3000 hrcC were examined for PTI. In a dark period-dependent manner, the mutants showed compromised induction of a PTI marker, and callose accumulation in response to the bacterial PAMP flagellin, flg22. In combination with weakened PTI responses in wild type by inhibition of the TCA cycle, the experiments determined the necessity of C-derived energy in establishing PTI. Global gene expression analyses identified flg22 responsive genes displaying C supply-dependent patterns. Nutrient recycling-related genes were regulated similarly by C-limitation and flg22, indicating re-arrangements of expression programs to redirect resources that establish or strengthen PTI. Ethylene and NAC transcription factors appear to play roles in these processes. Under C-limitation, PTI appears compromised based on suppression of genes required for continued biosynthetic capacity and defenses through flg22. Our results provide a foundation for the intuitive perception of the interplay between plant nutrition status and pathogen defense. PMID:25387755

  18. Molecular Dynamics Simulations of Surface Acoustic Waves on Patterned Layered Nanostructures

    NASA Astrophysics Data System (ADS)

    Bjornsson, Matteo; Connolly, Aine; Mahat, Sushant; Rachmilowitz, Bryan; Daly, Brian; Antonelli, George; Myers, Alan; Singh, Kanwal; Yoo, Hiu-Jae; King, Sean

    2015-03-01

    We report coarse-grained molecular dynamics (MD) simulations of surface acoustic waves on patterned layered nanostructures. The simulations were designed for comparison with samples consisting of the following patterned film stack: 25 nm physically vapor deposited TiN / 180 nm porous PECVD-grown a-SiOC:H / 12 nm non-porous PECVD-grown a-SiOC:H etch-stop / 100 nm CVD-grown a-SiO2 / Si (100) substrate. The TiN film was etched with lines of rectangular cross-section with pitch = 168 to 420 nm. Ultrafast optical experiments on these samples have detected high frequency surface waves in the range of 10's of GHz. The MD simulation demonstrates the presence of strongly excited modes at frequencies that closely match those found in the experiments. Moreover, the simulation predicts that the type of surface wave mode detected should change depending on the pitch. For larger pitch, Rayleigh-like waves are predicted, but for smaller pitch, Sezawa waves (surface waves with properties similar to free plate modes of the thin films) are predicted. The MD simulation also demonstrates the cutoff wavelength for the Sezawa modes, as is reflected in the experimental results and as is also predicted by isotropic elastic calculations of the surface modes of a thin film on an infinite substrate. This work was supported by NSF Award DMR1206681.

  19. Molecular characterization and expression patterns of myogenin in compensatory growth of Megalobrama amblycephala.

    PubMed

    Zhu, Kecheng; Chen, Liping; Zhao, Jinkun; Wang, Huijuan; Wang, Weimin; Li, Zhong; Wang, Huanling

    2014-04-01

    Myogenin (myog) is a muscle-specific basic helix-loop-helix (bHLH) transcription factor that plays an essential role in regulating skeletal muscle development and growth. To investigate molecular characterization of myog and the effect of starvation/refeeding on the gene expression, we isolated the myog cDNA sequence and analyzed the expression patterns using quantitative real-time polymerase chain reaction in Megalobrama amblycephala. Sequence analysis indicated that M. amblycephala myog shared an analogous structure with the highly conserved His/Cys-rich, bHLH and C-terminal helix III domains with other vertebrates. Sequence alignment and phylogenetic tree showed that M. amblycephala myog had the highest identity with the homologues of Ctenopharyngodon idella and Cyprinus carpio. Spatio-temporal expression patterns revealed that myog mRNA levels at the segmentation period and 12 h post-hatching (hph) were significantly higher than at other development stages (P<0.05). Furthermore, the highest myog expression level was predominantly observed in white muscle compared with the other types of muscle. Fish body weight continuously decreased during 21-day starvation and then significantly increased after 7days of refeeding and reached the similar level to the control at 21days of refeeding, indicating that the pattern of complete compensatory growth possibly occurred in M. amblycephala; meanwhile, the relative somatic growth rate after refeeding was also dramatically higher than the control group. In addition, the myog expression decreased during 21days of starvation and then exhibited a strong rebound effect after 7days of refeeding and subsequently declined gradually to the control level by 21days of refeeding. PMID:24440962

  20. Short communication: Single molecule, real-time sequencing technology revealed species- and strain-specific methylation patterns of 2 Lactobacillus strains.

    PubMed

    Zhang, Wenyi; Sun, Zhihong; Menghe, Bilige; Zhang, Heping

    2015-05-01

    Pacific Biosciences' (Menlo Park, CA) single molecule, real-time sequencing technology was reported to have some advantages in generating finished genomes and characterizing the epigenome of bacteria. In the present study, this technology was used to sequence 2 Lactobacillus strains, Lactobacillus casei Zhang and Lactobacillus plantarum P-8. Previously, the former bacterium was sequenced by an Applied Biosystems 3730 DNA analyzer (Grand Island, NY), whereas the latter one was analyzed with Roche 454 (Indianapolis, IN) and Illumina sequencing technologies (San Diego, CA). The results showed that single molecule, real-time sequencing resulted in high-quality, finished genomes for both strains. Interestingly, epigenome analysis indicates the presence of 1 active N(6)-methyladenine methyltransferase in L. casei Zhang, but none in L. plantarum P-8. Our study revealed for the first time a completely different methylation pattern in 2 Lactobacillus strains. PMID:25747834

  1. Adapting SAFT-? perturbation theory to site-based molecular dynamics simulation. III. Molecules with partial charges at bulk phases, confined geometries and interfaces

    NASA Astrophysics Data System (ADS)

    Ghobadi, Ahmadreza F.; Elliott, J. Richard

    2014-09-01

    In Paper I [A. F. Ghobadi and J. R. Elliott, J. Chem. Phys. 139(23), 234104 (2013)], we showed that how a third-order Weeks-Chandler-Anderson (WCA) Thermodynamic Perturbation Theory and molecular simulation can be integrated to characterize the repulsive and dispersive contributions to the Helmholtz free energy for realistic molecular conformations. To this end, we focused on n-alkanes to develop a theory for fused and soft chains. In Paper II [A. F. Ghobadi and J. R. Elliott, J. Chem. Phys. 141(2), 024708 (2014)], we adapted the classical Density Functional Theory and studied the microstructure of the realistic molecular fluids in confined geometries and vapor-liquid interfaces. We demonstrated that a detailed consistency between molecular simulation and theory can be achieved for both bulk and inhomogeneous phases. In this paper, we extend the methodology to molecules with partial charges such as carbon dioxide, water, 1-alkanols, nitriles, and ethers. We show that the electrostatic interactions can be captured via an effective association potential in the framework of Statistical Associating Fluid Theory (SAFT). Implementation of the resulting association contribution in assessing the properties of these molecules at confined geometries and interfaces presents satisfactory agreement with molecular simulation and experimental data. For example, the predicted surface tension deviates less than 4% comparing to full potential simulations. Also, the theory, referred to as SAFT-? WCA, is able to reproduce the specific orientation of hydrophilic head and hydrophobic tail of 1-alkanols at the vapor-liquid interface of water.

  2. Molecular profiling of experimental endometriosis identified gene expression patterns in common with human disease

    PubMed Central

    Flores, Idhaliz; Rivera, Elizabeth; Ruiz, Lynnette A.; Santiago, Olga I.; Vernon, Michael W.; Appleyard, Caroline B.

    2007-01-01

    OBJECTIVE To validate a rat model of endometriosis using cDNA microarrays by identifying common gene expression patterns beween experimental and natural disease. DESIGN Autotransplantation rat model. SETTING Medical school department. ANIMALS Female Sprague-Dawley rats. INTERVENTIONS Endometriosis was surgically-induced by suturing uterine horn implants next to the small intestine’s mesentery. Control rats received sutures with no implants. After 60 days, endometriotic implants and uterine horn were obtained. MAIN OUTCOME MEASURES Gene expression levels determined by cDNA microarrays and QRT-PCR. METHODS Cy5-labeled cDNA was synthesized from total RNA obtained from endometriotic implants. Cy3-labeled cDNA was synthesized using uterine RNA from a control rat. Gene expression levels were analyzed after hybridizing experimental and control labeled cDNA to PIQOR™ Toxicology Rat Microarrays (Miltenyi Biotec) containing 1,252 known genes. Cy5/Cy3 ratios were determined and genes with >2-fold higher or <0.5-fold lower expression levels were selected. Microarray results were validated by QRT-PCR. RESULTS We observed differential expression of genes previously shown to be upregulated in patients, including growth factors, inflammatory cytokines/receptors, tumor invasion/metastasis factors, adhesion molecules, and anti-apoptotic factors. CONCLUSIONS This study presents evidence in support of using this rat model to study the natural history of endometriosis and test novel therapeutics for this incurable disease. PMID:17478174

  3. Molecular characterization of peach PR genes and their induction kinetics in response to bacterial infection and signaling molecules.

    PubMed

    Sherif, S; Paliyath, G; Jayasankar, Subramanian

    2012-04-01

    'Venture' and 'BabyGold 5' are two peach cultivars with a demonstrated resistance and susceptibility, respectively, to bacterial spot disease caused by Xanthomonas campestris pv. pruni (Xcp). To explore the differences between these cultivars at the molecular level, two PR1 (Pp-PR1a, Pp-PR1b) and three PR5 (Pp-TLP1, Pp-TLP2 and Pp-TLP3) genes were isolated from peach (Prunus persica L.) and investigated by in silico and in situ approaches. The analysis of gene expression by qRT-PCR indicated that all PR genes, except Pp-PR1a, were induced to a significantly higher degree in the resistant cultivar. In response to signaling molecules, Pp-PR1a was induced chiefly by SA treatment, while other PR genes were induced mainly by ethephon or MeJA treatments. The induction of the same set of PR genes in response to bacterial infection, MeJA or ethephon suggests the involvement of jasmonic acid (JA)/ethylene (ET)-signaling pathways in mediating resistance against Xcp, which is consistent with the potential hemibiotrophic nature of this bacterium. The identification of binding sites for ERF and MYC2 transcription factors in the promoter of Pp-TLP1 and Pp-TLP2 genes further supported the role of JA/ET pathways in the transcription regulation of these genes. The role of stomata in defense against Xcp was also investigated by measuring stomatal apertures in both 'Venture' and 'BabyGold 5' leaves after 1 and 3 HPI. While most stomata closed in both cultivars within 1 HPI, stomata reopened again at 3 HPI with a higher percentage recorded for 'BabyGold 5', suggesting a potential role of stomata in the susceptibility of this cultivar. PMID:22101723

  4. Pattern Formation within Escherichia coli: Diffusion, Membrane Attachment, and Self-Interaction of MinD Molecules

    E-print Network

    Timmer, Jens

    -Interaction of MinD Molecules Rahul V. Kulkarni,1,* Kerwyn Casey Huang,1,2, Morten Kloster,1 and Ned S. Wingreen1,3 1 provide a model for the polar localization of MinD based only on diffusion, a delay for nucleotide analytically the probability density, and correspondingly the length scale, for MinD attachment zones. Our

  5. Toward a full structural characterization of G-quadruplex DNA in aqueous solution: Molecular dynamics simulations of four G-quadruplex molecules

    Microsoft Academic Search

    Ming-Hui Li; Quan Luo; Xiang-Gui Xue; Ze-Sheng Li

    2010-01-01

    A systematic study on guanine (G) quadruplex DNA flexibility was performed by using extended explicit molecular dynamics (MD) simulations on four quadruplex molecules containing one dimeric and three monomeric G-quadruplexes with the most used and recent modified versions of AMBER force fields (parm99 and parmbsc0). The detailed analyses of general structure and basic structural parameters were done for the G-DNA

  6. Strontium mono-chloride - A new molecule for the determination of chlorine using high-resolution graphite furnace molecular absorption spectrometry and direct solid sample analysis

    NASA Astrophysics Data System (ADS)

    Pereira, Éderson R.; Welz, Bernhard; Lopez, Alfredo H. D.; de Gois, Jefferson S.; Caramori, Giovanni F.; Borges, Daniel L. G.; Carasek, Eduardo; de Andrade, Jailson B.

    2014-12-01

    A new method has been developed for the determination of chlorine in biological reference materials using high-resolution continuum source graphite furnace molecular absorption spectrometry (HR-CS GF MAS) of the strontium mono-chloride (SrCl) molecule and direct solid sample analysis. The use of the SrCl molecule for high-temperature MAS was not described up to now in the literature. Preliminary time-dependent density functional theory calculations of the SrCl structure were carried out in order to obtain reasonable estimates of the absorption spectrum of the target molecule. The calculations, which were carried out at BHandHLyp/def2-QZVP level of theory, proved a very accurate and inexpensive way to get information about the spectrum of the SrCl molecule, which enabled us to perform the Cl determination with good sensitivity and specificity. The molecular absorption of the SrCl molecule has been measured using the wavelength at 635.862 nm, and zirconium and palladium have been evaluated as the chemical modifiers in order to increase the sensitivity of the gaseous SrCl molecule generated in the graphite furnace. The pyrolysis and vaporization temperatures were 600 °C and 2300 °C, respectively. Accuracy and precision of the method have been evaluated using biological certified reference materials of both animal and plant origins, showing good agreement with the informed and certified values. Limit of detection and characteristic mass were 1.0 and 2.2 ng, respectively. The results found using HR-CS GF MAS were in agreement (95% confidence level) compared to those obtained by electrothermal vaporization-inductively coupled plasma mass spectrometry.

  7. Complex temporal patterns in molecular dynamics: A direct measure of the phase-space exploration by the trajectory at macroscopic time scales

    E-print Network

    Nerukh, Dmitry

    Complex temporal patterns in molecular dynamics: A direct measure of the phase-space exploration how the trajectory explores the phase space and independent from the particular molecular signal used in liquids form complex patterns in the phase space. Because of the system's high dimensionality defined

  8. Laser guiding of cold molecules in a hollow optical fiber and continuous-wave cold molecular beam generation

    Microsoft Academic Search

    Liu Run-Qin; Yin Ya-Ling; Yin Jian-Ping

    2012-01-01

    A novel scheme for guiding arbitrary buffer-gas cooled neutral molecules in a hollow optical fiber (HOF) using a red-detuned HE11 mode is proposed and analysed theoretically. We give the electromagnetic field distribution of the HE11 mode in the HOF and calculate the optical potential of an I2 molecule, and study the molecule guiding mechanism using a classical Monte Carlo simulation.

  9. 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)

    Ebata, Takayuki; Kusaka, Ryoji; Inokuchi, Yoshiya; Xantheas, Sotiris S.

    2011-06-01

    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 molecular receptors, metal cation extraction agents, fluoro-ionophores and phase transfer catalytic media have been previously reported in a number of studies in the literature. One of the important aspects of these host/guest molecular assemblies is their selectivity in the encapsulation of guest species. Two important factors that control this selectivity are: (1) the size and the flexibility of the host cavity and (2) the properties of solvent molecules. Molecular complexes formed in supersonic jets provide ideal systems for the selective study of the conformational preference and micro-solvated effects under solvent-controlled conditions. This talk will review our spectroscopic and theoretical studies of the structures of dibenzo-18-crown-6-ether (DB18C6), benzo-18-crown-6-ether (B18C6), calix[4]arene (C4A) and their complexes with guest molecules. We apply laser-induced fluorescence (LIF), resonance enhanced two-photon ionization (R2PI) and UV-UV hole-burning (HB) spectroscopy for obtaining electronic spectra and IR-UV doubleresonance and IR photodissociation (IRPD) spectroscopy for the IR spectra. The electronic and IR spectra are compared with the corresponding results obtained by DFT calculations and high-level first principles electronic structure calculations [MP2 and CCSD(T)]. Based on these joint studies we can elucidate the nature of interactions that control the encapsulation of a guest molecular species as well as how the host can adjust its conformation to accommodate a specific guest, leading to the molecular recognition.

  10. The Plant Actin Cytoskeleton Responds to Signals from Microbe-Associated Molecular Patterns

    PubMed Central

    Henty-Ridilla, Jessica L.; Shimono, Masaki; Li, Jiejie; Chang, Jeff H.; Day, Brad; Staiger, Christopher J.

    2013-01-01

    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. PMID:23593000

  11. Moving Molecules!

    NSDL National Science Digital Library

    2014-06-24

    In this activity about molecular diffusion (located on page 2 of the PDF), learners will make predictions and move molecules of iodine through a seemingly solid plastic sandwich bag. The process of diffusion will be visually indicated by a color change when the iodine reacts with starch inside the bag. Information in the resource explains how this activity relates to nanoparticles and research. Related to linked video, DragonflyTV Nano: Nanosilver.

  12. Oxaliplatin induces different cellular and molecular chemoresistance patterns in colorectal cancer cell lines of identical origins

    PubMed Central

    2013-01-01

    Background Cancer cells frequently adopt cellular and molecular alterations and acquire resistance to cytostatic drugs. Chemotherapy with oxaliplatin is among the leading treatments for colorectal cancer with a response rate of 50%, inducing intrastrand cross-links on the DNA. Despite of this drug’s efficiency, resistance develops in nearly all metastatic patients. Chemoresistance being of crucial importance for the drug’s clinical efficiency this study aimed to contribute to the identification and description of some cellular and molecular alterations induced by prolonged oxaliplatin therapy. Resistance to oxaliplatin was induced in Colo320 (Colo320R) and HT-29 (HT-29R) colorectal adenocarcinoma cell lines by exposing the cells to increasing concentrations of the drug. Alterations in morphology, cytotoxicity, DNA cross-links formation and gene expression profiles were assessed in the parental and resistant variants with microscopy, MTT, alkaline comet and pangenomic microarray assays, respectively. Results Morphology analysis revealed epithelial-to-mesenchymal transition in the resistant vs parental cells suggesting alterations of the cells’ adhesion complexes, through which they acquire increased invasiveness and adherence. Cytotoxicity measurements demonstrated resistance to oxaliplatin in both cell lines; Colo320 being more sensitive than HT-29 to this drug (P?molecular chemoresistance patterns induced by prolonged treatment with oxaliplatin in cell lines with identical origins (colorectal adenocarcinomas). PMID:23865481

  13. The molecular yo-yo method: Live jump detection improves throughput of single-molecule force spectroscopy for out-of-equilibrium transitions

    NASA Astrophysics Data System (ADS)

    Mack, A. H.; Schlingman, D. J.; Kamenetska, M.; Collins, R.; Regan, L.; Mochrie, S. G. J.

    2013-08-01

    By monitoring multiple molecular transitions, force-clamp, and trap-position-clamp methods have led to precise determinations of the free energies and free energy landscapes for molecular states populated in equilibrium at the same or similar forces. Here, we present a powerful new elaboration of the force-clamp and force-jump methods, applicable to transitions far from equilibrium. Specifically, we have implemented a live jump detection and force-clamp algorithm that intelligently adjusts and maintains the force on a single molecule in response to the measured state of that molecule. We are able to collect hundreds of individual molecular transitions at different forces, many times faster than previously, permitting us to accurately determine force-dependent lifetime distributions and reaction rates. Application of our method to unwinding and rewinding the nucleosome inner turn, using optical tweezers reveals experimental lifetime distributions that comprise a statistically meaningful number of transitions, and that are accurately single exponential. These measurements significantly reduce the error in the previously measured rates, and demonstrate the existence of a single, dominant free energy barrier at each force studied. A key benefit of the molecular yo-yo method for nucleosomes is that it reduces as far as possible the time spent in the tangentially bound state, which minimizes the loss of nucleosomes by dissociation.

  14. Reconstruction of the Electron Density of Molecules with Single-Axis Alignment

    SciTech Connect

    Starodub, Dmitri

    2011-08-12

    Diffraction from the individual molecules of a molecular beam, aligned parallel to a single axis by a strong electric field or other means, has been proposed as a means of structure determination of individual molecules. As in fiber diffraction, all the information extractable is contained in a diffraction pattern from incidence of the diffracting beam normal to the molecular alignment axis. We present two methods of structure solution for this case. One is based on the iterative projection algorithms for phase retrieval applied to the coefficients of the cylindrical harmonic expansion of the molecular electron density. Another is the holographic approach utilizing presence of the strongly scattering reference atom for a specific molecule.

  15. Patterned self-assembly of magnetic biomolecules on semiconductor substrates

    NASA Astrophysics Data System (ADS)

    Sun, Kien Wen; Chang, Chia-Ching

    2007-05-01

    The paper reports on the methods of preparing and patterning magnetic metallothionein (Mn,Cd-MT-2) molecules on semiconductor surfaces. The molecules are placed into nanopores prepared on silicon (0 0 1) substrates. We observe the self-assembled growth of those MT molecules on the patterned Si surface. Dense arrays of molecular rods are demonstrated on templates with small pores and pitch sizes. Then the structures of the self-assembled protein are studied by atomic force microscopy (AFM) and magnetic force microscopy (MFM). Our measurements indicate that molecular self-assembly has a magnetic dipole moment which interacts with the applied magnetic field.

  16. The Role of Damage-Associated Molecular Patterns (DAMPs) in Human Diseases

    PubMed Central

    Land, Walter G.

    2015-01-01

    This article is the second part of a review that addresses the role of damage-associated molecular patterns (DAMPs) in human diseases by presenting examples of traumatic (systemic inflammatory response syndrome), cardiovascular (myocardial infarction), metabolic (type 2 diabetes mellitus), neurodegenerative (Alzheimer’s disease), malignant and infectious diseases. Various DAMPs are involved in the pathogenesis of all these diseases as they activate innate immune machineries including the unfolded protein response and inflammasomes. These subsequently promote sterile autoinflammation accompanied, at least in part, by subsequent adaptive autoimmune processes. This review article discusses the future role of DAMPs in routine practical medicine by highlighting the possibility of harnessing and deploying DAMPs either as biomarkers for the appropriate diagnosis and prognosis of diseases, as therapeutics in the treatment of tumours or as vaccine adjuncts for the prophylaxis of infections. In addition, this article examines the potential for developing strategies aimed at mitigating DAMPs-mediated hyperinflammatory responses, such as those seen in systemic inflammatory response syndrome associated with multiple organ failure. PMID:26052447

  17. Formation of Ga droplets on patterned GaAs (100) by molecular beam epitaxy

    PubMed Central

    2012-01-01

    In this paper, the formation of Ga droplets on photo-lithographically patterned GaAs (100) and the control of the size and density of Ga droplets by droplet epitaxy using molecular beam epitaxy are demonstrated. In extension of our previous result from the journal Physical Status Solidi A, volume 209 in 2012, the sharp contrast of the size and density of Ga droplets is clearly observed by high-resolution scanning electron microscope, atomic force microscope, and energy dispersive X-ray spectrometry. Also, additional monolayer (ML) coverage is added to strength the result. The density of droplets is an order of magnitude higher on the trench area (etched area), while the size of droplets is much larger on the strip top area (un-etched area). A systematic variation of ML coverage results in an establishment of the control of size and density of Ga droplets. The cross-sectional line profile analysis and root mean square roughness analysis show that the trench area (etched area) is?approximately?six times rougher. The atomic surface roughness is suggested to be the main cause of the sharp contrast of the size and density of Ga droplets and is discussed in terms of surface diffusion. PMID:23033893

  18. Microevolutionary Patterns and Molecular Markers: The Genetics of Geographic Variation in Ascaris suum

    PubMed Central

    Nadler, S. A.

    1996-01-01

    Molecular markers have been used only rarely to characterize the population genetic structure of nematodes. Published studies have suggested that different taxa may show distinct genetic architectures. Isoenzyme and RAPD markers have been used to investigate geographic variation of Ascaris suum at the level of infrapopulations (nematodes within individual hosts), within localities, and among geographic regions. Independent estimates of genetic differentiation among population samples based on isoenzyme and RAPD data showed similar patterns and substantial correlation. Heterozygote deficiencies within infrapopulations and large values for inbreeding coefficients among infrapopulations suggested that the composition of these populations was not consistent with a model of random recruitment from a large panmictic pool of life-cycle stages. Both isoenzyme and RAPD markers revealed moderate levels of genetic differentiation among samples representing infrapopulations and localities. Of total gene diversity, 9.4% (isoenzyme) and 9.2% (RAPD) was partitioned among infrapopulations. Geographic localities accounted for 7.8% (isoenzyme) and 6.2% (RAPD) of total diversity. Only infrapopulations from the same farm had low levels of differentiation. PMID:19277145

  19. In Situ Mapping of the Molecular Arrangement of Amphiphilic Dye Molecules at the TiO2 Surface of Dye-Sensitized Solar Cells.

    PubMed

    Voïtchovsky, Kislon; Ashari-Astani, Negar; Tavernelli, Ivano; Tétreault, Nicolas; Rothlisberger, Ursula; Stellacci, Francesco; Grätzel, Michael; Harms, Hauke A

    2015-05-27

    Amphiphilic sensitizers are central to the function of dye-sensitized solar cells. It is known that the cell's performance depends on the molecular arrangement and the density of the dye on the semiconductor surface, but a molecular-level picture of the cell-electrolyte interface is still lacking. Here, we present subnanometer in situ atomic force microscopy images of the Z907 dye at the surface of TiO2 in a relevant liquid. Our results reveal changes in the conformation and the lateral arrangement of the dye molecules, depending on their average packing density on the surface. Complementary quantitative measurements on the ensemble of the film are obtained by the quartz-crystal microbalance with dissipation technique. An atomistic picture of the dye coverage-dependent packing, the effectiveness of the hydrophobic alkyl chains as blocking layer, and the solvent accessibility is obtained from molecular dynamics simulations. PMID:25936429

  20. Engineering crystals of dendritic molecules.

    PubMed

    Lukin, Oleg; Schubert, Dirk; Müller, Claudia M; Schweizer, W Bernd; Gramlich, Volker; Schneider, Julian; Dolgonos, Grygoriy; Shivanyuk, Alexander

    2009-07-01

    A detailed single-crystal X-ray study of conformationally flexible sulfonimide-based dendritic molecules with systematically varied molecular architectures was undertaken. Thirteen crystal structures reported in this work include 9 structures of the second-generation dendritic sulfonimides decorated with different aryl groups, 2 compounds bearing branches of both second and first generation, and 2 representatives of the first generation. Analysis of the packing patterns of 9 compounds bearing second-generation branches shows that despite their lack of strong directive functional groups there is a repeatedly reproduced intermolecular interaction mode consisting in an anchor-type packing of complementary second-generation branches of neighbouring molecules. The observed interaction tolerates a wide range of substituents in meta- and para-positions of the peripheral arylsulfonyl rings. Quantum chemical calculations of the molecule-molecule interaction energies agree at the qualitative level with the packing preferences found in the crystalline state. The calculations can therefore be used as a tool to rationalize and predict molecular structures with commensurate and non-commensurate branches for programming of different packing modes in crystal. PMID:19549870

  1. The reactions of the molecular nitrogen doubly charged ion with neutral molecules of relevance to planetary ionospheres

    NASA Astrophysics Data System (ADS)

    Ricketts, Claire Louise

    Diatomic dications (e.g. C02+) have been known to exist for several decades and are believed to be important components of energised media. Molecular dications possess significant internal energy due to the Coulombic repulsion of their two positive charges, meaning that many possible reaction channels are available to dications in a collision with a neutral molecule. Modellers have recently predicted that N22+ is present in the ionosphere of Earth and Titan as well as the dications C>22+ and 02+ in the ionosphere of Earth and CC>22+ in the ionosphere of Mars. These recent predictions, of dications in planetary ionospheres, imply that dications, and processes involving dication-neutral collisions, may have more significance than previously thought in the upper atmospheres of planets. Therefore this thesis describes a study of the reactions between N2 dications and neutrals, potentially of relevance to the ionosphere of Earth and Titan. A position sensitive coincidence (PSCO) time-of flight (TOF) mass spectrometer is used to probe the reactivity, energetics and dynamics of the bimolecular reactions of N22 . Dication-neutrals reactions often result in a pair of singly charged ions. The PSCO experiment is used to collect these pairs of singly-charged ions in coincidence. From the position-sensitive data we extract the velocity vectors of the product ions, and if the reaction of interest involves the formation of a third, undetected, neutral species, its velocity can be determined via conservation of momentum. The electron transfer reactions between dications and neutrals have been well rationalized 2+ previously, so only the electron transfer reactions of N2 with Ne and NO are discussed in this thesis. This thesis concentrates on probing the less well rationalized, bond- forming reactions between dications and neutrals. The bond-forming reactions of N22+ with O2, CO2, H2O, C2H2, CH4, H2 and Ar have been investigated and discussed. Several new bond-forming reactions mechanisms are derived for example, the bond-forming reactions of N22+ with O2 proceed via a 'long' lived complex which dissociates via loss of a neutral and then charge separation, a mechanism which is also operating for one of the bond-forming reactions of N2 with CO2 and N2 with H2O. Additional bond-forming reactions are detected for N22+ with CO2 and H2O, which proceed via shorter lived collision complexes. The reactions of N22+ with C2H2, CH4, H2 and Ar all proceed via a variety of mechanisms involving short-lived collision complexes or H and electron stripping.

  2. MCL and Mincle: C-Type Lectin Receptors That Sense Damaged Self and Pathogen-Associated Molecular Patterns

    PubMed Central

    Richardson, Mark B.; Williams, Spencer J.

    2014-01-01

    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. PMID:25002863

  3. A Jump Distance Distribution-based Bayesian model selection procedure reliably extracts molecular motion features from single molecule tracking data

    E-print Network

    Tollis, Sylvain

    2015-01-01

    Single-molecule tracking (SMT) methods are under considerable expansion in many fields of cell biology, as the dynamics of cellular components in biological mechanisms becomes increasingly relevant. Despite the development of SMT technologies, it is still difficult to reconcile a sparse signal at all times (required to distinguish single molecules) with long individual trajectories, which would be required for efficient Mean-Square Displacement-based analysis, within confined regions of the cell and given experimental limitations. In this work, we develop and implement a new mathematical analysis method of SMT trajectories, which aims to take advantage of the (large) number of (short) trajectories that are typically obtained with cellular systems in vivo. The method is based on the fitting of the jump distance distribution, e.g. the distribution that represents how far molecules travel in a set time interval; it uses a Bayesian approach to compare plausible molecule motion and extract both qualitative and qua...

