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1

Endogenous Molecules Induced by a Pathogen-Associated Molecular Pattern (PAMP) Elicit Innate Immunity in Shrimp  

PubMed Central

Invertebrates rely on an innate immune system to combat invading pathogens. The system is initiated in the presence of cell wall components from microbes like lipopolysaccharide (LPS), ?-1,3-glucan (?G) and peptidoglycan (PG), altogether known as pathogen-associated molecular patterns (PAMPs), via a recognition of pattern recognition protein (PRP) or receptor (PRR) through complicated reactions. We show herein that shrimp hemocytes incubated with LPS, ?G, and PG caused necrosis and released endogenous molecules (EMs), namely EM-L, EM-?, and EM-P, and found that shrimp hemocytes incubated with EM-L, EM-?, and EM-P caused changes in cell viability, degranulation and necrosis of hemocytes, and increased phenoloxidase (PO) activity and respiratory burst (RB) indicating activation of immunity in vitro. We found that shrimp receiving EM-L, EM-?, and EM-P had increases in hemocyte count and other immune parameters as well as higher phagocytic activity toward a Vibrio pathogen, and found that shrimp receiving EM-L had increases in proliferation cell ratio and mitotic index of hematopoietic tissues (HPTs). We identified proteins of EMs deduced from SDS-PAGE and LC-ESI-MS/MS analyses. EM-L and EM-P contained damage-associated molecular patterns (DAMPs) including HMGBa, HMGBb, histone 2A (H2A), H2B, and H4, and other proteins including proPO, Rab 7 GPTase, and Rab 11 GPTase, which were not observed in controls (EM-C, hemocytes incubated in shrimp salt solution). We concluded that EMs induced by PAMPs contain DAMPs and other immune molecules, and they could elicit innate immunity in shrimp. Further research is needed to identify which individual molecule or combined molecules of EMs cause the results, and determine the mechanism of action in innate immunity. PMID:25517999

Chen, Yu-Yuan; Chen, Jiann-Chu; Lin, Yong-Chin; Kitikiew, Suwaree; Li, Hui-Fang; Bai, Jia-Chin; Tseng, Kuei-Chi; Lin, Bo-Wei; Liu, Po-Chun; Shi, Yin-Ze; Kuo, Yi-Hsuan; Chang, Yu-Hsuan

2014-01-01

2

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

PubMed Central

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

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

2014-01-01

3

1Modeling molecules 2Molecular . . .  

E-print Network

·Full Screen ·Close ·Quit 1. Modeling molecules (special graphs) - can we predict rigidity? Single atom ·Go Back ·Full Screen ·Close ·Quit Graph G of atoms and covalent bonds Body and hinge model Atoms1Modeling molecules 2Molecular . . . 3Realization in . . . Home Page Title Page Page 1 of 40 Go

Servatius, Brigitte

4

IgG antibodies from dourine infected horses identify a distinctive Trypanosoma equiperdum antigenic pattern of low molecular weight molecules.  

PubMed

Diagnosis and control of dourine is strongly based on serological evidence, but knowledge of the humoral response of horses during infection is limited. In this study we developed a chemiluminescent immunoblotting (cIB) assay to characterise the Trypanosoma equiperdum antigen pattern recognised by IgGs from naturally or experimentally dourine-infected horses and analyse the kinetics of IgG humoral response following the infection. One compounding factor is that sera from uninfected animals often cross-react with T. equiperdum antigens. Development of the cIB assay was based on the hypothesis that serum IgGs from healthy and infected animals recognise different T. equiperdum antigen patterns. We used sera from 8 naturally infected horses which had recovered from Italian outbreaks and 2 experimentally infected mares. In addition, sera from 10 healthy control animals, eight of which were CFT positive but IFA negative for dourine, were collected from disease free regions. Sera were compared by the complement fixation test (CFT), indirect immune fluorescence (IFA) and the cIB assay. cIB analysis revealed that IgGs from infected horses, in contrast to IgGs from healthy horses, specifically recognise a T. equiperdum antigenic profile with low molecular weight bands ranging between 16 and 35 kDa. A time course experiment indicated that IgGs specific for the 16-35 kDa parasite protein fraction appear 17 days post-infection. The cIB assay confirmed all ten infected animals as positive and all controls as negative. This study demonstrated that analysis of IgGs by cIB can provide clear confirmation of trypanosome infection in horses, suggesting that this technique can be applied as a confirmatory serological test for dourine infection. PMID:23218944

Luciani, M; Di Pancrazio, C; Di Febo, T; Tittarelli, M; Podaliri Vulpiani, M; Puglielli, M O; Naessens, J; Sacchini, F

2013-01-15

5

Programmable motion and patterning of molecules on solid surfaces  

PubMed Central

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

Suo, Z.; Hong, W.

2004-01-01

6

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

PubMed

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

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

2014-07-27

7

Sequence-Specific Molecular Lithography on Single DNA Molecules  

Microsoft Academic Search

Recent advances in the realization of individual molecular-scale electronic devices emphasize the need for novel tools and concepts capable of assembling such devices into large-scale functional circuits. We demonstrated sequence-specific molecular lithography on substrate DNA molecules by harnessing homologous recombination by RecA protein. In a sequence-specific manner, we patterned the coating of DNA with metal, localized labeled molecular objects and

Kinneret Keren; Michael Krueger; Rachel Gilad; Gdalyahu Ben-Yoseph; Uri Sivan; Erez Braun

2002-01-01

8

Structure factor and rheology of chain molecules from molecular dynamics  

NASA Astrophysics Data System (ADS)

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

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

2013-05-01

9

Integrated Analysis Identifies Interaction Patterns between Small Molecules and Pathways  

PubMed Central

Previous studies have indicated that the downstream proteins in a key pathway can be potential drug targets and that the pathway can play an important role in the action of drugs. So pathways could be considered as targets of small molecules. A link map between small molecules and pathways was constructed using gene expression profile, pathways, and gene expression of cancer cell line intervened by small molecules and then we analysed the topological characteristics of the link map. Three link patterns were identified based on different drug discovery implications for breast, liver, and lung cancer. Furthermore, molecules that significantly targeted the same pathways tended to treat the same diseases. These results can provide a valuable reference for identifying drug candidates and targets in molecularly targeted therapy. PMID:25114931

Li, Yan; Li, Weiguo; Chen, Xin; Sun, Jiatong; Chen, Huan; Lv, Sali

2014-01-01

10

Cold Molecular Ions:. Single Molecule Studies  

NASA Astrophysics Data System (ADS)

Single molecular ions can be sympathetically cooled to a temperature in the mK-range and become spatially localized within a few ?m3 through the Coulomb interaction with laser-cooled atomic ions, and hence be an excellent starting point for a variety of single molecule studies. By applying a rather simple, non-destructive technique for the identification of the individual molecular ions relying on an in situ mass measurement of the molecules, studies of the photofragmentation of singly-charged aniline ions (C6H7N+) as well as investigations of isotope effects in reactions of Mg+ ions with HD molecules have been carried out.

Drewsen, M.

2009-03-01

11

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

PubMed

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 mollusk, the sea hare Aplysia californica. The open reading frame of this cDNA encodes a protein of 147 amino acids. The molecular architecture of the deduced protein is highly homologous to that reported for the prepro-octopus GnRH (oct-GnRH) and consists of a putative signal peptide, a GnRH dodecapeptide, a downstream processing site, and a GnRH-associated peptide (GAP). The deduced amino acid sequence of the Aplysia GnRH (ap-GnRH) is QNYHFSNGWYAG and differs from oct-GnRH by only two amino acids. The transcript for ap-GnRH is widely expressed in the central nervous system (CNS), the ovotestis, and the atrial gland, an exocrine gland. Immunocytochemistry (ICC) using an antiserum against oct-GnRH detected immunoreactive neurons in all CNS ganglia examined, and the staining was abolished by the preadsorption of the antiserum with synthetic ap-GnRH. In sum, ap-GnRH sequence is the first gastropod GnRH-like molecule to be elucidated. Further, it represents one of the only two GnRH-like molecules found outside Phylum Chordata. These data refute the possibility that oct-GnRH arose singly in cephalopods by convergent evolution and provide valuable support for an ancient origin of GnRH during metazoan evolution. PMID:18178211

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

2008-04-01

12

Patterns and conformations in molecularly thin films  

NASA Astrophysics Data System (ADS)

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

Basnet, Prem B.

13

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

Microsoft Academic Search

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

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

2008-01-01

14

Single-Molecule Circuits with Well-Defined Molecular Conductance  

E-print Network

Single-Molecule Circuits with Well-Defined Molecular Conductance Latha Venkataraman,*,,| Jennifer E-terminated molecules by breaking Au point contacts in a molecular solution at room temperature. We find that the variability of the observed conductance for the diamine molecule-Au junctions is much less than

Hone, James

15

Molecular rearrangements observed by single-molecule microscopy  

Microsoft Academic Search

We have applied quantitative single-molecule photoluminescence microscopy for directly observing molecular rearrangements in a polymeric material subjected to tensile deformation. The system examined is a blend of fluorescent conjugated polymer molecules embedded in polyethylene, known to exhibit strong phase separation. Statistical analysis of the sizes of phase-separated domains reveals that during tensile deformation large domains of fluorescent molecules are transformed

W. Trabesinger; A. Renn; B. Hecht; U. P. Wild; A. Montali; P. Smith; Ch. Weder

2001-01-01

16

Interstellar Molecules: The New Frontiers for Molecular Data  

NASA Astrophysics Data System (ADS)

Although over 110 chemical species have been securely identified in the interstellar and circumstellar gas, there are still many data needs for molecular astrophysics. Among these needs are new high-resolution spectroscopic measurements of potential interstellar molecules, in particular organic radicals, metal-bearing molecules, and molecular ions. Ab initio studies that support these experimental investigations are necessary as well. Reaction rate measurements of many ion-molecule, neutral-neutral, and radiative association processes are also essential.

Ziurys, Lucy M.; Apponi, Aldo J.

2002-10-01

17

Separation of biological molecules using mesoporous molecular sieves  

Microsoft Academic Search

The selective separation and purification of biological molecules is important in a number of industries, especially those processing food or pharmaceuticals. However, the applications of molecular sieves for these separations have been limited by the available pore sizes (

Jenny M. Kisler; Antje Dähler; Geoffrey W. Stevens; Andrea J. O’Connor

2001-01-01

18

Mechanically Activated Molecular Switch through Single-Molecule Pulling  

SciTech Connect

We investigate a prototypical single-molecule switch marrying force spectroscopy and molecular electronics far from the thermodynamic limit. We use molecular dynamics to simulate a conducting atomic force microscope mechanically manipulating a molecule bound to a surface between a folded state and an unfolded state while monitoring the conductance. Both the complexity and the unique phenomenology of single-molecule experiments are evident in this system. As the molecule unfolds/refolds, the average conductance reversibly changes over 3 orders of magnitude; however, throughout the simulation the transmission fluctuates considerably, illustrating the need for statistical sampling in these systems. We predict that emergent single-molecule signatures will still be evident with conductance blinking, correlated with force blinking, being observable in a region of dynamic bistability. Finally, we illustrate some of the structure?function relationships in this system, mapping the dominant interactions in the molecule for mediating charge transport throughout the pulling simulation.

Franco, Ignacio; George, Christopher B.; Solomon, G. C.; Schatz, George C.; Ratner, Mark A.

2011-01-01

19

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

SciTech Connect

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

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

2010-01-12

20

Receptor-mediated signalling in plants: molecular patterns and programmes  

PubMed Central

A highly evolved surveillance system in plants is able to detect a broad range of signals originating from pathogens, damaged tissues, or altered developmental processes, initiating sophisticated molecular mechanisms that result in defence, wound healing, and development. Microbe-associated molecular pattern molecules (MAMPs), damage-associated molecular pattern molecules (DAMPs), virulence factors, secreted proteins, and processed peptides can be recognized directly or indirectly by this surveillance system. Nucleotide binding-leucine rich repeat proteins (NB-LRR) are intracellular receptors and have been targeted by breeders for decades to elicit resistance to crop pathogens in the field. Receptor-like kinases (RLKs) or receptor like proteins (RLPs) are membrane bound signalling molecules with an extracellular receptor domain. They provide an early warning system for the presence of potential pathogens and activate protective immune signalling in plants. In addition, they act as a signal amplifier in the case of tissue damage, establishing symbiotic relationships and effecting developmental processes. The identification of several important ligands for the RLK-type receptors provided an opportunity to understand how plants differentiate, how they distinguish beneficial and detrimental stimuli, and how they co-ordinate the role of various types of receptors under varying environmental conditions. The diverse roles of extra-and intracellular plant receptors are examined here and the recent findings on how they promote defence and development is reviewed. PMID:19628572

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

2009-01-01

21

Identifying molecular signatures in metal-molecule-metal junctions  

NASA Astrophysics Data System (ADS)

Single molecule identification in metal-molecule-metal junctions provides an ultimate probe that opens a new avenue for revolutionary advances in demonstrating single molecule device functions. Inelastic electron tunneling spectroscopy (IETS) is an ultra-sensitive method for probing vibrational characteristics of molecules with atomic resolution. State-of-the-art experiments on the inelastic transport in self-assembled monolayers of organic molecules have demonstrated the utility of the IETS technique to derive structural information concerning molecular conformations and contact configurations. Here we report the vibrational fingerprint of an individual ?-conjugated molecule sandwiched between gold nanoelectrodes. Our strategy combines analyses of single molecule conductance and vibrational spectra exploiting the nanofabricated mechanically-controllable break junction. We performed IETS measurements on 1,4-benzenedithiol and 2,5-dimercapto-1,3,4-thiadiazole to examine chemical discrimination at the single-molecule level. We found distinct IET spectra unique to the test molecules that agreed excellently with the Raman and theoretical spectra in the fingerprint region, and thereby succeeded in electrical identification of single molecule junctions.

Tsutsui, Makusu; Taniguchi, Masateru; Shoji, Kohei; Yokota, Kazumichi; Kawai, Tomoji

2009-09-01

22

A random rotor molecule: Vibrational analysis and molecular dynamics simulations  

NASA Astrophysics Data System (ADS)

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

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

2012-12-01

23

Designed DNA molecules: principles and applications of molecular nanotechnology  

Microsoft Academic Search

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

Anne Condon

2006-01-01

24

An extracellular adhesion molecule complex patterns dendritic branching and morphogenesis  

PubMed Central

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

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

2014-01-01

25

Imaging of Flow Patterns with Fluorescent Molecular Rotors  

PubMed Central

Molecular rotors are a group of fluorescent molecules that form twisted intramolecular charge transfer states (TICT) upon photoexcitation. Some classes of molecular rotors, among them those that are built on the benzylidene malononitrile motif, return to the ground state either by nonradiative intramolecular rotation or by fluorescence emission. In low-viscosity solvents, intramolecular rotation dominates, and the fluorescence quantum yield is low. Higher solvent viscosities reduce the intramolecular rotation rate, thus increasing the quantum yield. We recently described a different mechanism whereby the fluorescence quantum yield of the molecular rotor also depends on the shear stress of the solvent. In this study, we examined a possible application for shear-sensitive molecular rotors for imaging flow patterns in fluidic chambers. Flow chambers with different geometries were constructed from polycarbonate or acrylic. Solutions of molecular rotors in ethylene glycol were injected into the chamber under controlled flow rates. LED-induced fluorescence (LIF) images of the flow chambers were taken with a digital camera, and the intensity difference between flow and no-flow images was visualized and compared to computed fluid dynamics (CFD) simulations. Intensity differences were detectable with average flow rates as low as 0.1 mm/s, and an exponential association between flow rate and intensity increase was found. Furthermore, a good qualitative match to computed fluid dynamics simulations was seen. On the other hand, prolonged exposure to light reduced the emission intensity. With its high sensitivity and high spatial and temporal resolution, imaging of flow patterns with molecular rotors may become a useful tool in microfluidics, flow measurement, and control. PMID:20405175

Mustafic, Adnan; Huang, Hsuan-Ming; Theodorakis, Emmanuel A.

2010-01-01

26

Behavior of a Reverse Lamellar Phase in the Presence of Low Molecular Weight Triblock Molecules  

E-print Network

Behavior of a Reverse Lamellar Phase in the Presence of Low Molecular Weight Triblock Molecules N molecular weight triblock molecules. So, we can wonder if these effects can also be induced by low molec lamellar phase upon the insertion of low molecular weight triblock molecules. Materials and Methods

Urbach, Wladimir

27

Molecular Design of Branched and Binary Molecules at Ordered Interfaces  

SciTech Connect

This study examined five different branched molecular architectures to discern the effect of design on the ability of molecules to form ordered structures at interfaces. Photochromic monodendrons formed kinked packing structures at the air-water interface due to the cross-sectional area mismatch created by varying number of alkyl tails and the hydrophilic polar head group. The lower generations formed orthorhombic unit cell with long range ordering despite the alkyl tails tilted to a large degree. Favorable interactions between liquid crystalline terminal groups and the underlying substrate were observed to compel a flexible carbosilane dendrimer core to form a compressed elliptical conformation which packed stagger within lamellae domains with limited short range ordering. A twelve arm binary star polymer was observed to form two dimensional micelles at the air-water interface attributed to the higher polystyrene block composition. Linear rod-coil molecules formed a multitude of packing structures at the air-water interface due to the varying composition. Tree-like rod-coil molecules demonstrated the ability to form one-dimensional structures at the air-water interface and at the air-solvent interface caused by the preferential ordering of the rigid rod cores. The role of molecular architecture and composition was examined and the influence chemically competing fragments was shown to exert on the packing structure. The amphiphilic balance of the different molecular series exhibited control on the ordering behavior at the air-water interface and within bulk structures. The shell nature and tail type was determined to dictate the preferential ordering structure and molecular reorganization at interfaces with the core nature effect secondary.

Kirsten Larson Genson

2005-12-27

28

Apparatus and method of determining molecular weight of large molecules  

DOEpatents

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

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

1998-06-23

29

Apparatus and method of determining molecular weight of large molecules  

DOEpatents

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

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

1998-01-01

30

Optical molecular imaging for systems biology: from molecule to organism  

PubMed Central

The development of highly efficient analytical methods capable of probing biological systems at system level is an important task that is required in order to meet the requirements of the emerging field of systems biology. Optical molecular imaging (OMI) is a very powerful tool for studying the temporal and spatial dynamics of specific biomolecules and their interactions in real time in vivo. In this article, recent advances in OMI are reviewed extensively, such as the development of molecular probes that make imaging brighter, more stable and more informative (e.g., FPs and semiconductor nanocrystals, also referred to as quantum dots), the development of imaging approaches that provide higher resolution and greater tissue penetration, and applications for measuring biological events from molecule to organism level, including gene expression, protein and subcellular compartment localization, protein activation and interaction, and low-mass molecule dynamics. These advances are of great significance in the field of biological science and could also be applied to disease diagnosis and pharmaceutical screening. Further developments in OMI for systems biology are also proposed. PMID:16850295

Du, Wei; Wang, Ying; Luo, Qingming

2006-01-01

31

Molecules  

NSDL National Science Digital Library

The Switzerland-based society, Molecular Diversity Preservation International (MDPI) provides this free, online journal, Molecules. This journal of synthetic and natural product chemistry encourages chemists to publish their experimental detail, particularly synthetic procedures and characterization information. "Any scattered unassembled experimental data for individual compounds which is conventionally not publishable is particularly welcomed," says the site. The idea is to get information out as quickly as possible to the scientific community. To access Molecules, follow the instructions on how to request a username and password.

1995-01-01

32

Single-molecule transistor fabrication by self-aligned lithography and in situ molecular assembly  

E-print Network

Single-molecule transistor fabrication by self-aligned lithography and in situ molecular assembly J of single-molecule transistors by self-aligned lithography and in situ molecular assembly. Ultrathin metal electronics is the realization of electronic switches comprising individual molecules as the key functional

Hone, James

33

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...

34

Molecular line parameters for the atmospheric trace molecule spectroscopy experiment  

NASA Technical Reports Server (NTRS)

During its first mission in 1985 onboard Spacelab 3, the ATMOS (atmospheric trace molecule spectroscopy) instrument, a high speed Fourier transform spectrometer, produced a large number of high resolution infrared solar absorption spectra recorded in the occultation mode. The analysis and interpretation of these data in terms of composition, chemistry, and dynamics of the earth's upper atmosphere required good knowledge of the molecular line parameters for those species giving rise to the absorptions in the atmospheric spectra. This paper describes the spectroscopic line parameter database compiled for the ATMOS experiment and referenced in other papers describing ATMOS results. With over 400,000 entries, the linelist catalogs parameters of 46 minor and trace species in the 1-10,000/cm region.

Brown, L. R.; Farmer, C. B.; Toth, R. A.; Rinsland, Curtis P.

1987-01-01

35

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

PubMed Central

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

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

2013-01-01

36

Patterns of energy levels and spectra for polyatomic molecules  

SciTech Connect

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

Harter, W.G.

1983-01-01

37

Exploration of target molecules for molecular imaging of inflammatory bowel disease  

SciTech Connect

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

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

2011-07-08

38

High Speed Molecular Patterning via Massively-Parallel Dip-Pen Nanolithography  

NASA Astrophysics Data System (ADS)

We have demonstrated a high speed direct deposition method for patterning organic molecules onto solid substrates via massively-parallel dip-pen nanolithography (DPN). This technique relies on high density multiple AFM tips as writing tools, organic adsorbates as inks, and solid substrates as paper. Our presentation will address how DPN, with which we previously demonstrated 12 nm linewidth resolution, multiple pattern alignment, and potential for high speed parallel writing [1-3], can be extended to high speed molecular patterning applications. The molecular patterns have been analyzed via various scanning probe techniques. Present and future implications of this methodology will be addressed. ([1] S. Hong, C. A. Mirkin, Science 288, 1808 (2000). [2] S. Hong, J. Zhu, C. A. Mirkin, Science 286, 523 (1999). [3] R. Piner, J. Zhu, F. Xu, S. Hong, C. A. Mirkin, Science 283, 661 (1999).)

Hong, Seunghun; Mirkin, Chad; Zhang, Ming; Bullen, David; Liu, Chang

2001-03-01

39

Evolving Molecules for Drug Design Using Genetic Algorithms via Molecular Trees  

E-print Network

Evolving Molecules for Drug Design Using Genetic Algorithms via Molecular Trees Gerard Kian evolutionary computation can design acceptable molecular structures that are potentially useful for drug design endeavors. 1 INTRODUCTION One major strategy in drug design is to find or build molecules that target

Fernandez, Thomas

40

Neocortex Patterning by the Secreted Signaling Molecule FGF8  

E-print Network

and invertebrate embryonic patterning, in- cluding members of the fibroblast growth factor (FGF), Wingless-Int (WNT) (Fig. 1B), and the primordium itself shows A/P graded expression of genes encoding FGF receptors FGFR1

Born, Richard

41

Molecular dynamics simulation on evaporation molecules in a vapor-liquid equilibrium state  

NASA Astrophysics Data System (ADS)

By using molecular dynamics simulations of argon molecules, the present study investigates molecular evaporation and reflection in equilibrium at a vapor-liquid interface, which involves the kinetic boundary condition (KBC) of the Boltzmann equation. The present method allows evaporation and reflection molecules to be selected naturally at the vapor-liquid interphase. Based on the results, we confirm that the evaporation molecules in the equilibrium state behave almost similar to spontaneous-evaporation molecules (as determined by virtual-vacuum evaporation simulations). Furthermore, we find that the velocity distribution of reflection molecules in the normal direction to the boundary is lower than the Maxwell distribution at the liquid temperature.

Kobayashi, Kazumichi; Hori, Kazumasa; Yaguchi, Hisao; Watanabe, Masao

2014-12-01

42

Revisiting molecular ionization: Does a molecule like to share?  

NASA Astrophysics Data System (ADS)

The ever-increasing detail obtained in strong-field experiments calls for a deeper understanding of the laser-molecule interaction. For instance, recent measurements reported in PRL 107, 143004 (2011) reveal a limitation in understanding strong-field ionization dynamics in terms of the strong-field approximation. We have addressed the question of how the electron and the nuclei share the energy when H2^+ breaks up in the presence of an intense IR field via the process: H2^++n?->p+p+e^-. Solving the time-dependent Schr"odinger equation and calculating the ionization probability resolved as a function of the asymptotic electron energy and the nuclear kinetic energy release (KER) allow us to give an answer. The energy sharing is non-trivial and plays an important role in the prediction of, for instance, the KER. We also address the limitations of current understanding of molecular ionization by comparing to models like the strong-field approximation and the Floquet picture. Such benchmarking may be facilitated by XUV+IR pump-probe schemes and carrier-envelope-phase control that allow for time-resolved and spatial probing of the dynamics.

Madsen, C. B.; Esry, B. D.

2012-06-01

43

Sensing of protein molecules through nanopores: a molecular dynamics study  

NASA Astrophysics Data System (ADS)

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

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

2014-04-01

44

Molecular multipole moments of water molecules in ice Ih  

SciTech Connect

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.}

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

45

Molecular multipole moments of water molecules in ice Ih  

NASA Astrophysics Data System (ADS)

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

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

1998-09-01

46

Electron transport through heterocyclic molecule: ab initio molecular orbital theory  

Microsoft Academic Search

We have calculated the electron transport properties of molecule wires by an ab initio molecule orbital theory on the basis of the first-principles density functional theory (DFT) and the non-equilibrium Green function (NEGF) technique. The wires are made of heterocyclic molecule (furan, thiophene, and pyrrole, shown in first figure), in contact with the atomic scale Au electrodes. The results of

W. W. Cheng; Y. X. Liao; H. Chen; H. Mizuseki; Y. Kawazoe

2004-01-01

47

Conformation and Luminescence of Isolated Molecular Semiconductor Molecules  

E-print Network

as the active layer in optoelectronic devices such as organic light-emitting diodes (OLEDs) and lasers. Unlike of two small molecule organic semiconductors, oligo(phenylenvinylene) (OPV) molecules with chains of five efficiency of the molecules in each class, providing a direct correlation between the luminescence efficiency

Buratto, Steve

48

Molecular analyses of dinosaur osteocytes support the presence of endogenous molecules.  

PubMed

The discovery of soft, transparent microstructures in dinosaur bone consistent in morphology with osteocytes was controversial. We hypothesize that, if original, these microstructures will have molecular features in common with extant osteocytes. We present immunological and mass spectrometry evidence for preservation of proteins comprising extant osteocytes (Actin, Tubulin, PHEX, Histone H4) in osteocytes recovered from two non-avian dinosaurs. Furthermore, antibodies to DNA show localized binding to these microstructures, which also react positively with DNA intercalating stains propidium iodide (PI) and 4',6'-diamidino-2-phenylindole dihydrochloride (DAPI). Each antibody binds dinosaur cells in patterns similar to extant cells. These data are the first to support preservation of multiple proteins and to present multiple lines of evidence for material consistent with DNA in dinosaurs, supporting the hypothesis that these structures were part of the once living animals. We propose mechanisms for preservation of cells and component molecules, and discuss implications for dinosaurian cellular biology. PMID:23085295

Schweitzer, Mary Higby; Zheng, Wenxia; Cleland, Timothy P; Bern, Marshall

2013-01-01

49

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

NASA Astrophysics Data System (ADS)

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.

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

2014-10-01

50

Molecular Karyotype Analysis ofCryptosporidium parvum: Evidence for Eight Chromosomes and a Low-Molecular-Size Molecule  

Microsoft Academic Search

We report improved separation of chromosome-sized DNA molecules of the coccidian parasite Cryptospo- ridium parvumwith contour-clamped homogeneous electricfields (CHEF). We used scanning densitometry to determine that the most likely number of chromosomes is eight. Molecular probes consisting of cloned genes were used to distinguish each offive bands visible on CHEF gels. We have also identified a low-molecular-size DNA molecule possibly

DENNIS S. BLUNT; NIKOLAI V. KHRAMTSOV; STEVE J. UPTON; ANDBETH A. MONTELONE

1997-01-01

51

Elements of the theory of molecular spectra. [multiatomic molecules  

NASA Technical Reports Server (NTRS)

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

Gribov, L. A.

1979-01-01

52

Organic molecules as chemical fossils - The molecular fossil record  

NASA Technical Reports Server (NTRS)

The study of biochemical clues to the early earth and the origin of life is discussed. The methods used in such investigation are described, including the extraction, fractionation, and analysis of geolipids and the analysis of kerogen. The occurrence of molecular fossils in the geological record is examined, discussing proposed precursor-product relationships and the molecular assessment of deep sea sediments, ancient sediments, and crude petroleums. Alterations in the molecular record due to diagenesis and catagenesis are considered, and the use of microbial lipids as molecular fossils is discussed. The results of searches for molecular fossils in Precambrian sediments are assessed.

Eglinton, G.

1983-01-01

53

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

PubMed

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

Lépinay, Sandrine; Ianoul, Anatoli; Albert, Jacques

2014-10-01

54

A localized molecular-orbital assembler approach for Hartree-Fock calculations of large molecules  

NASA Astrophysics Data System (ADS)

We describe an alternative fragment-based method, the localized molecular-orbital assembler method, for Hartree-Fock (HF) calculations of macromolecules. In this approach, a large molecule is divided into many small-size fragments, each of which is capped by its local surroundings. Then the conventional HF calculations are preformed on these capped fragments (or subsystems) and the canonical molecular orbitals of these systems are transferred into localized molecular orbitals (LMOs). By assembling the LMOs of these subsystems into a set of LMOs of the target molecule, the total density matrix of the target molecule is constructed and correspondingly the HF energy or other molecular properties can be approximately computed. This approach computationally achieves linear scaling even for medium-sized systems. Our test calculations with double-zeta and polarized double-zeta basis sets demonstrate that the present approach is able to reproduce the conventional HF energies within a few millihartrees for a broad range of molecules.

Li, Wei; Li, Shuhua

2005-05-01

55

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

NSDL National Science Digital Library

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

Michael Eck (Harvard University)

2011-04-09

56

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

NSDL National Science Digital Library

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

Michael Eck (Harvard University)

2011-04-09

57

The Virtual Museum of Minerals and Molecules: Molecular Visualization in a Virtual Hands-On Museum  

ERIC Educational Resources Information Center

The Virtual Museum of Minerals and Molecules (VMMM) is a web-based resource presenting interactive, 3-D, research-grade molecular models of more than 150 minerals and molecules of interest to chemical, earth, plant, and environmental sciences. User interactivity with the 3-D display allows models to be rotated, zoomed, and specific regions of…

Barak, Phillip; Nater, Edward A.

2005-01-01

58

The benzene molecule as a molecular resonant-tunneling transistor M. Di Ventraa)  

E-print Network

The benzene molecule as a molecular resonant-tunneling transistor M. Di Ventraa) and S. T of transport through a benzene-1, 4-dithiolate molecule with a third capacitive terminal gate . We find rectification was demonstrated in 1993.2 More recently, Reed et al. investigated the benzene-1, 4-dithiol rings

Pantelides, Sokrates T.

59

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

E-print Network

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

Wilson, Mark R.

60

Characteristics and Biological Variations of M-Ficolin, a Pattern Recognition Molecule, in Plasma  

Microsoft Academic Search

The three human ficolins, H-ficolin, L-ficolin and M-ficolin, are pattern recognition molecules of the innate immune system. All three ficolins can activate the lectin pathway of the complement system after binding to pathogens. H- and L-ficolin are serum proteins with an average concentration of 18 and 3 ?g\\/ml, respectively. M-ficolin has been described as a membrane-associated pattern recognition receptor of

Thomas Wittenborn; Steffen Thiel; Lisbeth Jensen; Hans J. Nielsen; Jens C. Jensenius

2010-01-01

61

Three-dimensional Molecular Modeling with Single Molecule FRET  

PubMed Central

Single molecule fluorescence energy transfer experiments enable investigations of macromolecular conformation and folding by the introduction of fluorescent dyes at specific sites in the macromolecule. Multiple such experiments can be performed with different labeling site combinations in order to map complex conformational changes or interactions between multiple molecules. Distances that are derived from such experiments can be used for determination of the fluorophore positions by triangulation. When combined with a known structure of the macromolecule(s) to which the fluorophores are attached, a three-dimensional model of the system can be determined. However, care has to be taken to properly derive distance from fluorescence energy transfer efficiency and to recognize the systematic or random errors for this relationship. Here we review the experimental and computational methods used for three-dimensional modeling based on single molecule fluorescence resonance transfer, and describe recent progress in pushing the limits of this approach to macromolecular complexes. PMID:20837146

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

2011-01-01

62

Research Update: Molecular electronics: The single-molecule switch and transistor  

SciTech Connect

In order to design and realize single-molecule devices it is essential to have a good understanding of the properties of an individual molecule. For electronic applications, the most important property of a molecule is its conductance. Here we show how a single octanethiol molecule can be connected to macroscopic leads and how the transport properties of the molecule can be measured. Based on this knowledge we have realized two single-molecule devices: a molecular switch and a molecular transistor. The switch can be opened and closed at will by carefully adjusting the separation between the electrical contacts and the voltage drop across the contacts. This single-molecular switch operates in a broad temperature range from cryogenic temperatures all the way up to room temperature. Via mechanical gating, i.e., compressing or stretching of the octanethiol molecule, by varying the contact's interspace, we are able to systematically adjust the conductance of the electrode-octanethiol-electrode junction. This two-terminal single-molecule transistor is very robust, but the amplification factor is rather limited.

Sotthewes, Kai; Heimbuch, René, E-mail: r.heimbuch@utwente.nl; Kumar, Avijit; Zandvliet, Harold J. W. [Physics of Interfaces and Nanomaterials, MESA Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500AE Enschede (Netherlands); Geskin, Victor [Service de Chimie des Materiaux Nouveaux, University of Mons, Mons (Belgium)

2014-01-01

63

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

E-print Network

. Gauthier Groupe Nanosciences, CEMES-CNRS 29 rue Jeanne Marvig, F-31055 Toulouse, France Fax: (+33) 5 Community Sixth Framework Programme for RTD activities, under the STREP project NANOMAN (Control) (Fig. 1a and b) on Cu(100) by STM at room temperature (RT) under ultrahigh vacuum (UHV). This molecule

Paris-Sud XI, Université de

64

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

NASA Astrophysics Data System (ADS)

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

Miller, Michael Stephen

65

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

NASA Astrophysics Data System (ADS)

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

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

2014-07-01

66

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

PubMed

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

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

2014-07-01

67

Syntheses of molecularly imprinted polymers: Molecular recognition of cyproheptadine using original print molecules and azatadine as dummy templates.  

PubMed

The use of custom-made polymeric materials with high selectivities as target molecules in solid-phase extraction (SPE), known as molecularly imprinted solid-phase extraction (MISPE), is becoming an increasingly important sample preparation technique. However, the potential risk of leakage of the imprinting molecules during the desorption phase has limited application. The use of a mimicking template, called a dummy molecular imprinting polymer (DMIP), that bears the structure of a related molecule and acts as a putative imprinting molecule may provide a useful solution to this problem. In the current study, cyproheptadine (CPH) and azatadine (AZA) were used as templates in the development of an MIP and DMIP for acrylic acid and methacrylic acid monomers. Our results indicate that DMIPs have equal recognition of CPH, avoiding the problem of leakage of original template during the desorption phase relative to MIPs synthesized in presence of the print molecule CPH. Examination of the surface structure of the two polymer products by SEM shows appreciable differences in structural morphology and function of the monomers employed. These results are well supplemented by data obtained for swelling ratios and solvent uptake. Molecular modelling of CPH and AZA suggests that both substrates are similar in shape and volume. PMID:19084632

Feás, X; Seijas, J A; Vázquez-Tato, M P; Regal, P; Cepeda, A; Fente, C

2009-01-12

68

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

NASA Astrophysics Data System (ADS)

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.