  4. Method for imaging informational biological molecules on a semiconductor substrate

    NASA Technical Reports Server (NTRS)

    Coles, L. Stephen (Inventor)

    1994-01-01

    Imaging biological molecules such as DNA at rates several times faster than conventional imaging techniques is carried out using a patterned silicon wafer having nano-machined grooves which hold individual molecular strands and periodically spaced unique bar codes permitting repeatably locating all images. The strands are coaxed into the grooves preferably using gravity and pulsed electric fields which induce electric charge attraction to the molecular strands in the bottom surfaces of the grooves. Differential imaging removes substrate artifacts.

  5. Immune response and gene expression in shrimp ( Litopenaeus vannamei) hemocytes and hepatopancreas against some pathogen-associated molecular patterns

    Microsoft Academic Search

    Pei-Feng Ji; Cui-Luan Yao; Zhi-Yong Wang

    2009-01-01

    The effects of some pathogen-associated molecular patterns (PAMPs) (laminarin, LPS and poly I:C) on total hemocyte counts (THC), phenoloxidase (PO) activity, superoxide anion production and lectin, prophenoloxidase, lysozyme, cytosolic manganese superoxide dismutase (C-MnSOD) and catalase (CAT) gene expression were studied. The results showed that the production or activity of most tested immune factors and the expression of most tested genes

  6. Combined quantum mechanics/molecular mechanics (QM/MM) simulations for protein-ligand complexes: free energies of binding of water molecules in influenza neuraminidase.

    PubMed

    Woods, Christopher J; Shaw, Katherine E; Mulholland, Adrian J

    2015-01-22

    The applicability of combined quantum mechanics/molecular mechanics (QM/MM) methods for the calculation of absolute binding free energies of conserved water molecules in protein/ligand complexes is demonstrated. Here, we apply QM/MM Monte Carlo simulations to investigate binding of water molecules to influenza neuraminidase. We investigate five different complexes, including those with the drugs oseltamivir and peramivir. We investigate water molecules in two different environments, one more hydrophobic and one hydrophilic. We calculate the free-energy change for perturbation of a QM to MM representation of the bound water molecule. The calculations are performed at the BLYP/aVDZ (QM) and TIP4P (MM) levels of theory, which we have previously demonstrated to be consistent with one another for QM/MM modeling. The results show that the QM to MM perturbation is significant in both environments (greater than 1 kcal mol(-1)) and larger in the more hydrophilic site. Comparison with the same perturbation in bulk water shows that this makes a contribution to binding. The results quantify how electronic polarization differences in different environments affect binding affinity and also demonstrate that extensive, converged QM/MM free-energy simulations, with good levels of QM theory, are now practical for protein/ligand complexes. PMID:25340313

  7. Multiple binding modes of a small molecule to human Keap1 revealed by X-ray crystallography and molecular dynamics simulation

    PubMed Central

    Satoh, Mikiya; Saburi, Hajime; Tanaka, Tomoyuki; Matsuura, Yoshinori; Naitow, Hisashi; Shimozono, Rieko; Yamamoto, Naoyoshi; Inoue, Hideki; Nakamura, Noriko; Yoshizawa, Yoshitaka; Aoki, Takumi; Tanimura, Ryuji; Kunishima, Naoki

    2015-01-01

    Keap1 protein acts as a cellular sensor for oxidative stresses and regulates the transcription level of antioxidant genes through the ubiquitination of a corresponding transcription factor, Nrf2. A small molecule capable of binding to the Nrf2 interaction site of Keap1 could be a useful medicine. Here, we report two crystal structures, referred to as the soaking and the cocrystallization forms, of the Kelch domain of Keap1 with a small molecule, Ligand1. In these two forms, the Ligand1 molecule occupied the binding site of Keap1 so as to mimic the ETGE motif of Nrf2, although the mode of binding differed in the two forms. Because the Ligand1 molecule mediated the crystal packing in both the forms, the influence of crystal packing on the ligand binding was examined using a molecular dynamics (MD) simulation in aqueous conditions. In the MD structures from the soaking form, the ligand remained bound to Keap1 for over 20 ns, whereas the ligand tended to dissociate in the cocrystallization form. The MD structures could be classified into a few clusters that were related to but distinct from the crystal structures, indicating that the binding modes observed in crystals might be atypical of those in solution. However, the dominant ligand recognition residues in the crystal structures were commonly used in the MD structures to anchor the ligand. Therefore, the present structural information together with the MD simulation will be a useful basis for pharmaceutical drug development. PMID:26199865

  8. Microbe associated molecular patterns from rhizosphere bacteria trigger germination and Papaver somniferum metabolism under greenhouse conditions.

    PubMed

    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

    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

  9. Intratracheally administered pathogen-associated molecular patterns affect antibody responses of poultry.

    PubMed

    Ploegaert, T C W; De Vries Reilingh, G; Nieuwland, M G B; Lammers, A; Savelkoul, H F J; Parmentier, H K

    2007-08-01

    Various potential immune-modulating microbially derived pathogen-associated molecular patterns (PAMP), or so called homotopes, are present in high concentrations in the environment of food animals. In previous studies, intravenously administered PAMP had variable effects on specific primary and secondary immune responses of poultry to systemically administered antigens. In the present study, we evaluated the effects of intratracheal (i.t.) challenge with the PAMP lipopolysaccharide, lipoteichoic acid (LTA), and Zymosan-A (containing 1,3 beta-glucan) on primary and secondary (total) antibody (Ab) responses and (isotype) IgM, IgG, and IgA responses to systemically administered human serum albumin (HuSA), and Ab titers to infectious bursal disease (Gumboro virus) and infectious bronchitis vaccines in layer hens at 9 and 22 wk of age. Birds were challenged via the trachea with PAMP for 5 consecutive days prior to primary and secondary immunization with HuSA. Intratracheally administered LTA and, to a minor extent, lipopolysaccharide significantly enhanced secondary total and IgG Ab responses to HuSA. 1,3 beta-Glucan did not significantly affect Ab responses to HuSA. All birds challenged with PAMP showed a decreased BW. Higher total Ab titers to infectious bursal disease and infectious bronchitis were found in birds challenged with LTA. The present results indicate that i.t. administered PAMP affect the humoral immune responsiveness of poultry, which may lead to an enhanced status of immune reactivity. Furthermore, our results suggest that the hygienic status of the environment influences BW (gain). The consequences of immune modulation by airborne PAMP or hygienic conditions in chicken husbandry for vaccine delivery and immune responsiveness of poultry are discussed. PMID:17626812

  10. Positron-attachment to acetonitrile, acetaldehyde, and acetone molecules: Vibrational enhancement of positron affinities with configuration interaction level of multi-component molecular orbital approach

    NASA Astrophysics Data System (ADS)

    Tachikawa, Masanori

    2014-04-01

    To theoretically demonstrate the binding of a positron to acetonitrile, acetaldehyde, and acetone molecules, we have calculated the vibrational averaged positron affinity (PA) values along the local CN or CO vibrational contribution with the configuration interaction level of multi-component molecular orbital method. This method can take the electron-positron correlation contribution into account through single electronic - single positronic excitation configurations. The PA values are enhanced by including the local vibrational contribution from vertical PA values due to the anharmonicity of the potential. For acetonitrile, acetaldehyde, and acetone molecules, the PA values after averaging over the 1st vibrational state are 136, 55, and 96 meV, which can be compared with the corresponding experimental vlues of 180, 90, and 173 meV, respectively.

  11. Cellular/Molecular The Endurance and Selectivity of Spatial Patterns of

    E-print Network

    Segev, Idan

    potentiation/depression (LTP/LTD), and negative-feedback, homeostatic synaptic plasticity (HSP). A detailed may have an important role in selecting which spatial patterns of LTP/LTD are to last. Several spatial pattern of LTP/LTD. Under a local dendritic HSP mechanism, sparse patterns of LTP/LTD, which we

  12. An application of a statistical model for the calculation of the logarithmic mean excitation energy of molecules Molecular hydrogen

    Microsoft Academic Search

    Efstathios Kamaratos

    1985-01-01

    A statistical model, the local plasma approximation, is considered for the calculation of the logarithmic mean excitation energy for stopping power of chemically bound particles by taking into consideration chemical bonding. This statistical model is applied to molecular hydrogen and leads to results that suggest a value for the logarithmic mean excitation energy of molecular hydrogen that is larger than

  13. Application of multiresolution analyses to electron density maps of small molecules: Critical point representations for molecular superposition

    Microsoft Academic Search

    Laurence Leherte

    2001-01-01

    Three different methods are applied to generate low resolution molecular electron density (ED) distribution functions: a crystallography-based formalism, an analytical approach which allows the calculation of a promolecular ED distribution in terms of a weighted summation over atomic ED distributions, and a wavelet-based multiresolution analysis approach. Critical point graph representations of the molecular ED distributions are then generated by locating

  14. Effects of molecular potential and geometry on atomic core-level photoemission over an extended energy range - the case study of CO molecule

    NASA Astrophysics Data System (ADS)

    Kukk, E.; Ayuso, D.; Thomas, T. D.; Decleva, P.; Patanen, M.; Argenti, L.; Plésiat, E.; Palacios, A.; Kooser, K.; Travnikova, O.; Mondal, S.; Kimura, M.; Sakai, K.; Miron, C.; Martín, F.; Ueda, K.

    2014-04-01

    We report an experimental and theoretical study of single-molecule inner-shell photoemission over an extended range of photon energies. The vibrational ratios v=1/v=0 from the C 1s photoelectron spectra, although mostly determined by the bond length change, are shown to be affected also by photoelectron recoil and scattering on the neighboring oxygen atom. Density functional theory is used to encompass all these effect in unified treatment. It is also demonstrated that the DFT calculations can be used as a means to extract dynamic and static molecular geometry values.

  15. Spatiotemporal induction patterns of cytokine and related immune signal molecule mRNAs in response to intrastriatal injection of lipopolysaccharide.

    PubMed

    Stern, E L; Quan, N; Proescholdt, M G; Herkenham, M

    2000-09-22

    The brain's response to a direct immune challenge was examined by in situ hybridization histochemistry. Lipopolysaccharide (bacterial endotoxin) injected acutely into rat striatum induced mRNA expression for inhibitory factor kappaBalpha, interleukin (IL)-1beta, tumor necrosis factor-alpha, IL-6, IL-12 p35, inducible nitric oxide synthase, IL-1 receptor antagonist, and the type 1 IL-1 receptor. Expression patterns were evaluated at select time points ranging from 15 min to 3 days post-injection. Rats injected with vehicle alone were used to control for mechanical effects. Following lipopolysaccharide administration, a wave of mRNA induction within brain parenchyma radiated outward from the injection site, generally peaking in intensity at the 16-h time point. The individual profiles of cytokine mRNA induction patterns reveal that the brain's immune response to local inflammatory stimulation is quite elaborate and in many ways resembles the progression of cytokine induction customary of localized inflammation in peripheral tissues. PMID:10996227

  16. Chemical Bonds, Molecular Shapes, and Molecular Models

    NSDL National Science Digital Library

    Camp, David.

    This site, designed by doctors Anna Cavinato and David Camp, teaches students how to construct models of molecules using model kits. Definitions of molecular shape, electron pair geometry, and nonmetal bonding patterns begin the tutorial. After students build a knowledge base, they can then proceed to the demonstrations and specific examples of the models. A self-assessment quiz allows students to test their newly acquired knowledge of chemical shapes.

  17. Regulated In Situ Generation of Molecular Ions or Protonated Molecules under Atmospheric-Pressure Helium-Plasma-Ionization Mass Spectrometric Conditions.

    PubMed

    Gangam, Rekha; Pavlov, Julius; Attygalle, Athula B

    2015-07-01

    In an enclosed atmospheric-pressure helium-plasma ionization (HePI) source engulfed with dehumidified ambient gases, molecular cations are generated from compounds such as toluene, bromobenzene, and iodobenzene. Evidently, the ionization is effected by a direct Penning mechanism attributable to interactions of the gas-phase analyte with metastable helium atoms. It is widely known that secondary ions generated from ambient gases also play an important role in the overall ionization process. For example, when the ambient gases bear even traces of moisture, the analytes are ionized by proton transfer reactions with gaseous H3O(+). In this study, we demonstrate how a controlled variation of experimental conditions can manipulate the abundance of molecular ions and protonated molecules in a HePI source. Graphical Abstract ?. PMID:25804892

  18. Selective catalysts for the hydrogen oxidation and oxygen reduction reactions by patterning of platinum with calix[4]arene molecules.

    SciTech Connect

    Genorio, B.; Strmcnik, D.; Subbaraman, R.; Tripkovic, D.; Karapetrov, G.; Stamenkovic, V. R.; Pejovnik, S.; Markovic, N. M.; Univ. Ljubljana; National Inst. of Chemistry

    2010-12-01

    The design of new catalysts for polymer electrolyte membrane fuel cells must be guided by two equally important fundamental principles: optimization of their catalytic behaviour as well as the long-term stability of the metal catalysts and supports in hostile electrochemical environments. The methods used to improve catalytic activity are diverse, ranging from the alloying and de-alloying of platinum to the synthesis of platinum core-shell catalysts. However, methods to improve the stability of the carbon supports and catalyst nanoparticles are limited, especially during shutdown (when hydrogen is purged from the anode by air) and startup (when air is purged from the anode by hydrogen) conditions when the cathode potential can be pushed up to 1.5 V. Under the latter conditions, stability of the cathode materials is strongly affected (carbon oxidation reaction) by the undesired oxygen reduction reaction (ORR) on the anode side. This emphasizes the importance of designing selective anode catalysts that can efficiently suppress the ORR while fully preserving the Pt-like activity for the hydrogen oxidation reaction. Here, we demonstrate that chemically modified platinum with a self-assembled monolayer of calix[4]arene molecules meets this challenging requirement.

  19. Selective catalysts for the hydrogen oxidation and oxygen reduction reactions by patterning of platinum with calix[4]arene molecules

    NASA Astrophysics Data System (ADS)

    Genorio, Bostjan; Strmcnik, Dusan; Subbaraman, Ram; Tripkovic, Dusan; Karapetrov, Goran; Stamenkovic, Vojislav R.; Pejovnik, Stane; Markovi?, Nenad M.

    2010-12-01

    The design of new catalysts for polymer electrolyte membrane fuel cells must be guided by two equally important fundamental principles: optimization of their catalytic behaviour as well as the long-term stability of the metal catalysts and supports in hostile electrochemical environments. The methods used to improve catalytic activity are diverse, ranging from the alloying and de-alloying of platinum to the synthesis of platinum core-shell catalysts. However, methods to improve the stability of the carbon supports and catalyst nanoparticles are limited, especially during shutdown (when hydrogen is purged from the anode by air) and startup (when air is purged from the anode by hydrogen) conditions when the cathode potential can be pushed up to 1.5V (ref. 11). Under the latter conditions, stability of the cathode materials is strongly affected (carbon oxidation reaction) by the undesired oxygen reduction reaction (ORR) on the anode side. This emphasizes the importance of designing selective anode catalysts that can efficiently suppress the ORR while fully preserving the Pt-like activity for the hydrogen oxidation reaction. Here, we demonstrate that chemically modified platinum with a self-assembled monolayer of calix[4]arene molecules meets this challenging requirement.

  20. I. Microlithographic process for patterning conjugated emissive polymers. II. Fluorinated distyrylbenzene chromophores: Effect of fluorine regiochemistry on molecular properties and solid state organization

    NASA Astrophysics Data System (ADS)

    Renak, Michelle Lee

    Microlithographic techniques were developed for the spatially controlled light-directed synthesis of poly(p-phenylenevinylene) (PPV). Microscalar linear and circular patterns can be prepared in the 25 mum range. The procedure relies on the photogeneration of triflic acid to catalyze the formation of PPV. This site specific conversion gives complete control over pattern design and can be used to fabricate pixel-like electroluminescent devices. Microlithographic patterning of blends of poly [2-(2'-ethylhexyloxy)-5-methoxy-1,4-phenylenevinylene] (MEH-PPV) and poly(paracyclophene) was successfully used to create multi-colored emissive patterns within a continuous polymer film. Microlithographic techniques were also used to control the shapes and sizes of polymer light emitting diodes by patterning an insulating layer of novolac photoresist onto the electrode surface. A series of fluorinated distyrylbenzene (DSB) derivatives were synthesized and studied to probe the effect of fluorine substitution on molecular properties and on the arrangement of molecules in the solid state. Trans-trans-bis(4-fluorostyryl)benzene (2Ft), 1,4-bis(styryl)-2,5-difluorobenzene ( 2Fc), 1,4-bis(4-fluorostyryl)-2,5-difluorobenzene ( 2Fc2Ft), (2,5-difluorostyryl)benzene ( 4Ft), trans-trans-1,4-bis(pentaflourostyryl)-benzene ( 10Ft) and 1,4-bis(pentafluorostyryl)-2,5-difluorobenzene (2Fc10Ft) were prepared by Heck and Wittig coupling reactions. Absorption spectroscopy shows that DSB, 2F t, 2Fc, 2Fc2Ft, 4Ft, 10F t, and 2Fc10Ft have a lambda max at approximately 350 nm. Cyclic voltammetry shows that as the fluorine load increases, the reduction of the DSB framework becomes more facile. It is also shown that the regiochemistry of substitution makes an impact on the inductive ability of fluorine to facilitate reduction. The lattice properties of 2Fc, 2Fc2Ft, 4Ft, 10F t, and 2Fc10Ft were determined by X-ray diffraction experiments. Two structural motifs emerge from these studies. One is the tendency of the DSB framework to stack cofacially and form vertical "columns" within the crystal. The second motif is the alignment of these "columns" to maximize C-H···F electrostatic registry. Exciplex formation between all of the distyrylbenzene derivatives and dimethylaniline were also observed and studied spectroscopically.

  1. Molecular eigenstate spectroscopy: Application to the intramolecular dynamics of some polyatomic molecules in the 3000 to 7000 cm{sup {minus}1} region

    SciTech Connect

    Perry, D.S. [Univ. of Akron, OH (United States)

    1993-12-01

    Intramolecular vibrational redistribution (IVR) appears to be a universal property of polyatomic molecules in energy regions where the vibrational density of states is greater than about 5 to 30 states per cm{sup {minus}1}. Interest in IVR stems from its central importance to the spectroscopy, photochemistry, and reaction kinetics of these molecules. A bright state, {var_phi}{sub s}, which may be a C-H stretching vibration, carries the oscillator strength from the ground state. This bright state may mix with bath rotational-vibrational levels to form a clump of molecular eigenstates, each of which carries a portion of the oscillator strength from the ground state. In this work the authors explicitly resolve transitions to each of these molecular eigenstates. Detailed information about the nature of IVR is contained in the frequencies and intensities of the observed discrete transitions. The primary goal of this research is to probe the coupling mechanisms by which IVR takes place. The most fundamental distinction to be made is between anharmonic coupling which is independent of molecular rotation and rotationally-mediated coupling. The authors are also interested in the rate at which IVR takes place. Measurements are strictly in the frequency domain but information is obtained about the decay of the zero order state, {var_phi}{sub s}, which could be prepared in a hypothetical experiment as a coherent excitation of the clump of molecular eigenstates. As the coherent superposition dephases, the energy would flow from the initially prepared mode into nearby overtones and combinations of lower frequency vibrational modes. The decay of the initially prepared mode is related to a pure sequence infrared absorption spectrum by a Fourier transform.

  2. ATOMIC AND MOLECULAR PHYSICS: Theoretical Investigation of Femtosecond-Resolved Photoelectron Spectra of the Li2 Molecule

    NASA Astrophysics Data System (ADS)

    Liu, Yu-Fang; Liu, Rui-Qiong; Ding, Jun-Xia

    2009-07-01

    The time-dependent quantum wave packet method is used to investigate the dynamics for the Li2 molecule, and the time-resolved photoelectron spectra (TRPES) of the Li2 molecule are calculated. At the short delay time, the particular phenomenon of TRPES with four peaks is qualitatively interpreted in a dressed state picture by analyzing wave packet motion on light-induced potential (LIP). The significant difference in the electronic structure of between the inner and outer turning points has an impact on the TRPES. The control for the first excited state of the initial wave packet is discussed.

  3. Molecular Dynamics as a pattern recognition tool: an automated process detects peptides that preserve the 3D arrangement of Trypsin's Active Site.

    PubMed

    Tatsis, Vasileios A; Stavrakoudis, Athanassios; Demetropoulos, Ioannis N

    2008-03-01

    Recently, the synthesis of a molecule has been reported that belongs to a Lysine based, branched cyclic peptide class. This work explores the ability of such molecules to preserve the 3D geometry of the Trypsin's Active Site (TAS) by applying an integrated framework of automated computer procedures. The following four factors a) D/L chirality, b) different amino acids at different positions of the molecular scaffold's cyclic part, c) the application of AMBER and CHARMM force fields and d) different implicit solvation models were evaluated against TAS similarity. It was found that a number of molecules exhibit satisfactory geometric affinity to the TAS during extended Molecular Dynamics runs. We estimated that more than 2000 molecules (belonging to this class) could retain good similarity to the TAS arrangement. PMID:18177993

  4. Building Molecules

    NSDL National Science Digital Library

    Rensselaer Polytechnic Institute

    2005-01-01

    This online interactive has three activities in the NanoLab (press the upper right button): Build, Zoom, and Transform. In Build, learners build increasingly complex molecules out of carbon, oxygen, and hydrogen, and is useful for connecting subscripts and the number of atoms, and for introducing 3D molecular structures which are automatically built. Zoom is a "powers of 10" zoom-in ranging from 10,000 kilometers to 1 nanometer. Transform is a simulation of water changing phase from solid to liquid to gas. Through exploration of the site learners form a better understanding of the composition of matter.

  5. Binding of atoms and stability of molecules in Hartree and Thomas-Fermi type theories. Part I: A necessary and sufficient condition for the stability of general molecular systems

    SciTech Connect

    Catto, I.; Lions, P.L. (Universite Paris-Dauphine (France))

    1992-01-01

    The authors study here the binding of atoms and molecules and the stability of general molecular systems including molecular ions. This is the first paper of a series devoted to the study of these general problems. The authors obtain here a general necessary and sufficient condition for the stability of a general molecular system in the context of Thomas-Fermi-Von Weizsaecker, Thomas-Fermi-Dirac-Von Weizsaecker, Hartree or Hartree-Fock theories. 20 refs.

  6. Quantitative molecular graphics what is it? -use of molecular graphics at quantitative level employing high-quality pictures of molecules in various views (orthographic

    E-print Network

    Ferreira, Márcia M. C.

    employing high-quality pictures of molecules in various views (orthographic projections primarily instead of using expensive, sophisticated software; use of pictures that cannot be easily reproduced and frontier orbital isosurfaces were measured/calculated from high quality pictures by an empirical method

  7. Bcl::Cluster: A method for clustering biological molecules coupled with visualization in the Pymol Molecular Graphics System

    Microsoft Academic Search

    Nathan Alexander; Nils Woetzel; Jens Meiler

    2011-01-01

    Clustering algorithms are used as data analysis tools in a wide variety of applications in Biology. Clustering has become especially important in protein structure prediction and virtual high throughput screening methods. In protein structure prediction, clustering is used to structure the conformational space of thousands of protein models. In virtual high throughput screening, databases with millions of drug-like molecules are

  8. An application of a statistical model for the calculation of the logarithmic mean excitation energy of molecules Molecular hydrogen

    NASA Technical Reports Server (NTRS)

    Kamaratos, E.

    1985-01-01

    A statistical model, the local plasma approximation, is considered for the calculation of the logarithmic mean excitation energy for stopping power of chemically bound particles by taking into consideration chemical bonding. This statistical model is applied to molecular hydrogen and leads to results that suggest a value for the logarithmic mean excitation energy of molecular hydrogen that is larger than the accepted experimental and theoretical values.

  9. The Pattern of Secreted Molecules During the Co-Inoculation of Alfalfa Plants With Sinorhizobium meliloti and Delftia sp. strain JD2: An Interaction That Improves Plant Yield.

    PubMed

    Morel, M A; Cagide, C; Minteguiaga, M A; Dardanelli, M S; Castro-Sowinski, S

    2015-02-01

    Delftia sp. strain JD2 is a plant-growth-promoting bacterium that enhances legume nodulation and growth, acting as nodule-assisting bacterium during the co-inoculation of plants with rhizobial strains. In this work, we evaluate how the co-inoculation of alfalfa with Sinorhizobium meliloti U143 and JD2 increases plant yield under greenhouse conditions and we analyze the pattern of secreted bioactive compounds which may be involved in the microbe-plant communication. The chemical composition of extracellular cultures (EC) produced in hydroponic conditions (collected 4, 7, and 14 days after bacterial treatment) were characterized using different chromatographic and elucidation techniques. In addition, we assessed the effect that plant irrigation with cell-free EC, produced during co-inoculation experiments, would have on plant yield. Results showed increased alfalfa shoot and root matter, suggesting that U143-JD2 co-inoculation might be a beneficial agricultural practice. The pattern of secreted secondary metabolites among treatments showed important differences. Qualitative and quantitative changes in phenolic compounds (including flavonoids), organic acids, and volatile compounds were detected during the early microbe-plant interaction, suggesting that the production of some molecules positively affects the microbe-plant association. Finally, the irrigation of co-inoculated plants with cell-free EC under greenhouse conditions increased plant yield over agronomic expectations. This effect might be attributed to the bioactive secondary metabolites incorporated during the irrigation. PMID:25353366

  10. Decreased capacity of recombinant 45/47-kDa molecules (Apa) of Mycobacterium tuberculosis to stimulate T lymphocyte responses related to changes in their mannosylation pattern.

    PubMed

    Horn, C; Namane, A; Pescher, P; Rivière, M; Romain, F; Puzo, G; Bârzu, O; Marchal, G

    1999-11-01

    The Apa molecules secreted by Mycobacterium tuberculosis, Mycobacterium bovis, or BCG have been identified as major immunodominant antigens. Mass spectrometry analysis indicated similar mannosylation, a complete pattern from 1 up to 9 hexose residues/mole of protein, of the native species from the 3 reference strains. The recombinant antigen expressed in M. smegmatis revealed a different mannosylation pattern: species containing 7 to 9 sugar residues/mole of protein were in the highest proportion, whereas species bearing a low number of sugar residues were almost absent. The 45/47-kDa recombinant antigen expressed in E. coli was devoid of sugar residues. The proteins purified from M. tuberculosis, M. bovis, or BCG have a high capacity to elicit in vivo potent delayed-type hypersensitivity (DTH) reactions and to stimulate in vitro sensitized T lymphocytes of guinea pigs immunized with living BCG. The recombinant Apa expressed in Mycobacterium smegmatis was 4-fold less potent in vivo in the DTH assay and 10-fold less active in vitro to stimulate sensitized T lymphocytes than the native proteins. The recombinant protein expressed in Escherichia coli was nearly unable to elicit DTH reactions in vivo or to stimulate T lymphocytes in vitro. Thus the observed biological effects were related to the extent of glycosylation of the antigen. PMID:10542234

  11. Bifunctional role of a pattern recognition molecule ?-1,3 glucan binding protein purified from mangrove crab Episesarma tetragonum.