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

2013-10-01

69

The Role of Damage-Associated Molecular Patterns in Human Diseases  

PubMed Central

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

Land, Walter G.

2015-01-01

70

Atomistic theory of mesoscopic pattern formation induced by bimolecular surface reactions between oppositely charged molecules  

NASA Astrophysics Data System (ADS)

The kinetics of mesoscopic pattern formation is studied for a reversible A+B rightleftharpoons 0 reaction between mobile oppositely charged molecules at the interface. Using formalism of the joint correlation functions, non-equilibrium charge screening and reverse Monte Carlo methods, it is shown that labyrinth-like percolation structure induced by (even moderate-rate) reaction is principally non-steady-state one and is associated with permanently growing segregation of dissimilar reactants and aggregation of similar reactants into mesoscopic size domains. A role of short-range and long-range reactant interactions in pattern formation is discussed.

Kuzovkov, V. N.; Kotomin, E. A.; Zvejnieks, G.

2011-12-01

71

Molecular level studies on binding modes of labeling molecules with polyalanine peptides  

NASA Astrophysics Data System (ADS)

In this work, the binding modes of typical labeling molecules (thioflavin T (ThT), Congo red (CR) and copper(ii) phthalocyanine tetrasulfonic acid tetrasodium salt (PcCu(SO3Na)4)) on pentaalanine, which is a model peptide segment of amyloid peptides, have been resolved at the molecular level by using scanning tunneling microscopy (STM). In the STM images, ThT molecules are predominantly adsorbed parallel to the peptide strands and two binding modes could be identified. It was found that ThT molecules are preferentially binding on top of the peptide strand, and the mode of intercalated between neighboring peptides also exists. The parallel binding mode of CR molecules can be observed with pentaalanine peptides. Besides the binding modes of labeling molecules, the CR and PcCu(SO3Na)4 display different adsorption affinity with the pentaalanine peptides. The results could be beneficial for obtaining molecular level insight of the interactions between labeling molecules and peptides.In this work, the binding modes of typical labeling molecules (thioflavin T (ThT), Congo red (CR) and copper(ii) phthalocyanine tetrasulfonic acid tetrasodium salt (PcCu(SO3Na)4)) on pentaalanine, which is a model peptide segment of amyloid peptides, have been resolved at the molecular level by using scanning tunneling microscopy (STM). In the STM images, ThT molecules are predominantly adsorbed parallel to the peptide strands and two binding modes could be identified. It was found that ThT molecules are preferentially binding on top of the peptide strand, and the mode of intercalated between neighboring peptides also exists. The parallel binding mode of CR molecules can be observed with pentaalanine peptides. Besides the binding modes of labeling molecules, the CR and PcCu(SO3Na)4 display different adsorption affinity with the pentaalanine peptides. The results could be beneficial for obtaining molecular level insight of the interactions between labeling molecules and peptides. Electronic supplementary information (ESI) available. See DOI: 10.1039/c0nr00782j

Mao, Xiaobo; Wang, Chenxuan; Ma, Xiaojing; Zhang, Min; Liu, Lei; Zhang, Lan; Niu, Lin; Zeng, Qindao; Yang, Yanlian; Wang, Chen

2011-04-01

72

Carbon Nanotube Biosensors for Space Molecule Detection and Clinical Molecular Diagnostics  

NASA Technical Reports Server (NTRS)

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

Han, Jie

2001-01-01

73

A new graph-based molecular descriptor using the canonical representation of the molecule.  

PubMed

Molecular similarity is a pervasive concept in drug design. The basic idea underlying molecular similarity is the similar property principle, which states that structurally similar molecules will exhibit similar physicochemical and biological properties. In this paper, a new graph-based molecular descriptor (GBMD) is introduced. The GBMD is a new method of obtaining a rough description of 2D molecular structure in textual form based on the canonical representations of the molecule outline shape and it allows rigorous structure specification using small and natural grammars. Simulated virtual screening experiments with the MDDR database show clearly the superiority of the graph-based descriptor compared to many standard descriptors (ALOGP, MACCS, EPFP4, CDKFP, PCFP, and SMILE) using the Tanimoto coefficient (TAN) and the basic local alignment search tool (BLAST) when searches were carried. PMID:25140330

Hentabli, Hamza; Saeed, Faisal; Abdo, Ammar; Salim, Naomie

2014-01-01

74

A New Graph-Based Molecular Descriptor Using the Canonical Representation of the Molecule  

PubMed Central

Molecular similarity is a pervasive concept in drug design. The basic idea underlying molecular similarity is the similar property principle, which states that structurally similar molecules will exhibit similar physicochemical and biological properties. In this paper, a new graph-based molecular descriptor (GBMD) is introduced. The GBMD is a new method of obtaining a rough description of 2D molecular structure in textual form based on the canonical representations of the molecule outline shape and it allows rigorous structure specification using small and natural grammars. Simulated virtual screening experiments with the MDDR database show clearly the superiority of the graph-based descriptor compared to many standard descriptors (ALOGP, MACCS, EPFP4, CDKFP, PCFP, and SMILE) using the Tanimoto coefficient (TAN) and the basic local alignment search tool (BLAST) when searches were carried. PMID:25140330

Hentabli, Hamza; Abdo, Ammar; Salim, Naomie

2014-01-01

75

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

NASA Astrophysics Data System (ADS)

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

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

2011-06-01

76

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

NASA Astrophysics Data System (ADS)

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

Harter, William; Mitchell, Justin

2009-06-01

77

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

Microsoft Academic Search

The classical molecular dynamics (MD) simulations for the solvation properties of cis- and transplatins in water are performed with the Lennard-Jones plus Coulomb electrostatic potential parameters that are optimized with ab initio potential energies of the water-platin systems. Two hydration shells are found both for cis- and transplatins. The first shell of water molecules is closer to transplatin than cisplatin.

Cen-Feng Fu; Shan Xi Tian

2010-01-01

78

Atoms, Molecules and Photons: An Introduction to Atomic Molecular and Quantum Physics  

Microsoft Academic Search

This introduction to Atomic and Molecular Physics explains how our present model of atoms and molecules has been developed during the last two centuries by many experimental discoveries and from the theoretical side by the introduction of quantum physics to the adequate description of micro-particles. It illustrates the wave model of particles by many examples and shows the limits of

Wolfgang Demtröder

2006-01-01

79

Resonance enhanced multiphoton ionization spectra of molecules and molecular fragments. Technical report, January 1990--December 1990  

SciTech Connect

The objective of our effort is to carry out theoretical studies of resonance enhanced multiphoton ionization processes in molecules and molecular fragments. These studies are designed to provide a quantitatively robust analysis and prediction of key spectral features of interest in several ongoing experimental studies and applications of this technique.

NONE

1997-07-01

80

Single-Molecule Approach to Molecular Biology in Living Bacterial Cells  

Microsoft Academic Search

Recent developments on fluorescent proteins and microscopy tech- niques have allowed the probing of single molecules in a living bacterial cell with high specificity, millisecond time resolution, and nanometer spatial precision. Recording movies and analyzing dy- namics of individual macromolecules have brought new insights into the mechanisms of many processes in molecular biology, such as DNA-protein interactions, gene regulation, transcription,

X. Sunney Xie; Paul J. Choi; Gene-Wei Li; Nam Ki Lee; Giuseppe Lia

2008-01-01

81

Electronic Structures of Molecules XI. Electroaffinity, Molecular Orbitals and Dipole Moments  

Microsoft Academic Search

A convenient criterion for defining equal electronegativity of two atoms is stated in terms of coefficients in LCAO approximate molecular orbitals. Connections between relative electronegativities, coefficients in LCAO orbitals, effective charges on atoms in partially polar molecules, and dipole moments, are then analyzed, and various equations are obtained expressing these connections. The discussion is largely applicable to polyatomic as well

Robert S. Mulliken

1935-01-01

82

Micro-patternable nanoporous polymer integrated with microstructures for molecular filtration  

NASA Astrophysics Data System (ADS)

This paper proposes a facile method to fabricate nanoporous microstructures by a photo-patternable SU-8 photoresist, to serve as a molecular filter in microfluidic systems. The fabrication process involves solvent-controlled nanoporous structure formation combined with standard photolithography steps for microstructure fabrication. The self-formed nanoporous morphology embedded inside the microstructure exhibits a sufficient mechanical strength and eliminates complex processes or protocols for integration/assembly of nano- and microstructures. Field emission gun scanning electronic microscopy (FEGSEM) images showed the fabricated nanoporous morphologies with embedded nanogaps of about 6-10 nm. Atomic force microscopy (AFM) images also depicted a clear difference on the degree of porosity between the solvent-controlled SU-8 and the standard resist. Fluorescent dyes, namely Rhodamine-B and Rhodamine-6G, were employed to estimate the diffusivity of the fabricated SU-8 based nanofilter and demonstrated that the Rhodamine based fluorescent molecules can penetrate these nanosized filtration structures. The fabricated nanofilter was capable of providing a molecular weight cut-off range up to 70 kDa, estimated roughly for a molecule with a diameter of 6-10 nm. This simple process provides a novel way to integrate the nanofiltration capability into microstructures while maintaining a sufficient mechanical strength for molecular level filtration in lab-on-chip (LOC) systems.

Chang, Chia-Jung; Yang, Chung-Shi; Chuang, Yun-Ju; Khoo, Hwa-Seng; Tseng, Fan-Gang

2008-09-01

83

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

NASA Technical Reports Server (NTRS)

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

Byer, R. L.

1982-01-01

84

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

PubMed

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

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

2014-05-28

85

A quantum simulator for molecules: Imaging molecular orbitals and electronic dynamics with ultracold atoms  

E-print Network

In the recent years, ultracold atoms in optical lattices have proven their great value as quantum simulators for studying strongly-correlated phases and complex phenomena in solid-state systems. Here we reveal their potential as quantum simulators for molecular physics and propose a technique to image the three-dimensional molecular orbitals with high resolution. The outstanding tunability of ultracold atoms in terms of potential and interaction offer fully-adjustable model systems for gaining deep insight into the electronic structure of molecules. We study the orbitals of an artificial benzene molecule and discuss the effect of tunable interactions in its conjugated pi electron system with special regard to localization and spin order. The dynamical timescale of ultracold atom simulators are on the order milliseconds which allow for the time-resolved monitoring of a broad range of dynamical processes. As an example, we compute the hole dynamics in the conjugated pi system of the artificial benzene molecule.

Lühmann, Dirk-Sören; Sengstock, Klaus

2015-01-01

86

A scale-bridging modeling approach for anisotropic organic molecules at patterned semiconductor surfaces  

NASA Astrophysics Data System (ADS)

Hybrid systems consisting of organic molecules at inorganic semiconductor surfaces are gaining increasing importance as thin film devices for optoelectronics. The efficiency of such devices strongly depends on the collective behavior of the adsorbed molecules. In the present paper, we propose a novel, coarse-grained model addressing the condensed phases of a representative hybrid system, that is, para-sexiphenyl (6P) at zinc-oxide (ZnO). Within our model, intermolecular interactions are represented via a Gay-Berne potential (describing steric and van-der-Waals interactions) combined with the electrostatic potential between two linear quadrupoles. Similarly, the molecule-substrate interactions include a coupling between a linear molecular quadrupole to the electric field generated by the line charges characterizing ZnO(10-10). To validate our approach, we perform equilibrium Monte Carlo simulations, where the lateral positions are fixed to a 2D lattice, while the rotational degrees of freedom are continuous. We use these simulations to investigate orientational ordering in the condensed state. We reproduce various experimentally observed features such as the alignment of individual molecules with the line charges on the surface, the formation of a standing uniaxial phase with a herringbone structure, as well as the formation of a lying nematic phase.

Kleppmann, Nicola; Klapp, Sabine H. L.

2015-02-01

87

Angular distribution of photoelectrons in small molecules: A molecular quantum defect calculation  

NASA Astrophysics Data System (ADS)

The molecular quantum defect orbital (MQDO) method, previously used in the determination of molecular photoionization cross sections, is applied here to calculate the angular distribution of photoelectrons arising from the molecular photoionization. Calculations are performed for the ionization from outer valence orbitals of HF, H2O, NH3, N2O, and H2CO molecules. The results are compared with previous measurements and with theoretical curves found in the literature. Profiles of the angular distribution parameter as a function of photoelectron energy covering a range from the photoionization threshold to 120 eV are presented for the above molecules. The energy dependence of the angular distributions predicted by the MQDO calculations agrees fairly well with predictions from more sophisticated theories and with observed results.

Vega, M. V.; Lavín, C.; Velasco, A. M.

2012-06-01

88

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

PubMed Central

We present “molecular threading”, a surface independent tip-based method for stretching and depositing single and double-stranded DNA molecules. DNA is stretched into air at a liquid-air interface, and can be subsequently deposited onto a dry substrate isolated from solution. The design of an apparatus used for molecular threading is presented, and fluorescence and electron microscopies are used to characterize the angular distribution, straightness, and reproducibility of stretched DNA deposited in arrays onto elastomeric surfaces and thin membranes. Molecular threading demonstrates high straightness and uniformity over length scales from nanometers to micrometers, and represents an alternative to existing DNA deposition and linearization methods. These results point towards scalable and high-throughput precision manipulation of single-molecule polymers. PMID:23935923

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

2013-01-01

89

Metal-molecule contacts play a key role in defining electron transport in molecular electronics. However, the possibility of  

E-print Network

Metal-molecule contacts play a key role in defining electron transport in molecular electronics by the strong bonding of C60 molecules to step edges on a Ag surface. When free, the step edges move dynamically, it would limit the effective length of the step to the distance between C60 molecules. By fabricating step

Rubloff, Gary W.

90

Detecting differential patterns of interaction in molecular pathways.  

PubMed

We consider statistical inference for potentially heterogeneous patterns of association characterizing the expression of bio-molecular pathways across different biologic conditions. We discuss a modeling approach based on Gaussian-directed acyclic graphs and provide computational and methodological details needed for posterior inference. Our application finds motivation in reverse phase protein array data from a study on acute myeloid leukemia, where interest centers on contrasting refractory versus relapsed patients. We illustrate the proposed method through both synthetic and case study data. PMID:25519431

Yajima, Masanao; Telesca, Donatello; Ji, Yuan; Müller, Peter

2015-04-01

91

Identifying Molecular Dynamics in Single-Molecule FRET Experiments with Burst Variance Analysis  

PubMed Central

Histograms of single-molecule Förster resonance energy transfer (FRET) efficiency are often used to study the structures of biomolecules and relate these structures to function. Methods like probability distribution analysis analyze FRET histograms to detect heterogeneities in molecular structure, but they cannot determine whether this heterogeneity arises from dynamic processes or from the coexistence of several static structures. To this end, we introduce burst variance analysis (BVA), a method that detects dynamics by comparing the standard deviation of FRET from individual molecules over time to that expected from theory. Both simulations and experiments on DNA hairpins show that BVA can distinguish between static and dynamic sources of heterogeneity in single-molecule FRET histograms and can test models of dynamics against the observed standard deviation information. Using BVA, we analyzed the fingers-closing transition in the Klenow fragment of Escherichia coli DNA polymerase I and identified substantial dynamics in polymerase complexes formed prior to nucleotide incorporation; these dynamics may be important for the fidelity of DNA synthesis. We expect BVA to be broadly applicable to single-molecule FRET studies of molecular structure and to complement approaches such as probability distribution analysis and fluorescence correlation spectroscopy in studying molecular dynamics. PMID:21402040

Torella, Joseph P.; Holden, Seamus J.; Santoso, Yusdi; Hohlbein, Johannes; Kapanidis, Achillefs N.

2011-01-01

92

Theoretical Study of Donor - Spacer - Acceptor Structure Molecule for Molecular Rectifier  

NASA Astrophysics Data System (ADS)

Recently, the molecular electronics has attracted strong attention as a ``post-silicone technology'' to establish a future nanoscale electronic devices. To realize this molecular device, unimolecular rectifiering function is one of the most important constituents in nanotechnology [C. Majumder, H. Mizuseki, and Y. Kawazoe, Molecular Scale Rectifier: Theoretical Study, J. Phys. Chem. A, 105 (2001) 9454-9459.]. In the present study, the geometric and electronic structure of alkyl derivative C37H50N4O4 (PNX) molecule, (donor - spacer - acceptor), a leading candidate of molecular rectifying device, has been investigated theoretically using ab initio quantum mechanical calculation. The results suggest that in such donor-acceptor molecular complexes, while the lowest unoccupied orbital concentrates on the acceptor subunit, the highest occupied molecular orbital is localized on the donor subunit. The approximate potential differences for optimized PNX molecule have been estimated at the B3PW91/6-311g++(d,p) level of theory, which achieves quite good agreement with experimentally reported results. This study was performed through Special Coordination Funds for Promoting Science and Technology of the Ministry of Education, Culture, Sports, Science and Technology of the Japanese Government.

Mizuseki, Hiroshi; Kenji, Niimura; Belosludov, Rodion; Farajian, Amir; Kawazoe, Yoshiyuki

2003-03-01

93

SABRE: ligand/structure-based virtual screening approach using consensus molecular-shape pattern recognition.  