    PubMed

    Sivakamavalli, Jeyachandran; Vaseeharan, Baskaralingam

    2014-06-01

    ?-1,3-Glucan binding protein (?-GBP) was purified from the haemolymph of Episesarma tetragonum by affinity chromatography with epoxy-activated laminarin-sepharose CL-6B column. E. tetragonum ?-GBP exhibits a single band with a molecular weight of 100 kDa on SDS-PAGE and a pI of 5.9 in isoelectric focusing (IEF). The circular dichroism (CD) spectra result of E. tetragonum ?-GBP indicates that the negative ellipticity bands near 220 nm and 208 nm correspond to the ?-sheets in the secondary structure. Functional analysis results demonstrate that the purified E. tetragonum ?-GBP agglutinates fungal cells (Candida albicans) containing ?-glucan. This recognition and binding specificity leads to the activation of the prophenoloxidase (ProPO) cascade and enhance the phenoloxidase (PO) activity in a dose-dependent manner. Our finding discloses new insights in the ProPO activation and fungal agglutination of purified E. tetragonum ?-GBP. It seems to play a significant role in microbial uncovering mechanism in invertebrates. PMID:24681307

  12. Evolving patterns in boron cluster chemistry

    Microsoft Academic Search

    Mark A. Fox; Ken Wade

    2003-01-01

    This paper outlines the development of our knowledge and understanding of the structures and bonding of boron cluster compounds, with particular reference to the evolving complementary roles localized bonding and molecular orbital treatments have played in providing simple rationalizations of their polyhedral molecules. INTRODUCTION: EARLY DEVEL OPMENTS The polyhedral patterns that characterize boron cluster chemistry have provided rich pickings for

  13. Polyatomic molecules under intense femtosecond laser irradiation.

    PubMed

    Konar, Arkaprabha; Shu, Yinan; Lozovoy, Vadim V; Jackson, James E; Levine, Benjamin G; Dantus, Marcos

    2014-12-11

    Interaction of intense laser pulses with atoms and molecules is at the forefront of atomic, molecular, and optical physics. It is the gateway to powerful new tools that include above threshold ionization, high harmonic generation, electron diffraction, molecular tomography, and attosecond pulse generation. Intense laser pulses are ideal for probing and manipulating chemical bonding. Though the behavior of atoms in strong fields has been well studied, molecules under intense fields are not as well understood and current models have failed in certain important aspects. Molecules, as opposed to atoms, present confounding possibilities of nuclear and electronic motion upon excitation. The dynamics and fragmentation patterns in response to the laser field are structure sensitive; therefore, a molecule cannot simply be treated as a "bag of atoms" during field induced ionization. In this article we present a set of experiments and theoretical calculations exploring the behavior of a large collection of aryl alkyl ketones when irradiated with intense femtosecond pulses. Specifically, we consider to what extent molecules retain their molecular identity and properties under strong laser fields. Using time-of-flight mass spectrometry in conjunction with pump-probe techniques we study the dynamical behavior of these molecules, monitoring ion yield modulation caused by intramolecular motions post ionization. The set of molecules studied is further divided into smaller sets, sorted by type and position of functional groups. The pump-probe time-delay scans show that among positional isomers the variations in relative energies, which amount to only a few hundred millielectronvolts, influence the dynamical behavior of the molecules despite their having experienced such high fields (V/Å). High level ab initio quantum chemical calculations were performed to predict molecular dynamics along with single and multiphoton resonances in the neutral and ionic states. We propose the following model of strong-field ionization and subsequent fragmentation for polyatomic molecules: Single electron ionization occurs on a suboptical cycle time scale, and the electron carries away essentially all of the energy, leaving behind little internal energy in the cation. Subsequent fragmentation of the cation takes place as a result of further photon absorption modulated by one- and two-photon resonances, which provide sufficient energy to overcome the dissociation energy. The proposed hypothesis implies the loss of a photoelectron at a rate that is faster than intramolecular vibrational relaxation and is consistent with the observation of nonergodic photofragmentation of polyatomic molecules as well as experimental results from many other research groups on different molecules and with different pulse durations and wavelengths. PMID:25314590

  14. Investigating the Interaction Pattern and Structural Elements of a Drug-Polymer Complex at the Molecular Level.

    PubMed

    Nie, Haichen; Mo, Huaping; Zhang, Mingtao; Song, Yang; Fang, Ke; Taylor, Lynne S; Li, Tonglei; Byrn, Stephen R

    2015-07-01

    Strong associations between drug and polymeric carriers are expected to contribute to higher drug loading capacities and better physical stability of amorphous solid dispersions. However, molecular details of the interaction patterns and underlying mechanisms are still unclear. In the present study, a series of amorphous solid dispersions of clofazimine (CLF), an antileprosy drug, were prepared with different polymers by applying the solvent evaporation method. When using hypromellose phthalate (HPMCP) as the carrier, the amorphous solid dispersion system exhibits not only superior drug loading capacity (63% w/w) but also color change due to strong drug-polymer association. In order to further explain these experimental observations, the interaction between CLF and HPMCP was investigated in a nonpolar volatile solvent system (chloroform) prior to forming the solid dispersion. We observed significant UV/vis and (1)H NMR spectral changes suggesting the protonation of CLF and formation of ion pairs between CLF and HPMCP in chloroform. Furthermore, nuclear Overhauser effect spectroscopy (NOESY) and diffusion order spectroscopy (DOSY) were employed to evaluate the strength of associations between drug and polymers, as well as the molecular mobility of CLF. Finally, by correlating the experimental values with quantum chemistry calculations, we demonstrate that the protonated CLF is binding to the carboxylate group of HPMCP as an ion pair and propose a possible structural model of the drug-polymer complex. Understanding the drug and carrier interaction patterns from a molecular perspective is critical for the rational design of new amorphous solid dispersions. PMID:25988812

  15. The self-assembly of 5,6,7-trithiapentacene-13-one molecules on gold: from low-coverage molecular chains to monolayer coverage

    NASA Astrophysics Data System (ADS)

    Larson, Amanda; Tang, Jian-Ming; Pohl, Karsten

    2015-03-01

    Understanding electronic devices down to the atomic scale is essential for the development of novel organic molecule based nanotechnologies. 5,6,7-trithiapentacene-13-one (TTPO) is a promising organic semiconductor with potential applications in high temperature photovoltaic devices. Scanning tunneling microscopy (STM) of TTPO on the close-packed stepped Au (788) surface reveals interesting nanoscale surface structures ranging from molecular chains at low coverage to an ordered self-assembled monolayer. Density functional theory (DFT) calculations have been used to further probe this unique 3-D angular assembly, where the long-axis of TTPO is parallel to the gold surface, distinctive from previously observed pentacene and pentacene derivative assemblies on surfaces. It is the lateral arrangement of the underlying pentacene backbone of the molecule that is unique, causing the thiol substituent side of the molecule to be angled down towards the gold surface, with the oxygen angled away. Combining imaging with density functional theory calculations allows for classification of these self-assembled structures with particular interest being directed toward the interaction between TTPO and gold at this organic-metallic interface. Understanding of the structure of such interfaces can potentially guide nanoscale modifications for improved electrical transport and energy-conversion efficiency in future devices.

  16. Potent new small-molecule inhibitor of botulinum neurotoxin serotype A endopeptidase developed by synthesis-based computer-aided molecular design.

    PubMed

    Pang, Yuan-Ping; Vummenthala, Anuradha; Mishra, Rajesh K; Park, Jewn Giew; Wang, Shaohua; Davis, Jon; Millard, Charles B; Schmidt, James J

    2009-01-01

    Botulinum neurotoxin serotype A (BoNTA) causes a life-threatening neuroparalytic disease known as botulism. Current treatment for post exposure of BoNTA uses antibodies that are effective in neutralizing the extracellular toxin to prevent further intoxication but generally cannot rescue already intoxicated neurons. Effective small-molecule inhibitors of BoNTA endopeptidase (BoNTAe) are desirable because such inhibitors potentially can neutralize the intracellular BoNTA and offer complementary treatment for botulism. Previously we reported a serotype-selective, small-molecule BoNTAe inhibitor with a K(i) (app) value of 3.8+/-0.8 microM. This inhibitor was developed by lead identification using virtual screening followed by computer-aided optimization of a lead with an IC(50) value of 100 microM. However, it was difficult to further improve the lead from micromolar to even high nanomolar potency due to the unusually large enzyme-substrate interface of BoNTAe. The enzyme-substrate interface area of 4,840 A(2) for BoNTAe is about four times larger than the typical protein-protein interface area of 750-1,500 A(2). Inhibitors must carry several functional groups to block the unusually large interface of BoNTAe, and syntheses of such inhibitors are therefore time-consuming and expensive. Herein we report the development of a serotype-selective, small-molecule, and competitive inhibitor of BoNTAe with a K(i) value of 760+/-170 nM using synthesis-based computer-aided molecular design (SBCAMD). This new approach accounts the practicality and efficiency of inhibitor synthesis in addition to binding affinity and selectivity. We also report a three-dimensional model of BoNTAe in complex with the new inhibitor and the dynamics of the complex predicted by multiple molecular dynamics simulations, and discuss further structural optimization to achieve better in vivo efficacy in neutralizing BoNTA than those of our early micromolar leads. This work provides new insight into structural modification of known small-molecule BoNTAe inhibitors. It also demonstrates that SBCAMD is capable of improving potency of an inhibitor lead by nearly one order of magnitude, even for BoNTAe as one of the most challenging protein targets. The results are insightful for developing effective small-molecule inhibitors of protein targets with large active sites. PMID:19901994

  17. Potent New Small-Molecule Inhibitor of Botulinum Neurotoxin Serotype A Endopeptidase Developed by Synthesis-Based Computer-Aided Molecular Design

    PubMed Central

    Pang, Yuan-Ping; Vummenthala, Anuradha; Mishra, Rajesh K.; Park, Jewn Giew; Wang, Shaohua; Davis, Jon; Millard, Charles B.; Schmidt, James J.

    2009-01-01

    Botulinum neurotoxin serotype A (BoNTA) causes a life-threatening neuroparalytic disease known as botulism. Current treatment for post exposure of BoNTA uses antibodies that are effective in neutralizing the extracellular toxin to prevent further intoxication but generally cannot rescue already intoxicated neurons. Effective small-molecule inhibitors of BoNTA endopeptidase (BoNTAe) are desirable because such inhibitors potentially can neutralize the intracellular BoNTA and offer complementary treatment for botulism. Previously we reported a serotype-selective, small-molecule BoNTAe inhibitor with a Kiapp value of 3.8±0.8 µM. This inhibitor was developed by lead identification using virtual screening followed by computer-aided optimization of a lead with an IC50 value of 100 µM. However, it was difficult to further improve the lead from micromolar to even high nanomolar potency due to the unusually large enzyme-substrate interface of BoNTAe. The enzyme-substrate interface area of 4,840 Å2 for BoNTAe is about four times larger than the typical protein-protein interface area of 750–1,500 Å2. Inhibitors must carry several functional groups to block the unusually large interface of BoNTAe, and syntheses of such inhibitors are therefore time-consuming and expensive. Herein we report the development of a serotype-selective, small-molecule, and competitive inhibitor of BoNTAe with a Ki value of 760±170 nM using synthesis-based computer-aided molecular design (SBCAMD). This new approach accounts the practicality and efficiency of inhibitor synthesis in addition to binding affinity and selectivity. We also report a three-dimensional model of BoNTAe in complex with the new inhibitor and the dynamics of the complex predicted by multiple molecular dynamics simulations, and discuss further structural optimization to achieve better in vivo efficacy in neutralizing BoNTA than those of our early micromolar leads. This work provides new insight into structural modification of known small-molecule BoNTAe inhibitors. It also demonstrates that SBCAMD is capable of improving potency of an inhibitor lead by nearly one order of magnitude, even for BoNTAe as one of the most challenging protein targets. The results are insightful for developing effective small-molecule inhibitors of protein targets with large active sites. PMID:19901994

  18. Guided three-dimensional molecular self-assembly on silicon substrates

    NASA Astrophysics Data System (ADS)

    Chang, Chia-Ching; Sun, Kien Wen; Kan, Lou-Sing; Kuan, Chieh-Hsiung

    2006-06-01

    We demonstrate three-dimensional (3D) self-assemble growth of the metallothionein (Mn,Cd-MT-2) molecules on patterned semiconductor substrates. The MT molecules deposited on the patterned substrates were found to grow into 3D rod or ring-type nanostructures, depending on the shape of patterned nanostructures on the substrates. Dense arrays of 3D molecular nanorods or rings with an area density close to 1010cm-2 were demonstrated with a pore size of 20nm and a pitch size of 100nm. Those engineered molecular nanostructures provide an excellent opportunity for biological applications, sensing sources of nanodevices, biochemical reactions on surfaces, and even single molecule studies.

  19. Hydrogenation of carbon-cluster cations with molecular hydrogen: implications for the growth of carbon-cluster molecules

    NASA Astrophysics Data System (ADS)

    Bohme, Diethard K.; Wlodek, Stanislaw

    1990-12-01

    Experimental results are reviewed for the hydrogenation and deuteration of carbon-cluster cations in the gas phase. Emphasis is given to reactivity measurements performed with Fourier trasform ion-cyclotron resonance (FTICR) spectrometry for large cluster ions derived from graphite and diamond by laser vaporization, and reactivity measurements performed with selected-ion flow tube (SIFT) mass spectrometry for small cluster ions derived from benzene by electron impact. New SIFT measurements are presented for reactivities of small cluster ions primarily produced from acyclic hydrocarbon molecules by electron impact. Attention is given to the insight provided by these reactivity measurements into the influence of the morphology of carbon-cluster cations on the efficiency of their hydrogenation and deuteration and on the growth of carbon-cluster molecules as it is perceived to occur in interstellar chemistry.

  20. ATOMIC AND MOLECULAR PHYSICS: Accurate One-Centre Method for Hydrogen Molecule Ions in Strong Magnetic Field

    Microsoft Academic Search

    Yue-Xia Zhang; Shuai Kang; Ting-Yun Shi

    2008-01-01

    An accurate one-centre method for the hydrogen molecule ion is tested. The slow convergence and singularities at the nuclear positions that are problems in the general one-centre method are solved well by employing the optimal radial and angular B-spline basis. Therefore, the accuracy of the one-centre method is improved observably. For the ground state of the H2+ in the free

  1. The spin-unrestricted molecular Kohn-Sham solution and the analogue of Koopmans's theorem for open-shell molecules

    Microsoft Academic Search

    O. V. Gritsenko; E. J. Baerends

    2004-01-01

    Spin-unrestricted Kohn-Sham (KS) solutions are constructed from accurate ab initio spin densities for the prototype doublet molecules NO2, ClO2, and NF2 with the iterative local updating procedure of van Leeuwen and Baerends (LB). A qualitative justification of the LB procedure is given with a ``strong'' form of the Hohenberg-Kohn theorem. The calculated energies ?isigma of the occupied KS spin orbitals

  2. Molecular mechanisms of regeneration initiation and dorsal-ventral patterning in planarians

    E-print Network

    Gaviño, Michael A. (Michael Alexander)

    2013-01-01

    Regeneration is widespread among animals, yet very little is known about the molecular mechanisms that govern regenerative processes. Planarians have emerged in recent years as a powerful model for studying regeneration ...

  3. FINDING FLEXIBLE PATTERNS IN A TEXT -AN APPLICATION TO 3D MOLECULAR MATCHING

    E-print Network

    Soldano, Henry

    areas, for instance in the analysis of biological molecules such as nucleic acids or proteins. In the latter case, the text may be sequences of amino acids or a linear coding of 3D structures definition of the concept of multiple comparison. Another important motivation for this work is therefore

  4. Energetics and Dynamics of a Cyclic Oligosaccharide Molecule in a Confined Protein Pore Environment. A Molecular Dynamics Study

    E-print Network

    Kurnikova, Maria

    between a transmembrane pore protein R-hemolysin and a cyclic oligosaccharide -cyclodextrin results protein-carbohydrate complex, whose structural, dynamical and energetic properties can be helpful interactions in such complexes is, therefore, of wide interest. We have performed a set of molecular dynamics

  5. Understanding the Molecular Mechanism of Interventions in Treating Rheumatoid Arthritis Patients with Corresponding Traditional Chinese Medicine Patterns Based on Bioinformatics Approach

    PubMed Central

    Jiang, Miao; Lu, Cheng; Chen, Gao; Xiao, Cheng; Zha, Qinglin; Niu, Xuyan; Chen, Shilin; Lu, Aiping

    2012-01-01

    Better effectiveness would be achieved when interventions are used in treating patients with a specific traditional Chinese medicine (TCM) pattern. In this paper, the effectiveness in treating rheumatoid arthritis (RA) patients in a randomized clinical trial as reanalyzed after the patients were classified into different TCM patterns and the underlying mechanism of how the TCM pattern influences the clinical effectiveness of interventions (TCM and biomedicine therapy) was explored. The pharmacological networks of interventions were builtup with protein and protein interaction analyses based on all the related targeted proteins obtained from PubChem. The underlying mechanism was explored by merging the pharmacological networks with the molecular networks of TCM cold and hot patterns in RA. The results show that the TCM therapy is better in treating the RA patients with TCM hot pattern, and the biomedical therapy is better in the RA patients with cold pattern. The pharmacological network of TCM intervention is merged well with the molecular network of TCM hot pattern, and the pharmacological network of biomedical therapy is merged well with the network of cold pattern. The finding indicates that molecular network analysis could give insight into the full understanding of the underlying mechanism of how TCM pattern impacts the efficacy. PMID:23118783

  6. Computational mass spectrometry for small molecules

    PubMed Central

    2013-01-01

    The identification of small molecules from mass spectrometry (MS) data remains a major challenge in the interpretation of MS data. This review covers the computational aspects of identifying small molecules, from the identification of a compound searching a reference spectral library, to the structural elucidation of unknowns. In detail, we describe the basic principles and pitfalls of searching mass spectral reference libraries. Determining the molecular formula of the compound can serve as a basis for subsequent structural elucidation; consequently, we cover different methods for molecular formula identification, focussing on isotope pattern analysis. We then discuss automated methods to deal with mass spectra of compounds that are not present in spectral libraries, and provide an insight into de novo analysis of fragmentation spectra using fragmentation trees. In addition, this review shortly covers the reconstruction of metabolic networks using MS data. Finally, we list available software for different steps of the analysis pipeline. PMID:23453222

  7. Computational mass spectrometry for small molecules.

    PubMed

    Scheubert, Kerstin; Hufsky, Franziska; Böcker, Sebastian

    2013-01-01

    : The identification of small molecules from mass spectrometry (MS) data remains a major challenge in the interpretation of MS data. This review covers the computational aspects of identifying small molecules, from the identification of a compound searching a reference spectral library, to the structural elucidation of unknowns. In detail, we describe the basic principles and pitfalls of searching mass spectral reference libraries. Determining the molecular formula of the compound can serve as a basis for subsequent structural elucidation; consequently, we cover different methods for molecular formula identification, focussing on isotope pattern analysis. We then discuss automated methods to deal with mass spectra of compounds that are not present in spectral libraries, and provide an insight into de novo analysis of fragmentation spectra using fragmentation trees. In addition, this review shortly covers the reconstruction of metabolic networks using MS data. Finally, we list available software for different steps of the analysis pipeline. PMID:23453222

  8. Molecular Universe

    NSDL National Science Digital Library

    Catlow, C. R. A. (Charles Richard Arthur), 1947-

    This fantastic resource for college-level students of chemistry provides abundant images and explanatory text on molecules and molecular systems. The site's main provider is Richard Catlow, Director of the Davy Faraday Research Laboratory at the Royal Institution of Great Britain. Molecular Universe presents a collection of lessons, arranged into categories such as Building in Three Dimensions, Boundaries and Barriers, and The Molecules of Life. The sleek color illustrations demonstrate everything from diamond structure to a DNA molecule. Highlights of the site include a detailed look at protein folding, how molecules taste, and molecules and computers. Both students and professors should journey to the Molecular Universe.

  9. Pattern Transformation with DNA Circuits

    PubMed Central

    Chirieleison, Steven M.; Allen, Peter B.; Simpson, Zack B.; Ellington, Andrew D.; Chen, Xi

    2014-01-01

    Readily programmable chemical networks are important tools as the scope of chemistry expands from individual molecules to larger molecular systems. While many complex systems have been constructed using conventional organic and inorganic chemistry, the programmability of biological molecules such as nucleic acids allows for precise, high-throughput, and automated design, as well as simple, rapid, and robust implementation. Here we show that systematic and quantitative control over the diffusivity and reactivity of DNA molecules yields highly programmable chemical reaction networks (CRNs) that execute at the macroscale. In particular, we design and implement non-enzymatic DNA circuits capable of performing pattern transformation algorithms such as edge detection. We also show that it is possible to fine-tune and multiplex such circuits. We believe these strategies will provide programmable platforms for prototyping CRNs, for discovering bottom-up construction principles, and for generating patterns in materials. PMID:24256862

  10. Different polysialic acid-neural cell adhesion molecule expression patterns in distinct types of mossy fiber boutons in the adult hippocampus.

    PubMed

    Seki, T; Arai, Y

    1999-07-19

    Dentate granule cells continue to be generated in the adult hippocampus, and the newly generated granule cells express the highly polysialylated neural cell adhesion molecule (PSA-NCAM), which has been shown to be important in neural development and plasticity. In the present study, the PSA-NCAM expression pattern in morphologically distinct types of mossy fiber boutons in adult rats was examined by immunoelectron and confocal laser scanning microscopy. Although many unmyelinated axons within the mossy fiber bundles expressed PSA-NCAM, most of the mature type of mossy fiber boutons were negative for polysialic acid (PSA) but positive for NCAM peptides, suggesting that NCAM is less polysialylated in the mature mossy fiber boutons. On the other hand, PSA was expressed by small round varicosities, irregularly shaped boutons, and the presumptive immature type of mossy fiber boutons. The PSA-positive small boutons were found to make synaptic contacts with CA3 pyramidal cells and nonpyramidal cells. The PSA-expressing presumptive immature boutons contained fewer clear synaptic vesicles and mitochondria, and, in some instances, they were invaginated by the PSA-positive, finger-like dendritic outgrowths arising from the dendritic shafts of the pyramidal cells, which are known to develop into a mossy fiber bouton-thorny excrescence complex. These findings indicate that distinct types of the mossy fiber boutons possess different PSA expression patterns in the adult hippocampus, and they also imply that PSA expression allows the mossy fibers to have the ability to regulate the bouton formation and remodeling that accompany synapse formation at the contact sites with pyramidal cells and nonpyramidal cells. PMID:10397399

  11. Histidine-rich glycoprotein is a novel plasma pattern recognition molecule that recruits IgG to facilitate necrotic cell clearance via FcgammaRI on phagocytes.

    PubMed

    Poon, Ivan K H; Hulett, Mark D; Parish, Christopher R

    2010-03-25

    Under normal physiologic conditions, necrotic cells resulting from tissue injury are rapidly removed from the circulation and tissues by phagocytes, thus preventing the exposure of intracellular antigenic and immunostimulatory molecules that can aid the development of autoimmune disease. Histidine-rich glycoprotein (HRG), a relatively abundant plasma glycoprotein, has a multidomain structure that can interact with many ligands including components of the fibrinolytic and immune systems. Recently, it has been reported that HRG can bind strongly to cytoplasmic ligand(s) exposed in necrotic cells to enhance clearance by phagocytes. Here we describe the molecular mechanisms underpinning this process. A complex consisting of both HRG and immunoglobulin G (IgG) was found as necessary to aid necrotic cell uptake by monocytes, predominantly via an FcgammaRI-dependent mechanism. The findings in this study also show that HRG can potentially interact with anionic phospholipids exposed in necrotic cells. Furthermore, the enhanced phagocytosis of necrotic cells induced by HRG-IgG complexes triggers phagocytes to release proinflammatory cytokines such as interleukin-8 and tumor necrosis factor. Thus, HRG has the unique property of complexing with IgG and facilitating a proinflammatory innate immune response to promote the clearance of necrotic cells. PMID:20071662

  12. Covalent Immobilization of Microtubules on Glass Surfaces for Molecular Motor Force Measurements and Other Single-Molecule Assays

    PubMed Central

    Nicholas, Matthew P.; Rao, Lu; Gennerich, Arne

    2014-01-01

    Rigid attachment of microtubules (MTs) to glass cover slip surfaces is a prerequisite for a variety of microscopy experiments in which MTs are used as substrates for MT-associated proteins, such as the molecular motors kinesin and cytoplasmic dynein. We present an MT-surface coupling protocol in which aminosilanized glass is formylated using the cross-linker glutaraldehyde, fluorescence-labeled MTs are covalently attached, and the surface is passivated with highly pure beta-casein. The technique presented here yields rigid MT immobilization while simultaneously blocking the remaining glass surface against nonspecific binding by polystyrene optical trapping microspheres. This surface chemistry is straightforward and relatively cheap and uses a minimum of specialized equipment or hazardous reagents. These methods provide a foundation for a variety of optical tweezers experiments with MT-associated molecular motors and may also be useful in other assays requiring surface-immobilized proteins. PMID:24633798

  13. Pores in Bilayer Membranes of Amphiphilic Molecules: Coarse-Grained Molecular Dynamics Simulations Compared with Simple Mesoscopic Models

    E-print Network

    Claire Loison; Michel Mareschal; Friederike Schmid

    2005-01-05

    We investigate pores in fluid membranes by molecular dynamics simulations of an amphiphile-solvent mixture, using a molecular coarse-grained model. The amphiphilic membranes self-assemble into a lamellar stack of amphiphilic bilayers separated by solvent layers. We focus on the particular case of tension less membranes, in which pores spontaneously appear because of thermal fluctuations. Their spatial distribution is similar to that of a random set of repulsive hard discs. The size and shape distribution of individual pores can be described satisfactorily by a simple mesoscopic model, which accounts only for a pore independent core energy and a line tension penalty at the pore edges. In particular, the pores are not circular: their shapes are fractal and have the same characteristics as those of two dimensional ring polymers. Finally, we study the size-fluctuation dynamics of the pores, and compare the time evolution of their contour length to a random walk in a linear potential.

  14. Isolation and Molecular Characterization of Biofouling Bacteria and Profiling of Quorum Sensing Signal Molecules from Membrane Bioreactor Activated Sludge

    PubMed Central

    Lade, Harshad; Paul, Diby; Kweon, Ji Hyang

    2014-01-01

    The formation of biofilm in a membrane bioreactor depends on the production of various signaling molecules like N-acyl homoserine lactones (AHLs). In the present study, a total of 200 bacterial strains were isolated from membrane bioreactor activated sludge and screened for AHLs production using two biosensor systems, Chromobacterium violaceum CV026 and Agrobacterium tumefaciens A136. A correlation between AHLs production and biofilm formation has been made among screened AHLs producing strains. The 16S rRNA gene sequence analysis revealed the dominance of Aeromonas and Enterobacter sp. in AHLs production; however few a species of Serratia, Leclercia, Pseudomonas, Klebsiella, Raoultella and Citrobacter were also identified. The chromatographic characterization of sludge extract showed the presence of a broad range of quorum sensing signal molecules. Further identification of sludge AHLs by thin layer chromatography bioassay and high performance liquid chromatography confirms the presence of C4-HSL, C6-HSL, C8-HSL, 3-oxo-C8-HSL, C10-HSL, C12-HSL, 3-oxo-C12-HSL and C14-HSL. The occurrence of AHLs in sludge extract and dominance of Aeromonas and Enterobacter sp. in activated sludge suggests the key role of these bacterial strains in AHLs production and thereby membrane fouling. PMID:24499972

  15. Investigation of molecular interactions between (10, 10) single-walled nanotube and Epon 862 resin\\/DETDA curing agent molecules

    Microsoft Academic Search

    Zhiyong Liang; Chuck Zhang; Ben Wang; Leslie Kramer

    2004-01-01

    Single-walled nanotubes (SWNTs) are considered a promising reinforcement material for the next generation of high-performance structural and multifunctional composites. Unlike conventional fibrous reinforcement materials, SWNTs have a unique electronic structure, nanoscale diameter, high curvature and extra-large surface area, which lead to different wetting behaviors in the processing of SWNT–epoxy nanocomposites. In this research, molecular dynamics (MD) simulations were used to

  16. Probing molecular orientation in corrosion inhibition via a NEXAFS study of benzotriazole and related molecules on Cu(100)

    Microsoft Academic Search

    J. F. Walsh; H. S. Dhariwal; A. Gutiérrez-Sosa; P. Finetti; C. A. Muryn; N. B. Brookes; R. J. Oldman; G. Thornton

    1998-01-01

    The orientation of benzotriazole on Cu(100) has been studied using near-edge X-ray absorption fine structure (NEXAFS) at the C and N K-edges. At submonolayer coverage, benzotriazole (C6H5N3) is found to adsorb with the molecular plane close to perpendicular to the Cu(100) surface, as indicated by the polarization dependence of the ?? features. The orientation of benzimidazole (C7H6N2) and 1-methyl benzotriazole

  17. Directed assembly of high molecular weight block copolymers: highly ordered line patterns of perpendicularly oriented lamellae with large periods.

    PubMed

    Kim, Eunhye; Ahn, Hyungju; Park, Sungmin; Lee, Hoyeon; Lee, Moongyu; Lee, Sumi; Kim, Taewoo; Kwak, Eun-Ae; Lee, Jun Han; Lei, Xie; Huh, June; Bang, Joona; Lee, Byeongdu; Ryu, Du Yeol

    2013-03-26

    The directed assembly of block copolymer nanostructures with large periods exceeding 100 nm remains challenging because the translational ordering of long-chained block copolymer is hindered by its very low chain mobility. Using a solvent-vapor annealing process with a neutral solvent, which was sequentially combined with a thermal annealing process, we demonstrate the rapid evolution of a perpendicularly oriented lamellar morphology in high molecular weight block copolymer films on neutral substrate. The synergy with the topographically patterned substrate facilitated unidirectionally structural development of ultrahigh molecular weight block copolymer thin films-even for the structures with a large period of 200 nm-leading to perfectly guided, parallel, and highly ordered line-arrays of perpendicularly oriented lamellae in the trenched confinement. This breakthrough strategy, which is applicable to nanolithographic pattern transfer to target substrates, can be a simple and efficient route to satisfy the demand for block copolymer assemblies with larger feature sizes on hundreds of nanometers scale. PMID:23441640

  18. The Impact of Staphylococcus aureus-Associated Molecular Patterns on Staphylococcal Superantigen-Induced Toxic Shock Syndrome and Pneumonia

    PubMed Central

    David, Chella S.

    2014-01-01

    Staphylococcus aureus is capable of causing a spectrum of human illnesses. During serious S. aureus infections, the staphylococcal pathogen-associated molecular patterns (PAMPs) such as peptidoglycan, lipoteichoic acid, and lipoproteins and even intact S. aureus, are believed to act in conjunction with the staphylococcal superantigens (SSAg) to activate the innate and adaptive immune system, respectively, and cause immunopathology. However, recent studies have shown that staphylococcal PAMPs could suppress inflammation by several mechanisms and protect from staphylococcal toxic shock syndrome, a life-threatening systemic disease caused by toxigenic S. aureus. Given the contradictory pro- and anti-inflammatory roles of staphylococcal PAMPs, we examined the effects of S. aureus-derived molecular patterns on immune responses driven by SSAg in vivo using HLA-DR3 and HLA-DQ8 transgenic mice. Our study showed that neither S. aureus-derived peptidoglycans (PGN), lipoteichoic acid (LTA), nor heat-killed Staphylococcus aureus (HKSA) inhibited SSAg-induced T cell proliferation in vitro. They failed to antagonize the immunostimulatory effects of SSAg in vivo as determined by their inability to attenuate systemic cytokine/chemokine response and reduce SSAg-induced T cell expansion. These staphylococcal PAMPs also failed to protect HLA-DR3 as well as HLA-DQ8 transgenic mice from either SSAg-induced toxic shock or pneumonia induced by a SSAg-producing strain of S. aureus. PMID:25024509

  19. Effects of molecular potential and geometry on atomic core-level photoemission over an extended energy range: The case study of the CO molecule

    NASA Astrophysics Data System (ADS)

    Kukk, E.; Ayuso, D.; Thomas, T. D.; Decleva, P.; Patanen, M.; Argenti, L.; Plésiat, E.; Palacios, A.; Kooser, K.; Travnikova, O.; Mondal, S.; Kimura, M.; Sakai, K.; Miron, C.; Martín, F.; Ueda, K.