PubMed

We present an efficient and rational ligand/structure shape-based virtual screening approach combining our previous ligand shape-based similarity SABRE (shape-approach-based routines enhanced) and the 3D shape of the receptor binding site. Our approach exploits the pharmacological preferences of a number of known active ligands to take advantage of the structural diversities and chemical similarities, using a linear combination of weighted molecular shape density. Furthermore, the algorithm generates a consensus molecular-shape pattern recognition that is used to filter and place the candidate structure into the binding pocket. The descriptor pool used to construct the consensus molecular-shape pattern consists of four dimensional (4D) fingerprints generated from the distribution of conformer states available to a molecule and the 3D shapes of a set of active ligands computed using SABRE software. The virtual screening efficiency of SABRE was validated using the Database of Useful Decoys (DUD) and the filtered version (WOMBAT) of 10 DUD targets. The ligand/structure shape-based similarity SABRE algorithm outperforms several other widely used virtual screening methods which uses the data fusion of multiscreening tools (2D and 3D fingerprints) and demonstrates a superior early retrieval rate of active compounds (EF(0.1%) = 69.0% and EF(1%) = 98.7%) from a large size of ligand database (?95,000 structures). Therefore, our developed similarity approach can be of particular use for identifying active compounds that are similar to reference molecules and predicting activity against other targets (chemogenomics). An academic license of the SABRE program is available on request. PMID:24328054

Wei, Ning-Ning; Hamza, Adel

2014-01-27

94

A tensor model for nematic phases of bent-core molecules based on molecular theory  

E-print Network

A tensor model for nematic phases of bent-core molecules is presented. The model is derived from the second virial expansion. The terms in the model are determined by the $C_{2v}$ symmetry of the molecule, and the coefficients are estimated from molecular parameters. An extension of the Bingham closure is employed that is able to restrict the tensors in physical range. The model can describe the homogeneous uniaxial and biaxial nematics, as well as the twist-bend and the splay-bend modulation. Two new modulated phases are found. Some of the phase sequences we obtain have been observed experimentally.

Jie Xu; Pingwen Zhang

2014-08-16

95

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

NASA Astrophysics Data System (ADS)

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

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

2008-03-01

96

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

SciTech Connect

The objective of the research under this contract is to carry out studies of resonant enhanced multiphoton ionization (REMPI) processes in molecules. In the (n+1)-REMPI process of interest an atom or molecule in a specific initial state absorbs n photons making a transition to an intermediate state from which it is subsequently ionized by absorption of an additional photon. The studies are designed to provide a quantitatively robust analysis and prediction of key spectral features in several ongoing experimental studies and potentially practical applications of this technique. The specific problems of interest to the authors in these studied are (1) the vibrational distributions of ions that can be expected in REMPI of small molecules and molecular fragments with particular emphasis on their non-Franck-Condon behavior. Such non-Franck-Condon behavior introduces serious complications in the use of the technique for state-specific production of ions, e.g., O{sub 2}{sup +}({nu}) and OH{sup +}({nu}), and in the extraction of state populations from REMPI signals, (2) rotational distributions of ions that can be produced in various REMPI schemes and how these distributions can be tuned by choice of the resonant state and influenced by the molecular character of the photoelectron, and (3) the circular dichroism in photoelectron angular distributions, i.e., the difference in photoelectron angular distributions produced by right- and left-circularly polarized, and their use as a probe of molecular alignment. Here the author will summarize the progress that has been made to date in the studies of these features and applications of REMPI of molecules and molecular fragments. A significant feature of these studies, which will be explicitly assumed throughout the discussion below, is that they are carried out using quantitatively reliable molecular photoelectron orbitals.

NONE

1988-12-31

97

Molecular Dynamics Simulations of RNA: An In Silico Single Molecule Approach  

PubMed Central

RNA molecules are now known to be involved in the processing of genetic information at all levels, taking on a wide variety of central roles in the cell. Understanding how RNA molecules carry out their biological functions will require an understanding of structure and dynamics at the atomistic level, which can be significantly improved by combining computational simulation with experiment. This review provides a critical survey of the state of molecular dynamics (MD) simulations of RNA, including a discussion of important current limitations of the technique and examples of its successful application. Several types of simulations are discussed in detail, including those of structured RNA molecules and their interactions with the surrounding solvent and ions, catalytic RNAs, and RNA–small molecule and RNA–protein complexes. Increased cooperation between theorists and experimentalists will allow expanded judicious use of MD simulations to complement conceptually related single molecule experiments. Such cooperation will open the door to a fundamental understanding of the structure–function relationships in diverse and complex RNA molecules. PMID:17080418

McDowell, S. Elizabeth; Špa?ková, Nad'a; Šponer, Ji?í; Walter, Nils G.

2007-01-01

98

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

SciTech Connect

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{sub 12}O{sub 40}{sup 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.

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

99

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

NASA Astrophysics Data System (ADS)

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 PW12O403-, 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.

Balliou, A.; Douvas, A. M.; Normand, P.; Tsikritzis, D.; Kennou, S.; Argitis, P.; Glezos, N.

2014-10-01

100

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

PubMed

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

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

2014-02-01

101

Molecular physics. Production of trilobite Rydberg molecule dimers with kilo-Debye permanent electric dipole moments.  

PubMed

Permanent electric dipole moments are important for understanding symmetry breaking in molecular physics, control of chemical reactions, and realization of strongly correlated many-body quantum systems. However, large molecular permanent electric dipole moments are challenging to realize experimentally. We report the observation of ultralong-range Rydberg molecules with bond lengths of ~100 nanometers and kilo-Debye permanent electric dipole moments that form when an ultracold ground-state cesium (Cs) atom becomes bound within the electronic cloud of an extended Cs electronic orbit. The electronic character of this hybrid class of "trilobite" molecules is dominated by degenerate Rydberg manifolds, making them difficult to produce by conventional photoassociation. We used detailed coupled-channel calculations to reproduce their properties quantitatively. Our findings may lead to progress in ultracold chemistry and strongly correlated many-body physics. PMID:25838380

Booth, D; Rittenhouse, S T; Yang, J; Sadeghpour, H R; Shaffer, J P

2015-04-01

102

Small molecules make big differences: molecular doping effects on electronic and optical properties of phosphorene  

NASA Astrophysics Data System (ADS)

Systematical computations on the density functional theory were performed to investigate the adsorption of three typical organic molecules, tetracyanoquinodimethane (TCNQ), tetracyanoethylene (TCNE) and tetrathiafulvalene (TTF), on the surface of phosphorene monolayers and thicker layers. There exist considerable charge transfer and strong non-covalent interaction between these molecules and phosphorene. In particular, the band gap of phosphorene decreases dramatically due to the molecular modification and can be further tuned by applying an external electric field. Meanwhile, surface molecular modification has proven to be an effective way to enhance the light harvesting of phosphorene in different directions. Our results predict a flexible method toward modulating the electronic and optical properties of phosphorene and shed light on its experimental applications.

Jing, Yu; Tang, Qing; He, Peng; Zhou, Zhen; Shen, Panwen

2015-03-01

103

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

SciTech Connect

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.

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

2011-04-15

104

Small molecules make big differences: molecular doping effects on electronic and optical properties of phosphorene.  

PubMed

Systematical computations on the density functional theory were performed to investigate the adsorption of three typical organic molecules, tetracyanoquinodimethane (TCNQ), tetracyanoethylene (TCNE) and tetrathiafulvalene (TTF), on the surface of phosphorene monolayers and thicker layers. There exist considerable charge transfer and strong non-covalent interaction between these molecules and phosphorene. In particular, the band gap of phosphorene decreases dramatically due to the molecular modification and can be further tuned by applying an external electric field. Meanwhile, surface molecular modification has proven to be an effective way to enhance the light harvesting of phosphorene in different directions. Our results predict a flexible method toward modulating the electronic and optical properties of phosphorene and shed light on its experimental applications. PMID:25665596

Jing, Yu; Tang, Qing; He, Peng; Zhou, Zhen; Shen, Panwen

2015-03-01

105

Binding assay for low molecular weight analytes based on reflectometry of absorbing molecules in porous substrates.  

PubMed

Small molecule sensing is of great importance in pharmaceutical research. While there exist well established screening methods such as EMSA (electrophoretic motility shift assay) or biointeraction chromatography to report on successful binding interactions, there are only a few techniques that allow studying and quantifying the interaction of low molecular weight analytes with a binding partner directly. We report on a binding assay for small molecules based on the reflectivity change of a porous transparent film upon immobilisation of an absorbing substance on the pore walls. The porous matrix acts as a thin optical transparent film to produce interference fringes and accumulates molecules at the inner wall to amplify the sensor response. The benefits and limits of the assay are demonstrated by investigating the binding of biotin labelled with an atto dye to avidin physisorbed within an anodic aluminium oxide membrane. PMID:24599267

Stephan, Milena; Kramer, Corinna; Steinem, Claudia; Janshoff, Andreas

2014-04-21

106

Phase and orientational ordering of low molecular weight rod molecules in a quenched liquid crystalline polymer matrix with mobile side  

E-print Network

Phase and orientational ordering of low molecular weight rod molecules in a quenched liquid interaction among the host and the low molecular weight guest. Control and manipulation of properties of the short LC molecular rods is crucial for practical applications.1 Below we review theoretical

Cao, Jianshu

107

Strong-Field Photoionization of Sputtered Neutral Molecules for Molecular Depth Profiling  

Microsoft Academic Search

Molecular depth profiles of an organic thin film of guanine vapor deposited onto a Ag substrate are obtained using a 40 keV C60 + cluster ion beam in conjunction with time-of-flight secondary ion mass spectrometric (ToF-SIMS) detection. Strong-field, femtosecond photoionization of intact guanine molecules is used to probe the neutral component of the profile for direct comparison with the secondary

D. Willingham; D. A. Brenes; A. Wucher; N. Winograd

2009-01-01

108

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

PubMed

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

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

2014-10-28

109

Molecular cloning and characterization of avian sarcoma virus circular DNA molecules.  

PubMed Central

Supercoiled DNA molecules were used for the molecular cloning of full-length avian sarcoma virus (ASV) DNA. Viral DNA produced by the Schmidt-Ruppin A (SR-A) strain of ASV was isolated from acutely infected transformed quail cells. Supercoiled DNA was separated from linear and open circular DNA by acid phenol extraction, opened into a full-length linear form by cleavage with the restriction endonuclease SacI, and cloned into lambda gtWES x lambda B. Four different cloned viral DNA molecules were isolated: SRA-1 contains two copies of the 330-base pair terminal redundancy normally found at each end of the linear DNA molecules, but harbors a 63-base pair deletion that spans the site at which the two copies of the terminal redundancy are joined in circular DNA molecules; SRA-2 contains two complete copies of the terminal redundancy; SRA-3 probably contains only one copy of the terminal redundancy but in all other respects appears to be similar to SRA-2; SRA-4 contains a 2,500-base pair deletion that removes all of the src gene (the gene responsible for transformation by ASVs) plus additional nucleotides adjacent to the src gene whose precise locations have not been determined. Transfection of chicken embryo fibroblasts by either SRA-1 or SRA-2 resulted both in the appearance of transformed cells and in the production of infectious virus. These results demonstrate that the cloned DNA molecules are functionally identical to viral DNA produced in vivo; therefore, molecular cloning did not cause any major alterations of the DNA. The infectivity of SRA-1 DNA indicates that the 63 base pairs missing from that molecule are not required for the initiation of viral RNA synthesis, even though the deletion is located in a copy of the terminal redundancy thought to carry a promoter for RNA synthesis. This suggests that the deletion does not remove any sequences required for the initiation of transcription. Images PMID:6255214

DeLorbe, W J; Luciw, P A; Goodman, H M; Varmus, H E; Bishop, J M

1980-01-01

110

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

SciTech Connect

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.

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

2011-03-02

111

Single-molecule toroics in Ising-type lanthanide molecular clusters.  

PubMed

Single-molecule toroics (SMTs) are defined, by analogy with single-molecule magnets, as bistable molecules with a toroidal magnetic state, and seem to be most promising for future applications in quantum computing and information storage and use as multiferroic materials with magnetoelectric effect. As an interdisciplinary research area that spans chemistry, physics and material sciences, synthetic chemists have produced systems suitable for detailed study by physicists and materials scientists, while ab initio calculations have been playing a major role in the detection of toroidal magnetization and the advancement of this field. In this tutorial review, we demonstrate the research developed in the fascinating and challenging field of molecular-based SMTs with particular focus on how recent studies tend to address the issue of toroidal arrangement of the magnetic moment in these systems. Herein, nine typical SMTs are summarized, showing that the assembly of wheel-shaped complexes with the high symmetry of the molecule unit and strong intra-molecular dipolar interactions using strong anisotropy metal ions represents the most promising route toward the design of a toroidal moment. Furthermore, the linkage of such robust toroidal moment units with ferromagnetic type through appropriate bridging ligands enhances the toroidal magnetic moment per unit cell. PMID:24975197

Ungur, Liviu; Lin, Shuang-Yan; Tang, Jinkui; Chibotaru, Liviu F

2014-10-21

112

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

NASA Astrophysics Data System (ADS)

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

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

2012-08-01

113

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

NASA Astrophysics Data System (ADS)

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

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

2010-03-01

114

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

PubMed Central

The multifunctional protein, ?-catenin, has essential roles in cell adhesion and, through the Wnt signaling pathway, in controlling cell differentiation, development, and generation of cancer. Could distinct molecular forms of ?-catenin underlie these two functions? Our single-molecule force spectroscopy of armadillo ?-catenin, with molecular dynamics (MD) simulation, suggests a model in which the cell generates various forms of ?-catenin, in equilibrium. We find ?-catenin and the transcriptional factor Tcf4 form two complexes with different affinities. Specific cellular response is achieved by the ligand binding to a particular matching preexisting conformer. Our MD simulation indicates that complexes derive from two conformers of the core region of the protein, whose preexisting molecular forms could arise from small variations in flexible regions of the ?-catenin main binding site. This mechanism for the generation of the various forms offers a route to tailoring future therapeutic strategies. PMID:17660262

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

2007-01-01

115

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

PubMed

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

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

2007-09-01

116

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

PubMed Central

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

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

2014-01-01

117

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

PubMed

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

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

2014-06-10

118

Exploring the aqueous vertical ionization of organic molecules by molecular simulation and liquid microjet photoelectron spectroscopy.  

PubMed

To study the influence of aqueous solvent on the electronic energy levels of dissolved organic molecules, we conducted liquid microjet photoelectron spectroscopy (PES) measurements of the aqueous vertical ionization energies (VIEaq) of aniline (7.49 eV), veratrole alcohol (7.68 eV), and imidazole (8.51 eV). We also reanalyzed previously reported experimental PES data for phenol, phenolate, thymidine, and protonated imidazolium cation. We then simulated PE spectra by means of QM/MM molecular dynamics and EOM-IP-CCSD calculations with effective fragment potentials, used to describe the aqueous vertical ionization energies for six molecules, including aniline, phenol, veratrole alcohol, imidazole, methoxybenzene, and dimethylsulfide. Experimental and computational data enable us to decompose the VIEaq into elementary processes. For neutral compounds, the shift in VIE upon solvation, ?VIEaq, was found to range from ?-0.5 to -0.91 eV. The ?VIEaq was further explained in terms of the influence of deforming the gas phase solute into its solution phase conformation, the influence of solute hydrogen-bond donor and acceptor interactions with proximate solvent molecules, and the polarization of about 3000 outerlying solvent molecules. Among the neutral compounds, variability in ?VIEaq appeared largely controlled by differences in solute-solvent hydrogen-bonding interactions. Detailed computational analysis of the flexible molecule veratrole alcohol reveals that the VIE is strongly dependent on molecular conformation in both gas and aqueous phases. Finally, aqueous reorganization energies of the oxidation half-cell ionization reaction were determined from experimental data or estimated from simulation for the six compounds aniline, phenol, phenolate, veratrole alcohol, dimethylsulfide, and methoxybenzene, revealing a surprising constancy of 2.06 to 2.35 eV. PMID:25516011

Tentscher, Peter R; Seidel, Robert; Winter, Bernd; Guerard, Jennifer J; Arey, J Samuel

2015-01-01

119

Distance-dependent patterns of molecular divergences in tuatara mitogenomes  

PubMed Central

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

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

2015-01-01

120

Distance-dependent patterns of molecular divergences in Tuatara mitogenomes.  

PubMed

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

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

2015-01-01

121

Synthesis and Electrical Characterization of Metal-Molecule-Metal Nanowires for Nanoscale and Molecular Electronics  

NASA Astrophysics Data System (ADS)

Considerable attention has been devoted to developing molecular-scale devices that function as nonlinear circuit elements and nanowires that interconnect these circuit elements. In this talk, we will present an overview of our research on the electrical characterization of metal-molecule-metal nanowires fabricated by template-directed synthesis. Polycarbonate membranes were used for the electrochemical preparation of nanowires with diameter of 30 - 40 nm and length of 2 - 4 microns. Functionalized dithioacetyl-molecules were adsorbed to the tips of the first Au or Pd segment of the nanowire using a potential-assisted assembly method, which resulted in ordered and uniform self-assembled monolayers (SAMs). A thin layer of seed metal was then deposited on top of the SAM by reduction of metal ions to form Ag or Pd nanoparticles prior to growing the second Au or Pd metal nanowire segment. The resulting in-wire devices were aligned and attached to pairs of large-area Au electrodes using an electrofluidic assembly technique. Electrical measurements were conducted at room temperature for nanowires with SAMs of C12, oligo (phenylene ethynylene) (OPE), and oligo(phenylene vinylene) (OPV) molecules, and with Pd and Au metal contacts. For biases between +/-1 V, the OPV molecular junctions had higher conductance than the OPE junctions. Both of these molecular wire junctions had current that was several orders of magnitude higher than the insulating C12 molecular junction. Comparison of OPE junctions formed with Au-Pd, Ag-Pd, and Pd-Pd contacts showed that the conductance of the Pd-Pd contact was the largest of the three investigated.