    2013-09-01

    We report an experimental and theoretical study of single-molecule inner-shell photoemission measured over an extended range of photon energies. The vibrational intensity ratios I(?=1)/I(?=0) from the C 1s photoelectron spectra of carbon monoxide, although mostly determined by the bond length change upon ionization, are shown to be affected also by photoelectron recoil and by scattering from the neighboring oxygen atom. Static-exchange density functional theory (DFT) is used to encompass all these effects in a unified theoretical treatment. The ab initio calculations show that the vibrational ratio as a function of the photoelectron momentum is sensitive to both the ground-state internuclear distance and its contraction upon photoionization. We present a proof-of-principle application of DFT calculations as a quantitative structural analysis tool for extracting the dynamic and static molecular geometry parameters simultaneously.

  20. Ion-molecule interactions in solutions of lithium perchlorate in propylene carbonate + diethyl carbonate mixtures: an IR and molecular orbital study.

    PubMed

    Wang, Jianji; Wu, Yanping; Xuan, Xiaopeng; Wang, Hanqing

    2002-08-01

    FTIR spectra have been recorded and analyzed for solutions of lithium perchlorate in propylene carbonate (PC), diethyl carbonate (DEC), and PC + DEC mixtures. It has been shown that the carbonyl stretch bands for PC and DEC are very sensitive to the interaction between Li+ and the solvent molecules. They split with addition of LiClO4, indicating a strong interaction of Li+ with PC and DEC through the oxygen group of PC and both oxygen and ether oxygen atoms of DEC. In conjunction with molecular orbital calculation, the optimized geometries of solvation are given. In addition, solvent separated ion pairs and contact ion pairs were observed in LiClO4/DEC solutions, and no preferential solvation of Li+ in LiClO4/PC + DEC solutions were detected. PMID:12212734

  1. Virtual screening of natural inhibitors to the predicted HBx protein structure of Hepatitis B Virus using molecular docking for identification of potential lead molecules for liver cancer

    PubMed Central

    Pathak, Rajesh Kumar; Baunthiyal, Mamta; Taj, Gohar; Kumar, Anil

    2014-01-01

    The HBx protein in Hepatitis B Virus (HBV) is a potential target for anti-liver cancer molecules. Therefore, it is of interest to screen known natural compounds against the HBx protein using molecular docking. However, the structure of HBx is not yet known. Therefore, the predicted structure of HBx using threading in LOMET was used for docking against plant derived natural compounds (curcumin, oleanolic acid, resveratrol, bilobetin, luteoline, ellagic acid, betulinic acid and rutin) by Molegro Virtual Docker. The screening identified rutin with binding energy of -161.65 Kcal/mol. Thus, twenty derivatives of rutin were further designed and screened against HBx. These in silico experiments identified compounds rutin01 (-163.16 Kcal/mol) and rutin08 (- 165.76 Kcal/mol) for further consideration and downstream validation. PMID:25187683

  2. Polyuronides in Avocado (Persea americana) and Tomato (Lycopersicon esculentum) Fruits Exhibit Markedly Different Patterns of Molecular Weight Downshifts during Ripening.

    PubMed Central

    Huber, D. J.; O'Donoghue, E. M.

    1993-01-01

    Avocado (Persea americana) fruit experience a rapid and extensive loss of firmness during ripening. In this study, we examined whether the chelator solubility and molecular weight of avocado polyuronides paralleled the accumulation of polygalacturonase (PG) activity and loss in fruit firmness. Polyuronides were derived from ethanolic precipitates of avocado mesocarp prepared using a procedure to rapidly inactivate endogenous enzymes. During ripening, chelator (cyclohexane-trans-1,2-diamine tetraacetic acid [CDTA])-soluble polyuronides increased from approximately 30 to 40 [mu]g of galacturonic acid equivalents (mg alcohol-insoluble solids)-1 in preripe fruit to 150 to 170 [mu]g mg-1 in postclimacteric fruit. In preripe fruit, chelator-extractable polyuronides were of high molecular weight and were partially excluded from Sepharose CL- 2B-300 gel filtration media. Avocado polyuronides exhibited marked downshifts in molecular weight during ripening. At the postclimacteric stage, nearly all chelator-extractable polyuronides, which constituted from 75 to 90% of total cell wall uronic acid content, eluted near the total volume of the filtration media. Rechromatography of low molecular weight polyuronides on Bio-Gel P-4 disclosed that oligomeric uronic acids are produced in vivo during avocado ripening. The gel filtration behavior and pattern of depolymerization of avocado polyuronides were not influenced by the polyuronide extraction protocol (imidazole versus CDTA) or by chromatographic conditions designed to minimize interpolymeric aggregation. Polyuronides from ripening tomato (Lycopersicon esculentum) fruit extracted and chromatographed under conditions identical with those used for avocado polyuronides exhibited markedly less rapid and less extensive downshifts in molecular weight during the transition from mature-green to fully ripe. Even during a 9-d period beyond the fully ripe stage, tomato fruit polyuronides exhibited limited additional depolymerization and did not include oligomeric species. A comparison of the data for the avocado and tomato fruit indicates that downshifts in polyuronide molecular weight are a prominent feature of avocado ripening and may also explain why molecular down-regulation of PG (EC 3.2.1.15) in tomato fruit has resulted in minimal effects on fruit performance until the terminal stages of ripening. PMID:12231835

  3. Experimental and theoretical investigation of the molecular structure, conformational stability, hyperpolarizability, electrostatic potential, thermodynamic properties and NMR spectra of pharmaceutical important molecule: 4'-methylpropiophenone.

    PubMed

    Karunakaran, V; Balachandran, V

    2014-07-15

    Combined experimental and theoretical studies have been performed on the structure and vibrational spectra (IR and Raman spectra) of 4'-methylpropiophenone (MPP). The FT-IR and FT-Raman spectra of 4'-methylpropiophenone (MPP) have been recorded in the region 4000-400 cm(-1) and 3500-100 cm(-1), respectively. The harmonic vibrational frequencies were calculated and the scaled values have been compared with experimental FT-IR and FT-Raman spectra. A detailed interpretation of the infrared and Raman spectra of MPP are also reported based on total energy distribution (TED). The observed and the calculated frequencies are found to be in good agreement. The (1)H and (13)C NMR chemical shifts have been calculated by Gauge-Independent Atomic Orbital (GIAO) method with B3LYP/6-311++G(d,p). The natural bond orbital (NBO), natural hybrid orbital (NHO) analysis and electronic properties, such as HOMO and LUMO energies, were performed by DFT approach. The calculated HOMO and LUMO energies show that charge transfer occurs within molecule. The first order hyperpolarizability (?0) of the novel molecular system and related properties (?tot, ?0 and ??) of MPP are calculated using DFT/6-311++G(d,p) method on the finite-field approach. The Mulliken charges, the values of electric dipole moment (?) of the molecule were computed using DFT calculations. The thermodynamic functions of the title compound were also performed at the above method and basis set. PMID:24657464

  4. Experimental and theoretical investigation of the molecular structure, conformational stability, hyperpolarizability, electrostatic potential, thermodynamic properties and NMR spectra of pharmaceutical important molecule: 4?-Methylpropiophenone

    NASA Astrophysics Data System (ADS)

    Karunakaran, V.; Balachandran, V.

    2014-07-01

    Combined experimental and theoretical studies have been performed on the structure and vibrational spectra (IR and Raman spectra) of 4?-methylpropiophenone (MPP). The FT-IR and FT-Raman spectra of 4?-methylpropiophenone (MPP) have been recorded in the region 4000-400 cm-1 and 3500-100 cm-1, respectively. The harmonic vibrational frequencies were calculated and the scaled values have been compared with experimental FT-IR and FT-Raman spectra. A detailed interpretation of the infrared and Raman spectra of MPP are also reported based on total energy distribution (TED). The observed and the calculated frequencies are found to be in good agreement. The 1H and 13C NMR chemical shifts have been calculated by Gauge-Independent Atomic Orbital (GIAO) method with B3LYP/6-311++G(d,p). The natural bond orbital (NBO), natural hybrid orbital (NHO) analysis and electronic properties, such as HOMO and LUMO energies, were performed by DFT approach. The calculated HOMO and LUMO energies show that charge transfer occurs within molecule. The first order hyperpolarizability (?0) of the novel molecular system and related properties (?tot, ?0 and ??) of MPP are calculated using DFT/6-311++G(d,p) method on the finite-field approach. The Mulliken charges, the values of electric dipole moment (?) of the molecule were computed using DFT calculations. The thermodynamic functions of the title compound were also performed at the above method and basis set.

  5. A sodium channel variant in Aedes aegypti as a candidate pathogen sensor for viral-associated molecular patterns.

    PubMed

    Lee, Cara; Jones, Alexis; Kainz, Danielle; Khan, Faatima; Carrithers, Michael D

    2015-08-01

    Recent work demonstrated that a splice variant of a human macrophage voltage-gated sodium channel expressed on endosomes acts as an intracellular sensor for dsRNA, a viral-associated molecular pattern. Here our goal was to identify a candidate gene in a clinically relevant invertebrate model with related cellular and pattern recognition properties. The para gene in drosophila and other insects encodes voltage-gated sodium channels with similar electrophysiological properties to those found in vertebrate excitable membranes. A database search revealed that the AAEL006019 gene in Aedes aegypti, the yellow fever mosquito, encodes a voltage-gated sodium channel that is distinct from genes that encode para-like sodium channels. As compared to para-like channels, the protein products from this gene have deletions in the N-terminus and in the DII-DIII linker region. When over-expressed in an Aedes aegypti cell line, CCL-125, the AAEL006019 channel demonstrated cytoplasmic expression on vesicular-like organelles. Electrophysiologic analysis revealed that the channel mediates small inward currents that are enhanced by synthetic mimics of viral-derived ssRNA, R848 and ORN02, but not the dsRNA mimic, poly I:C. R848 treatment of CCL-125 cells that express high levels of the channels led to increased expression of RelA and Ago2, two mediators of insect innate immunity. These results suggest that the AAEL006019 channel acts as an intracellular pathogen sensor for ssRNA molecular patterns. PMID:26086103

  6. Octupolar molecules for nonlinear optics: from molecular design to crystals and films with large second-harmonic generation.

    PubMed

    Jeong, Mi-Yun; Cho, Bong Rae

    2015-02-01

    We summarize the nonlinear optical (NLO) properties of octupolar molecules, crystals, and films developed in our laboratory. We present the design strategy, structure-property relationship, and second-order NLO properties of 1,3,5-trinitro- and 1,3,5-tricyano-2,4,6-tris(p-diethylaminostyryl)benzene (TTB) derivatives, TTB crystals, and films prepared by free-casting TTB in poly(methyl methacrylate) (PMMA). The first hyperpolarizability of TTB was fivefold larger than that of the dipolar analogue. Moreover, the TTB crystal showed unprecedentedly large second-harmonic generation (SHG). While TTB crystal films (20 wt% TTB/PMMA) on various substrates showed appreciable SHG values, the cylinder film exhibited much larger SHG values and large electro-optic (EO) coefficients. The large SHG values and EO coefficients, as well as the high thermal stability of the cylinder film, will make it a potential candidate for NLO device applications. PMID:25315898

  7. VUV Photolysis of NH_3: a Matrix Isolation Study of the Molecular Interactions Between Amidogen Radical and Ammonia Molecules

    NASA Astrophysics Data System (ADS)

    Krim, L.; Zins, E. L.

    2013-06-01

    The presence of NH_3 in the interstellar medium is very promising in terms of possible exobiologically-relevant reactions. This is the reason why numerous laboratory investigations on reactions involving NH_3 were carried out in the context of astrochemistry. Among other reactions, the photolysis of NH_3 was widely investigated. IR spectroscopy in solid phase as well as in rare-gas matrices suggested the formation of NH_2 radicals. In most of these experiments, samples containing NH_3 were prepared at cryogenic temperatures and further irradiated. On the other hand, since the penetration of the photons inside the solid ices as well as inside matrices is limited, the concentration of the photoproducts is weak, thus hindering possible secondary reaction studies. Furthermore, in addition with ice-grain irradiations, in the interstellar clouds, the gaseous species may be subjected to irradiation during their condensation on ice grains. In order to reproduce this effect, instead of irradiating samples obtained by condensation of NH_3 or NH_3/Ne gases at low temperatures, we carried experiments in which irradiation was carried out during the sample deposition. Thus, the amidogen radical and complexes between this radical and ammonia molecules were prepared and isolated in a neon matrix. The formation of (NH_2)(NH_3), (NH_2)(NH_3)_2 and (NH_2)(NH_3)_3 was clearly established thanks to the comparison between the theoretical and the experimental vibrational frequencies. Thus, such ammonia-containing aggregates may be formed in the interstellar clouds. These complexes, as solvated radicals, may further react with carbon- and oxygen-containing species present on the surface of ice grains. Such reactions may be a first step toward the formation of prebiotic molecules.

  8. Patterns of inheritance with RAPD molecular markers reveal novel types of polymorphism in the honey bee

    Microsoft Academic Search

    Greg J. Hunt; Robert E. Page

    1992-01-01

    The polymerase chain reaction (PCR) was used to generate random amplified polymorphic DNA (RAPD) from honey bee DNA samples in order to follow the patterns of inheritance of RAPD markers in a haplodiploid insect. The genomic DNA samples from two parental bees, a haploid drone and a diploid queen, were screened for polymorphism with 68 different tennucleotide primers of random

  9. Molecular classification of head and neck squamous cell carcinomas using patterns of gene expression

    Microsoft Academic Search

    Christine H. Chung; Joel S. Parker; Gamze Karaca; Junyuan Wu; William K Funkhouser; Dominic Moore; Dale Butterfoss; Dong Xiang; Adam Zanation; Xiaoying Yin; William W Shockley; Mark C Weissler; Lynn G Dressler; Carol G Shores; Wendell G Yarbrough; Charles M Perou

    2004-01-01

    The prognostication of head and neck squamous cell carcinoma (HNSCC) is largely based upon the tumor size and location and the presence of lymph node metastases. Here we show that gene expression patterns from 60 HNSCC samples assayed on cDNA microarrays allowed categorization of these tumors into four distinct subtypes. These subtypes showed statistically significant differences in recurrence-free survival and

  10. DISPERSAL PATTERN OF BLACK-BILLED MAGPIES (PICA HUDSONIA) MEASURED BY MOLECULAR GENETIC (RAPD) ANALYSIS

    Microsoft Academic Search

    XIAO-HONG WANGAND; Charles H. Trost

    2001-01-01

    Black-billed Magpies (Pica hudsonia) are a relatively sedentary corvid, with greater dispersal of females than males. To genetically confirm that dispersal pattern, 29 reproductively active adults were captured over two years and were scored for primer-spe- cific random amplified polymorphic DNA (RAPD) bands (53 polymorphic bands in 1996 and 104 in 1997). In both years, we captured more previously banded

  11. Evidence that ultraviolet markings are associated with patterns of molecular gene flow

    E-print Network

    Danchin, Etienne

    , and approved February 1, 2001 (received for review December 5, 2000) Recent studies have shown UV vision its potential importance in sexual selection. However, there has been no genetic evidence that UV that UV markings are associated with the pattern of gene flow in the Tenerife lizard (Gallotia galloti

  12. Viral Pathogen-Associated Molecular Patterns Regulate Blood-Brain Barrier Integrity via Competing Innate Cytokine Signals

    PubMed Central

    Daniels, Brian P.; Holman, David W.; Cruz-Orengo, Lillian; Jujjavarapu, Harsha; Durrant, Douglas M.

    2014-01-01

    ABSTRACT Pattern recognition receptor (PRR) detection of pathogen-associated molecular patterns (PAMPs), such as viral RNA, drives innate immune responses against West Nile virus (WNV), an emerging neurotropic pathogen. Here we demonstrate that WNV PAMPs orchestrate endothelial responses to WNV via competing innate immune cytokine signals at the blood-brain barrier (BBB), a multicellular interface with highly specialized brain endothelial cells that normally prevents pathogen entry. While Th1 cytokines increase the permeability of endothelial barriers, type I interferon (IFN) promoted and stabilized BBB function. Induction of innate cytokines by pattern recognition pathways directly regulated BBB permeability and tight junction formation via balanced activation of the small GTPases Rac1 and RhoA, which in turn regulated the transendothelial trafficking of WNV. In vivo, mice with attenuated type I IFN signaling or IFN induction (Ifnar?/? Irf7?/?) exhibited enhanced BBB permeability and tight junction dysregulation after WNV infection. Together, these data provide new insight into host-pathogen interactions at the BBB during neurotropic viral infection. PMID:25161189

  13. Heterogeneity of Molecular Resistance Patterns in Antimony-Resistant Field Isolates of Leishmania Species from the Western Mediterranean Area

    PubMed Central

    Mary, Charles; Aoun, Karim; Harrat, Zoubir; Bouratbine, Aïda; Faraut, Françoise; Benikhlef, Rezika; Pomares, Christelle; Pratlong, Francine; Marty, Pierre; Piarroux, Renaud

    2014-01-01

    Antimonials remain the first-line treatment for the various manifestations of leishmaniasis in most areas where the disease is endemic, and increasing cases of therapeutic failure associated with parasite resistance have been reported. In this study, we assessed the molecular status of 47 clinical isolates of Leishmania causing visceral and cutaneous leishmaniasis from Algeria, Tunisia, and southern France. In total, we examined 14 genes that have been shown to exhibit significant variations in DNA amplification, mRNA levels, or protein expression with respect to resistance to antimonials. The gene status of each clinical isolate was assessed via qPCR and qRT-PCR. We then compared the molecular pattern against the phenotype determined via an in vitro sensitivity test of the clinical isolates against meglumine antimoniate, which is considered the reference technique. Our results demonstrate significant DNA amplification and/or RNA overexpression in 56% of the clinical isolates with the resistant phenotype. All clinical isolates that exhibited significant overexpression of at least 2 genes displayed a resistant phenotype. Among the 14 genes investigated, 10 genes displayed either significant amplification or overexpression in at least 1 clinical isolate; these genes are involved in several metabolic pathways. Moreover, various gene associations were observed depending on the clinical isolates, supporting the multifactorial nature of Leishmania resistance. Molecular resistance features were found in the 3 Leishmania species investigated (Leishmania infantum, Leishmania major, and Leishmania killicki). To our knowledge, this is the first report of the involvement of molecular resistance genes in field isolates of Leishmania major and Leishmania killicki with the resistance phenotype. PMID:24913173

  14. Drug Delivery Through the Skin: Molecular Simulations of Barrier Lipids to Design more Effective Noninvasive Dermal and Transdermal Delivery Systems for Small Molecules Biologics and Cosmetics

    SciTech Connect

    J Torin Huzil; S Sivaloganathan; M Kohandel; M Foldvari

    2011-12-31

    The delivery of drugs through the skin provides a convenient route of administration that is often preferable to injection because it is noninvasive and can typically be self-administered. These two factors alone result in a significant reduction of medical complications and improvement in patient compliance. Unfortunately, a significant obstacle to dermal and transdermal drug delivery alike is the resilient barrier that the epidermal layers of the skin, primarily the stratum corneum, presents for the diffusion of exogenous chemical agents. Further advancement of transdermal drug delivery requires the development of novel delivery systems that are suitable for modern, macromolecular protein and nucleotide therapeutic agents. Significant effort has already been devoted to obtain a functional understanding of the physical barrier properties imparted by the epidermis, specifically the membrane structures of the stratum corneum. However, structural observations of membrane systems are often hindered by low resolutions, making it difficult to resolve the molecular mechanisms related to interactions between lipids found within the stratum corneum. Several models describing the molecular diffusion of drug molecules through the stratum corneum have now been postulated, where chemical permeation enhancers are thought to disrupt the underlying lipid structure, resulting in enhanced permeability. Recent investigations using biphasic vesicles also suggested a possibility for novel mechanisms involving the formation of complex polymorphic lipid phases. In this review, we discuss the advantages and limitations of permeation-enhancing strategies and how computational simulations, at the atomic scale, coupled with physical observations can provide insight into the mechanisms of diffusion through the stratum corneum.

  15. Computational study of the vibrational spectroscopic studies, natural bond orbital, frontier molecular orbital and second-order non-linear optical properties of acetophenone thiosemicarbazone molecule.

    PubMed

    Li, Xiao-Hong; Mei, Zheng; Zhang, Xian-Zhou

    2014-01-24

    The vibrational frequencies of acetophenone thiosemicarbazone in the ground state have been calculated using density functional method (B3LYP) with 6-31G(d), 6-31G(d,p) and 6-311++G(d,p) basis sets. The analysis of natural bond orbital was also performed. The IR spectra were obtained and interpreted by means of potential energies distributions (PEDs) using MOLVIB program. In addition, the results show that there exist N-H…N and N-H…S hydrogen bonds in the title compound, which play a major role in stabilizing the molecule and are confirmed by the natural bond orbital analysis. The predicted NLO properties show that the title compound is a good candidate as second-order NLO material. In addition, the frontier molecular orbitals were analyzed and the crystal structure obtained by molecular mechanics belongs to the Pbca space group, with lattice parameters Z=8, a=16.0735 Å, b=7.1719 Å, c=7.8725 Å, ?=0.808 g/cm(3). PMID:24084483

  16. Contrasted Patterns of Molecular Evolution in Dominant and Recessive Self-Incompatibility Haplotypes in Arabidopsis

    Microsoft Academic Search

    Pauline M. Goubet; Hélène Bergès; Arnaud Bellec; Elisa Prat; Nicolas Helmstetter; Sophie Mangenot; Sophie Gallina; Anne-Catherine Holl; Isabelle Fobis-Loisy; Xavier Vekemans; Vincent Castric

    2012-01-01

    Self-incompatibility has been considered by geneticists a model system for reproductive biology and balancing selection, but our understanding of the genetic basis and evolution of this molecular lock-and-key system has remained limited by the extreme level of sequence divergence among haplotypes, resulting in a lack of appropriate genomic sequences. In this study, we report and analyze the full sequence of

  17. Expression of pattern in plants: combining molecular and calculus-based biophysical paradigms.

    PubMed

    Green, P B

    1999-08-01

    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 that structural specification at each scale is highly efficient if the pertinent gene activity is manifested in two complementary biophysical categories. At large scale, one category is the tendency of the formative tissue to fold with a certain spatial periodicity determined by its material properties (e.g., bending stiffness from cellulose content). This latent tendency is formalized in a differential equation for physical buckling. The second category at this scale comprises boundary conditions that specify how the latent tendency is manifested as topography: whether tissue humps occur as whorls or Fibonacci spirals. This versatile combinatorial format accounts for the relative stability of alternative organ patterning as well as alternative organ shaping (e.g., stamens vs. carpels). It also accounts for the structural shifts seen in normal development and after mutation or chemical/physical intervention. At small scale, the latent differential activity is the tendency for groups of dividing cells to co-align their cytoskeletons. The curvature of the surface opposes this tendency. The least curved part of a new primordium is its quasicylindrical midportion. There, by aligning microtubules and cellulose coherently around the organ, a new growth direction is set. Thus large-scale buckling produces curvature variation, which, in turn, affects the localization and orientation of the cytoskeleton. This scheme for the coherent production of diverse geometrical features, involving calculus at two structural levels, is supported by complex organogenetic responses to simple physical intervention. Also, many morphological alternatives, wild type vs. mutant, reflect single changes in parameters in this differential-integral format. PMID:10449383

  18. Antibiotic Sensitivity Patterns and Molecular Typing of Shigella sonnei Strains Using ERIC-PCR

    PubMed Central

    Ranjbar, Reza; Mirsaeed Ghazi, Farzaneh

    2013-01-01

    Abstract Background Shigella sonnei is considered as a major cause of diarrheal disease in both developing and developed countries. Iran is one of the endemic areas of shigellosis. The present study was undertaken to investigate the antibiotic susceptibility and genetic relatedness of S. sonnei strains isolated from pediatric patients in Tehran, Iran. Methods The study included all S. sonnei strains isolated from pediatric patients with diarrhea admitted to several hospitals in Tehran, Iran, during 2008-2010. Shigella spp. strains were recovered from patients using standard microbiological methods. S. sonnei strains were further studied by antimicrobial susceptibility testing and Enterobacterial Repetitive Intergenic Consensus (ERIC) - PCR analysis. Results Eighty nine Shigella isolates were isolated. S. sonnei was themost prevalent Shigella species (60.7%) followed by, S. flexneri (31.5%). Eleven antimicrobial resistance patterns (R1-R11) were identified among S. sonnei isolates. The majority of the strains were resistant to trimethoprim-sulfamethoxazole, tetracycline and streptomycin. All isolates were susceptible to ciprofloxacin, ceftizoxime and chloramphenicol. All strains were typable by ERIC-PCR. Five ERIC-PCR patterns (E1-E5) were found among S. sonnei isolates; however the half of the isolates was clustered in E4 pattern. Conclusion The antibiotic resistance rates are increasing among S. sonnei strains. Moreover, a predominant clone or limited clones of S. sonnei were responsible for shigellosis caused by this Shigella species in pediatric patients in Tehran, Iran.

  19. Molecular architecture of a complex between an adhesion protein from the malaria parasite and intracellular adhesion molecule 1.

    PubMed

    Brown, Alan; Turner, Louise; Christoffersen, Stig; Andrews, Katrina A; Szestak, Tadge; Zhao, Yuguang; Larsen, Sine; Craig, Alister G; Higgins, Matthew K

    2013-02-22

    The adhesion of Plasmodium falciparum-infected erythrocytes to human tissues or endothelium is central to the pathology caused by the parasite during malaria. It contributes to the avoidance of parasite clearance by the spleen and to the specific pathologies of cerebral and placental malaria. The PfEMP1 family of adhesive proteins is responsible for this sequestration by mediating interactions with diverse human ligands. In addition, as the primary targets of acquired, protective immunity, the PfEMP1s are potential vaccine candidates. PfEMP1s contain large extracellular ectodomains made from CIDR (cysteine-rich interdomain regions) and DBL (Duffy-binding-like) domains and show extensive variation in sequence, size, and domain organization. Here we use biophysical methods to characterize the entire ?300-kDa ectodomain from IT4VAR13, a protein that interacts with the host receptor, intercellular adhesion molecule-1 (ICAM-1). We show through small angle x-ray scattering that IT4VAR13 is rigid, elongated, and monomeric. We also show that it interacts with ICAM-1 through the DBL? domain alone, forming a 1:1 complex. These studies provide a first low resolution structural view of a PfEMP1 ectodomain in complex with its ligand. They show that it combines a modular domain arrangement consisting of individual ligand binding domains, with a defined higher order architecture that exposes the ICAM-1 binding surface to allow adhesion. PMID:23297413

  20. Biological and Molecular Effects of Small Molecule Kinase Inhibitors on Low-Passage Human Colorectal Cancer Cell Lines

    PubMed Central

    Lange, Falko; Franz, Benjamin; Maletzki, Claudia; Linnebacher, Michael; Hühns, Maja; Jaster, Robert

    2014-01-01

    Low-passage cancer cell lines are versatile tools to study tumor cell biology. Here, we have employed four such cell lines, established from primary tumors of colorectal cancer (CRC) patients, to evaluate effects of the small molecule kinase inhibitors (SMI) vemurafenib, trametinib, perifosine, and regorafenib in an in vitro setting. The mutant BRAF (V600E/V600K) inhibitor vemurafenib, but also the MEK1/2 inhibitor trametinib efficiently inhibited DNA synthesis, signaling through ERK1/2 and expression of genes downstream of ERK1/2 in BRAF mutant cells only. In case of the AKT inhibitor perifosine, three cell lines showed a high or intermediate responsiveness to the drug while one cell line was resistant. The multikinase inhibitor regorafenib inhibited proliferation of all CRC lines with similar efficiency and independent of the presence or absence of KRAS, BRAF, PIK3CA, and TP53 mutations. Regorafenib action was associated with broad-range inhibitory effects at the level of gene expression but not with a general inhibition of AKT or MEK/ERK signaling. In vemurafenib-sensitive cells, the antiproliferative effect of vemurafenib was enhanced by the other SMI. Together, our results provide insights into the determinants of SMI efficiencies in CRC cells and encourage the further use of low-passage CRC cell lines as preclinical models. PMID:25309914

  1. Dynamic fluctuations in single-molecule biophysics experiments. Comment on "Extracting physics of life at the molecular level: A review of single-molecule data analyses" by W. Colomb and S.K. Sarkar

    NASA Astrophysics Data System (ADS)

    Krapf, Diego

    2015-06-01

    Single-molecule biophysics includes the study of isolated molecules and that of individual molecules within living cells. In both cases, dynamic fluctuations at the nanoscale play a critical role. Colomb and Sarkar emphasize how different noise sources affect the analysis of single molecule data [1]. Fluctuations in biomolecular systems arise from two very different mechanisms. On one hand thermal fluctuations are a predominant feature in the behavior of individual molecules. On the other hand, non-Gaussian fluctuations can arise from inter- and intramolecular interactions [2], spatial heterogeneities [3], non-Poisson external perturbations [4] and complex non-linear dynamics in general [5,6].

  2. A CD83-like molecule in sea bass (Dicentrarchus labrax): molecular characterization and modulation by viral and bacterial infection.