Mayer, Theresa

2003-03-01

122

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

Microsoft Academic Search

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

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

2007-01-01

123

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 ...

124

Extracellular matrix molecules exhibit unique expression pattern in the climbing fiber-generating precerebellar nucleus, the inferior olive.  

PubMed

Extracellular matrix (ECM) accumulates around different neuronal compartments of the central nervous system (CNS) or appears in diffuse reticular form throughout the neuropil. In the adult CNS, the perineuronal net (PNN) surrounds the perikarya and dendrites of various neuron types, whereas the axonal coats are aggregations of ECM around the individual synapses, and the nodal ECM is localized at the nodes of Ranvier. Previous studies in our laboratory demonstrated on rats that the heterogeneous distribution and molecular composition of ECM is associated with the variable cytoarchitecture and hodological organization of the vestibular nuclei and may also be related to their specific functions in gaze and posture control as well as in the compensatory mechanisms following vestibular lesion. Here, we investigated the ECM expression pattern in the climbing fiber-generating inferior olive (IO), which is functionally related to the vestibular nuclei. By using histochemical and immunohistochemical methods, the most characteristic finding was the lack of PNNs, presumably due to the absence of synapses on the perikarya and proximal dendrites of IO neurons. On the other hand, the darkly stained dots or ring-like structures in the neuropil might represent the periaxonal coats around the axon terminals of olivary synaptic glomeruli. We have observed positive ECM reaction for the hyaluronan, tenascin-R, hyaluronan and proteoglycan link protein 1 (HAPLN1) and various chondroitin sulfate proteoglycans. The staining intensity and distribution of ECM molecules revealed a number of differences between the functionally different subnuclei of IO. We hypothesized that the different molecular composition and intensity differences of ECM reaction is associated with different control mechanisms of gaze and posture control executed by the visuomotor-vestibular, somatosensory and integrative subnuclei of the IO. PMID:25445196

Kecskes, S; Gaál, B; Rácz, É; Birinyi, A; Hunyadi, A; Matesz, C

2015-01-22

125

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

SciTech Connect

The objective of our research under this contract is to carry out studies of resonant enhanced multiphoton ionization (REMPI) processes in molecules. In the (n + 1) - REMPI process of interest an atom or molecule in a specific initial state absorbs n photons making a transition to an intermediate state from which it is subsequently ionized by absorption of an additional photon. A remarkable feature of resonant enhanced multiphoton ionization is that the narrow bandwidth radiation of lasers makes it possible (i) to select a specific rovibrational level in the initial state of a molecule or fragment, (ii) to resonantly pump this level up to a selected rotational-vibrational level of an excited electronic state, and (iii) to subsequently photoionize the state that has been resonantly excited. The extreme state-selectivity and sensitivity make REMPI both a tool with several practical applications and an important technique for probing the photoionization dynamics of vibrationally and electronically excited states. Some significant applications of this technique include its use for state-specific detection of species and diagnostics in combustion and chemical etching media and plasmas, (ii) for state-specific generation of molecular ions for use in ion-molecule reaction studies, and (iii) as a probe of photofragmentation and gas-surface scattering including alignment and orientation effects in these processes.

NONE

1997-07-01

126

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

NASA Technical Reports Server (NTRS)

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

Neufeld, David A.; Dalgarno, A.

1989-01-01

127

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

PubMed Central

All cells have developed various mechanisms to respond and adapt to a variety of environmental challenges, including stresses that damage cellular proteins. One such response, the heat shock response (HSR), leads to the transcriptional activation of a family of molecular chaperone proteins that promote proper folding or clearance of damaged proteins within the cytosol. In addition to its role in protection against acute insults, the HSR also regulates lifespan and protects against protein misfolding that is associated with degenerative diseases of aging. As a result, identifying pharmacological regulators of the HSR has become an active area of research in recent years. Here, we review progress made in identifying small molecule activators of the HSR, what cellular targets these compounds interact with to drive response activation, and how such molecules may ultimately be employed to delay or reverse protein misfolding events that contribute to a number of diseases. PMID:22799889

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

2012-01-01

128

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

NASA Astrophysics Data System (ADS)

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.

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

2015-03-01

129

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

NASA Technical Reports Server (NTRS)

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

Srivastava, Deepak; Saini, Subhash (Technical Monitor)

1998-01-01

130

Molecular orbital tomography for adsorbed molecules: is a correct description of the final state really unimportant?  

NASA Astrophysics Data System (ADS)

The application of the ‘orbital tomography’ technique to obtain direct images of molecular orbitals of adsorbed molecules from angle-resolved photoemission data, first proposed by Puschnig et al (2009 Science 326 702), is an extremely attractive idea, but is based on the assumption that the photoemission can be described by a plane wave final state. It is well known that this neglect of the spherical-wave nature of the initial emission and of the role of final state scattering both within the molecule and from the substrate can lead to serious errors. Despite this, in the albeit simple systems studied so far the method appears to work reasonably well. Here we provide a detailed critique of this problem, highlight situations in which the orbital tomography approach is likely to lead to major errors, and propose test experiments that could provide clear information on the extent of these problems.

Bradshaw, A. M.; Woodruff, D. P.

2015-01-01

131

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

PubMed

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. PMID:25698329

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

2015-03-01

132

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

PubMed Central

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

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

2014-01-01

133

Circular dichroism in molecular-frame photoelectron angular distributions in the dissociative photoionization of H2 and D2 molecules  

NASA Astrophysics Data System (ADS)

The presence of net circular dichroism in the photoionization of nonchiral homonuclear molecules has been put in evidence recently through the measurement of molecular-frame photoelectron angular distributions in dissociative photoionization of H2 [Dowek et al., Phys. Rev. Lett. 104, 233003 (2010), 10.1103/PhysRevLett.104.233003]. In this work we present a detailed study of circular dichroism in the photoelectron angular distributions of H2 and D2 molecules, oriented perpendicularly to the propagation vector of the circularly polarized light, at different photon energies (20, 27, and 32.5 eV). Circular dichroism in the angular distributions at 20 and to a large extent 27 eV exhibits the usual pattern in which inversion symmetry is preserved. In contrast, at 32.5 eV, the inversion symmetry breaks down, which eventually leads to total circular dichroism after integration over the polar emission angle. Time-dependent ab initio calculations support and explain the observed results for H2 in terms of quantum interferences between direct photoionization and delayed autoionization from the Q1 and Q2 doubly excited states into ionic states (1 s ?g and 2 p ?u ) of different inversion symmetry. Nevertheless, for D2 at 32.5 eV, there is a particular case where theory and experiment disagree in the magnitude of the symmetry breaking: when D+ ions are produced with an energy of around 5 eV. This reflects the subleties associated to such simple molecules when exposed to this fine scrutiny.

Pérez-Torres, J. F.; Sanz-Vicario, J. L.; Veyrinas, K.; Billaud, P.; Picard, Y. J.; Elkharrat, C.; Poullain, S. Marggi; Saquet, N.; Lebech, M.; Houver, J. C.; Martín, F.; Dowek, D.

2014-10-01

134

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

SciTech Connect

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

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

2005-08-12

135

On the separability of the extended molecule: Constructing the best localized molecular orbitals for an organic molecule bridging two model electrodes  

SciTech Connect

Based on a quantum chemical valence formalism that allows the rigorous construction of best-localized molecular orbitals on specific parts of an extended system, we examined the separability of individual components of model systems relevant to the description of electron transport in molecular devices. We started by examining how to construct the maximally localized electronic density at the tip of a realistic model of a gold electrode. By varying the number of gold atoms included in the local region where to project the total electronic density, we quantitatively assess how many molecular orbitals are entirely localized in that region. We then considered a 1,4-benzene-di-thiol molecule connected to two model gold electrodes and examined how to localize the electronic density of the total system in the extended molecule, a fractional entity comprising the organic molecule plus an increasing number of the closest metal atoms. We were able to identify in a rigorous manner the existence of three physically different electronic populations, each one corresponding to a distinct set of molecular orbitals. First, there are those entirely localized in the extended molecule, then there is a second group of those completely distributed in the gold atoms external to that region, and, finally, there are those delocalized over the entire system. This latter group can be associated to the shared electronic population between the extended molecule and the rest of the system. We suggest that the treatment here presented could be useful in the theoretical analysis of the electronic transport in nanodevices whenever the use of localized molecular states are required by the physics of the specific problem, such as in cases of weak coupling and super-exchange limits.

Moreira, Rodrigo A.; Melo, Celso P. de, E-mail: celso@df.ufpe.br [Departamento de Física, Universidade Federal de Pernambuco, Recife-PE 50670-901 (Brazil)

2014-09-28

136

On the separability of the extended molecule: Constructing the best localized molecular orbitals for an organic molecule bridging two model electrodes.  

PubMed

Based on a quantum chemical valence formalism that allows the rigorous construction of best-localized molecular orbitals on specific parts of an extended system, we examined the separability of individual components of model systems relevant to the description of electron transport in molecular devices. We started by examining how to construct the maximally localized electronic density at the tip of a realistic model of a gold electrode. By varying the number of gold atoms included in the local region where to project the total electronic density, we quantitatively assess how many molecular orbitals are entirely localized in that region. We then considered a 1,4-benzene-di-thiol molecule connected to two model gold electrodes and examined how to localize the electronic density of the total system in the extended molecule, a fractional entity comprising the organic molecule plus an increasing number of the closest metal atoms. We were able to identify in a rigorous manner the existence of three physically different electronic populations, each one corresponding to a distinct set of molecular orbitals. First, there are those entirely localized in the extended molecule, then there is a second group of those completely distributed in the gold atoms external to that region, and, finally, there are those delocalized over the entire system. This latter group can be associated to the shared electronic population between the extended molecule and the rest of the system. We suggest that the treatment here presented could be useful in the theoretical analysis of the electronic transport in nanodevices whenever the use of localized molecular states are required by the physics of the specific problem, such as in cases of weak coupling and super-exchange limits. PMID:25273466

Moreira, Rodrigo A; de Melo, Celso P

2014-09-28

137

Controlling on-surface molecular diffusion behaviors by functionalizing the organic molecules with tert-butyl groups  

NASA Astrophysics Data System (ADS)

We have performed the systematic studies on three structurally similar aromatic molecules with different functional groups on a Cu(110) surface and investigated their on-surface molecular diffusion behaviors by the interplay of scanning tunneling microscopy imaging and density functional theory calculations. We have found that the tert-butyl groups could significantly affect the molecular adsorption geometries and moreover the mobility of the molecules on the surface. These findings could give further insights into the understanding of diffusion behaviors of organic molecules specifically with tert-butyl groups on surfaces.

Sun, Qiang; Zhang, Chi; Li, Zhiwen; Sheng, Kai; Kong, Huihui; Wang, Likun; Pan, Yunxiang; Tan, Qinggang; Hu, Aiguo; Xu, Wei

2013-07-01

138

ORIGINAL ARTICLE Patterns of molecular evolution of the germ line specification  

E-print Network

the Oskar proteins of D. melanogaster and D. virilis. This molecular evolutionary analysis thus representsORIGINAL ARTICLE Patterns of molecular evolution of the germ line specification gene oskar suggest an important role in posterior patterning. A novel N-terminal domain of oskar(the Long Oskar domain) evolved

Extavour, Cassandra

139

Bicelles: A natural ‘molecular goniometer’ for structural, dynamical and topological studies of molecules in membranes  

PubMed Central

Major biological processes occur at the biological membrane. One of the great challenges is to understand the function of chemical or biological molecules inside the membrane; as well of those involved in membrane trafficking. This requires obtaining a complete picture of the in situ structure and dynamics as well as the topology and orientation of these molecules in the membrane lipid bilayer. These led to the creation of several innovative models of biological membranes in order to investigate the structure and dynamics of amphiphilic molecules, as well as integral membrane proteins having single or multiple transmembrane segments. Because the determination of the structure, dynamics and topology of molecules in membranes requires a macroscopic alignment of the system, a new membrane model called ‘bicelles’ that represents a crossover between lipid vesicles and classical micelles has become very popular due to its property of spontaneous self-orientation in magnetic fields. In addition, crucial factors involved in mimicking natural membranes, such as sample hydration, pH and salinity limits, are easy to control in bicelle systems. Bicelles are composed of mixtures of long chain (14–18 carbons) and short chain phospholipids (6–8 carbons) hydrated up to 98% with buffers and may adopt various morphologies depending on lipid composition, temperature and hydration. We have been developing bicelle systems under the form of nano-discs made of lipids with saturated or biphenyl-containing fatty acyl chains. Depending on the lipid nature, these membranous nano-discs may be macroscopically oriented with their normal perpendicular or parallel to the magnetic field, providing a natural ‘molecular goniometer’ for structural and topological studies, especially in the field of NMR. Bicelles can also be spun at the magic angle and lead to the 3D structural determination of molecules in membranes. PMID:19248817

Diller, Anna; Loudet, Cécile; Aussenac, Fabien; Raffard, Gérard; Fournier, Sylvie; Laguerre, Michel; Grélard, Axelle; Opella, Stanley J.; Marassi, Francesca M.; Dufourc, Erick J.

2010-01-01

140

MOLECULAR WEIGHT, ELECTROCHEMICAL AND BIOLOGICAL PROPERTIES OF TUBERCULIN PROTEIN AND POLYSACCHARIDE MOLECULES  

PubMed Central

Studies have been made by means of sedimentation in the ultracentrifuge, and by diffusion and electrophoresis, to determine the molecular weights and homogeneity of the tuberculin protein and polysaccharide molecules as found in their natural state in the unchanged filtrates from culture media after growth of tubercle bacilli. These results have been compared with data obtained on fractions isolated by chemical procedures from them or from old tuberculin. By means of electrophoresis in the Tiselius apparatus it was possible to separate the protein from the polysaccharide, as these two fractions occur naturally in the original culture medium filtrates of acid-fast bacilli. The protein from the bovine strain of bacillus proved to be homogeneous in sedimentation (S20 = 1.6), diffusion (D20 = 12.0) and electrophoresis, with a molecular weight of about 10,000. The tuberculin polysaccharide isolated in electrophoresis appeared to be practically the same in sedimentation and in precipitin reaction as the polysaccharide isolated by chemical procedure. The latter proved to be homogeneous in sedimentation (S20 = 1.6) and diffusion (D20 = 11.0) with a molecular weight of about 9000. A practically homogeneous protein was isolated from the culture filtrate of the human tubercle bacillus H 37 by fractional ammonium sulfate precipitation, with a molecular weight of 32,000 (S20 = 3.3; D20 = 8.2). It was electrochemically homogeneous, with an isoelectric point at pH 4.3 and an isoionic point at pH 4.7. It could be dried or frozen with no loss in homogeneity. It was highly antigenic in the precipitin reaction and produced the anaphylactic type of local skin reaction in tuberculous guinea pigs, in contrast to the true tuberculin type of reaction caused by a purified PPD fraction. Furthermore death resulted in tuberculous guinea pigs from intracutaneous injection of exceptionally small amounts. A protein with molecular weight of about 17,000 was isolated from the filtrate from cultures of the timothy bacillus. The nucleic acid originally occurring in old tuberculin (OT) seems to be responsible for the high electrochemical mobility observed. From OT and the PPD made from it, potent but non-antigenic molecules of 16,000 and 9000 weight and with a low content of nucleic acid were isolated. With increase in size these deviated much from the normal compact spherical shape, and aggregation was evident from the tendency toward gel formation. The smallest molecule (9000) was homogeneous (S20 = 1.0; D20 = 10.0) and had lost some tuberculin potency. PMID:19870796

Seibert, Florence B.; Pedersen, Kai O.; Tiselius, Arne

1938-01-01

141

Disintegration of argon clusters in collisions with highly vibrationally excited SF6 molecules in crossed molecular and cluster beams  

NASA Astrophysics Data System (ADS)

It has been found that collisions of highly vibrationally excited SF6 molecules (with the vibrational energy E vib ? 0.5-2.0 eV) with Ar N clusters (where N ? 30-40 is the number of atoms in a cluster) in crossed molecular and cluster beams result in capture of molecules followed by complete disintegration of the clusters. Possible applications of the effect for selective doping of clusters with molecules, laser separation of isotopes, and selective transport of molecules to the surface are discussed.

Makarov, G. N.; Petin, A. N.

2013-03-01

142

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

PubMed

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

Horton, Nathan C; Mathew, Porunelloor A

2015-01-01

143

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

PubMed Central

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

Horton, Nathan C.; Mathew, Porunelloor A.

2015-01-01

144

First principles investigations of vinazene molecule and molecular crystal: a prospective candidate for organic photovoltaic applications.  