    PubMed

    Buonocore, Francesco; Randelli, Elisa; Tranfa, Paola; Scapigliati, Giuseppe

    2012-06-01

    The CD83 cell surface marker is an important and intriguing component of immune system. It is considered the best marker for mature human dendritic cells, but it is also important for thymic development of T cells, and it also plays a role as a regulator of peripheral B-cell function and homeostasis. A CD83-like molecule was identified in sea bass (Dicentrarchus labrax) by EST sequencing of a thymus cDNA library; the CD83 cDNA is composed of 816 bp and the mature CD83 peptide consists of 195 amino acids, with a putative signal peptide of 18 amino acids and two possible N-glycosylation sites. The comparison of sea bass CD83 sequence with its homologues in other fish species and mammals shows some differences, with two cysteine residues conserved from fish to mammals and a high variability both in the total number of cysteines and in mature CD83 sequence polypeptide length. Basal transcripts levels of CD83 mRNA are highest in liver, followed by thymus. The in vitro treatment of head kidney leukocytes with LPS resulted in a down-regulation on CD83 mRNA leves both after 4 and 24 h, whereas with poly I:C an up-regulation after 4h followed by a down-regulation at 24 h was observed. An in vivo infection of sea bass juveniles with nodavirus induced an increase of CD83 expression on head kidney leukocytes both after 6 and 24 h and a decrease after 72 h. On the other hand, an in vivo infection with Photobacterium damselae bacteria induced a decrease of CD83 transcript levels after 6 and 24 h and an increase after 72 h. These findings suggest in sea bass CD83 expression could be modulated by viral and bacterial immune response. PMID:22554578

  3. Systematic studies of molecular vibrational anharmonicity and vibration-rotation interaction by self-consistent-field higher derivative methods: Applications to asymmetric and symmetric top and linear polyatomic molecules

    SciTech Connect

    Clabo, D.A. Jr.

    1987-04-01

    Inclusion of the anharmonicity normal mode vibrations (i.e., the third and fourth (and higher) derivatives of a molecular Born-Oppenheimer potential energy surface) is necessary in order to theoretically reproduce experimental fundamental vibrational frequencies of a molecule. Although ab initio determinations of harmonic vibrational frequencies may give errors of only a few percent by the inclusion of electron correlation within a large basis set for small molecules, in general, molecular fundamental vibrational frequencies are more often available from high resolution vibration-rotation spectra. Recently developed analytic third derivatives methods for self-consistent-field (SCF) wavefunctions have made it possible to examine with previously unavailable accuracy and computational efficiency the anharmonic force fields of small molecules.

  4. Final Report for Integrated Multiscale Modeling of Molecular Computing Devices

    SciTech Connect

    Glotzer, Sharon C.

    2013-08-28

    In collaboration with researchers at Vanderbilt University, North Carolina State University, Princeton and Oakridge National Laboratory we developed multiscale modeling and simulation methods capable of modeling the synthesis, assembly, and operation of molecular electronics devices. Our role in this project included the development of coarse-grained molecular and mesoscale models and simulation methods capable of simulating the assembly of millions of organic conducting molecules and other molecular components into nanowires, crossbars, and other organized patterns.

  5. David Adler Lectureship Award Talk: Friction and energy dissipation mechanisms in adsorbed molecules and molecularly thin films

    NASA Astrophysics Data System (ADS)

    Krim, Jacqueline

    2015-03-01

    Studies of the fundamental origins of friction have undergone rapid progress in recent years, with the development of new experimental and computational techniques for measuring and simulating friction at atomic length and time scales. The increased interest has sparked a variety of discussions and debates concerning the nature of the atomic-scale and quantum mechanisms that dominate the dissipative process by which mechanical energy is transformed into heat. Measurements of the sliding friction of physisorbed monolayers and bilayers can provide information on the relative contributions of these various dissipative mechanisms. Adsorbed films, whether intentionally applied or present as trace levels of physisorbed contaminants, moreover are ubiquitous at virtually all surfaces. As such, they impact a wide range of applications whose progress depends on precise control and/or knowledge of surface diffusion processes. Examples include nanoscale assembly, directed transport of Brownian particles, material flow through restricted geometries such as graphene membranes and molecular sieves, passivation and edge effects in carbon-based lubricants, and the stability of granular materials associated with frictional and frictionless contacts. Work supported by NSFDMR1310456.

  6. Molecular cloning and characterisation of peroxinectin, a cell adhesion molecule, from the giant freshwater prawn Macrobrachium rosenbergii.

    PubMed

    Hsu, Pei-I; Liu, Chun-Hung; Tseng, Deng-Yu; Lee, Pai-Po; Cheng, Winton

    2006-07-01

    Expression of peroxinectin cDNA was determined from haemocytes of giant freshwater prawn Macrobrachium rosenbergii using oligonucleotide primers and reverse transcription polymerase chain reaction (RT-PCR) based on the peroxinectin sequence of white shrimp Litopenaeus vannamei, tiger shrimp Penaeus monodon, and freshwater crayfish Pacifastacus leniusculus. The peroxinectin of M. rosenbergii was constitutively expressed. Analysis of the nucleotide sequence revealed that the cDNA clone has an open reading frame of 2,403 bp encoding a protein of 801 amino acids including a 20 amino acid signal peptide. The calculated molecular mass of the mature protein (781 amino acids) was 88.7 kDa with an estimated pI of 6.8. A putative peroxidase domain and a putative integrin-binding motif, KGD (Lys-Gly-Asp) were observed in prawn peroxinectin at the C-terminal. Sequence comparison showed that peroxinectin deduced amino acid of M. rosenbergii had an overall similarity of 62%, 64%, and 66% to that of P. leniusculus, P. monodon, and L. vannamei, respectively. Quantitative real-time PCR analysis showed that peroxinectin transcript in haemocyte of M. rosenbergii decreased significantly after 3, 6 and 12h injection with Lactococcus garvieae. PMID:16377210

  7. Making teeth to order: conserved genes reveal an ancient molecular pattern in paddlefish (Actinopterygii).

    PubMed

    Smith, Moya M; Johanson, Zerina; Butts, Thomas; Ericsson, Rolf; Modrell, Melinda; Tulenko, Frank J; Davis, Marcus C; Fraser, Gareth J

    2015-04-22

    Ray-finned fishes (Actinopterygii) are the dominant vertebrate group today (+30 000 species, predominantly teleosts), with great morphological diversity, including their dentitions. How dental morphological variation evolved is best addressed by considering a range of taxa across actinopterygian phylogeny; here we examine the dentition of Polyodon spathula (American paddlefish), assigned to the basal group Acipenseriformes. Although teeth are present and functional in young individuals of Polyodon, they are completely absent in adults. Our current understanding of developmental genes operating in the dentition is primarily restricted to teleosts; we show that shh and bmp4, as highly conserved epithelial and mesenchymal genes for gnathostome tooth development, are similarly expressed at Polyodon tooth loci, thus extending this conserved developmental pattern within the Actinopterygii. These genes map spatio-temporal tooth initiation in Polyodon larvae and provide new data in both oral and pharyngeal tooth sites. Variation in cellular intensity of shh maps timing of tooth morphogenesis, revealing a second odontogenic wave as alternate sites within tooth rows, a dental pattern also present in more derived actinopterygians. Developmental timing for each tooth field in Polyodon follows a gradient, from rostral to caudal and ventral to dorsal, repeated during subsequent loss of teeth. The transitory Polyodon dentition is modified by cessation of tooth addition and loss. As such, Polyodon represents a basal actinopterygian model for the evolution of developmental novelty: initial conservation, followed by tooth loss, accommodating the adult trophic modification to filter-feeding. PMID:25788604

  8. Symmetry breaking in nanostructure development of carbogenic molecular sieves: Effects of morphological pattern formation on oxygen and nitrogen transport

    SciTech Connect

    Kane, M.S.; Goellner, J.F.; Foley, H.C. [Univ. of Delaware, Newark, DE (United States)] [and others] [Univ. of Delaware, Newark, DE (United States); and others

    1996-08-01

    A comprehensive study has been undertaken to establish the primary factors that control transport of oxygen and nitrogen in polymer-derived carbogenic molecular sieves (CMS). Characterization of the nanostructure of CMS derived from poly(furfuryl alcohol) (PFA) indicates that significant physical and chemical reorganization occurs as a function of synthesis temperature. Spectroscopic measurements show a drastic decrease in oxygen and hydrogen functionality with increasing pyrolysis temperature. Structural reorganization and elimination of these heteroatoms lead to a measurable increase in the unpaired electron density in these materials. High-resolution transmission electron microscopy and powder neutron diffraction are used to probe the corresponding changes in the physical structural features in the CMS. These indicate that as the pyrolysis temperature is increased, the structure of the CMS transforms from one that is disordered and therefore highly symmetric to one that is more ordered on a length scale of 15 {Angstrom} and hence less symmetric. This structural transformation process, one of symmetry breaking and pattern formation, if often observed in other nonlinear dissipative systems, but not in solids. Symmetry breaking provides the driving force for these high-temperature reorganizations, but unlike most dissipative systems, these less-symmetric structures remain frozen in place when energy is no longer applied. The impact of these nanostructural reorganizations on the molecular sieving character of the CMS is studied in terms of the physical separation of oxygen and nitrogen. 40 refs., 14 figs., 3 tabs.

  9. Molecular detection of hematozoa infections in tundra swans relative to migration patterns and ecological conditions at breeding grounds.

    PubMed

    Ramey, Andrew M; Ely, Craig R; Schmutz, Joel A; Pearce, John M; Heard, Darryl J

    2012-01-01

    Tundra swans (Cygnus columbianus) are broadly distributed in North America, use a wide variety of habitats, and exhibit diverse migration strategies. We investigated patterns of hematozoa infection in three populations of tundra swans that breed in Alaska using satellite tracking to infer host movement and molecular techniques to assess the prevalence and genetic diversity of parasites. We evaluated whether migratory patterns and environmental conditions at breeding areas explain the prevalence of blood parasites in migratory birds by contrasting the fit of competing models formulated in an occupancy modeling framework and calculating the detection probability of the top model using Akaike Information Criterion (AIC). We described genetic diversity of blood parasites in each population of swans by calculating the number of unique parasite haplotypes observed. Blood parasite infection was significantly different between populations of Alaska tundra swans, with the highest estimated prevalence occurring among birds occupying breeding areas with lower mean daily wind speeds and higher daily summer temperatures. Models including covariates of wind speed and temperature during summer months at breeding grounds better predicted hematozoa prevalence than those that included annual migration distance or duration. Genetic diversity of blood parasites in populations of tundra swans appeared to be relative to hematozoa prevalence. Our results suggest ecological conditions at breeding grounds may explain differences of hematozoa infection among populations of tundra swans that breed in Alaska. PMID:23049862

  10. Molecular evolution patterns reveal life history features of mycoplasma-related endobacteria associated with arbuscular mycorrhizal fungi.

    PubMed

    Toomer, Kevin H; Chen, Xiuhua; Naito, Mizue; Mondo, Stephen J; den Bakker, Henk C; VanKuren, Nicholas W; Lekberg, Ylva; Morton, Joseph B; Pawlowska, Teresa E

    2015-07-01

    The mycoplasma-related endobacteria (MRE), representing a recently discovered lineage of Mollicutes, are widely distributed across arbuscular mycorrhizal fungi (AMF, Glomeromycota). AMF colonize roots of most terrestrial plants and improve plant mineral nutrient uptake in return for plant-assimilated carbon. The role of MRE in the biology of their fungal hosts is unknown. To start characterizing this association, we assessed partitioning of MRE genetic diversity within AMF individuals and across the AMF phylogeographic range. We further used molecular evolution patterns to make inferences about MRE codivergence with AMF, their lifestyle and antiquity of the Glomeromycota-MRE association. While we did not detect differentiation between MRE derived from different continents, high levels of diversity were apparent in MRE populations within AMF host individuals. MRE exhibited significant codiversification with AMF over ecological time and the absence of codivergence over evolutionary time. Moreover, genetic recombination was evident in MRE. These patterns indicate that, while MRE transmission is predominantly vertical, their complex intrahost populations are likely generated by horizontal transmission and recombination. Based on predictions of evolutionary theory, we interpreted these observations as a suggestion that MRE may be antagonists of AMF. Finally, we detected a marginally significant signature of codivergence of MRE with Glomeromycota and the Endogone lineage of Mucoromycotina, implying that the symbiosis between MRE and fungi may predate the divergence between these two groups of fungi. PMID:26011293

  11. Molecular detection of hematozoa infections in tundra swans relative to migration patterns and ecological conditions at breeding grounds

    USGS Publications Warehouse

    Ramey, Andrew M.; Ely, Craig R.; Schmutz, Joel A.; Pearce, John M.; Heard, Darryl J.

    2012-01-01

    Tundra swans (Cygnus columbianus) are broadly distributed in North America, use a wide variety of habitats, and exhibit diverse migration strategies. We investigated patterns of hematozoa infection in three populations of tundra swans that breed in Alaska using satellite tracking to infer host movement and molecular techniques to assess the prevalence and genetic diversity of parasites. We evaluated whether migratory patterns and environmental conditions at breeding areas explain the prevalence of blood parasites in migratory birds by contrasting the fit of competing models formulated in an occupancy modeling framework and calculating the detection probability of the top model using Akaike Information Criterion (AIC). We described genetic diversity of blood parasites in each population of swans by calculating the number of unique parasite haplotypes observed. Blood parasite infection was significantly different between populations of Alaska tundra swans, with the highest estimated prevalence occurring among birds occupying breeding areas with lower mean daily wind speeds and higher daily summer temperatures. Models including covariates of wind speed and temperature during summer months at breeding grounds better predicted hematozoa prevalence than those that included annual migration distance or duration. Genetic diversity of blood parasites in populations of tundra swans appeared to be relative to hematozoa prevalence. Our results suggest ecological conditions at breeding grounds may explain differences of hematozoa infection among populations of tundra swans that breed in Alaska.

  12. Toll-like receptor 9-mediated protection of enterovirus 71 infection in mice is due to the release of danger-associated molecular patterns.

    PubMed

    Hsiao, Hung-Bo; Chou, Ai-Hsiang; Lin, Su-I; Chen, I-Hua; Lien, Shu-Pei; Liu, Chia-Chyi; Chong, Pele; Liu, Shih-Jen

    2014-10-01

    Enterovirus 71 (EV71), a positive-stranded RNA virus, is the major cause of hand, foot, and mouth disease (HFMD) with severe neurological symptoms. Antiviral type I interferon (alpha/beta interferon [IFN-?/?]) responses initiated from innate receptor signaling are inhibited by EV71-encoded proteases. It is less well understood whether EV71-induced apoptosis provides a signal to activate type I interferon responses as a host defensive mechanism. In this report, we found that EV71 alone cannot activate Toll-like receptor 9 (TLR9) signaling, but supernatant from EV71-infected cells is capable of activating TLR9. We hypothesized that TLR9-activating signaling from plasmacytoid dendritic cells (pDCs) may contribute to host defense mechanisms. To test our hypothesis, Flt3 ligand-cultured DCs (Flt3L-DCs) from both wild-type (WT) and TLR9 knockout (TLR9KO) mice were infected with EV71. More viral particles were produced in TLR9KO mice than by WT mice. In contrast, alpha interferon (IFN-?), monocyte chemotactic protein 1 (MCP-1), tumor necrosis factor-alpha (TNF-?), IFN-?, interleukin 6 (IL-6), and IL-10 levels were increased in Flt3L-DCs from WT mice infected with EV71 compared with TLR9KO mice. Seven-day-old TLR9KO mice infected with a non-mouse-adapted EV71 strain developed neurological lesion-related symptoms, including hind-limb paralysis, slowness, ataxia, and lethargy, but WT mice did not present with these symptoms. Lung, brain, small intestine, forelimb, and hind-limb tissues collected from TLR9KO mice exhibited significantly higher viral loads than equivalent tissues collected from WT mice. Histopathologic damage was observed in brain, small intestine, forelimb, and hind-limb tissues collected from TLR9KO mice infected with EV71. Our findings demonstrate that TLR9 is an important host defense molecule during EV71 infection. Importance: The host innate immune system is equipped with pattern recognition receptors (PRRs), which are useful for defending the host against invading pathogens. During enterovirus 71 (EV71) infection, the innate immune system is activated by pathogen-associated molecular patterns (PAMPs), which include viral RNA or DNA, and these PAMPs are recognized by PRRs. Toll-like receptor 3 (TLR3) and TLR7/8 recognize viral nucleic acids, and TLR9 senses unmethylated CpG DNA or pathogen-derived DNA. These PRRs stimulate the production of type I interferons (IFNs) to counteract viral infection, and they are the major source of antiviral alpha interferon (IFN-?) production in pDCs, which can produce 200- to 1,000-fold more IFN-? than any other immune cell type. In addition to PAMPs, danger-associated molecular patterns (DAMPs) are known to be potent activators of innate immune signaling, including TLR9. We found that EV71 induces cellular apoptosis, resulting in tissue damage; the endogenous DNA from dead cells may activate the innate immune system through TLR9. Therefore, our study provides new insights into EV71-induced apoptosis, which stimulates TLR9 in EV71-associated infections. PMID:25078697

  13. Molecular Menagerie

    NSDL National Science Digital Library

    Howard Hughes Medical Institute

    2002-01-01

    In this activity, learners use molecular model kits to construct familiar molecules like lactose, caffeine, and Aspirin. This activity helps learners understand how scientists use models to study molecules as well as how advances in 3-D graphics have made the use of computer models much easier. This activity guide includes chemical formulas and 3-D structural diagrams of various natural and artificial molecules. Note: the cost of molecular model kits is included in the estimated cost of materials.

  14. A molecular mechanism that confines the activity pattern of miR165 in Arabidopsis leaf primordia.

    PubMed

    Tatematsu, Kiyoshi; Toyokura, Koichi; Miyashima, Shunsuke; Nakajima, Keiji; Okada, Kiyotaka

    2015-05-01

    In Arabidopsis leaf primordia, the expression of HD-Zip III, which promotes tissue differentiation on the adaxial side of the leaf primordia, is repressed by miRNA165/166 (miR165/166). Small RNAs, including miRNAs, can move from cell to cell. In this study, HD-Zip III expression was strikingly repressed by miR165/166 in the epidermis and parenchyma cells on the abaxial side of the leaf primordia compared with those on the adaxial side. We also found that the MIR165A locus, which was expressed in the abaxial epidermis, was sufficient to establish the rigid repression pattern of HD-Zip III expression in the leaf primordia. Ectopic expression analyses of MIR165A showed that the abaxial-biased miR165 activity in the leaf primordia was formed neither by a polarized distribution of factors affecting miR165 activity nor by a physical boundary inhibiting the cell-to-cell movement of miRNA between the adaxial and abaxial sides. We revealed that cis-acting factors, including the promoter, backbone, and mature miRNA sequence of MIR165A, are necessary for the abaxial-biased activity of miR165 in the leaf primordia. We also found that the abaxial-determining genes YABBYs are trans-acting factors that are necessary for the miR165 activity pattern, resulting in the rigid determination of the adaxial-abaxial boundary in leaf primordia. Thus, we proposed a molecular mechanism in which the abaxial-biased patterning of miR165 activity is confined. PMID:25788175

  15. Mighty Molecules

    NSDL National Science Digital Library

    Carlyn Little

    1997-01-01

    In this activity, learners use marshmallows and gum drops to construct seven models of molecules. Learners classify (solid, liquid or gas) and draw diagrams of the molecules. Learners can also create a table showing the chemical formula for each molecule and identify a common use for each chemical. Use this activity to introduce learners to molecules, compounds, and bonds.

  16. Mobility of signaling molecules: the key to deciphering plant organogenesis.

    PubMed

    Kawade, Kensuke; Tanimoto, Hirokazu

    2015-01-01

    Signaling molecules move between cells to form a characteristic distribution pattern within a developing organ; thereafter, they spatiotemporally regulate organ development. A key question in this process is how the signaling molecules robustly form the precise distribution on a tissue scale in a reproducible manner. Despite of an increasing number of quantitative studies regarding the mobility of signaling molecules, the detail mechanism of organogenesis via intercellular signaling is still unclear. We here review the potential advantages of plant development to address this question, focusing on the cytoplasmic continuity of plant cells through the plasmodesmata. The plant system would provide a unique opportunity to define the simple transportation mode of diffusion process, and, hence, the mechanism of organogenesis via intercellular signaling. Based on the advances in the understanding of intercellular signaling at the molecular level and in the quantitative imaging techniques, we discuss our current challenges in measuring the mobility of signaling molecules for deciphering plant organogenesis. PMID:25516503

  17. Surface Patterning of Benzene Carboxylic Acids on Graphite: Influence of structure, solvent, and concentration on molecular self-assembly

    NASA Astrophysics Data System (ADS)

    Florio, Gina; Stiso, Kimberly; Campanelli, Joseph; Dessources, Kimberly; Folkes, Trudi

    2012-02-01

    Scanning tunneling microscopy (STM) was used to investigate the molecular self-assembly of four different benzene carboxylic acid derivatives at the liquid/graphite interface: pyromellitic acid (1,2,4,5-benzenetetracarboxylic acid), trimellitic acid (1,2,4-benzenetricarboxylic acid), trimesic acid (1,3,5-benzenetricarboxylic acid), and 1,3,5-benzenetriacetic acid. A range of two dimensional networks are observed that depend sensitively on the number of carboxylic acids present, the nature of the solvent, and the solution concentration. We will describe our recent efforts to determine (a) the preferential two-dimensional structure(s) for each benzene carboxylic acid at the liquid/graphite interface, (b) the thermodynamic and kinetic factors influencing self-assembly (or lack thereof), (c) the role solvent plays in the assembly, (e) the effect of in situ versus ex situ dilution on surface packing density, and (f) the temporal evolution of the self-assembled monolayer. Results of computational analysis of analog molecules and model monolayer films will also be presented to aid assignment of network structures and to provide a qualitative picture of surface adsorption and network formation.

  18. Single molecule data under scrutiny. Comment on "Extracting physics of life at the molecular level: A review of single-molecule data analyses" by W. Colomb & S.K. Sarkar

    NASA Astrophysics Data System (ADS)

    Wohland, Thorsten

    2015-06-01

    Single Molecule Detection and Spectroscopy have grown from their first beginnings into mainstream, mature research areas that are widely applied in the biological sciences. However, despite the advances in technology and the application of many single molecule techniques even in in vivo settings, the data analysis of single molecule experiments is complicated by noise, systematic errors, and complex underlying processes that are only incompletely understood. Colomb and Sarkar provide in this issue an overview of single molecule experiments and the accompanying problems in data analysis, which have to be overcome for a proper interpretation of the experiments [1].

  19. JCE Featured Molecules

    NSDL National Science Digital Library

    These interactive images are linked to molecular structures or other graphic images from articles in our print Journal. Many articles in the Journal of Chemical Education include molecular structures naturally in a two-dimensional representation. This collection of interactive Chime-based structures are chosen from some of these molecules. While many such Web-based structure collections exist, having the structures in a single location and linked to specific articles in JCE (and vice versa) will benefit both teachers and students. In addition to static images, two fully manipulable versions (Jmol, MDL Chime) of these molecules are available.

  20. Disclosure pattern and follow-up after the molecular diagnosis of BRCA/CHEK2 mutations.

    PubMed

    Kegelaers, D; Merckx, W; Odeurs, P; van den Ende, J; Blaumeiser, B

    2014-04-01

    Five to 10% of all breast cancer cases are due to mutations of high penetrance susceptibility genes, especially BRCA1 and BRCA2. In families with known BRCA mutations, disclosure of genetic test results could induce relatives to undergo genetic testing themselves and adopt cancer risk management strategies, if necessary. This study examines disclosure patterns of individuals tested for mutations in the BRCA1, BRCA2 and CHEK2 genes to first-degree relatives with emphasis on a possible gender difference. It also assesses which management strategy is preferred by mutation-positive women in Belgium and the influence of psychological characteristics on communication and choice of management strategy. Ninety-nine adults from BRCA/CHEK2 families, selected from the Centre of Medical Genetics of Antwerp, were included in the study. They were provided with medical and psychological questionnaires, the latter being the Self-Assessment Questionnaire, which is the Dutch version of the Spielberger State-Trait Anxiety Inventory and the Dutch version of the Coping Inventory for Stressful Situations (CISS-NL). The survey focused on disclosure, coping and management strategies with special attention on possible gender differences. The influence of socio-demographic and medical data on disclosure and cancer risk management as well as the influence of psychological features were examined by means of various statistical analyses. Ninety-nine patients were included, of whom 25 (25 %) were male. Eighty-seven percent of the participants informed all of their adult first-degree relatives about their mutation status without any gender discrimination. Seventy-eight percent of highly-educated participants informed all of their adult first-degree relatives, compared to 98 % of less formally-educated participants (p?=?0.006). The majority of mutation-positive women preferred prophylactic surgery to surveillance. Psychological differences appeared to have little influence on disclosure patterns and management strategies. The gender difference seems to be less pronounced than previously assumed. A striking observation, however, is the fact that significantly more participants who were less formally-educated informed all of their adult first-degree relatives, compared to participants who were highly-educated. In our study population, most female mutation carriers opted for prophylactic surgery. Since the study population is small, further studies are needed to enhance the generalizability of these results. PMID:24114282

  1. Effect of substituent pattern and molecular weight of cellulose ethers on interactions with different bile salts.

    PubMed

    Torcello-Gómez, Amelia; Fernández Fraguas, Cristina; Ridout, Mike J; Woodward, Nicola C; Wilde, Peter J; Foster, Timothy J

    2015-03-11

    Some known mechanisms proposed for the reduction of blood cholesterol by dietary fibre are: binding with bile salts in the duodenum and prevention of lipid absorption, which can be partially related with the bile salt binding. In order to gain new insights into the mechanisms of the binding of dietary fibre to bile salts, the goal of this work is to study the main interactions between cellulose derivatives and two types of bile salts. Commercial cellulose ethers: methyl (MC), hydroxypropyl (HPC) and hydroxypropylmethyl cellulose (HPMC), have been chosen as dietary fibre due to their highly functional properties important in manufactured food products. Two types of bile salts: sodium taurocholate (NaTC) and sodium taurodeoxycholate (NaTDC), have been chosen to understand the effect of the bile salt type. Interactions in the bulk have been investigated by means of differential scanning calorimetry (DSC) and linear mechanical spectroscopy. Results show that both bile salts have inhibitory effects on the thermal structuring of cellulose ethers and this depends on the number and type of substitution in the derivatised celluloses, and is not dependent upon molecular weight. Concerning the bile salt type, the more hydrophobic bile salt (NaTDC) has greater effect on these interactions, suggesting more efficient adsorption onto cellulose ethers. These findings may have implications in the digestion of cellulose-stabilised food matrices, providing a springboard to develop new healthy cellulose-based food products with improved functional properties. PMID:25679293

  2. HIV-1 molecular epidemiology evidence and transmission patterns in the Middle East and North Africa.

    PubMed

    Mumtaz, Ghina; Hilmi, Nahla; Akala, Francisca Ayodeji; Semini, Iris; Riedner, Gabriele; Wilson, David; Abu-Raddad, Laith J

    2011-03-01

    The distribution of HIV-1 subtypes in a population tracks the spread and evolution of the epidemic. This study is a systematic review of all available evidence on HIV-1 molecular epidemiology and subtype distribution in the Middle East and North Africa. Sources of data included Medline and various institutional documents and databases. In several countries, a diverse distribution of HIV-1 subtypes was observed principally reflecting travel-related exogenous exposures. A trend for a dominant HIV-1 subtype was observed in a few other settings and was often linked to HIV transmission within specific high-risk groups such as subtype A and CRF35_AD among injecting drug users and subtype C among commercial sex networks. Multiple exogenous introductions of HIV-1 variants seemed common to all countries, as observed from the high diversity in subtypes, or the high genetic divergence among any specific subtype even if predominant. In several countries though, epidemic-type clustering of specific subtypes suggests established or nascent HIV epidemics among classic core risk groups for HIV infection. HIV prevention efforts in MENA must be prioritized for these high-risk groups. PMID:21036790

  3. Self-assembly of ?-6T Molecule on Ag(100) and Related STM Induced Luminescence

    NASA Astrophysics Data System (ADS)

    Chen, Liu-guo; Zhang, Chao; Zhang, Rui; Dong, Zhen-chao

    2011-12-01

    We have investigated the self-assembly and light emission properties of organic ?-sexithiophene (?-6T) molecules on Ag(100) under different coverage by scanning tunneling microscopy (STM). At very low coverage, the ?-6T molecules form a unique enantiomer by grouping four molecules into a windmill supermolecular structure. As the coverage is increased, ?-6T molecules tend to pack side by side into a denser stripe structure. Further increase of the coverage will lead to the layer-by-layer growth of molecules on Ag(100) with the lower-layer stripe pattern serving as a template. Molecular fluorescence for ?-6T molecules on Ag(100) at a coverage of five monolayers has been detected by light excitations, which indicates a well decoupled electronic states for the top-layer ?-6T molecules. However, the STM induced luminescent spectra for the same sample reveal only plasmonic-like emission. The absence of intramolecular fluorescence in this case suggests that the electronic decoupling is not a sufficient condition for generating photon emission from molecules. For intramolecular fluorescence to occur, the orientation of the dynamic dipole moment of molecules and the energy-level alignment at the molecule-metal interface are also important so that molecules can be effectively excited through efficient dipolar coupling with local plasmons and by injecting holes into the molecules.

  4. Complex patterns of continental speciation: molecular phylogenetics and biogeography of sub-Saharan puddle frogs (Phrynobatrachus).