PubMed

Escalating demand for sustainable energy resources, because of the rapid exhaustion of conventional energy resources as well as to maintain the environmental level of carbon dioxide (CO2) to avoid its adverse effect on the climate, has led to the exploitation of photovoltaic technology manifold more than ever. In this regard organic materials have attracted great attention on account of demonstrating their potential to harvest solar energy at an affordable rate for photovoltaic technology. 2-vinyl-4,5-dicyanoimidazole (vinazene) is considered as a suitable material over the fullerenes for photovoltaic applications because of its particular chemical and physical nature. In the present study, DFT approaches are employed to provide an exposition of optoelectronic properties of vinazene molecule and molecular crystal. To gain insight into its properties, different forms of exchange correlation energy functional/potential such as LDA, GGA, BLYP, and BL3YP are used. Calculated electronic structure of vinazene molecule has been displayed via HOMO-LUMO isosurfaces, whereas electronic structure of the vinazene molecular crystal, via electronic band structure, is presented. The calculated electronic and optical properties were analyzed and compared as well. Our results endorse vinazene as a suitable material for organic photovoltaic applications. PMID:25631921

Mohamad, Mazmira; Ahmed, Rashid; Shaari, Amirudin; Goumri-Said, Souraya

2015-02-01

145

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

SciTech Connect

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

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

2012-05-01

146

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

NASA Astrophysics Data System (ADS)

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 PE molecule and the armchair SWNTs is largest among eight kinds of chiral SWNTs. The interaction energy decreases with the increase of temperature or the SWNT radius. The methyl, phenyl, hydroxyl, carboxyl, -F, and amino groups, have been introduced onto the surface of the SWNTs by the simulation software and the influence of SWNT chemical modification has also been investigated. The interaction energy between PE and chemically modified SWNTs is larger than that between PE and pristine SWNTs, and increases with increasing the concentration of the modified groups monotonously. In addition, the group electronegativity and van der Waals force will affect the interaction energy between PE and chemically modified SWNTs greatly, which can be attributed to the electronic structures of the chemically modified groups. This study can provide some useful suggestions for the composite material design and drug transport.

Li, Qun; He, Guofang; Zhao, Rengao; Li, Yanfei

2011-09-01

147

Image patterned molecular delivery into live cells using gold particle coated substrates  

PubMed Central

An image-patterned molecular delivery system for mammalian cells is demonstrated by pulsed laser irradiation of gold particles immobilized on a substrate below a cell monolayer. Patterned cavitation bubble nucleation was captured using a time-resolved imaging system and molecular delivery verified by observing the uptake of a membrane-impermeable fluorescent dye, calcein. Delivery efficiency as high as 90% was observed and multiplexed, patterned dye delivery was demonstrated. PMID:20173916

Wu, Ting-Hsiang; Kalim, Sheraz; Callahan, Caitlin; Teitell, Michael A.; Chiou, Pei-Yu

2010-01-01

148

[Current progress in functions of axon guidance molecule Slit and underlying molecular mechanism].  

PubMed

The axon guidance molecule Slit is a secreted glucoprotein which is conserved during evolution. Slit has been implicated in regulating a variety of life activities, such as axon guidance, neuronal migration, neuronal morphological differentiation, tumor metastasis, angiogenesis and heart morphogenesis. Slit function mainly depends on the binding of its LRR-2 domain to the Ig1 domain of Roundabout (Robo) receptor, meanwhile Slit function is also mediated by a range of signaling molecules, including the heparan sulfate proteoglycans (HSPGs), GTPase-activating proteins (GAPs), tyrosine kinase Abelson, calcium ions, MicroRNA-218 and other axon guidance molecules. Several transcription factors, including Single-minded, Irx and Midline, were shown to regulate slit expression. In addition, multiple Slit isoforms exist as a consequence of alternative spliced transcripts. The research on guidance mechanism of Slit will facilitate the understanding of molecular mechanism underlying neural networks formation in the process of neural development and regeneration. Meanwhile, the studying of Slit guidance mechanism could promote the prevention and treatment of human neurological diseases and cancer metastasis. PMID:22513474

Yu, Qi; Zhou, Qi-Sheng; Zhao, Xiao; Liu, Qing-Xin

2012-04-25

149

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

PubMed

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

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

2010-01-01

150

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

NASA Astrophysics Data System (ADS)

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

Küpper, Jochen

2011-06-01

151

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

E-print Network

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

Perrimon, Norbert

152

Molecular resonant dissociation of surface-adsorbed molecules by plasmonic nanoscissors  

NASA Astrophysics Data System (ADS)

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.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. Electronic supplementary information (ESI) available: Further experimental spectra and theoretical calculations. See DOI: 10.1039/c3nr06799h

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

2014-04-01

153

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

SciTech Connect

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.

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

2009-01-01

154

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

SciTech Connect

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.

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

2011-12-31

155

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

PubMed

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

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

2014-05-01

156

Nanomechanical recognition measurements of individual DNA molecules reveal epigenetic methylation patterns  

Microsoft Academic Search

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

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

157

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

SciTech Connect

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

Chu, P.M.Y.

1991-10-01

158

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

PubMed Central

Adolescent males have an increased risk of developing schizophrenia, implicating testosterone in the precipitation of dopamine-related psychopathology. Evidence from adult rodent brain indicates that testosterone can modulate nigrostriatal dopamine. However, studies are required to understand the role testosterone plays in maturation of dopamine pathways during adolescence and to elucidate the molecular mechanism(s) by which testosterone exerts its effects. We hypothesized that molecular indices of dopamine neurotransmission [synthesis (tyrosine hydroxylase), breakdown (catechol-O-methyl transferase; monoamine oxygenase), transport [vesicular monoamine transporter (VMAT), dopamine transporter (DAT)] and receptors (DRD1-D5)] would be changed by testosterone or its metabolites, dihydrotestosterone and 17?-estradiol, in the nigrostriatal pathway of adolescent male rats. We found that testosterone and dihydrotestosterone increased DAT and VMAT mRNAs in the substantia nigra and that testosterone increased DAT protein at the region of the cell bodies, but not in target regions in the striatum. Dopamine receptor D2 mRNA was increased and D3 mRNA was decreased in substantia nigra and/or striatum by androgens. These data suggest that increased testosterone at adolescence may change dopamine responsivity of the nigrostriatal pathway by modulating, at a molecular level, the capacity of neurons to transport and respond to dopamine. Further, dopamine turnover was increased in the dorsal striatum following gonadectomy and this was prevented by testosterone replacement. Gene expression changes in the dopaminergic cell body region may serve to modulate both dendritic dopamine feedback inhibition and reuptake in the dopaminergic somatodendritic field as well as dopamine release and re-uptake dynamics at the presynaptic terminals in the striatum. These testosterone-induced changes of molecular indices of dopamine neurotransmission in males are primarily androgen receptor-driven events as estradiol had minimal effect. We conclude that nigrostriatal responsivity to dopamine may be modulated by testosterone acting via androgen receptors to alter gene expression of molecules involved in dopamine signaling during adolescence. PMID:24618531

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

2014-01-01

159

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

Microsoft Academic Search

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,

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

1998-01-01

160

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

PubMed

The classical molecular dynamics (MD) simulations for the solvation properties of cis- and transplatins in water are performed with the Lennard-Jones plus Coulomb electrostatic potential parameters that are optimized with ab initio potential energies of the water-platin systems. Two hydration shells are found both for cis- and transplatins. The first shell of water molecules is closer to transplatin than cisplatin. The average number and lifetime of the intermolecular hydrogen bonds (HBs) estimated from the MD trajectories indicate that the Cl and NH(3) ligands are the main groups involved in the intermolecular HBs with water. In comparison with cisplatin, there are more HBs around transplatin and these HBs show the longer lifetime. The distinctly different solvation structures between cis- and transplatins are further revealed with the spatially anisotropic distributions of the first hydration shells. PMID:20459174

Fu, Cen-Feng; Tian, Shan Xi

2010-05-01

161

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

NASA Astrophysics Data System (ADS)

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

Fu, Cen-Feng; Tian, Shan Xi

2010-05-01

162

Link molecule method for quantum mechanical/molecular mechanical hybrid simulations  

SciTech Connect

We present a new coupling method for hybrid simulations in which the system is partitioned into covalently linked quantum mechanical (QM) and molecular mechanical (MM) regions. Our method, called the 'link molecule method (LMM),' is substantially different from the link atom methods in that LMM is free from the delicate issue of how to remove the additional degrees of freedom with respect to the position of the virtual atoms linking the QM and the MM regions. The force acting on the atom at the regional boundary is obtained in a simple form based on the total energy conservation. The accuracy of LMM is demonstrated in detail using a system of silicon partitioned into the QM and the MM region at the (1 0 0) boundary plane. This condition has been difficult to simulate by conventional methods employing the link atoms because of the strong repulsion between the nearby link atoms.

Nakamura, Yoshimichi [Institute of Industrial Science, University of Tokyo, 4-6-1 Komaba, Megro, Tokyo 153-8505 (Japan) and Computational Materials Science Center, National Institute for Materials Science (NIMS), 1-2-1 Sengen, Tsukuba, Ibaraki 305-0047 (Japan)]. E-mail: NAKAMURA.Yoshimichi@nims.go.jp; Takahashi, Norihiko [Computational Materials Science Center, National Institute for Materials Science (NIMS), 1-2-1 Sengen, Tsukuba, Ibaraki 305-0047 (Japan); Okamoto, Masakuni [Mechanical Engineering Research Laboratory, Hitachi Ltd., 832-2 Horiguchi, Hitachinaka, Ibaraki 312-0034 (Japan); Uda, Tsuyoshi [Institute of Industrial Science, University of Tokyo, 4-6-1 Komaba, Megro, Tokyo 153-8505 (Japan); AdvanceSoft Corporation, 4-6-1 Komaba, Megro, Tokyo 153-8904 (Japan); Ohno, Takahisa [Institute of Industrial Science, University of Tokyo, 4-6-1 Komaba, Megro, Tokyo 153-8505 (Japan) and Computational Materials Science Center, National Institute for Materials Science (NIMS), 1-2-1 Sengen, Tsukuba, Ibaraki 305-0047 (Japan)]. E-mail: OHNO.Takahisa@nims.go.jp

2007-08-10

163

Low-temperature collisions between neutral molecules in merged molecular beams.  

PubMed

We have developed an experiment for the investigation of neutral molecular collisions in the gas phase at temperatures as low as 100 mK. These low temperatures are obtained by merging two supersonic expansions, using an electric and a magnetic guide, and by matching the velocities of the beams. Since the energy available for the collisions, or the temperature, is determined only by the relative velocity of the reaction partners this enables the study of chemical processes at very low temperatures without the need to prepare slow molecules in the laboratory frame of reference. This paper describes the method and presents results on the Ne((3)P2)+NH3 Penning ionization. PMID:24983610

Bertsche, Benjamin; Jankunas, Justin; Osterwalder, Andreas

2014-01-01

164

Rotation commensurate echo of asymmetric molecules—Molecular fingerprints in the time domain  

NASA Astrophysics Data System (ADS)

Using the pulses of terahertz free electron laser and ultra-fast Schottky diode detectors, we observed the coherent transients within a free induction decay of gaseous nitrogen dioxide NO2. The laser excited different sub-bands of rotation spectra of NO2 containing about 50-70 lines. The free induction signal continued more than 30 ns and consisted of many echo-like bursts duration about 0.2 ns. Unlike the similar effect observed previously for linear and symmetric top molecules, the sequence of echo bursts is not periodic. The values for delay of individual echo are stable, and the set of these delays can be considered as a "molecular fingerprint" in the time domain.

Chesnokov, E. N.; Kubarev, V. V.; Koshlyakov, P. V.

2014-12-01

165

Surface-bound norbornylogous bridges as molecular rulers for investigating interfacial electrochemistry and as single molecule switches.  

PubMed

Electron transfer (ET) reactions through molecules attached to surfaces, whether they are through single molecules or ensembles, are the subject of much research in molecular electronics, bioelectronics, and electrochemistry. Therefore, understanding the factors that govern ET is of high importance. The availability of rigid hydrocarbon molecular scaffolds possessing well-defined configurations and lengths that can be systematically varied is crucial to the development of such devices. In this Account, we demonstrate how suitably functionalized norbornylogous (NB) systems can provide important insights into interfacial ET processes and electrical conduction through single molecules. To this end, we created NB bridges with vic-trans-bismethylenethiol groups at one end so they can assemble on gold electrodes and redox species at the distal ends. With these in hand, we then formed mixed self-assembled monolayers (SAMs) containing a small proportion of the NB bridges diluted with alkanethiols. As such, the NB bridges served as molecular rulers for probing the environment above the surface defined by the diluent species. Using this construct, we were able to measure the interfacial potential distribution above the diluent surface, and track how variation in the ionic distribution in the electrical double layer impacts ET kinetics. Using the same construct, but with a redox molecule that remains neutral in both oxidized and reduced states, we could explore the impact of the chemical environment near a surface on ET processes. These results are important, because with conventional surface constructs, ET occurs across this interfacial region. Such knowledge is therefore relevant to the design of molecular systems at surfaces involving ET. With a second family of molecules, we investigated aspects of single-molecule electrical conduction using NB bridges bearing vic-trans-bismethylenethiol groups at both ends of the bridge. This gave us insights into distance-dependent electron transport through single molecules and introduced a method of boosting the conductance of saturated molecules by incorporating aromatic moieties in their backbone. These partially conjugated NB molecules represent a new class of molecular wires with far greater stability than conventional completely conjugated molecular wires. Of particular note was our demonstration of a single molecule switch, using a NB bridge containing an embedded anthraquinone redox group, the switching mechanism being via electrochemically controlled quantum interference. PMID:24160945

Darwish, Nadim; Paddon-Row, Michael N; Gooding, J Justin

2014-02-18

166

Prediction of metabolic reactions based on atomic and molecular properties of small-molecule compounds  

PubMed Central

Motivation: Our knowledge of the metabolites in cells and their reactions is far from complete as revealed by metabolomic measurements that detect many more small molecules than are documented in metabolic databases. Here, we develop an approach for predicting the reactivity of small-molecule metabolites in enzyme-catalyzed reactions that combines expert knowledge, computational chemistry and machine learning. Results: We classified 4843 reactions documented in the KEGG database, from all six Enzyme Commission classes (EC 1–6), into 80 reaction classes, each of which is marked by a characteristic functional group transformation. Reaction centers and surrounding local structures in substrates and products of these reactions were represented using SMARTS. We found that each of the SMARTS-defined chemical substructures is widely distributed among metabolites, but only a fraction of the functional groups in these substructures are reactive. Using atomic properties of atoms in a putative reaction center and molecular properties as features, we trained support vector machine (SVM) classifiers to discriminate between functional groups that are reactive and non-reactive. Classifier accuracy was assessed by cross-validation analysis. A typical sensitivity [TP/(TP+FN)] or specificity [TN/(TN+FP)] is ?0.8. Our results suggest that metabolic reactivity of small-molecule compounds can be predicted with reasonable accuracy based on the presence of a potentially reactive functional group and the chemical features of its local environment. Availability: The classifiers presented here can be used to predict reactions via a web site (http://cellsignaling.lanl.gov/Reactivity/). The web site is freely available. Contact: fmu@lanl.gov Supplementary information: Supplementary data are available at Bioinformatics online. PMID:21478194

Mu, Fangping; Unkefer, Clifford J.; Unkefer, Pat J.; Hlavacek, William S.

2011-01-01

167

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

E-print Network

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.

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

2007-05-11

168

Kinetics of molecular transitions with dynamic disorder in single-molecule pulling experiments  

NASA Astrophysics Data System (ADS)

Macromolecular transitions are subject to large fluctuations of rate constant, termed as dynamic disorder. The individual or intrinsic transition rates and activation free energies can be extracted from single-molecule pulling experiments. Here we present a theoretical framework based on a generalized Langevin equation with fractional Gaussian noise and power-law memory kernel to study the kinetics of macromolecular transitions to address the effects of dynamic disorder on barrier-crossing kinetics under external pulling force. By using the Kramers' rate theory, we have calculated the fluctuating rate constant of molecular transition, as well as the experimentally accessible quantities such as the force-dependent mean lifetime, the rupture force distribution, and the speed-dependent mean rupture force. Particular attention is paid to the discrepancies between the kinetics with and without dynamic disorder. We demonstrate that these discrepancies show strong and nontrivial dependence on the external force or the pulling speed, as well as the barrier height of the potential of mean force. Our results suggest that dynamic disorder is an important factor that should be taken into account properly in accurate interpretations of single-molecule pulling experiments.

Zheng, Yue; Li, Ping; Zhao, Nanrong; Hou, Zhonghuai

2013-05-01

169

Nonadiabatic quantum molecular dynamics with hopping. III. Photoinduced excitation and relaxation of organic molecules  

NASA Astrophysics Data System (ADS)

Photoinduced excitation and relaxation of organic molecules (C2H4 and CH2NH2+) are investigated by means of nonadiabatic quantum molecular dynamics with hopping (NA-QMD-H), developed recently [Fischer, Handt, and Schmidt, paper I of this series, Phys. Rev. A 90, 012525 (2014), 10.1103/PhysRevA.90.012525]. This method is first applied to molecules assumed to be initially ad hoc excited to an electronic surface. Special attention is drawn to elaborate the role of electron-nuclear correlations, i.e., of quantum effects in the nuclear dynamics. It is found that they are essential for a realistic description of the long-time behavior of the electronic relaxation process, but only of minor importance to portray the short-time scenario of the nuclear dynamics. Migration of a hydrogen atom, however, is identified as a quantum effect in the nuclear motion. Results obtained with explicit inclusion of an fs-laser field are presented as well. It is shown that the laser-induced excitation process generally leads to qualitatively different gross features of the relaxation dynamics, as compared to the field-free case. Nevertheless, the nuclear wave packet contains all subtleties of the cis-trans isomerization mechanism as observed without a laser field.

Fischer, M.; Handt, J.; Schmidt, R.

2014-07-01

170

Effect of doping and molecular coverage on the I-V characteristics of organic molecules on silicon surfaces  

NASA Astrophysics Data System (ADS)

Quantum transport properties of organic molecules on the silicon (001) surface have been studied by ab initio non- equilibrium Green function calculations in a basis of optimal localized orbitals. Our calculated results provide a qualitative picture and quantitative understanding of the importance of self-consistent screening and broadening of quasi- molecular orbitals under a large bias. Negative Differential Resistance (NDR) is found to be a general feature of organic molecules on Si surfaces [1]. By comparing the I-V characteristics of a monolayer of cyclopentene molecules with that of a single molecule, we show that interactions between the molecules attenuate the NDR, as seen in experiments. We have also investigated the effects of proximal dopant atoms on the NDR in a large unit cell. [1]. W. Lu, V. Meunier, J. Bernholc, Phys. Rev. Lett. 95, 206805 (2005).