    PubMed

    Zimkus, Breda M; Rödel, Mark-Oliver; Hillers, Annika

    2010-06-01

    Puddle frogs (Anura: Phrynobatrachidae) are one of the most species-rich sub-Saharan amphibian groups, occupying an extraordinarily diverse range of habitats. We construct the first phylogeny of puddle frogs, utilizing mitochondrial (12S rRNA, valine-tRNA, and 16S rRNA) and nuclear (RAG-1) DNA. Phylogenetic analyses are conducted using separate and combined partitions under maximum parsimony, maximum likelihood, and Bayesian criterion. Monophyly of the Phrynobatrachidae is well supported, and three major clades of Phrynobatrachus are identified. We reconstructed a biogeographic history using habitat preference, elevation, and geographic distribution. Habitat niches appear to be conserved between sister species, with the majority of species favoring forest over savanna habitats and the most recent common ancestor of the Phrynobatrachidae reconstructed as a forest species. Analyses of elevational data identify three independent colonizations of highland regions, one in each of the three major clades. Ancestral reconstructions support an East African origination of puddle frogs. Most species are restricted to one of five sub-Saharan regions and are distributed within the Eastern, Central, and Western zones with far fewer species in Southern Africa. These results elucidate the complex patterns of spatial niche partitioning that have contributed to the diversification of this widely distributed, sub-Saharan genus. PMID:20034584

  5. Molecular characterization of three gonadotropin subunits and their expression patterns during ovarian maturation in Cynoglossus semilaevis.

    PubMed

    Shi, Bao; Liu, Xuezhou; Xu, Yongjiang; Wang, Shanshan

    2015-01-01

    The endocrine regulation of reproduction in a multiple spawning flatfish with an ovary of asynchronous development remains largely unknown. The objectives of this study were to monitor changes in mRNA expression patterns of three gonadotropin hormone (GTH) subunits (FSH?, LH? and CG?) and plasma GTH levels during ovarian maturation of half-smooth tongue sole Cynoglossus semilaevis. Cloning and sequence analysis revealed that the cDNAs of FSH?, LH? and CG? were 541, 670 and 685 bp in length, and encode for peptides of 130, 158 and 127 amino acids, respectively. The number of cysteine residues and potential N-linked glycosylation sites of the flatfish GTHs were conserved among teleosts. However, the primary structure of GTHs in Pleuronectiformes appeared to be highly divergent. The FSH? transcriptional level in the pituitary remained high during the vitellogenic stage while plasma levels of FSH peaked and oocyte development was stimulated. The LH? expression in the pituitary and ovary reached the maximum level during oocyte maturation stages when the plasma levels of LH peaked. The brain GTHs were expressed at the different ovarian stages. These results suggested that FSH and LH may simultaneously regulate ovarian development and maturation through the brain-pituitary-ovary axis endocrine system in tongue sole. PMID:25633101

  6. Molecular imaging coupled to pattern recognition distinguishes response to temozolomide in preclinical glioblastoma.

    PubMed

    Delgado-Goñi, Teresa; Julià-Sapé, Margarida; Candiota, Ana Paula; Pumarola, Martí; Arús, Carles

    2014-11-01

    Non-invasive monitoring of response to treatment of glioblastoma (GB) is nowadays carried out using MRI. MRS and MR spectroscopic imaging (MRSI) constitute promising tools for this undertaking. A temozolomide (TMZ) protocol was optimized for GL261 GB. Sixty-three mice were studied by MRI/MRS/MRSI. The spectroscopic information was used for the classification of control brain and untreated and responding GB, and validated against post-mortem immunostainings in selected animals. A classification system was developed, based on the MRSI-sampled metabolome of normal brain parenchyma, untreated and responding GB, with a 93% accuracy. Classification of an independent test set yielded a balanced error rate of 6% or less. Classifications correlated well both with tumor volume changes detected by MRI after two TMZ cycles and with the histopathological data: a significant decrease (p < 0.05) in the proliferation and mitotic rates and a 4.6-fold increase in the apoptotic rate. A surrogate response biomarker based on the linear combination of 12 spectral features has been found in the MRS/MRSI pattern of treated tumors, allowing the non-invasive classification of growing and responding GL261 GB. The methodology described can be applied to preclinical treatment efficacy studies to test new antitumoral drugs, and begets translational potential for early response detection in clinical studies. PMID:25208348

  7. Patterns of molecular variation in a species-wide germplasm set of Brassica napus.

    PubMed

    Bus, Anja; Körber, Niklas; Snowdon, Rod J; Stich, Benjamin

    2011-12-01

    Rapeseed (Brassica napus L.) is the leading European oilseed crop serving as source for edible oil and renewable energy. The objectives of our study were to (i) examine the population structure of a large and diverse set of B. napus inbred lines, (ii) investigate patterns of genetic diversity within and among different germplasm types, (iii) compare the two genomes of B. napus with regard to genetic diversity, and (iv) assess the extent of linkage disequilibrium (LD) between simple sequence repeat (SSR) markers. Our study was based on 509 B. napus inbred lines genotyped with 89 genome-specific SSR primer combinations. Both a principal coordinate analysis and software STRUCTURE revealed that winter types, spring types, and swedes were assigned to three major clusters. The genetic diversity of winter oilseed rape was lower than the diversity found in other germplasm types. Within winter oilseed rape types, a decay of genetic diversity with more recent release dates and reduced levels of erucic acid and glucosinolates was observed. The percentage of linked SSR loci pairs in significant (r (2) > Q (95 unlinked loci pairs)) LD was 6.29% for the entire germplasm set. Furthermore, LD decayed rapidly with distance, which will allow a relatively high mapping resolution in genome-wide association studies using our germplasm set, but, on the other hand, will require a high number of markers. PMID:21847624

  8. Molecular Properties by Quantum Monte Carlo: An Investigation on the Role of the Wave Function Ansatz and the Basis Set in the Water Molecule

    PubMed Central

    Zen, Andrea; Luo, Ye; Sorella, Sandro; Guidoni, Leonardo

    2014-01-01

    Quantum Monte Carlo methods are accurate and promising many body techniques for electronic structure calculations which, in the last years, are encountering a growing interest thanks to their favorable scaling with the system size and their efficient parallelization, particularly suited for the modern high performance computing facilities. The ansatz of the wave function and its variational flexibility are crucial points for both the accurate description of molecular properties and the capabilities of the method to tackle large systems. In this paper, we extensively analyze, using different variational ansatzes, several properties of the water molecule, namely, the total energy, the dipole and quadrupole momenta, the ionization and atomization energies, the equilibrium configuration, and the harmonic and fundamental frequencies of vibration. The investigation mainly focuses on variational Monte Carlo calculations, although several lattice regularized diffusion Monte Carlo calculations are also reported. Through a systematic study, we provide a useful guide to the choice of the wave function, the pseudopotential, and the basis set for QMC calculations. We also introduce a new method for the computation of forces with finite variance on open systems and a new strategy for the definition of the atomic orbitals involved in the Jastrow-Antisymmetrised Geminal power wave function, in order to drastically reduce the number of variational parameters. This scheme significantly improves the efficiency of QMC energy minimization in case of large basis sets. PMID:24526929

  9. Molecular properties by Quantum Monte Carlo: an investigation on the role of the wave function ansatz and the basis set in the water molecule

    E-print Network

    Andrea Zen; Ye Luo; Sandro Sorella; Leonardo Guidoni

    2013-09-02

    Quantum Monte Carlo methods are accurate and promising many body techniques for electronic structure calculations which, in the last years, are encountering a growing interest thanks to their favorable scaling with the system size and their efficient parallelization, particularly suited for the modern high performance computing facilities. The ansatz of the wave function and its variational flexibility are crucial points for both the accurate description of molecular properties and the capabilities of the method to tackle large systems. In this paper, we extensively analyze, using different variational ansatzes, several properties of the water molecule, namely: the total energy, the dipole and quadrupole momenta, the ionization and atomization energies, the equilibrium configuration, and the harmonic and fundamental frequencies of vibration. The investigation mainly focuses on variational Monte Carlo calculations, although several lattice regularized diffusion Monte Carlo calculations are also reported. Through a systematic study, we provide a useful guide to the choice of the wave function, the pseudo potential, and the basis set for QMC calculations. We also introduce a new strategy for the definition of the atomic orbitals involved in the Jastrow - Antisymmetrised Geminal power wave function, in order to drastically reduce the number of variational parameters. This scheme significantly improves the efficiency of QMC energy minimization in case of large basis sets.

  10. Calculation of total cross sections for charge exchange in molecular collisions

    NASA Technical Reports Server (NTRS)

    Ioup, J.

    1979-01-01

    Areas of investigation summarized include nitrogen ion-nitrogen molecule collisions; molecular collisions with surfaces; molecular identification from analysis of cracking patterns of selected gases; computer modelling of a quadrupole mass spectrometer; study of space charge in a quadrupole; transmission of the 127 deg cylindrical electrostatic analyzer; and mass spectrometer data deconvolution.

  11. Molecular genetics of pattern formation in the inner ear: do compartment boundaries play a role?

    PubMed

    Brigande, J V; Kiernan, A E; Gao, X; Iten, L E; Fekete, D M

    2000-10-24

    The membranous labyrinth of the inner ear establishes a precise geometrical topology so that it may subserve the functions of hearing and balance. How this geometry arises from a simple ectodermal placode is under active investigation. The placode invaginates to form the otic cup, which deepens before pinching off to form the otic vesicle. By the vesicle stage many genes expressed in the developing ear have assumed broad, asymmetrical expression domains. We have been exploring the possibility that these domains may reflect developmental compartments that are instrumental in specifying the location and identity of different parts of the ear. The boundaries between compartments are proposed to be the site of inductive interactions required for this specification. Our work has shown that sensory organs and the endolymphatic duct each arise near the boundaries of broader gene expression domains, lending support to this idea. A further prediction of the model, that the compartment boundaries will also represent lineage-restriction compartments, is supported in part by fate mapping the otic cup. Our data suggest that two lineage-restriction boundaries intersect at the dorsal pole of the otocyst, a convergence that may be critical for the specification of endolymphatic duct outgrowth. We speculate that the patterning information necessary to establish these two orthogonal boundaries may emanate, in part, from the hindbrain. The compartment boundary model of ear development now needs to be tested through a variety of experimental perturbations, such as the removal of boundaries, the generation of ectopic boundaries, and/or changes in compartment identity. PMID:11050198

  12. Unique Patterns of Molecular Profiling between Human Prostate Cancer LNCaP and PC-3 Cells

    PubMed Central

    Dozmorov, Mikhail G.; Hurst, Robert E.; Culkin, Daniel J.; Kropp, Bradley P.; Frank, Mark Barton; Osban, Jeanette; Penning, Trevor M.; Lin, Hsueh-Kung

    2009-01-01

    BACKGROUND Human prostate cancer LNCaP and PC-3 cell lines have been extensively used to study prostate cancer progression and to develop therapeutic agents. Although LNCaP and PC-3 cells are generally assumed to represent early and late stages of prostate cancer, respectively, there is limited information regarding gene expression patterns between these two cell lines and its relationship to prostate cancer. METHODS Comprehensive gene expression analysis was performed. Total RNA was isolated from cultured cells and hybridized to Illumina human BeadChips representing 24,526 transcripts. Bioinformatics analysis was applied to identify cell line specific genes as well as biological mechanisms, pathways, and functions related to the genes. RESULTS A total of 2,198 genes were differentially expressed between LNCaP and PC-3 cells. Using a robust statistical analysis and high significance criteria, 115 and 188 genes were identified to be unique to LNCaP and PC-3 cells, respectively. LNCaP cells maintained various metabolic pathways including a gene cluster that encodes UDP-glucuronosyltransferases. Several transcription factors including Tal?/?, GATA-1, and c-Myc/Max may be responsible for regulating LNCaP cell specific genes. By contrast, PC-3 cells were characterized by their unique expression of cytoskeleton-related genes and other genes including VEGFC, IL8, and TGF?2. CONCLUSIONS This study showed that LNCaP and PC-3 cells represent two distinct prostate cancer cell lineages. LNCaP cells retain many prostate cell specific properties, whereas PC-3 cells have acquired a more aggressive phenotype. Future studies for prostate cancer research need to consider similarities and differences between these two cells and their relationship to prostate cancer. PMID:19343732

  13. Reactive microCP on ultrathin block copolymer films: investigation of the microCP mechanism and application to sub-microm (bio)molecular patterning.

    PubMed

    Feng, Chuan Liang; Vancso, G Julius; Schönherr, Holger

    2007-01-30

    In this paper, the mechanism of the recently introduced soft lithographic patterning approach of reactive microcontact printing on thin substrate-supported polystyrene-block-poly(tert-butyl acrylate) (PS690-b-PtBA1210) films using trifluoroacetic acid (TFA)-inked elastomeric poly(dimethylsiloxane) (PDMS) stamps is investigated in detail. In this approach, solventless deprotection reactions are carried out with very high spatial definition using TFA as a volatile reagent that partitions into the PtBA skin layer. On the basis of a systematic investigation of the process, ink loading was identified as a crucial parameter for obtaining faithful pattern transfer. Using optimized conditions, submicrometer-sized patterns were successfully fabricated. In combination with subsequent wet chemical covalent coupling of various (bio)molecules, reactive microCP is established as an approach to afford positive, as well as negative, images of the features of the stamps used. In addition, the size of the patterned areas was manipulated by exploiting the controlled spreading of the ink; thus, stamps with identical features yield patterns with different sizes, yet identical periodicity, as shown for bovine serum albumin (BSA)-poly(ethylene glycol) patterns. The reactive microCP methodology affords new pathways for submicrometer-scale patterning of bioreactive surfaces. PMID:17241023

  14. Two Metallothionein Genes in Oxya chinensis: Molecular Characteristics, Expression Patterns and Roles in Heavy Metal Stress

    PubMed Central

    Liu, Yaoming; Wu, Haihua; Kou, Lihua; Liu, Xiaojian; Zhang, Jianzhen; Guo, Yaping; Ma, Enbo

    2014-01-01

    Metallothioneins (MTs) are small, cysteine-rich, heavy metal-binding proteins involved in metal homeostasis and detoxification in living organisms. In the present study, we cloned two MT genes (OcMT1 and OcMT2) from Oxya chinensis, analyzed the expression patterns of the OcMT transcripts in different tissues and at varying developmental stages using real-time quantitative PCR (RT-qPCR), evaluated the functions of these two MTs using RNAi and recombinant proteins in an E. coli expression system. The full-length cDNAs of OcMT1 and OcMT2 encoded 40 and 64 amino acid residues, respectively. We found Cys-Cys, Cys-X-Cys and Cys-X-Y-Z-Cys motifs in OcMT1 and OcMT2. These motifs might serve as primary chelating sites, as in other organisms. These characteristics suggest that OcMT1 and OcMT2 may be involved in heavy metal detoxification by capturing the metals. Two OcMT were expressed at all developmental stages, and the highest levels were found in the eggs. Both transcripts were expressed in all eleven tissues examined, with the highest levels observed in the brain and optic lobes, followed by the fat body. The expression of OcMT2 was also relatively high in the ovaries. The functions of OcMT1 and OcMT2 were explored using RNA interference (RNAi) and different concentrations and treatment times for the three heavy metals. Our results indicated that mortality increased significantly from 8.5% to 16.7%, and this increase was both time- and dose-dependent. To evaluate the abilities of these two MT proteins to confer heavy metal tolerance to E. coli, the bacterial cells were transformed with pET-28a plasmids containing the OcMT genes. The optical densities of both the MT-expressing and control cells decreased with increasing concentrations of CdCl2. Nevertheless, the survival rates of the MT-overexpressing cells were higher than those of the controls. Our results suggest that these two genes play important roles in heavy metal detoxification in O. chinensis. PMID:25391131

  15. Molecular Interactions of the Min Protein System Reproduce Spatiotemporal Patterning in Growing and Dividing Escherichia coli Cells.

    PubMed

    Walsh, James C; Angstmann, Christopher N; Duggin, Iain G; Curmi, Paul M G

    2015-01-01

    Oscillations of the Min protein system are involved in the correct midcell placement of the divisome during Escherichia coli cell division. Based on molecular interactions of the Min system, we formulated a mathematical model that reproduces Min patterning during cell growth and division. Specifically, the increase in the residence time of MinD attached to the membrane as its own concentration increases, is accounted for by dimerisation of membrane-bound MinD and its interaction with MinE. Simulation of this system generates unparalleled correlation between the waveshape of experimental and theoretical MinD distributions, suggesting that the dominant interactions of the physical system have been successfully incorporated into the model. For cells where MinD is fully-labelled with GFP, the model reproduces the stationary localization of MinD-GFP for short cells, followed by oscillations from pole to pole in larger cells, and the transition to the symmetric distribution during cell filamentation. Cells containing a secondary, GFP-labelled MinD display a contrasting pattern. The model is able to account for these differences, including temporary midcell localization just prior to division, by increasing the rate constant controlling MinD ATPase and heterotetramer dissociation. For both experimental conditions, the model can explain how cell division results in an equal distribution of MinD and MinE in the two daughter cells, and accounts for the temperature dependence of the period of Min oscillations. Thus, we show that while other interactions may be present, they are not needed to reproduce the main characteristics of the Min system in vivo. PMID:26018614

  16. Molecular Interactions of the Min Protein System Reproduce Spatiotemporal Patterning in Growing and Dividing Escherichia coli Cells

    PubMed Central

    Walsh, James C.; Angstmann, Christopher N.; Duggin, Iain G.; Curmi, Paul M. G.

    2015-01-01

    Oscillations of the Min protein system are involved in the correct midcell placement of the divisome during Escherichia coli cell division. Based on molecular interactions of the Min system, we formulated a mathematical model that reproduces Min patterning during cell growth and division. Specifically, the increase in the residence time of MinD attached to the membrane as its own concentration increases, is accounted for by dimerisation of membrane-bound MinD and its interaction with MinE. Simulation of this system generates unparalleled correlation between the waveshape of experimental and theoretical MinD distributions, suggesting that the dominant interactions of the physical system have been successfully incorporated into the model. For cells where MinD is fully-labelled with GFP, the model reproduces the stationary localization of MinD-GFP for short cells, followed by oscillations from pole to pole in larger cells, and the transition to the symmetric distribution during cell filamentation. Cells containing a secondary, GFP-labelled MinD display a contrasting pattern. The model is able to account for these differences, including temporary midcell localization just prior to division, by increasing the rate constant controlling MinD ATPase and heterotetramer dissociation. For both experimental conditions, the model can explain how cell division results in an equal distribution of MinD and MinE in the two daughter cells, and accounts for the temperature dependence of the period of Min oscillations. Thus, we show that while other interactions may be present, they are not needed to reproduce the main characteristics of the Min system in vivo. PMID:26018614

  17. Vibronic spectra of single dibenzoterrylene molecules in anthracene and 2,3-dimethylanthracene crystals

    NASA Astrophysics Data System (ADS)

    Makarewicz, A.; Deperasi?ska, I.; Karpiuk, E.; Nowacki, J.; Kozankiewicz, B.

    2012-05-01

    The vibronic structure of fluorescence excitation spectra of single molecules of dibenzoterrylene (DBT) in anthracene (Ac) and in 2,3-dimethylanthracene (2,3-DMA) crystals were studied at 5 K. The vibronic patterns observed for different single molecules in the same crystal site were explained as fingerprints of the molecular geometry, which according to the ONIOM calculations are strongly dependent on the local insertion cavity. The 'dipolar' disorder encountered in the 2,3-DMA crystals led to a broad frequency distribution of the purely electronic lines of single molecules. The saturation curves for the (0, 0) and vibronic transitions were studied.

  18. Molecular fountain.

    SciTech Connect

    Strecker, Kevin E.; Chandler, David W.

    2009-09-01

    A molecular fountain directs slowly moving molecules against gravity to further slow them to translational energies that they can be trapped and studied. If the molecules are initially slow enough they will return some time later to the position from which they were launched. Because this round trip time can be on the order of a second a single molecule can be observed for times sufficient to perform Hz level spectroscopy. The goal of this LDRD proposal was to construct a novel Molecular Fountain apparatus capable of producing dilute samples of molecules at near zero temperatures in well-defined user-selectable, quantum states. The slowly moving molecules used in this research are produced by the previously developed Kinematic Cooling technique, which uses a crossed atomic and molecular beam apparatus to generate single rotational level molecular samples moving slowly in the laboratory reference frame. The Kinematic Cooling technique produces cold molecules from a supersonic molecular beam via single collisions with a supersonic atomic beam. A single collision of an atom with a molecule occurring at the correct energy and relative velocity can cause a small fraction of the molecules to move very slowly vertically against gravity in the laboratory. These slowly moving molecules are captured by an electrostatic hexapole guiding field that both orients and focuses the molecules. The molecules are focused into the ionization region of a time-of-flight mass spectrometer and are ionized by laser radiation. The new molecular fountain apparatus was built utilizing a new design for molecular beam apparatus that has allowed us to miniaturize the apparatus. This new design minimizes the volumes and surface area of the machine allowing smaller pumps to maintain the necessary background pressures needed for these experiments.

  19. Beyond experimental noise: Analyzing single-molecule data of heterogeneous systems. Comment on "Extracting physics of life at the molecular level: A review of single-molecule data analyses" by W. Colomb and S.K. Sarkar

    NASA Astrophysics Data System (ADS)

    Meroz, Yasmine

    2015-06-01

    In the 1980s the world witnessed the advent of single-molecule experiments. The first atomic resolution characterization of a surface was reported by scanning tunneling microscope (STM) in 1982 [1], followed by atomic force microscope (AFM) in 1986 [2]. The first optical detection and spectroscopy of a single molecule in a solid took place in 1989 [3,4], in a time where essentially all chemical experiments were made on bulk, i.e. averaging over millions of copies of the same molecule.

  20. The microgeographical patterns of morphological and molecular variation of a mixed ploidy population in the species complex Actinidia chinensis.

    PubMed

    Liu, Yifei; Li, Dawei; Yan, Ling; Huang, Hongwen

    2015-01-01

    Polyploidy and hybridization are thought to have significant impacts on both the evolution and diversification of the genus Actinidia, but the structure and patterns of morphology and molecular diversity relating to ploidy variation of wild Actinidia plants remain much less understood. Here, we examine the distribution of morphological variation and ploidy levels along geographic and environmental variables of a large mixed-ploidy population of the A. chinensis species complex. We then characterize the extent of both genetic and epigenetic diversity and differentiation exhibited between individuals of different ploidy levels. Our results showed that while there are three ploidy levels in this population, hexaploids were constituted the majority (70.3%). Individuals with different ploidy levels were microgeographically structured in relation to elevation and extent of niche disturbance. The morphological characters examined revealed clear difference between diploids and hexaploids, however tetraploids exhibited intermediate forms. Both genetic and epigenetic diversity were high but the differentiation among cytotypes was weak, suggesting extensive gene flow and/or shared ancestral variation occurred in this population even across ploidy levels. Epigenetic variation was clearly correlated with changes in altitudes, a trend of continuous genetic variation and gradual increase of epigenomic heterogeneities of individuals was also observed. Our results show that complex interactions between the locally microgeographical environment, ploidy and gene flow impact A. chinensis genetic and epigenetic variation. We posit that an increase in ploidy does not broaden the species habitat range, but rather permits A. chinensis adaptation to specific niches. PMID:25658107

  1. Molecular Biogeography of Tribe Thermopsideae (Leguminosae): A Madrean-Tethyan Disjunction Pattern with an African Origin of Core Genistoides.

    PubMed

    Zhang, Ming-Li; Huang, Jian-Feng; Sanderson, Stewart C; Yan, Ping; Wu, Yu-Hu; Pan, Bo-Rong

    2015-01-01

    Thermopsideae has 45 species and exhibits a series of interesting biogeographical distribution patterns, such as Madrean-Tethyan disjunction and East Asia-North America disjunction, with a center of endemism in the Qinghai-Xizang Plateau (QTP) and Central Asia. Phylogenetic analysis in this paper employed maximum likelihood using ITS, rps16, psbA-trnH, and trnL-F sequence data; biogeographical approaches included BEAST molecular dating and Bayesian dispersal and vicariance analysis (S-DIVA). The results indicate that the core genistoides most likely originated in Africa during the Eocene to Oligocene, ca. 55-30?Ma, and dispersed eastward to Central Asia at ca. 33.47?Ma. The origin of Thermopsideae is inferred as Central Asian and dated to ca. 28.81?Ma. Ammopiptanthus is revealed to be a relic. Birth of the ancestor of Thermopsideae coincided with shrinkage of the Paratethys Sea at ca. 30?Ma in the Oligocene. The Himalayan motion of QTP uplift of ca. 20?Ma most likely drove the diversification between Central Asia and North America. Divergences in East Asia, Central Asia, the Mediterranean, and so forth, within Eurasia, except for Ammopiptanthus, are shown to be dispersals from the QTP. The onset of adaptive radiation at the center of the tribe, with diversification of most species in Thermopsis and Piptanthus at ca. 4-0.85?Ma in Tibet and adjacent regions, seems to have resulted from intense northern QTP uplift during the latter Miocene to Pleistocene. PMID:26114116

  2. Cellulose Binding Domains of a Phytophthora Cell Wall Protein Are Novel Pathogen-Associated Molecular Patterns[W

    PubMed Central

    Gaulin, Elodie; Dramé, Nani; Lafitte, Claude; Torto-Alalibo, Trudy; Martinez, Yves; Ameline-Torregrosa, Carine; Khatib, Moustafa; Mazarguil, Honoré; Villalba-Mateos, François; Kamoun, Sophien; Mazars, Christian; Dumas, Bernard; Bottin, Arnaud; Esquerré-Tugayé, Marie-Thérèse; Rickauer, Martina

    2006-01-01

    The cellulose binding elicitor lectin (CBEL) from Phytophthora parasitica nicotianae contains two cellulose binding domains (CBDs) belonging to the Carbohydrate Binding Module1 family, which is found almost exclusively in fungi. The mechanism by which CBEL is perceived by the host plant remains unknown. The role of CBDs in eliciting activity was investigated using modified versions of the protein produced in Escherichia coli or synthesized in planta through the potato virus X expression system. Recombinant CBEL produced by E. coli elicited necrotic lesions and defense gene expression when injected into tobacco (Nicotiana tabacum) leaves. CBEL production in planta induced necrosis. Site-directed mutagenesis on aromatic amino acid residues located within the CBDs as well as leaf infiltration assays using mutated and truncated recombinant proteins confirmed the importance of intact CBDs to induce defense responses. Tobacco and Arabidopsis thaliana leaf infiltration assays using synthetic peptides showed that the CBDs of CBEL are essential and sufficient to stimulate defense responses. Moreover, CBEL elicits a transient variation of cytosolic calcium levels in tobacco cells but not in protoplasts. These results define CBDs as a novel class of molecular patterns in oomycetes that are targeted by the innate immune system of plants and might act through interaction with the cell wall. PMID:16766692

  3. S100B Protein, A Damage-Associated Molecular Pattern Protein in the Brain and Heart, and Beyond

    PubMed Central

    Sorci, Guglielmo; Bianchi, Roberta; Riuzzi, Francesca; Tubaro, Claudia; Arcuri, Cataldo; Giambanco, Ileana; Donato, Rosario

    2010-01-01

    S100B belongs to a multigenic family of Ca2+-binding proteins of the EF-hand type and is expressed in high abundance in the brain. S100B interacts with target proteins within cells thereby altering their functions once secreted/released with the multiligand receptor RAGE. As an intracellular regulator, S100B affects protein phosphorylation, energy metabolism, the dynamics of cytoskeleton constituents (and hence, of cell shape and migration), Ca2+ homeostasis, and cell proliferation and differentiation. As an extracellular signal, at low, physiological concentrations, S100B protects neurons against apoptosis, stimulates neurite outgrowth and astrocyte proliferation, and negatively regulates astrocytic and microglial responses to neurotoxic agents, while at high doses S100B causes neuronal death and exhibits properties of a damage-associated molecular pattern protein. S100B also exerts effects outside the brain; as an intracellular regulator, S100B inhibits the postinfarction hypertrophic response in cardiomyocytes, while as an extracellular signal, (high) S100B causes cardiomyocyte death, activates endothelial cells, and stimulates vascular smooth muscle cell proliferation. PMID:20827421

  4. Molecular Biogeography of Tribe Thermopsideae (Leguminosae): A Madrean-Tethyan Disjunction Pattern with an African Origin of Core Genistoides

    PubMed Central

    Zhang, Ming-Li; Huang, Jian-Feng; Sanderson, Stewart C.; Yan, Ping; Wu, Yu-Hu; Pan, Bo-Rong

    2015-01-01

    Thermopsideae has 45 species and exhibits a series of interesting biogeographical distribution patterns, such as Madrean-Tethyan disjunction and East Asia-North America disjunction, with a center of endemism in the Qinghai-Xizang Plateau (QTP) and Central Asia. Phylogenetic analysis in this paper employed maximum likelihood using ITS, rps16, psbA-trnH, and trnL-F sequence data; biogeographical approaches included BEAST molecular dating and Bayesian dispersal and vicariance analysis (S-DIVA). The results indicate that the core genistoides most likely originated in Africa during the Eocene to Oligocene, ca. 55-30?Ma, and dispersed eastward to Central Asia at ca. 33.47?Ma. The origin of Thermopsideae is inferred as Central Asian and dated to ca. 28.81?Ma. Ammopiptanthus is revealed to be a relic. Birth of the ancestor of Thermopsideae coincided with shrinkage of the Paratethys Sea at ca. 30?Ma in the Oligocene. The Himalayan motion of QTP uplift of ca. 20?Ma most likely drove the diversification between Central Asia and North America. Divergences in East Asia, Central Asia, the Mediterranean, and so forth, within Eurasia, except for Ammopiptanthus, are shown to be dispersals from the QTP. The onset of adaptive radiation at the center of the tribe, with diversification of most species in Thermopsis and Piptanthus at ca. 4-0.85?Ma in Tibet and adjacent regions, seems to have resulted from intense northern QTP uplift during the latter Miocene to Pleistocene. PMID:26114116

  5. Hypericin-based photodynamic therapy induces surface exposure of damage-associated molecular patterns like HSP70 and calreticulin.