Lu, Wenchang; Meunier, V.; Wang, S.; Zhao, Q.; Bernholc, J.

2006-03-01

171

Thermodynamic stability of water molecules in the bacteriorhodopsin proton channel: a molecular dynamics free energy perturbation study.  

PubMed Central

The proton transfer activity of the light-driven proton pump, bacteriorhodopsin (bR) in the photochemical cycle might imply internal water molecules. The free energy of inserting water molecules in specific sites along the bR transmembrane channel has been calculated using molecular dynamics simulations based on a microscopic model. The existence of internal hydration is related to the free energy change on transfer of a water molecule from bulk solvent into a specific binding site. Thermodynamic integration and perturbation methods were used to calculate free energies of hydration for each hydrated model from molecular dynamics simulations of the creation of water molecules into specific protein-binding sites. A rigorous statistical mechanical formulation allowing the calculation of the free energy of transfer of water molecules from the bulk to a protein cavity is used to estimate the probabilities of occupancy in the putative bR proton channel. The channel contains a region lined primarily by nonpolar side-chains. Nevertheless, the results indicate that the transfer of four water molecules from bulk water to this apparently hydrophobic region is thermodynamically permitted. The column forms a continuous hydrogen-bonded chain over 12 A between a proton donor, Asp 96, and the retinal Schiff base acceptor. The presence of two water molecules in direct hydrogen-bonding association with the Schiff base is found to be strongly favorable thermodynamically. The implications of these results for the mechanism of proton transfer in bR are discussed. PMID:8842206

Roux, B; Nina, M; Pomès, R; Smith, J C

1996-01-01

172

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

Cancer.gov

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

173

Selective Non-Templated Adsorption of Organic Molecules on Nanofacets and the Role of Bonding Patterns  

SciTech Connect

A key element of functionalizing nanocrystals with organic molecules is the non-templated selective adsorption of different molecules on different facets. Here we report scanning-tunneling-microscopy images of PTCDA and DMe-DCNQI on silver, demonstrating selective adsorption on different facets. We also report first-principles calculations that account for the data and show that bonding, which controls selectivity, occurs via the end-atoms, while the molecule's mid-region arches away from the substrate. The results are also consistent with data that have been interpreted in terms of bonding via the mid-region.

Du, S X [Chinese Academy of Sciences; Gao, Hongjun [ORNL; Seidel, Christine [ORNL; Tsetseris, Leonidas [ORNL; Ji, W. [Chinese Academy of Sciences; Kopf, H. [University of Munster, Germany; Chi, L. F. [University of Munster, Germany; Fuchs, H. [University of Munster, Germany; Pennycook, Stephen J [ORNL; Pantelides, Sokrates T [ORNL

2006-01-01

174

Molecular dynamics simulations on the aggregation behavior of indole type organic dye molecules in dye-sensitized solar cells.  

PubMed

In Ti0(2) nanostructured dye-sensitized solar cells indole based organic dyes D149, D205 exhibits greater power conversion efficiency. Such organic dye molecules are easily undergone for aggregation. Aggregation in dye molecules leads to reduce electron transfer process in dye-sensitized solar cells. Therefore, anti-aggregating agents such as chenodeoxycholic acid are commonly added to organic dye solution in DSSCs. Studying aggregation of such dye molecules in the absence of semiconductors gives a detailed influence of anti-aggregating agents on dye molecules. Atomistic level of molecular dynamics (MD) simulations were performed on aggregation of indole type dye molecules D149, D205 and D205-F with anti-aggregating agent chenodeoxy cholic acid using AMBER program. The trajectories of the MD simulations were analyzed with order parameters such as radial atom pair distribution functions g(r), diffusion coefficients and root mean square deviations values. MD results suggest that addition of chenodeoxy cholic acid to dyes significantly reduces structural arrangement and increases conformational flexibility and mobility of dye molecules. The influence of semi-perfluorinated alkyl chains in indole dye molecules was analyzed. The parameters such as open-circuit voltage (V(oc)) and power conversion efficiency (?) of dye-sensitized solar cells are corroborated with flexibility and diffusion values of dye molecules. PMID:21904812

Selvaraj, Ananda Rama Krishnan; Hayase, Shuji

2012-05-01

175

Molecular dynamics simulations of side chain liquid crystal polymer molecules in isotropic and liquid-crystalline melts  

E-print Network

Molecular dynamics simulations of side chain liquid crystal polymer molecules in isotropic side chain liquid crystal polymer SCLCP . The simulations use a coarse-grained model composed.1063/1.1948376 I. INTRODUCTION Liquid crystal polymers LCPs may be classified ac- cording to the location

Wilson, Mark R.

176

PHYSICAL REVIEW A 82, 035402 (2010) Effect of an improved molecular potential on strong-field tunneling ionization of molecules  

E-print Network

approximation (SFA) [11,12], or the molecular tunneling ionization theory (MO-ADK) [13] are quite desirable. In particular, the simple MO-ADK theory is of wide interest. According to MO-ADK [13], alignment- dependent for the molecule are obtained. In MO-ADK theory, the ionization rate depends on the instantaneous electric field

Lin, Chii-Dong

177

Evolution of complex organic molecules in hot molecular cores. Synthetic spectra at (sub-)mm wavebands  

NASA Astrophysics Data System (ADS)

Context. Hot molecular cores (HMCs) are intermediate stages of high-mass star formation and are also known for their rich chemical reservoirs and emission line spectra at (sub-)mm wavebands. Complex organic molecules (COMs) such as methanol (CH3OH), ethanol (C2H5OH), dimethyl ether (CH3OCH3), and methyl formate (HCOOCH3) produce most of these observed lines. The observed spectral feature of HMCs such as total number of emission lines and associated line intensities are also found to vary with evolutionary stages. Aims: We aim to investigate the spectral evolution of these COMs to explore the initial evolutionary stages of high-mass star formation including HMCs. Methods: We developed various 3D models for HMCs guided by the evolutionary scenarios proposed by recent empirical and modeling studies. We then investigated the spatio-temporal variation of temperature and molecular abundances in HMCs by consistently coupling gas-grain chemical evolution with radiative transfer calculations. We explored the effects of varying physical conditions on molecular abundances including density distribution and luminosity evolution of the central protostar(s) among other parameters. Finally, we simulated the synthetic spectra for these models at different evolutionary timescales to compare with observations. Results: Temperature has a profound effect on the formation of COMs through the depletion and diffusion on grain surface to desorption and further gas-phase processing. The time-dependent temperature structure of the hot core models provides a realistic framework for investigating the spatial variation of ice mantle evaporation as a function of evolutionary timescales. We find that a slightly higher value (15 K) than the canonical dark cloud temperature (10 K) provides a more productive environment for COM formation on grain surface. With increasing protostellar luminosity, the water ice evaporation font (~100 K) expands and the spatial distribution of gas phase abundances of these COMs also spreads out. We calculated the temporal variation of the radial profiles of these COMs for different hot core models. These profiles resemble the so-called jump profiles with relative abundances higher than 10-9 within the evaporation font will furthermore be useful to model the observed spectra of hot cores. We present the simulated spectra of these COMs for different hot core models at various evolutionary timescales. A qualitative comparison of the simulated and observed spectra suggests that these self-consistent hot core models can reproduce the notable trends in hot core spectral variation within the typical hot core timescales of 105 year. These models predict that the spatial distribution of various emission line maps will also expand with evolutionary time; this feature can be used to constrain the relative desorption energies of the molecules that mainly form on the grain surface and return to the gas phase via thermal desorption. The detailed modeling of the thermal structure of hot cores with similar masses along with the characterization of the desorption energies of different molecules can be used to constrain the luminosity evolution of the central protostars. The model predictions can be compared with high resolution observation that can probe scales of a few thousand AU in high-mass star forming regions such as from Atacama Large Millimeter/submillimeter Array (ALMA). We used a spectral fitting method to analyze the simulated spectra and find that it significantly underestimates some of the physical parameters such as temperature. The coupling of chemical evolution with radiative transfer models will be particularly useful to decipher the physical structure of hot cores and also to constrain the initial evolutionary stages of high-mass star formation. Appendices are available in electronic form at http://www.aanda.org

Choudhury, R.; Schilke, P.; Stéphan, G.; Bergin, E.; Möller, T.; Schmiedeke, A.; Zernickel, A.

2015-03-01

178

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

NASA Astrophysics Data System (ADS)

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

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

179

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

SciTech Connect

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

Wasielewski, M.R.

1997-01-01

180

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

PubMed

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

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

2014-05-23

181

Determination of NMR lineshape anisotropy of guest molecules within inclusion complexes from molecular dynamics simulations.  

PubMed

Nonspherical cages in inclusion compounds can result in non-uniform motion of guest species in these cages and anisotropic lineshapes in NMR spectra of the guest. Herein, we develop a methodology to calculate lineshape anisotropy of guest species in cages based on molecular dynamics simulations of the inclusion compound. The methodology is valid for guest atoms with spin 1/2 nuclei and does not depend on the temperature and type of inclusion compound or guest species studied. As an example, the nonspherical shape of the structure I (sI) clathrate hydrate large cages leads to preferential alignment of linear CO(2) molecules in directions parallel to the two hexagonal faces of the cages. The angular distribution of the CO(2) guests in terms of a polar angle theta and azimuth angle phi and small amplitude vibrational motions in the large cage are characterized by molecular dynamics simulations at different temperatures in the stability range of the CO(2) sI clathrate. The experimental (13)C NMR lineshapes of CO(2) guests in the large cages show a reversal of the skew between the low temperature (77 K) and the high temperature (238 K) limits of the stability of the clathrate. We determine the angular distributions of the guests in the cages by classical MD simulations of the sI clathrate and calculate the (13)C NMR lineshapes over a range of temperatures. Good agreement between experimental lineshapes and calculated lineshapes is obtained. No assumptions regarding the nature of the guest motions in the cages are required. PMID:18386265

Alavi, Saman; Dornan, Peter; Woo, Tom K

2008-04-21

182

Molecular-orbital decomposition of the ionization continuum for a diatomic molecule by angle-and energy-resolved photoelectron spectroscopy.  

E-print Network

photoionization cross sections can now be calculated for small molecules almost quantitatively using ab initio- and energy-resolved photo- electron spectroscopy.10­12 By ionizing optically aligned NO A 2 0 moleculesMolecular-orbital decomposition of the ionization continuum for a diatomic molecule by angle

Zare, Richard N.

183

Resonance enhanced multiphoton ionization spectra of molecules and molecular fragments. Annual technical report  

SciTech Connect

Resonance Enhanced Multiphoton Ionization (REMPI) utilizes pulsed laser radiation to prepare a molecule in an excited state via absorption of one or more photons and to subsequently ionize that state before it can decay. A remarkable feature of REMPI, and one that is very basic to many of its applications and uses, is that the very narrow bandwidth of the {open_quotes}pump{close_quotes} laser makes it possible to select a specific vibrational and rotational level in the initial state and to prepare the excited state of interest in a single vibrational and rotational level. Thus, by suitable choice of the photon pump transition, it is possible to selectively ionize a species of interest without ionizing any other species that might be present. This feature makes REMPI one of the most powerful tools for ultrasensitive detection of species. With REMPI it is also possible to study the photoionization dynamics of a single rotational level of an excited electronic state. Such state-resolved studies can certainly be expected to provide significant insight into the underlying dynamics of molecular photoionization.

NONE

1997-07-01

184

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

NASA Astrophysics Data System (ADS)

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. Perhaps remarkably, but apparently because of electrostatic repulsion, the direction of rotation is the same for both reactions.

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

2015-02-01

185

A tripodal molecule on a gold surface: orientation-dependent coupling and electronic properties of the molecular legs.  

PubMed

The realization of molecular electronics demands a detailed knowledge of the correlation between chemical groups and electronic function. It has become obvious during the last years that the conformation of a molecule and its coupling to the connecting electrodes plays a crucial role in its conductance behavior and its electronic function, e.g., as a switch. Knowledge about these relationships is therefore essential for future design of molecular electronic building blocks. We present a new three-dimensional molecule, consisting of three identical molecular wires connected to a headgroup. Due to the well-defined spatial arrangement of the molecule in a nonplanar geometry, it is possible to investigate the conductance behavior of these wires with respect to their position and coupling to the surface electrode with the submolecular resolution of a scanning tunneling microscope. The experimental findings are supported by calculations of the electronic structure and conformation of the molecule on the surface by density functional theory with dispersion corrections. PMID:23790078

Lukas, Maya; Dössel, Kerrin; Schramm, Alexandrina; Fuhr, Olaf; Stroh, Christophe; Mayor, Marcel; Fink, Karin; v Löhneysen, Hilbert

2013-07-23

186

Different molecular patterns in glioblastoma multiforme subtypes upon recurrence  

Microsoft Academic Search

One of the hallmarks of glioblastoma is its inherent tendency to recur. At this point patients with relapsed GBM show a survival\\u000a time of only few months. The molecular basis of the recurrence process in GBM is still poorly understood. The aim of the present\\u000a study was to investigate the genetic profile of relapsed GBM compared to their respective primary

Ramon Martinez; Veit Rohde; Gabriele Schackert

2010-01-01

187

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

E-print Network

Dynamics of Single-Molecule Rotations on Surfaces that Depend on Symmetry, Interactions Rotating surface-mounted molecules have attracted the attention of many research groups as a way to develop new nanoscale devices and materials. However, mechanisms of motion of these rotors at the single-molecule

188

Gene expression pattern Neuralin-1 is a novel Chordin-related molecule expressed in the mouse  

E-print Network

of the neural crest cells. During organogenesis, neuralin-1 presents a broad expression pattern in many tissues; Extracellular matrix; Neural plate; Organogenesis; Forebrain; Neural crest; Dorsal root ganglion; Branchial arch

De Robertis, Eddy M.

189

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

NASA Astrophysics Data System (ADS)

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

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

2010-10-01

190

Electronic transport in biphenyl single-molecule junctions with carbon nanotubes electrodes: The role of molecular conformation and chirality  

SciTech Connect

We investigate, by means of ab initio calculations, electronic transport in molecular junctions composed of a biphenyl molecule attached to metallic carbon nanotubes. We find that the conductance is proportional to cos{sup 2} {theta}, with {theta} the angle between phenyl rings, when the Fermi level of the contacts lies within the frontier molecular orbitals energy gap. This result, which agrees with experiments in biphenyl junctions with nonorganic contacts, suggests that the cos{sup 2} {theta} law has a more general applicability, irrespective of the nature of the electrodes. We calculate the geometrical degree of chirality of the junction, which only depends on the atomic positions, and demonstrate that it is not only proportional to cos{sup 2} {theta} but also is strongly correlated with the current through the system. These results indicate that molecular conformation plays the preponderant role in determining transport properties of biphenyl-carbon nanotubes molecular junctions.

Brito Silva, C. A. Jr.; Granhen, E. R. [Pos-Graduacao em Engenharia Eletrica, Universidade Federal do Para, 66075-900 Belem, PA (Brazil); Silva, S. J. S. da; Leal, J. F. P. [Pos-Graduacao em Fisica, Universidade Federal do Para, 66075-110 Belem, PA (Brazil); Del Nero, J. [Departamento de Fisica, Universidade Federal do Para, 66075-110 Belem, PA (Brazil); Divisao de Metrologia de Materiais, Instituto Nacional de Metrologia, Normalizacao e Qualidade Industrial, 25250-020 Duque de Caxias, RJ (Brazil); Instituto de Fisica, Universidade Federal do Rio de Janeiro, 21941-972 Rio de Janeiro, RJ (Brazil); Pinheiro, F. A. [Instituto de Fisica, Universidade Federal do Rio de Janeiro, 21941-972 Rio de Janeiro, RJ (Brazil)

2010-08-15

191

Functionality in single-molecule devices: Model calculations and applications of the inelastic electron tunneling signal in molecular junctions  

NASA Astrophysics Data System (ADS)

We analyze how functionality could be obtained within single-molecule devices by using a combination of non-equilibrium Green's functions and ab initio calculations to study the inelastic transport properties of single-molecule junctions. First, we apply a full non-equilibrium Green's function technique to a model system with electron-vibration coupling. We show that the features in the inelastic electron tunneling spectra (IETS) of the molecular junctions are virtually independent of the nature of the molecule-lead contacts. Since the contacts are not easily reproducible from one device to another, this is a very useful property. The IETS signal is much more robust versus modifications at the contacts and hence can be used to build functional nanodevices. Second, we consider a realistic model of a organic conjugated molecule. We use ab initio calculations to study how the vibronic properties of the molecule can be controlled by an external electric field which acts as a gate voltage. The control, through the gate voltage, of the vibron frequencies and (more importantly) of the electron-vibron coupling enables the construction of functionality: nonlinear amplification and/or switching is obtained from the IETS signal within a single-molecule device.

Dash, L. K.; Ness, H.; Verstraete, M. J.; Godby, R. W.

2012-02-01

192

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

PubMed Central

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

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

2013-01-01

193

A two-color tunable infrared/vacuum ultraviolet spectrometer for high-resolution spectroscopy of molecules in molecular beams  

NASA Astrophysics Data System (ADS)

We describe here the key technical elements of a two-color tunable IR/VUV photoionization TOF mass spectrometer system which allows a wide-range of high-resolution experiments to be performed on a diverse range of cold molecules and clusters in a molecular beam. In particular we highlight the methods we have applied to provide efficient wavelength separation of the VUV radiation from the longer wavelength components used to generate it and discuss a number of systems that we have studied with the instrument which highlight its flexibility for use in the study of molecular spectroscopy.