    PubMed

    Garg, Abhishek D; Krysko, Dmitri V; Vandenabeele, Peter; Agostinis, Patrizia

    2012-02-01

    Surface-exposed HSP70 and calreticulin are damage-associated molecular patterns (DAMPs) crucially involved in modulating the success of cancer therapy. Photodynamic therapy (PDT) involves the administration of a photosensitising (PTS) agent followed by visible light-irradiation. The reactive oxygen species that are thus generated directly kill tumours by damaging their microvasculature and inducing a local inflammatory reaction. PDT with the PTS photofrin is associated with DAMPs exposure, but the same is not true for other PTSs. Here, we show that when cancer cells are treated with hypericin-based PDT (Hyp-PDT), they surface-expose both HSP70 and calreticulin (CRT). Induction of CRT exposure was not accompanied by co-exposure of ERp57, but this did not compromise the ability of the exposed CRT to regulate the phagocytosis of Hyp-PDT-treated cancer cells by dendritic cells. Interestingly, we found that Hyp-PDT-induced CRT exposure (in contrast to anthracycline-induced CRT exposure) was independent of the presence of ERp57. Our results indicate that Hyp-PDT is a potential anti-cancer immunogenic modality. PMID:22193987

  6. Characterization of the molecular features and expression patterns of two serine proteases in Hermetia illucens (Diptera: Stratiomyidae) larvae.

    PubMed

    Kim, Wontae; Bae, Sungwoo; Kim, Ayoung; Park, Kwanho; Lee, Sangbeom; Choi, Youngcheol; Han, Sangmi; Park, Younghan; Koh, Youngho

    2011-06-01

    To investigate the molecular scavenging capabilities of the larvae of Hermetia illucens, two serine proteases (SPs) were cloned and characterized. Multiple sequence alignments and phylogenetic tree analysis of the deduced amino acid sequences of Hi-SP1 and Hi-SP2 were suggested that Hi-SP1 may be a chymotrypsin- and Hi-SP2 may be a trypsin-like protease. Hi-SP1 and Hi-SP2 3-D homology models revealed that a catalytic triad, three disulfide bonds, and a substrate-binding pocket were highly conserved, as would be expected of a SP. E. coli expressed Hi-SP1 and Hi-SP2 showed chymotrypsin or trypsin activities, respectively. Hi-SP2 mRNAs were consistently expressed during larval development. In contrast, the expression of Hi-SP1 mRNA fluctuated between feeding and molting stages and disappeared at the pupal stages. These expression pattern differences suggest that Hi-SP1 may be a larval specific chymotrypsin-like protease involved with food digestion, while Hi-SP2 may be a trypsin-like protease with diverse functions at different stages. PMID:21699751

  7. Molecular cloning of IGF-1 and IGF-1 receptor and their expression pattern in the Chilean flounder (Paralichthys adspersus).

    PubMed

    Escobar, Sebastian; Fuentes, Eduardo N; Poblete, Erika; Valdés, Juan A; Safian, Diego; Reyes, Ariel E; Alvarez, Marco; Molina, Alfredo

    2011-07-01

    Insulin-like growth factor-1 and insulin-like growth factor-1 receptor (IGF-1 and IGF-1R) play main roles in vertebrate growth and development. In fish, besides contributing to somatic growth, both molecules exhibit pleiotropic functions. We isolated complete cDNAs sequences encoding for both IGF-1 and IGF-1R in the Chilean flounder by using RT-PCR and rapid amplification of cDNAs ends (RACE) techniques. We analyzed gene expression in pre-metamorphic larvae and different organs of juvenile fish through whole mount in situ hybridization and RT-PCR, respectively. In addition, we studied the presence of calcified skeletal structures in pre-metamorphic larvae through the fluorescent chromophore calcein. The IGF-1 cDNA sequence displays an open reading frame of 558 nucleotides, encoding a 185 amino acid preproIGF-1. Moreover, IGF-1R contains an open reading frame spanning 4239 nucleotides, rendering a 702 amino acid subunit alpha and a 676 amino acid subunit beta. The deduced mature IGF-1 and IGF-1R exhibited high sequence identities with their corresponding orthologs in fishes, especially those domains involved in biological activity. RT-PCR showed expression of IGF-1 and IGF-1R transcripts in all studied tissues, consistent with their pleiotropic functions. Furthermore, we observed IGF-1 expression in notochord and IGF-1R expression in notochord, somites and head in larvae of 8 and 9 days post fertilization. Complementarily, we detected in larvae of 8 days post fertilization the presence of calcified skeletal structures in notochord and head. Interestingly, both mRNAs and calcified structures were found in territories such as notochord, an embryonic midline structure essential for the pattern of surrounding tissues as nervous system and mesoderm. Our results suggest that IGF-1 and its receptor play an important role in the development of the nervous system, muscle and bone-related structures during larval stages. PMID:21447399

  8. Molecular and Thermal Diffusion Coefficients of Alkane-Alkane and Alkane-Aromatic Binary Mixtures: Effect of Shape and Size of Molecules

    E-print Network

    Firoozabadi, Abbas

    Molecular and Thermal Diffusion Coefficients of Alkane-Alkane and Alkane-Aromatic Binary Mixtures Form: October 27, 2006 New molecular and thermal diffusion coefficients of binary mixtures of normal-molecular diffusion coefficient for nC10 from binary data. I. Introduction Molecular and thermal diffusion processes

  9. Correcting for bias of molecular confinement parameters induced by small-time-series sample sizes in single-molecule trajectories containing measurement noise.

    PubMed

    Calderon, Christopher P

    2013-07-01

    Several single-molecule studies aim to reliably extract parameters characterizing molecular confinement or transient kinetic trapping from experimental observations. Pioneering works from single-particle tracking (SPT) in membrane diffusion studies [Kusumi et al., Biophys. J. 65, 2021 (1993)] appealed to mean square displacement (MSD) tools for extracting diffusivity and other parameters quantifying the degree of confinement. More recently, the practical utility of systematically treating multiple noise sources (including noise induced by random photon counts) through likelihood techniques has been more broadly realized in the SPT community. However, bias induced by finite-time-series sample sizes (unavoidable in practice) has not received great attention. Mitigating parameter bias induced by finite sampling is important to any scientific endeavor aiming for high accuracy, but correcting for bias is also often an important step in the construction of optimal parameter estimates. In this article, it is demonstrated how a popular model of confinement can be corrected for finite-sample bias in situations where the underlying data exhibit Brownian diffusion and observations are measured with non-negligible experimental noise (e.g., noise induced by finite photon counts). The work of Tang and Chen [J. Econometrics 149, 65 (2009)] is extended to correct for bias in the estimated "corral radius" (a parameter commonly used to quantify confinement in SPT studies) in the presence of measurement noise. It is shown that the approach presented is capable of reliably extracting the corral radius using only hundreds of discretely sampled observations in situations where other methods (including MSD and Bayesian techniques) would encounter serious difficulties. The ability to accurately statistically characterize transient confinement suggests additional techniques for quantifying confined and/or hop diffusion in complex environments. PMID:23944492

  10. Intermolecular Forces for Polyatomic Molecules

    Microsoft Academic Search

    Taro Kihara

    1967-01-01

    Part I is a review of papers dealing with the convex-core potential (sometimes called the Kihara potential) of intermolecular forces, which is a useful mathematical model for the interaction between polyatomic molecules in gases. For molecular crystals electric multipoles of the molecules often play a decisive role in the crystal structures. This fact is demonstrated in Part II by use

  11. Loosely-Bound Diatomic Molecules.

    ERIC Educational Resources Information Center

    Balfour, W. J.

    1979-01-01

    Discusses concept of covalent bonding as related to homonuclear diatomic molecules. Article draws attention to the existence of bound rare gas and alkaline earth diatomic molecules. Summarizes their molecular parameters and offers spectroscopic data. Strength and variation with distance of interatomic attractive forces is given. (Author/SA)

  12. Effect of Al Concentration in AlGaAs Oxide Mask Pattern on Faceting Kinetics during Selective Area Growth of GaAs by Molecular Beam Epitaxy

    NASA Astrophysics Data System (ADS)

    Matsuda, Kazuhiro; Hayashi, Shota; Ushio, Shoji; Kaneko, Tadaaki

    2011-04-01

    An oxidized AlGaAs layer is used as an inorganic negative resist for low-energy electron-beam lithography. The patterned oxide can function as an ultrathin template for selectively growing GaAs mesa structures having side facets vertical to a GaAs(001) substrate by molecular beam epitaxy. With increase in the Al concentration in the oxide, the geometric shape of the structures with lateral growth on the oxide surface changes from triangular to pentagonal. This change is explained by a minimization effect of the total surface energy of the structure, including the interfacial energy between the lateral growth region and the patterned oxide mask.

  13. A Molecular–Structure Hypothesis

    PubMed Central

    Boeyens, Jan C. A.

    2010-01-01

    The self-similar symmetry that occurs between atomic nuclei, biological growth structures, the solar system, globular clusters and spiral galaxies suggests that a similar pattern should characterize atomic and molecular structures. This possibility is explored in terms of the current molecular structure-hypothesis and its extension into four-dimensional space-time. It is concluded that a quantum molecule only has structure in four dimensions and that classical (Newtonian) structure, which occurs in three dimensions, cannot be simulated by quantum-chemical computation. PMID:21151437

  14. A molecular-structure hypothesis.

    PubMed

    Boeyens, Jan C A

    2010-01-01

    The self-similar symmetry that occurs between atomic nuclei, biological growth structures, the solar system, globular clusters and spiral galaxies suggests that a similar pattern should characterize atomic and molecular structures. This possibility is explored in terms of the current molecular structure-hypothesis and its extension into four-dimensional space-time. It is concluded that a quantum molecule only has structure in four dimensions and that classical (Newtonian) structure, which occurs in three dimensions, cannot be simulated by quantum-chemical computation. PMID:21151437

  15. Molecules into Cells: Specifying Spatial Architecture

    PubMed Central

    Harold, Franklin M.

    2005-01-01

    A living cell is not an aggregate of molecules but an organized pattern, structured in space and in time. This article addresses some conceptual issues in the genesis of spatial architecture, including how molecules find their proper location in cell space, the origins of supramolecular order, the role of the genes, cell morphology, the continuity of cells, and the inheritance of order. The discussion is framed around a hierarchy of physiological processes that bridge the gap between nanometer-sized molecules and cells three to six orders of magnitude larger. Stepping stones include molecular self-organization, directional physiology, spatial markers, gradients, fields, and physical forces. The knowledge at hand leads to an unconventional interpretation of biological order. I have come to think of cells as self-organized systems composed of genetically specified elements plus heritable structures. The smallest self that can be fairly said to organize itself is the whole cell. If structure, form, and function are ever to be computed from data at a lower level, the starting point will be not the genome, but a spatially organized system of molecules. This conclusion invites us to reconsider our understanding of what genes do, what organisms are, and how living systems could have arisen on the early Earth. PMID:16339735

  16. Cold collisions between boson or fermion molecules

    SciTech Connect

    Kajita, Masatoshi [Communications Research Laboratory, 4-2-1, Nukui-Kitamachi, Koganei, Tokyo 184-8795 (Japan)

    2004-01-01

    We theoretically investigate collisions between electrostatically trapped cold polar molecules and compare boson and fermion isotopes. Evaporative cooling seems possible for fermion molecules as the ratio of the collision loss cross section to the elastic collision cross section (R) gets smaller as the molecular temperature T lowers. With boson molecules, R gets larger as T lowers, which makes evaporative cooling difficult. The elastic collision cross section between fermion molecules can be larger than that for boson molecules with certain conditions.

  17. Dissociation energy of molecules in dense gases

    NASA Technical Reports Server (NTRS)

    Kunc, J. A.

    1992-01-01

    A general approach is presented for calculating the reduction of the dissociation energy of diatomic molecules immersed in a dense (n = less than 10 exp 22/cu cm) gas of molecules and atoms. The dissociation energy of a molecule in a dense gas differs from that of the molecule in vacuum because the intermolecular forces change the intramolecular dynamics of the molecule, and, consequently, the energy of the molecular bond.

  18. Cancer Invasion: Patterns and Mechanisms

    PubMed Central

    Krakhmal, N. V.; Zavyalova, M. V.; Denisov, E. V.; Vtorushin, S. V.; Perelmuter, V. M.

    2015-01-01

    Cancer invasion and the ability of malignant tumor cells for directed migration and metastasis have remained a focus of research for many years. Numerous studies have confirmed the existence of two main patterns of cancer cell invasion: collective cell migration and individual cell migration, by which tumor cells overcome barriers of the extracellular matrix and spread into surrounding tissues. Each pattern of cell migration displays specific morphological features and the biochemical/molecular genetic mechanisms underlying cell migration. Two types of migrating tumor cells, mesenchymal (fibroblast-like) and amoeboid, are observed in each pattern of cancer cell invasion. This review describes the key differences between the variants of cancer cell migration, the role of epithelial-mesenchymal, collective-amoeboid, mesenchymal-amoeboid, and amoeboid- mesenchymal transitions, as well as the significance of different tumor factors and stromal molecules in tumor invasion. The data and facts collected are essential to the understanding of how the patterns of cancer cell invasion are related to cancer progression and therapy efficacy. Convincing evidence is provided that morphological manifestations of the invasion patterns are characterized by a variety of tissue (tumor) structures. The results of our own studies are presented to show the association of breast cancer progression with intratumoral morphological heterogeneity, which most likely reflects the types of cancer cell migration and results from different activities of cell adhesion molecules in tumor cells of distinct morphological structures. PMID:26085941

  19. Crystal structure, dielectric properties and molecular motions of molecules in thiazolium halometalates(III): (C3H4NS)6M4Br18·2H2O (M = Sb, Bi)

    NASA Astrophysics Data System (ADS)

    Piecha, A.; Jakubas, R.; Kinzhybalo, V.; Medycki, W.

    2012-04-01

    Two thiazolium analogs, (C3H4NS)6Sb4Br18·2H2O (TBA) and (C3H4NS)6Bi4Br18·2H2O (TBB), have been synthesized and structurally characterized. The compounds appeared to be isomorphous and crystallize in the triclinic symmetry, space group P1¯ (at 100 K). These ionic complexes are built up of thiazolium cations, centrosymmetric [M4Br18]6- anions (M = Sb, Bi) and water molecules. One of three independent thiazolium cations was found to be disordered (two-site model). The cations are hydrogen bonded to [M4Br18]6- moieties and water molecules. The water molecule (Ow) acts as a donor of the O-H⋯Br and an acceptor of the N-H⋯O types of hydrogen bonds. The dielectric dispersion studies disclosed a low frequency relaxation process characterized by a significant slowing down of two independent dielectric relaxators. The dielectric behavior was explained by the motion of thiazolium cations and water molecules The molecular motions of the thiazolium and water molecules were studied by means of the 1H NMR spin-lattice relaxation time (T1) measurements.

  20. Adsorption-geometry induced transformation of self-assembled nanostructures of an aldehyde molecule on Cu(110)

    NASA Astrophysics Data System (ADS)

    Zhang, Chi; Sun, Qiang; Sheng, Kai; Tan, Qinggang; Xu, Wei

    2014-09-01

    From an interplay of high-resolution STM imaging/manipulation and DFT calculations, we have revealed that different self-assembled nanostructures of BA molecules on Cu(110) are attributable to specific molecular adsorption geometries, and thus the corresponding intermolecular hydrogen bonding patterns. The STM manipulations demonstrate the feasibility of switching such weak-hydrogen-bonding patterns.From an interplay of high-resolution STM imaging/manipulation and DFT calculations, we have revealed that different self-assembled nanostructures of BA molecules on Cu(110) are attributable to specific molecular adsorption geometries, and thus the corresponding intermolecular hydrogen bonding patterns. The STM manipulations demonstrate the feasibility of switching such weak-hydrogen-bonding patterns. Electronic supplementary information (ESI) available: Supplementary STM images and DFT calculation results. See DOI: 10.1039/c4nr03754e

  1. Wavelength Dependent Photofragmentation Patterns of Tris(2,2,6,6-tetramethyl-3,5-heptanedionato)Ln (III) (Ln = Eu, Tb, Gd) in a Molecular Beam

    Microsoft Academic Search

    Franklin P. Ow; Mary T. Berry; P. Stanley May; Jeffrey I. Zink

    2006-01-01

    Laser photoionization and ligand photodissociation in Ln(thd) 3 (Ln ) Eu, Tb, Gd; thd ) 2,2,6,6-tetramethyl- 3,5-heptanedionato) are studied in a molecular beam via time-of-flight mass spectrometry. The fragmentation patterns are strongly wavelength dependent. With 355 nm excitation, the mass spectrum is dominated by Ln 2+ ,L n + , and LnO + fragments. The bare Ln ions are believed

  2. Hierarchy and Roles of Pathogen-Associated Molecular Pattern-Induced Responses in Nicotiana benthamiana1[W

    PubMed Central

    Segonzac, Cécile; Feike, Doreen; Gimenez-Ibanez, Selena; Hann, Dagmar R.; Zipfel, Cyril; Rathjen, John P.

    2011-01-01

    Our current understanding of pathogen-associated molecular pattern (PAMP)-triggered immunity signaling pathways in plants is limited due to the redundancy of several components or the lethality of mutants in Arabidopsis (Arabidopsis thaliana). To overcome this, we used a virus-induced gene silencing-based approach in combination with pharmacological studies to decipher links between early PAMP-triggered immunity events and their roles in immunity following PAMP perception in Nicotiana benthamiana. Two different calcium influx inhibitors suppressed the reactive oxygen species (ROS) burst: activation of the mitogen-activated protein kinases (MAPKs) and PAMP-induced gene expression. The calcium burst was unaffected in plants specifically silenced for components involved in ROS generation or for MAPKs activated by PAMP treatment. Importantly, the ROS burst still occurred in plants silenced for the two major defense-associated MAPK genes NbSIPK (for salicylic acid-induced protein kinase) and NbWIPK (for wound-induced protein kinase) or for both genes simultaneously, demonstrating that these MAPKs are dispensable for ROS production. We further show that NbSIPK silencing is sufficient to prevent PAMP-induced gene expression but that both MAPKs are required for bacterial immunity against two virulent strains of Pseudomonas syringae and their respective nonpathogenic mutants. These results suggest that the PAMP-triggered calcium burst is upstream of separate signaling branches, one leading to MAPK activation and then gene expression and the other to ROS production. In addition, this study highlights the essential roles of NbSIPK and NbWIPK in antibacterial immunity. Unexpectedly, negative regulatory mechanisms controlling the intensity of the PAMP-triggered calcium and ROS bursts were also revealed by this work. PMID:21478366

  3. One short cysteine-rich sequence pattern - two different disulfide-bonded structures - a molecular dynamics simulation study.

    PubMed

    Dames, Sonja A

    2015-06-01

    The nematocyst walls of Hydra are formed by proteins containing small cysteine-rich domains (CRDs) of ~25 amino acids. The first CRD of nematocyst outer all antigen (NW1) and the C-terminal CRD of minicollagen-1 (Mcol1C) contain six cysteines at identical sequence positions, however adopt different disulfide bonded structures. NW1 shows the disulfide connectivities C2-C14/C6-C19/C10-C18 and Mcol1C C2-C18/C6-C14/C10-C19. To analyze if both show structural preferences in the open, non-disulfide bonded form, which explain the formation of either disulfide connectivity pattern, molecular dynamics (MD) simulations at different temperatures were performed. NW1 maintained in the 100-ns MD simulations at 283?K a rather compact fold that is stabilized by specific hydrogen bonds. The Mcol1C structure fluctuated overall more, however stayed most of the time also rather compact. The analysis of the backbone ?/? angles indicated different turn propensities for NW1 and Mcol1C, which mostly can be explained based on published data about the influence of different amino acid side chains on the local backbone conformation. Whereas a folded precursor mechanism may be considered for NW1, Mcol1C may fold according to the quasi-stochastic folding model involving disulfide bond reshuffling and conformational changes, locking the native disulfide conformations. The study further demonstrates the power of MD simulations to detect local structural preferences in rather dynamic systems such as the open, non-disulfide bonded forms of NW1 and Mcol1C, which complement published information from NMR backbone residual dipolar couplings. Because the backbone structural preferences encoded by the amino acid sequence embedding the cysteines influence which disulfide connectivities are formed, the data are generally interesting for a better understanding of oxidative folding and the design of disulfide stabilized therapeutics. Copyright © 2015 European Peptide Society and John Wiley & Sons, Ltd. PMID:25781269

  4. Following several methodological developments, molecular dynamics simulations are now able to reproduce essential features of the solvation shell of biological molecules deduced

    E-print Network

    Westhof, Eric

    Summary Following several methodological developments, molecular dynamics simulations are now able-ray crystallography. Here we how molecular dynamics simulations can comple- ment experimental data by providing clues.auffinger@ibmc.u-strasbg.fr Hydrogens in RNA as visualized by molecular dynamics simulations AUFFINGER, Pascal / VAIANA, Andrea C

  5. Mighty Molecule Models

    NSDL National Science Digital Library

    Greg Rushton

    2008-01-01

    As part of the SMATHematics Project: The Wonder of Science, The Power of Mathematics--a collaborative partnership between Kennesaw State University and two local school districts, fifth graders had the opportunity to puzzle out chemical formulas of propane, methanol, and other important molecules. In addition, they explored properties that characterize certain molecules and then used their newly acquired knowledge of atoms' bonding requirements to help them build three-dimensional molecular models. The effort is succeeding--as you can see by the fifth-grade classroom experience described here.

  6. Dynamics of confined water molecules

    PubMed Central

    Gilijamse, J. J.; Lock, A. J.; Bakker, H. J.

    2005-01-01

    We present femtosecond midinfrared pump–probe measurements of the molecular motion and energy-transfer dynamics of a water molecule that is enclosed by acetone molecules. These confined water molecules show hydrogen-bond and orientational dynamics that are much slower than in bulk liquid water. This behavior is surprising because the hydrogen bonds to the C=O groups of the acetone molecules are weaker than the hydrogen bonds in bulk water. The energy transfer between the O—H groups of the confined water molecules has a time constant of 1.3 ± 0.2 ps, which is >20 times slower than in bulk water. We find that this energy transfer is governed completely by the rate at which hydrogen bonds are broken and reformed, and we identify the short-lived molecular complex that forms the transition state of this process. PMID:15722413

  7. Aromatic molecules as spintronic devices

    SciTech Connect

    Ojeda, J. H., E-mail: judith.ojeda@uptc.edu.co [Instituto de Alta investigación, Universidad de Tarapacá, Casilla 7D Arica (Chile); Grupo de Física de Materiales, Universidad Pedagógica y Tecnológica de Colombia, Tunja (Colombia); Orellana, P. A. [Departamento de Física, Universidad Técnica Federico Santa María, Casilla 110-V, Valparaíso (Chile)] [Departamento de Física, Universidad Técnica Federico Santa María, Casilla 110-V, Valparaíso (Chile); Laroze, D. [Instituto de Alta investigación, Universidad de Tarapacá, Casilla 7D Arica (Chile)] [Instituto de Alta investigación, Universidad de Tarapacá, Casilla 7D Arica (Chile)

    2014-03-14

    In this paper, we study the spin-dependent electron transport through aromatic molecular chains attached to two semi-infinite leads. We model this system taking into account different geometrical configurations which are all characterized by a tight binding Hamiltonian. Based on the Green's function approach with a Landauer formalism, we find spin-dependent transport in short aromatic molecules by applying external magnetic fields. Additionally, we find that the magnetoresistance of aromatic molecules can reach different values, which are dependent on the variations in the applied magnetic field, length of the molecules, and the interactions between the contacts and the aromatic molecule.

  8. Capture of an electron by ions in methionine and norleucine molecules

    NASA Astrophysics Data System (ADS)

    Afrosimov, V. V.; Basalaev, A. A.; Morozov, Yu. G.; Panov, M. N.; Smirnov, O. V.; Tropp, E. A.

    2013-09-01

    The relative cross sections of processes taking place when H+ and He2+ ions with an energy of 6 z keV ( z is the ionic charge) capture an electron from molecules of C5H11NO2S methionine (proteogenic amino acid) and C6H13NO2 norleucine (nonproteogenic amino acid) are measured by time-of-flight mass spectrometry (a methionine molecule transforms into a norleucine molecule by substituting the CH2 group for the S heteroatom). The fragmentation pattern of resulting molecular ions is established from correlation analysis of the detection times of all fragment ions. The results are compared with experimental data for fragmentation of the same molecules ionized by electrons and photons. In these amino acids, the pattern of molecular ion fragmentation is found to depend on the type of molecule ionization. However, the detachment cross section of the COOH neutral group or residue (neutral or charged) R of a side chain of the amino acid is invariably among the largest. The relative cross sections of capture with single and double ionization of molecules are measured.

  9. Microbe-Associated Molecular Patterns-Triggered Root Responses Mediate Beneficial Rhizobacterial Recruitment in Arabidopsis1[C][W][OA

    PubMed Central

    Lakshmanan, Venkatachalam; Kitto, Sherry L.; Caplan, Jeffrey L.; Hsueh, Yi-Huang; Kearns, Daniel B.; Wu, Yu-Sung; Bais, Harsh P.

    2012-01-01

    This study demonstrated that foliar infection by Pseudomonas syringae pv tomato DC3000 induced malic acid (MA) transporter (ALUMINUM-ACTIVATED MALATE TRANSPORTER1 [ALMT1]) expression leading to increased MA titers in the rhizosphere of Arabidopsis (Arabidopsis thaliana). MA secretion in the rhizosphere increased beneficial rhizobacteria Bacillus subtilis FB17 (hereafter FB17) titers causing an induced systemic resistance response in plants against P. syringae pv tomato DC3000. Having shown that a live pathogen could induce an intraplant signal from shoot-to-root to recruit FB17 belowground, we hypothesized that pathogen-derived microbe-associated molecular patterns (MAMPs) may relay a similar response specific to FB17 recruitment. The involvement of MAMPs in triggering plant innate immune response is well studied in the plant’s response against foliar pathogens. In contrast, MAMPs-elicited plant responses on the roots and the belowground microbial community are not well understood. It is known that pathogen-derived MAMPs suppress the root immune responses, which may facilitate pathogenicity. Plants subjected to known MAMPs such as a flagellar peptide, flagellin22 (flg22), and a pathogen-derived phytotoxin, coronatine (COR), induced a shoot-to-root signal regulating ALMT1 for recruitment of FB17. Micrografts using either a COR-insensitive mutant (coi1) or a flagellin-insensitive mutant (fls2) as the scion and ALMT1pro:?-glucuronidase as the rootstock revealed that both COR and flg22 are required for a graft transmissible signal to recruit FB17 belowground. The data suggest that MAMPs-induced signaling to regulate ALMT1 is salicylic acid and JASMONIC ACID RESISTANT1 (JAR1)/JASMONATE INSENSITIVE1 (JIN1)/MYC2 independent. Interestingly, a cell culture filtrate of FB17 suppressed flg22-induced MAMPs-activated root defense responses, which are similar to suppression of COR-mediated MAMPs-activated root defense, revealing a diffusible bacterial component that may regulate plant immune responses. Further analysis showed that the biofilm formation in B. subtilis negates suppression of MAMPs-activated defense responses in roots. Moreover, B. subtilis suppression of MAMPs-activated root defense does require JAR1/JIN1/MYC2. The ability of FB17 to block the MAMPs-elicited signaling pathways related to antibiosis reflects a strategy adapted by FB17 for efficient root colonization. These experiments demonstrate a remarkable strategy adapted by beneficial rhizobacteria to suppress a host defense response, which may facilitate rhizobacterial colonization and host-mutualistic association. PMID:22972705

  10. The formation of interstellar diatomic molecules

    NASA Technical Reports Server (NTRS)

    Stecher, T. P.; Williams, D. A.

    1972-01-01

    Reactions between atoms and ions of the interstellar medium and vibrationally excited molecular hydrogen are shown to produce a specific set of molecules. Molecules such as CO and CN can readily be produced in abundances greater than those of corresponding hydrides. When quantified in a simple manner the equilibrium density of molecules compares well with the observed values for the star Oph.

  11. Ultracold dipolar collisions of KRb molecules

    Microsoft Academic Search

    Goulven Quemener; John Bohn; Kang-Kuen Ni; Silke Ospelkaus; Dajun Wang; Brian Neyenhuis; Marcio de Miranda; Jun Ye; Deborah Jin

    2010-01-01

    Ultracold fermionic polar molecules of ^40K^87Rb in their absolute rovibronic anf hyperfine state [1] have been recently created in a magnetic trap. This enables experiments to probe ultracold molecular chemistry of polar molecules [2] in well defined quantum states. In addition, KRb molecules are polar and can be manipulated by an electric field. We present theoretical predictions for ultracold dipolar

  12. A component's framework based on the MVC pattern for the integration of data and tools on the molecular biology domain

    Microsoft Academic Search

    Luiz Roberto Lombardo; Mauro Biajiz; Antônio Francisco Do Prado

    2006-01-01

    In the domain of molecular biology, applications extract and analyze information of heterogeneous sources of data, distributed in different databases and text files. These applications can also use many different tools available in the domain of molecular biology to analyze and format the information extracted from these data sources. This diversity of data sources and tools make difficult the integration

  13. Microbial response to modified precipitation patterns in tallgrass prairie soil: molecular mechanisms, activity rates and organic matter dynamics

    NASA Astrophysics Data System (ADS)

    Zeglin, L. H.; David, M.; Bottomley, P.; Hettich, R. L.; Jansson, J.; Jumpponen, A.; Rice, C. W.; Tringe, S.; VerBerkmoes, N. C.; Myrold, D.

    2011-12-01

    A significant amount of carbon (C) is processed and stored in prairie soils: grasslands cover 6.1-7.4% of the earth's land surface and hold 7.3-11.4% of global soil C. Global change models predict that the future precipitation regime across the North American Great Plains will entail less frequent but larger rainfall events. The response of prairie soil microbial C processing and allocation to this scenario of higher hydrologic variability is not known, but will be a key determiner of the future capacity for prairie soil C sequestration. We are approaching this problem by assessing soil microbial function (respiration, C utilization efficiency, extracellular enzyme activity) and molecular indicators of dominant C allocation pathways (soil transcriptome, proteome and metabolome) under ambient and experimentally modified precipitation regimes. The rainfall manipulation plots (RaMPs) at the Konza Prairie Long-Term Ecological Research (LTER) site in eastern Kansas, USA is a replicated field manipulation of the magnitude and frequency of natural precipitation that was established in 1998. We collected soil before, during and after a rainfall event in both ambient and modified precipitation treatments and measured the microbial response. Microbial respiration doubled in both treatments during the water addition, and cellobiohydrolase enzyme potential activity (a catalyst of cellulose hydrolysis) increased slightly, but no significant effect of altered precipitation treatment has emerged. The fungal and bacterial ribosomal gene composition was also similar between precipitation treatments. Although pools of genes and extracellular enzymes may be relatively static during short-term dynamic conditions, transcript and intracellular protein abundances may be more indicative of the active microbial metabolic response to rapid shifts in soil moisture. Thus, analysis of transcript and protein composition is underway. In addition, we have implemented a series of lab experiments to optimize and link transcript and protein recovery and analysis procedures using the model soil bacterium Arthrobacter chlorophenicolus strain A6 (ArtchA6). Konza prairie soil was inoculated with ArchA6 and incubated for 72 h with no supplemental C, with acetate or with 4-chlorophenol (a xenobiotic compound that ArtchA6 can utilize as its sole C source), then RNA and protein were extracted from the soil. Quantitatively representative recovery of ArtchA6 genes, rRNA, mRNA and protein was successful. The ratio of ArtchA6 isocitrate lyase (icl, indicative of 2-C metabolism) to succinyl CoA synthetase (suCAB, indicative of total respiratory activity) transcript was highest in soils amended with acetate. Proteomic signatures were distinct in soils with different supplemental C sources. This experiment confirms our capability of recovering transcript and protein from the study soil and of identifying the functional molecules representative of distinct C metabolism pathways.

  14. Let's Make Molecules

    NSDL National Science Digital Library

    Sciencenter

    2010-01-01

    In this activity, learners use gumdrops and toothpicks to model the composition and molecular structure of three greenhouse gases: carbon dioxide (CO2), water vapor (H2O) and methane (CH4). Learners explore how greenhouse gases are released into the atmosphere as well as how these gases contribute to global climate change. This activity guide includes an extension activity in which learners move their bodies to model the arrangement of atoms in a methane molecule.

  15. Strange skyrmion molecules

    NASA Astrophysics Data System (ADS)

    Kopeliovich, Vladimir B.; Stern, Boris E.

    1997-05-01

    Composed skyrmions with B=2, strangeness content close to 0.5 and the binding energy of several tens of Mev are described. These skyrmions are obtained starting from the system of two B=1 hedgehogs located in different SU(2) subgroups of SU(3) and have the mass and baryon number distribution of molecular (dipole) type. The quantization of zero modes of skyrmion molecules and physics consequences of their existence are discussed.

  16. Subtractive Patterning via Chemical Lift-Off Lithography

    NASA Astrophysics Data System (ADS)

    Liao, Wei-Ssu; Cheunkar, Sarawut; Cao, Huan H.; Bednar, Heidi R.; Weiss, Paul S.; Andrews, Anne M.

    2012-09-01

    Conventional soft-lithography methods involving the transfer of molecular “inks” from polymeric stamps to substrates often encounter micrometer-scale resolution limits due to diffusion of the transferred molecules during printing. We report a “subtractive” stamping process in which silicone rubber stamps, activated by oxygen plasma, selectively remove hydroxyl-terminated alkanethiols from self-assembled monolayers (SAMs) on gold surfaces with high pattern fidelity. The covalent interactions formed at the stamp-substrate interface are sufficiently strong to remove not only alkanethiol molecules but also gold atoms from the substrate. A variety of high-resolution patterned features were fabricated, and stamps were cleaned and reused many times without feature deterioration. The remaining SAM acted as a resist for etching exposed gold features. Monolayer backfilling into the lift-off areas enabled patterned protein capture, and 40-nanometer chemical patterns were achieved.

  17. Single Molecule Electronics and Devices

    PubMed Central

    Tsutsui, Makusu; Taniguchi, Masateru

    2012-01-01

    The manufacture of integrated circuits with single-molecule building blocks is a goal of molecular electronics. While research in the past has been limited to bulk experiments on self-assembled monolayers, advances in technology have now enabled us to fabricate single-molecule junctions. This has led to significant progress in understanding electron transport in molecular systems at the single-molecule level and the concomitant emergence of new device concepts. Here, we review recent developments in this field. We summarize the methods currently used to form metal-molecule-metal structures and some single-molecule techniques essential for characterizing molecular junctions such as inelastic electron tunnelling spectroscopy. We then highlight several important achievements, including demonstration of single-molecule diodes, transistors, and switches that make use of electrical, photo, and mechanical stimulation to control the electron transport. We also discuss intriguing issues to be addressed further in the future such as heat and thermoelectric transport in an individual molecule. PMID:22969345

  18. How to get more from less. Comments on "Extracting physics of life at the molecular level: A review of single-molecule data analyses" by W. Colomb and S.K. Sarkar

    NASA Astrophysics Data System (ADS)

    Sachs, Frederick; Flomenbom, Ophir

    2015-06-01

    Measuring individual entities at room temperature has become routine due to improvements in technology. We can study ion channels (since the 70s), quantum dots (since the 80s), and receptors, molecular engines and enzymes (since the 90s). The inherent nature of these small systems is that the standard deviation of the measurement is comparable to the mean - the definition of a small system [1]. Individual probes are detected, measured, and the trajectories are then analyzed to extract the mean properties of the system. The review [2] provides links to many examples of single molecule studies, mostly those using optical probes.

  19. Molecular features of colorectal polyps presenting Kudo’s type II mucosal crypt pattern: are they based on the same mechanism of tumorigenesis?

    PubMed Central

    Shinmura, Kensuke; Konishi, Kazuo; Yamochi, Toshiko; Kubota, Yutaro; Yano, Yuichiro; Katagiri, Atsushi; Muramoto, Takashi; Kihara, Toshihiro; Tojo, Masayuki; Konda, Kenichi; Tagawa, Teppei; Yanagisawa, Fumito; Kogo, Mari; Makino, Reiko; Takimoto, Masafumi; Yoshida, Hitoshi

    2014-01-01

    Background and study aims: The molecular features of serrated polyps (SPs) with hyperplastic crypt pattern, also called Kudo’s type II observed by chromoendoscopy, were evaluated. Methods: The clinicopathological and molecular features of 114 SPs with a hyperplastic pit pattern detected under chromoendoscopy (five dysplastic SPs, 63 sessile serrated adenoma/polyps (SSA/Ps), 36 microvesicular hyperplastic polyps (MVHPs), and 10 goblet cell-rich hyperplastic polyps (GCHPs)) were examined. The frequency of KRAS and BRAF mutations and CpG island methylator phenotype (CIMP) were investigated. Results: Dysplastic SPs and SSA/Ps were frequently located in the proximal colon compared to others (SSA/Ps vs. MVHPs or GCHPs, P?molecular features were observed between proximal and distal SPs with hyperplastic crypt pattern. Proximal MVHPs may develop more frequently through SSA/Ps to CIMP cancers than distal MVHPs.

  20. Wave and Particle in Molecular Interference Lithography

    SciTech Connect

    Juffmann, Thomas; Truppe, Stefan; Geyer, Philipp; Major, Andras G.; Arndt, Markus [Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna (Austria); Deachapunya, Sarayut [Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna (Austria); Department of Physics, Faculty of Science, Burapha University, Chonburi 20131 (Thailand); Ulbricht, Hendrik [Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna (Austria); School of Physics and Astronomy, University of Southampton, SO17 1BJ (United Kingdom)

    2009-12-31

    The wave-particle duality of massive objects is a cornerstone of quantum physics and a key property of many modern tools such as electron microscopy, neutron diffraction or atom interferometry. Here we report on the first experimental demonstration of quantum interference lithography with complex molecules. Molecular matter-wave interference patterns are deposited onto a reconstructed Si(111) 7x7 surface and imaged using scanning tunneling microscopy. Thereby both the particle and the quantum wave character of the molecules can be visualized in one and the same image. This new approach to nanolithography therefore also represents a sensitive new detection scheme for quantum interference experiments.

  1. Oscillation of Angiogenesis and Vascular Dropout in Progressive Human Vascular Disease. [Vascular Pattern as Useful Read-Out of Complex Molecular Signaling

    NASA Technical Reports Server (NTRS)

    Parsons-Wingerter, Patricia

    2010-01-01

    When analyzed by VESsel GENeration Analysis (VESGEN) software, vascular patterns provide useful integrative read-outs of complex, interacting molecular signaling pathways. Using VESGEN, we recently discovered and published our innovative, surprising findings that angiogenesis oscillated with vascular dropout throughout progression of diabetic retinopathy, a blinding vascular disease. Our findings provide a potential paradigm shift in the current prevailing view on progression and treatment of this disease, and a new early-stage window of regenerative therapeutic opportunities. The findings also suggest that angiogenesis may oscillate with vascular disease in a homeostatic-like manner during early stages of other inflammatory progressive diseases such as cancer and coronary vascular disease.

  2. The emergence of sarcomeric, graded-polarity and spindle-like patterns in bundles of short cytoskeletal polymers and two opposite molecular motors

    PubMed Central

    Craig, EM; Dey, S; Mogilner, A

    2011-01-01

    We use linear stability analysis and numerical solutions of partial differential equations to investigate pattern formation in the one-dimensional system of short dynamic polymers and one (plus-end directed) or two (one is plus-end, another minus-end directed) molecular motors. If polymer sliding and motor gliding rates are slow and/or the polymer turnover rate is fast, then the polymer–motor bundle has mixed polarity and homogeneous motor distribution. However, if motor gliding is fast, a sarcomeric pattern with periodic bands of alternating polymer polarity separated by motor aggregates evolves. On the other hand, if polymer sliding is fast, a graded-polarity bundle with motors at the center emerges. In the presence of the second, minus-end directed motor, the sarcomeric pattern is more ubiquitous, while the graded-polarity pattern is destabilized. However, if the minus-end motor is weaker than the plus-end directed one, and/or polymer nucleation is autocatalytic, and/or long polymers are present in the bundle, then a spindle-like architecture with a sorted-out polarity emerges with the plus-end motors at the center and minus-end motors at the edges. We discuss modeling implications for actin–myosin fibers and in vitro and meiotic spindles. PMID:21862843

  3. From macroscopic to molecular scale investigations of mass transfer of small molecules through edible packaging applied at interfaces of multiphase food products

    Microsoft Academic Search

    Thomas Karbowiak; Frédéric Debeaufort; Andrée Voilley; Gilles Trystram

    2009-01-01

    This paper presents a multi-scale approach to investigate mass transfer properties of edible films that integrates some published data and new original results. The transport of small molecules, such as water, between the different parts of multiphase food products leads to quality deterioration and thus requires the use of barrier edible films or coatings. Therefore, it is necessary to characterise

  4. Molecular dynamics simulation of vibrational energy relaxation of highly excited molecules in fluids. III. Equilibrium simulations of vibrational energy relaxation of azulene in carbon dioxide

    Microsoft Academic Search

    C. Heidelbach; V. S. Vikhrenko; D. Schwarzer; I. I. Fedchenia; J. Schroeder

    1999-01-01

    The expressions for vibrational energy relaxation (VER) rates of polyatomic molecules in terms of equilibrium capacity time correlation functions (TCFs) derived in the first paper of this series [J. Chem. Phys. 110, 5273 (1999)] are used for the investigation of VER of azulene in carbon dioxide at low (3.2 MPa) and high (270 MPa) pressure. It is shown that for

  5. Cellular and Molecular Requirements for Association of the Murine Cytomegalovirus Protein m4\\/gp34 with Major Histocompatibility Complex Class I Molecules

    Microsoft Academic Search

    Xiuju Lu; Daniel G. Kavanagh; Ann B. Hill

    2006-01-01

    The murine cytomegalovirus (MCMV) protein m4\\/gp34 is unique among known viral genes that target the major histocompatibility complex (MHC) class I pathway of antigen presentation in the following two ways: it is found in association with class I MHC molecules at the cell surface, and it inhibits antigen presentation without reducing cell surface class I levels. The current study was

  6. Patterns in the quinary structures of proteins: plasticity and inequivalence of individual molecules in helical arrays of sickle cell hemoglobin and tubulin

    SciTech Connect

    Edelstein, S.J.

    1980-10-01

    The four recognized levels of organization of protein structure (primary through quaternary) are extended to add the designation quinary structure for the interactions within helical arrays, such as found for sickle cell hemoglobin fibers of tubulin units in microtubules. For sickle cell hemoglobin the main quinary structure is a 14-filament fiber, with a number of other minor forms also encountered. Degenerate forms of the 14-filament fibers can be characterized that lack specific pairs of filaments; evidence is presented which suggests an overall organization of the 14 filaments in pairs, with particular pairs aligned in an antiparallel orientation. For tubulin, a range of quinary structures can be detected depending on the number of protofilaments and whether adjacent protofilaments composed of alternating ..cap alpha..- and ..beta..-subunits are aligned with contacts between like or unlike subunits and with parallel or antiparallel polarity. Thus, in contrast to quarternary structure, which generally involves a fixed number of subunits, the quinary structures of proteins can exhibit marked plasticity and inequivalence in the juxtaposition of constituent molecules.

  7. A molecular communication interface using liposomes with gap junction proteins

    Microsoft Academic Search

    Yuki Moritani; Shin-ichiro M. Nomura; Satoshi Hiyama; Kazunari Akiyoshi; Tatsuya Suda

    2006-01-01

    Molecular communication [1]-[2] is an emerging communication paradigm that uses molecules as a communication medium. Molecular communication allows biological and artificially created nano- or cell-scale devices to communicate with each other. In molecular communication, senders encode information onto molecules (called information molecules), and information molecules are then loaded onto carrier molecules and transported to a receiver. Upon arriving at a

  8. Whispering gallery microresonators for second harmonic light generation from a low number of small molecules

    PubMed Central

    Dominguez-Juarez, J.L.; Kozyreff, G.; Martorell, Jordi

    2011-01-01

    Unmarked sensitive detection of molecules is needed in environmental pollution monitoring, disease diagnosis, security screening systems and in many other situations in which a substance must be identified. When molecules are attached or adsorbed onto an interface, detecting their presence is possible using second harmonic light generation, because at interfaces the inversion symmetry is broken. However, such light generation usually requires either dense matter or a large number of molecules combined with high-power laser sources. Here we show that using high-Q spherical microresonators and low average power, between 50 and 100 small non-fluorescent molecules deposited on the outer surface of the microresonator can generate a detectable change in the second harmonic light. This generation requires phase matching in the whispering gallery modes, which we achieved using a new procedure to periodically pattern, with nanometric precision, a molecular surface monolayer. PMID:21448153

  9. The Transcriptional Complex Between the BCL2 i-Motif and hnRNP LL Is a Molecular Switch for Control of Gene Expression That Can Be Modulated by Small Molecules

    PubMed Central

    2015-01-01

    In a companion paper (DOI: 10.021/ja410934b) we demonstrate that the C-rich strand of the cis-regulatory element in the BCL2 promoter element is highly dynamic in nature and can form either an i-motif or a flexible hairpin. Under physiological conditions these two secondary DNA structures are found in an equilibrium mixture, which can be shifted by the addition of small molecules that trap out either the i-motif (IMC-48) or the flexible hairpin (IMC-76). In cellular experiments we demonstrate that the addition of these molecules has opposite effects on BCL2 gene expression and furthermore that these effects are antagonistic. In this contribution we have identified a transcriptional factor that recognizes and binds to the BCL2 i-motif to activate transcription. The molecular basis for the recognition of the i-motif by hnRNP LL is determined, and we demonstrate that the protein unfolds the i-motif structure to form a stable single-stranded complex. In subsequent experiments we show that IMC-48 and IMC-76 have opposite, antagonistic effects on the formation of the hnRNP LL–i-motif complex as well as on the transcription factor occupancy at the BCL2 promoter. For the first time we propose that the i-motif acts as a molecular switch that controls gene expression and that small molecules that target the dynamic equilibrium of the i-motif and the flexible hairpin can differentially modulate gene expression. PMID:24559432

  10. IPET and FETR: experimental approach for studying molecular structure dynamics by cryo-electron tomography of a single-molecule structure.

    PubMed

    Zhang, Lei; Ren, Gang

    2012-01-01

    The dynamic personalities and structural heterogeneity of proteins are essential for proper functioning. Structural determination of dynamic/heterogeneous proteins is limited by conventional approaches of X-ray and electron microscopy (EM) of single-particle reconstruction that require an average from thousands to millions different molecules. Cryo-electron tomography (cryoET) is an approach to determine three-dimensional (3D) reconstruction of a single and unique biological object such as bacteria and cells, by imaging the object from a series of tilting angles. However, cconventional reconstruction methods use large-size whole-micrographs that are limited by reconstruction resolution (lower than 20 Å), especially for small and low-symmetric molecule (<400 kDa). In this study, we demonstrated the adverse effects from image distortion and the measuring tilt-errors (including tilt-axis and tilt-angle errors) both play a major role in limiting the reconstruction resolution. Therefore, we developed a "focused electron tomography reconstruction" (FETR) algorithm to improve the resolution by decreasing the reconstructing image size so that it contains only a single-instance protein. FETR can tolerate certain levels of image-distortion and measuring tilt-errors, and can also precisely determine the translational parameters via an iterative refinement process that contains a series of automatically generated dynamic filters and masks. To describe this method, a set of simulated cryoET images was employed; to validate this approach, the real experimental images from negative-staining and cryoET were used. Since this approach can obtain the structure of a single-instance molecule/particle, we named it individual-particle electron tomography (IPET) as a new robust strategy/approach that does not require a pre-given initial model, class averaging of multiple molecules or an extended ordered lattice, but can tolerate small tilt-errors for high-resolution single "snapshot" molecule structure determination. Thus, FETR/IPET provides a completely new opportunity for a single-molecule structure determination, and could be used to study the dynamic character and equilibrium fluctuation of macromolecules. PMID:22291925

  11. Functional dissection of the PROPEP2 and PROPEP3 promoters reveals the importance of WRKY factors in mediating microbe-associated molecular pattern-induced expression.

    PubMed

    Logemann, Elke; Birkenbihl, Rainer P; Rawat, Vimal; Schneeberger, Korbinian; Schmelzer, Elmon; Somssich, Imre E

    2013-06-01

    · In Arabidopsis thaliana, small peptides (AtPeps) encoded by PROPEP genes act as damage-associated molecular patterns (DAMPs) that are perceived by two leucine-rich repeat receptor kinases, PEPR1 and PEPR2, to amplify defense responses. In particular, expression of PROPEP2 and PROPEP3 is strongly and rapidly induced by AtPeps, in response to bacterial, oomycete, and fungal pathogens, and microbe-associated molecular patterns (MAMPs). · The cis-regulatory modules (CRMs) within the PROPEP2 and PROPEP3 promoters that mediate MAMP responsiveness were delineated, employing parsley (Petroselinum crispum) protoplasts and transgenic A. thaliana plants harboring promoter-reporter constructs. By chromatin immunoprecipitation in vivo, DNA interactions with a specific transcription factor were detected. Furthermore, the PHASTCONS program was used to identify conserved regions of the PROPEP3 locus in different Brassicaceae species. · The major MAMP-responsive CRM within the PROPEP2 promoter is composed of several W boxes and an as1/OCS (activation sequence-1/octopine synthase) enhancer element, while in the PROPEP3 promoter the CRM is comprised of six W boxes. The WRKY33 transcription factor binds in vivo to these promoter regions in a MAMP-dependent manner. Both the position and orientation of the six W boxes are conserved within the PROPEP3 promoters of four other Brassicaceae family members. · WRKY factors are the major regulators of MAMP-induced PROPEP2 and PROPEP3 expression. PMID:23496690

  12. Biological Molecules

    NSDL National Science Digital Library

    Paul Anderson

    2013-03-12

    Paul Anderson describes the four major biological molecules found in living things. He begins with a brief discussion of polymerization. Dehydration synthesis is used to connect monomers into polymers and hydrolysis breaks them down again. The major characteristics of nucleic acids are described as well as there directionality from 3' to 5' end.

  13. Coherent Dynamics Following Strong Field Ionization of Polyatomic Molecules

    NASA Astrophysics Data System (ADS)

    Konar, Arkaprabha; Shu, Yinan; Lozovoy, Vadim; Jackson, James; Levine, Benjamin; Dantus, Marcos

    2015-03-01

    Molecules, as opposed to atoms, present confounding possibilities of nuclear and electronic motion upon strong field ionization. The dynamics and fragmentation patterns in response to the laser field are structure sensitive; therefore, a molecule cannot simply be treated as a ``bag of atoms'' during field induced ionization. We consider here to what extent molecules retain their molecular identity and properties under strong laser fields. Using time-of-flight mass spectrometry in conjunction with pump-probe techniques we study the dynamical behavior of these molecules, monitoring ion yield modulation caused by intramolecular motions post ionization. The delay scans show that among positional isomers the variations in relative energies, amounting to only a few hundred meVs, influence the dynamical behavior of the molecules despite their having experienced such high fields (V/Å). Ab initio calculations were performed to predict dynamics along with single and multiphoton resonances in the neutral and ionic states. We propose that single electron ionization occurs within an optical cycle with the electron carrying away essentially all of the energy, leaving behind little internal energy in the cation. Evidence for this observation comes from coherent vibrational motion governed by the potential energy surface of the ground state of the cation. Subsequent fragmentation of the cation takes place as a result of further photon absorption modulated by one- and two-photon resonances, which provide sufficient energy to overcome the dissociation energy.

  14. Quantum transport through aromatic molecules

    SciTech Connect

    Ojeda, J. H., E-mail: judith.ojeda@uptc.edu.co [Instituto de Alta investigación, Universidad de Tarapaca, Casilla 7D Arica (Chile); Grupo de Física de Materiales, Escuela de Física, Universidad Pedagógica y Tecnológica de Colombia, Tunja (Colombia); Rey-González, R. R. [Departamento de Física, Universidad Nacional de Colombia, Bogotá D. C. (Colombia); Laroze, D. [Instituto de Alta investigación, Universidad de Tarapaca, Casilla 7D Arica (Chile)

    2013-12-07

    In this paper, we study the electronic transport properties through aromatic molecules connected to two semi-infinite leads. The molecules are in different geometrical configurations including arrays. Using a nearest neighbor tight-binding approach, the transport properties are analyzed into a Green's function technique within a real-space renormalization scheme. We calculate the transmission probability and the Current-Voltage characteristics as a function of a molecule-leads coupling parameter. Our results show different transport regimes for these systems, exhibiting metal-semiconductor-insulator transitions and the possibility to employ them in molecular devices.

  15. Molecular cloning and characterisation of a pattern recognition molecule, lipopolysaccharide- and ?-1,3-glucan binding protein (LGBP) from the white shrimp Litopenaeus vannamei

    Microsoft Academic Search

    Winton Cheng; Chun-Hung Liu; Chiung-Hui Tsai; Jiann-Chu Chen

    2005-01-01

    A lipopolysaccharide- and ?-1,3-glucan binding protein (LGBP) cDNA was cloned from the haemocyte and hepatopancreas of white shrimp Litopenaeus vannamei using oligonucleotide primers and RT-PCR. Both 3?- and 5?-regions were isolated by rapid amplification of cDNA end RACE method. Analysis of nucleotide sequence revealed that the cDNA clone has an open reading frame of 1101bp encoding a protein of 367

  16. Non perturbative approach for a polar and polarizable linear molecule in an inhomogeneous electric field: Application to molecular beam deviation experiments

    NASA Astrophysics Data System (ADS)

    Benichou, E.; Allouche, A. R.; Antoine, R.; Aubert-Frecon, M.; Bourgoin, M.; Broyer, M.; Dugourd, Ph.; Hadinger, G.; Rayane, D.

    A non perturbative approach is used to solve the problem of a rigid linear molecule with both a permanent dipole moment and a static dipole polarizability, in a static electric field. Eigenenergies are obtained and compared to perturbative low field and high field approximations. Analytical expressions for the orientation parameters and for the gradient of the energy are given. This non perturbative approach is applied to the simulation of beam deviation experiments in strong electric field. Results of simulations are given for inhomogeneous alkali dimers. For LiNa, the simulations are compared to experimental data. For LiK, deviation profiles have been simulated in order to prepare future experiments on this molecule.

  17. Digging deeper into noise. Reply to comment on "Extracting physics of life at the molecular level: A review of single-molecule data analyses"

    NASA Astrophysics Data System (ADS)

    Colomb, Warren; Sarkar, Susanta K.

    2015-06-01

    We would like to thank all the commentators for their constructive comments on our paper. Commentators agree that a proper analysis of noisy single-molecule data is important for extracting meaningful and accurate information about the system. We concur with their views and indeed, motivating an accurate analysis of experimental data is precisely the point of our paper. After a model about the system of interest is constructed based on the experimental single-molecule data, it is very helpful to simulate the model to generate theoretical single-molecule data and analyze exactly the same way. In our experience, such self-consistent approach involving experiments, simulations, and analyses often forces us to revise our model and make experimentally testable predictions. In light of comments from the commentators with different expertise, we would also like to point out that a single model should be able to connect different experimental techniques because the underlying science does not depend on the experimental techniques used. Wohland [1] has made a strong case for fluorescence correlation spectroscopy (FCS) as an important experimental technique to bridge single-molecule and ensemble experiments. FCS is a very powerful technique that can measure ensemble parameters with single-molecule sensitivity. Therefore, it is logical to simulate any proposed model and predict both single-molecule data and FCS data, and confirm with experimental data. Fitting the diffraction-limited point spread function (PSF) of an isolated fluorescent marker to localize a labeled biomolecule is a critical step in many single-molecule tracking experiments. Flyvbjerg et al. [2] have rigorously pointed out some important drawbacks of the prevalent practice of fitting diffraction-limited PSF with 2D Gaussian. As we try to achieve more accurate and precise localization of biomolecules, we need to consider subtle points as mentioned by Flyvbjerg et al. Shepherd [3] has mentioned specific examples of PSF that have been used for localization and has rightly mentioned the importance of detector noise in single-molecule localization. Meroz [4] has pointed out more clearly that the signal itself could be noisy and it is necessary to distinguish the noise of interest from the background noise. Krapf [5] has pointed out different origins of fluctuations in biomolecular systems and commented on their possible Gaussian and non-Gaussian nature. Importance of noise along with the possibility that the noise itself can be the signal of interest has been discussed in our paper [6]. However, Meroz [4] and Krapf [5] have provided specific examples to guide the readers in a better way. Sachs et al. [7] have discussed kinetic analysis in the presence of indistinguishable states and have pointed to the free software for the general kinetic analysis that originated from their research.

  18. Molecular composition of the node of Ranvier: identification of ankyrin- binding cell adhesion molecules neurofascin (mucin+\\/third FNIII domain- ) and NrCAM at nodal axon segments

    Microsoft Academic Search

    Jonathan Q. Davis; Stephen Lambert; Vann Bennett

    1996-01-01

    Neurofascin, NrCAM, L1, and NgCAM are a family of Ig\\/FNIII cell adhesion molecules that share ankyrin-binding activity in their cytoplasmic domains, and are candidates to form membrane-spanning com- plexes with members of the ankyrin family of spectrin- binding proteins in a variety of cellular contexts in the nervous system. Specialized forms of ankyrin, 270 kD and\\/or 480 kD ankyrinG are

  19. Muonic molecular formation under laser irradiation and in the clustered ion molecule (The effect of protonium additive on the muon catalyzed fusion cycle)

    SciTech Connect

    Takahashi, Hiroshi

    1988-01-01

    The formation rate of the dt..mu.. molecule is very sensitive to the differences in the vibrational rotational level between D/sub 2/ and ((dt..mu..)-d-2e/) molecules. The density effect of the normalized reaction rate has been studied by the resonance broadening due to collisional quenching. The surrounding molecules of the molecule forming dt/mu/ act as the third body which takes out the excess energy forming dt/mu/ from t/mu/, and the formation reaction occurs with the excitation of the vibrational state just below the threshold energy. By using the laser as the third body, the rate of resonance formation can be increased. In my last paper, the formation rate was calculated under high-intensity laser irradiation, using Vinitsky's model assuming that the laser interacts directly with the deuteron and modulates the interaction between t/mu/ and d/sub 2/ nuclei. However, the laser interacts more strongly with the electrons, because the interaction energy of the laser and the charged particle is proportional to the velocity of the particle's motion, and the velocity of the electron is a few thousand times greater than the velocity of the nuclei. This interaction with electrons was neglected in my last paper. In the present paper, the enhancement of the dt/mu/ formation rates by the strong laser irradiation is studied, taking into account the laser electron interaction; It was shown that the enhancement can be achieved by an intensity lower than the one described previously. 29 refs., 5 figs., 3 tabs.

  20. Potent New Small-Molecule Inhibitor of Botulinum Neurotoxin Serotype A Endopeptidase Developed by Synthesis-Based Computer-Aided Molecular Design

    Microsoft Academic Search

    Yuan-Ping Pang; Anuradha Vummenthala; Rajesh K. Mishra; Shaohua Wang; Jon Davis; Charles B. Millard; James J. Schmidt

    2009-01-01

    Botulinum neurotoxin serotype A (BoNTA) causes a life-threatening neuroparalytic disease known as botulism. Current treatment for post exposure of BoNTA uses antibodies that are effective in neutralizing the extracellular toxin to prevent further intoxication but generally cannot rescue already intoxicated neurons. Effective small-molecule inhibitors of BoNTA endopeptidase (BoNTAe) are desirable because such inhibitors potentially can neutralize the intracellular BoNTA and