Woodward, Jonathan R.; Watanabe, Hirokazu; Ishiuchi, Shun-Ichi; Fujii, Masaaki

2012-01-01

194

A two-color tunable infrared/vacuum ultraviolet spectrometer for high-resolution spectroscopy of molecules in molecular beams  

SciTech Connect

We describe here the key technical elements of a two-color tunable IR/VUV photoionization TOF mass spectrometer system which allows a wide-range of high-resolution experiments to be performed on a diverse range of cold molecules and clusters in a molecular beam. In particular we highlight the methods we have applied to provide efficient wavelength separation of the VUV radiation from the longer wavelength components used to generate it and discuss a number of systems that we have studied with the instrument which highlight its flexibility for use in the study of molecular spectroscopy.

Woodward, Jonathan R.; Watanabe, Hirokazu; Ishiuchi, Shun-Ichi; Fujii, Masaaki [Chemical Resources Laboratory, Tokyo Institute of Technology, Yokohama (Japan)

2012-01-15

195

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

E-print Network

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.

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

2013-01-01

196

A Purification Method for a Molecular Complex in Which a Scaffold Molecule Is Fully Loaded with Heterogeneous Molecules  

PubMed Central

An affinity resin-based pull-down method is convenient for the purification of biochemical materials. However, its use is difficult for the isolation of a molecular complex fully loaded with multiple components from a reaction mixture containing the starting materials and intermediate products. To overcome this problem, we have developed a new purification procedure that depends on sequential elimination of the residues. In practice, two affinity resins were used for purifying a triangular-shaped RNP (RNA-protein complex) consisting of three ribosomal proteins (L7Ae) bound to an RNA scaffold. First, a resin with immobilized L7Ae protein captured the incomplete RNP complexes and the free RNA scaffold. Next, another resin with an immobilized chemically modified RNA of a derivative of Box C/D motif, the binding partner of L7Ae, was used to capture free protein. The complete triangular RNP was successfully purified from the mixture by these two steps. Obviously, the purified triangular RNP displaying three protein-binding peptides exhibited an improved performance when compared with the unrefined product. Conceptually, this purification procedure should be applicable for the purification of a variety of complexes consisting of multiple components other than RNP. PMID:25781936

Ohuchi, Shoji J.; Sagawa, Fumihiko; Ohno, Hirohisa; Inoue, Tan

2015-01-01

197

Designing of multi-targeted molecules using combination of molecular screening and in silico drug cardiotoxicity prediction approaches.  

PubMed

We have previously investigated and reported a set of phenol- and indole-based derivatives at the binding pockets of carbonic anhydrase isoenzymes using in silico and in vitro analyses. In this study, we extended our analysis to explore multi-targeted molecules from this set of compounds. Thus, 26 ligands are screened at the binding sites of 229 proteins from 5 main enzyme family classes using molecular docking algorithms. Derived docking scores are compared with reported results of ligands at carbonic anhydrase I and II isoenzymes. Results showed potency of multi-targeted drugs of a few compounds from investigated ligand set. These promising ligands are then tested in silico for their cardiotoxicity risks. Results of this work can be used to improve the desired effects of these compounds by molecular engineering studies. In addition these results may lead to further investigation of studied molecules by medicinal chemists to explore different therapeutic aims. PMID:24699019

Buturak, Birce; Durdagi, Serdar; Noskov, Sergei Y; Ildeniz, A Tugba Ozal

2014-05-01

198

Molecular model of biaxial ordering in nematic liquid crystals composed of flat molecules with four mesogenic groups  

NASA Astrophysics Data System (ADS)

Relative stability of uniaxial and biaxial nematic phases is analyzed in a model nematic liquid crystal composed of flat molecules of C2h symmetry with four mesogenic groups rigidly linked to the same center. The generalized effective quadrupole mean-field potential is proposed and its constants are evaluated numerically for the pair intermolecular potential based on Gay-Berne interaction between mesogenic groups. The dependencies of the constants on molecular shape parameters are systematically analyzed. Order parameters of the uniaxial and biaxial nematic phases are evaluated by direct minimization of the free energy at different temperatures. The corresponding phase diagrams are obtained enabling one to study the effects of molecular model parameters on the stability regions of uniaxial and biaxial phases. The results are used to clarify the nature of experimentally observed biaxial ordering in nematic liquid crystals composed of tetrapode molecules with the same symmetry.

Gorkunov, M. V.; Osipov, M. A.; Kocot, A.; Vij, J. K.

2010-06-01

199

On Discrete to Continuum Transformations and the Universal Molecule Model—A Mathematical Chemistry Perspective of Molecular Families  

NASA Astrophysics Data System (ADS)

By replacing the discrete parameters and descriptors of molecules with continuous variables, for example, by considering the number of nuclei, the number of electrons, the nuclear charges, or the serial numbers of electronic excited states and their various multiplicities themselves as continuous parameters, a rather general molecular model can be constructed that in the extreme case provides a unified framework for the study of interrelations among all molecules. Whereas with rare exceptions only those specific cases correspond to physical reality where these continuous variables take integer values, nevertheless, this Universal Molecule model has several advantages and provides a novel perspective on several earlier results. (This paper is dedicated to the memory of Professor István Lukovits).

Mezey, Paul G.

2007-12-01

200

Resonance enhanced multiphoton ionization spectra of molecules and molecular fragments. Annual technical report, March 1991--February 1992  

SciTech Connect

Resonance Enhanced Multiphoton Ionization (REMPI) utilizes pulsed laser radiation to prepare a molecule in an excited state via absorption of one or more photons and to subsequently ionize that state before it can decay. The overall objective of this effort is to carry out theoretical studies of these REMPI processes in molecules and molecular fragments which are designed to provide a robust analysis and prediction of key spectral features of interest in several experimental studies and applications of this technique. A specific and very important objective of the effort is to predict the vibrational and rotational ion distributions which result from REMPI of representative molecules and to understand the underlying mechanisms that give use to these ion distributions. The author highlights progress made during this period.

NONE

1993-12-31

201

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

PubMed Central

The identification of synthesizable substructural domains within more complex structural targets is of significant value in designing a workable plan of synthesis. We term this process “pattern recognition analysis” (PRA). In this paper we continued to build on the theme of PRA as a potential resource in retrosynthetic blueprints to reach highly challenging targets. The paper operates at two levels. First, there is provided a clear sense of definitions of categories by which patterns are related to hypothetical reaction types. Although the required reaction type may for the moment not exist, we believe that this method of analysis is likely to promote innovation that identifies unmet needs and opportunities to advance the cause of complex target synthesis. In addition, we describe reductions to practice in expanding the menu of achievable patterns. It is likely that the future value of PRA will be associated with its utility in leading the way to new and exploitable chemical innovation. PMID:23784777

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

2013-01-01

202

Measurement of Single-Molecule Resistance by Repeated Formation of Molecular Junctions  

Microsoft Academic Search

The conductance of a single molecule connected to two gold electrodes was determined by repeatedly forming thousands of gold-molecule-gold junctions. Conductance histograms revealed well-defined peaks at integer multiples of a fundamental conductance value, which was used to identify the conductance of a single molecule. The resistances near zero bias were 10.5 +\\/- 0.5, 51 +\\/- 5, 630 +\\/- 50, and

Bingqian Xu; Nongjian J. Tao

2003-01-01

203

Image Intensification of X-Ray Diffraction Patterns from Protein Molecules  

Microsoft Academic Search

An image intensifier film system has been used to obtain X-ray diffraction patterns suitable for quantitative measurements of protein structure. Relevant image tube characteristics have been measured, as have the corresponding TV vidicon parameters for extension of the systems to on-line digital recording and analysis.

J. R. Milch; Geo. T. Reynolds; T. C. Minor

1975-01-01

204

The expression pattern of classical MHC class I molecules in the development of mouse central nervous system.  

PubMed

Classical major histocompatibility complex (MHC) class I, first identified in the immune system, is also expressed in the developing and adult central nervous system (CNS). Although the MHC class I molecules have been found to be expressed in the CNS of different species, a necessary step to elucidate the temporal and spatial expression patterns of MHC class I molecules in the brain development has never been taken. Frozen sections were made from the brains of embryonic and postnatal C57BL/6 J mice, and the expression of H-2D(b) mRNA was examined by in situ hybridization. Immunofluorescence was also performed to define the cell types that express H2-D(b) in P15 mice. At E10.5, the earliest stage we examined, H2-D(b) was expressed in neuroepithelium of the brain vesicles. From E12.5 to P0, H2-D(b) expression was mainly located at cerebral cortex, neuroepithelium of the lateral ventricle, neuroepithelium of aquaeductus and developing cerebellum. From P4 to adult, H2-D(b) mRNA was detected at olfactory bulb, hippocampus, cerebellum and some nerve nuclei. The major cell types expressing H-2D(b) in P15 hippocampus, cerebral cortex and olfactory bulb were neuron. H2-K(b) signal paralleled that of H2-D(b) and the expression levels of the two molecules were comparable throughout the brain. The investigation of the expression pattern of H-2D(b) at both embryonic and postnatal stages is important for further understanding the physiological and pathological roles of H2-D(b) in the developing CNS. PMID:23161087

Liu, Jiane; Shen, Yuqing; Li, Mingli; Shi, Qian; Zhang, Aifeng; Miao, Fengqin; Liu, Junhua; Wu, Xiaojing; He, Youji; Zhang, Jianqiong

2013-02-01

205

Differential patterns of molecular evolution among Haemosporidian parasite groups.  

PubMed

Malaria parasites have had profound effects on human populations for millennia, but other terrestrial vertebrates are impacted by malaria as well. Entire species of birds have been driven to extinction, and many others are threatened by population declines. Recent studies have shown that host-switching is quite common among malaria parasite lineages, and these switches often involve a significant shift in the environment in which the parasites find themselves, including nucleated vs non-nucleated red blood cells and red vs white blood cells. Therefore, it is important to understand how parasites adapt to these different host environments. The mitochondrial cytochrome b (cyt b) gene shows evidence of adaptive molecular evolution among malaria parasite groups, putatively because of its critical role in the electron transport chain (ETC) in cellular metabolism. Two hypotheses were addressed here: (1) mitochondrial components of the ETC (cyt b and cytochrome oxidase 1 [COI]) should show evidence of adaptive evolution (i.e. selection) and (2) selection should be evident in host switches. Overall we found a signature of constraint (e.g. purifying selection) across the four genes included here, but we also found evidence of positive selection associated with host switches in cyt b and, surprisingly, in (apicoplast) caseinolytic protease C. These results suggest that evidence of selection should be widespread across these parasite genomes. PMID:25351897

Outlaw, Robert K; Counterman, Brian; Outlaw, Diana C

2015-04-01

206

Genetic basis of dental agenesis - molecular genetics patterning clinical dentistry  

PubMed Central

Tooth agenesis is one of the most common congenital malformations in humans. Hypodontia can either occur as an isolated condition (non-syndromic hypodontia) or can be associated with a syndrome (syndromic hypodontia), highlighting the heterogeneity of the condition. Though much progress has been made to identify the developmental basis of tooth formation, knowledge of the etiological basis of inherited tooth loss is still lacking. To date, the mutation spectra of non-syndromic form of familial and sporadic tooth agenesis in humans have revealed defects in various such genes that encode transcription factors, MSX1 and PAX9 or genes that code for a protein involved in canonical Wnt signaling (AXIN2), and a transmembrane receptor of fibroblast growth factors (FGFR1). The aim of this paper is to review the current literature on the molecular mechanisms responsible for selective hypodontia in humans and to present a detailed overview of causative genes and syndromes associated with hypodontia. Key words:Tooth agenesis, hypodontia, growth factors, mutations. PMID:24121910

Goswami, Mridula; Chhabra, Anuj

2014-01-01

207

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

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

W. H. Flygare; R. C. Benson

1971-01-01

208

What can be learned about molecular reorientation from single molecule polarization microscopy?  

Microsoft Academic Search

We have developed a general approach for the calculation of the single molecule polarization correlation function C(t), which delivers a correlation of the emission dichroisms at time 0 and t. The approach is model independent and valid for general asymmetric top molecules. The key dynamic quantities of our analysis are the even-rank orientational correlation functions, the weighted sum of which

M. F. Gelin; D. S. Kosov

2006-01-01

209

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

Microsoft Academic Search

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

Paul K. Hansma

2000-01-01

210

Ultracold molecular spectroscopy: toward the narrow-line cooling of molecules  

NASA Astrophysics Data System (ADS)

A new spectroscopic method that utilizes microwave transition of ultracold molecules is demonstrated. The narrow spectral linewidth (approximately 100 Hz) was guaranteed by preparing molecules at low temperature, and a high signal-to-noise ratio was achieved by preparing a significant fraction of molecules in the target internal state. The repetition rate of the experiment was approximately 10 Hz, which was only limited by the time needed to load ultracold atoms into the magneto-optical trap. To demonstrate the performance, we investigated the hyperfine structures of the vibrational ground states of the {{X}1}{{? }+} and {{b}3}{{\\Pi }{{0+}}} states of KRb molecules. This technique not only allows us to pursue the narrow-line laser cooling of KRb molecules, but also provided us with essential information for realizing precision spectroscopies e.g., the search for the temporal variation of the electron-to-proton mass ratio.

Kobayashi, Jun; Ogino, Atsushi; Inouye, Shin

2015-03-01

211

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

Microsoft Academic Search

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

John Christoffersen Pearson

1995-01-01

212

Theoretical Study of Donor - Spacer - Acceptor Structure Molecule for Molecular Rectifier  

Microsoft Academic Search

Recently, the molecular electronics has attracted strong attention as a ``post-silicone technology'' to establish a future nanoscale electronic devices. To realize this molecular device, unimolecular rectifiering function is one of the most important constituents in nanotechnology [C. Majumder, H. Mizuseki, and Y. Kawazoe, Molecular Scale Rectifier: Theoretical Study, J. Phys. Chem. A, 105 (2001) 9454-9459.]. In the present study, the

Hiroshi Mizuseki; Niimura Kenji; Rodion Belosludov; Amir Farajian; Yoshiyuki Kawazoe; C. Majumder

2003-01-01

213

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

Microsoft Academic Search

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

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

2003-01-01

214

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

EPA Science Inventory

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

215

Targeted expression of the signaling molecule decapentaplegic induces pattern duplications and growth alterations in Drosophila wings.  

PubMed Central

In the wing imaginal disc, the decapentaplegic (dpp) gene is expressed in a stripe of anterior cells near the anterior-posterior compartment boundary, and it is required solely in these cells for the entire disc to develop. In some viable segment polarity mutants, alterations in dpp expression have been demonstrated that correlate with changes in wing morphology. To test the hypothesis that the abnormal patterns of dpp expression are responsible directly for the mutant phenotypes, we have expressed dpp in ectopic places in wing imaginal discs, and we have found that dpp is able to cause overgrowth and pattern duplications in both anterior and posterior compartments of the wing disc. The alterations of the anterior compartment are strikingly similar to those observed in some viable segment polarity mutants. Thus, ectopic dpp alone can account for the phenotype of these mutants. We also show that ectopic expression of the segment polarity gene hedgehog (hh) gives similar morphological changes and activates dpp expression in the anterior compartment. This strongly suggests that the organizating activity of hh is mediated by dpp. We propose that the expression of dpp near the anterior-posterior compartment boundary is directed by the interaction between patched and hh, and that dpp itself could act as a general organizer of the patterning in the wing imaginal disc. Images PMID:7925288

Capdevila, J; Guerrero, I

1994-01-01

216

Molecular rectification of a helical peptide with a redox group in the metal-molecule-metal junction.  

PubMed

A helical hexadecapeptide immobilized on gold via a thiophenyl group at the N-terminal was analyzed by scanning tunneling microscopy under ultrahigh vacuum to obtain the I-V response at a molecular level. The attenuation factor of the electron transfer through the hexadecapeptide was determined by applying the Simons model to the I-V response to show better molecular conductance of the hexadecapeptide than dodecanethiol. Chemical modification at the C-terminal of the hexadecapeptide with a ferrocene unit, on the other hand, brought about significant changes in the I-V response, where the helical peptide became more conductive at the negative bias voltage. The molecular rectification behavior is due to the ferrocene unit regulating the direction of the electron transfer at the metal-molecule junction. PMID:16852745

Kitagawa, Kazuya; Morita, Tomoyuki; Kimura, Shunsaku

2005-07-28

217

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

PubMed

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

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

2014-03-18

218

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

PubMed Central

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

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

2014-01-01

219

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

NASA Astrophysics Data System (ADS)

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

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

2014-01-01

220

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

PubMed

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

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

221

Imaging Molecular Structure through Femtosecond Photoelectron Diffraction on Aligned and Oriented Gas-Phase Molecules  

E-print Network

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 (C8H5F) and dissociating, laseraligned 1,4-dibromobenzene (C6H4Br2) 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.

Boll, R; Adolph, M; Anielski, D; Aquila, A; Bari, S; Bomme, C; Bostedt, C; Bozek, J D; Chapman, H N; Christensen, L; Coffee, R; Coppola, N; De, S; Decleva, P; Epp, S W; Erk, B; Filsinger, F; Foucar, L; Gorkhover, T; Gumprecht, L; Hoemke, A; Holmegaard, L; Johnsson, P; Kienitz, J S; Kierspel, T; Krasniqi, F; Kuehnel, K -U; Maurer, J; Messerschmidt, M; Moshammer, R; Mueller, Nele L M; Rudek, B; Savelyev, E; Schlichting, I; Schmidt, C; Scholz, F; Schorb, S; Schulz, J; Seltmann, J; Stener, M; Stern, S; Techert, S; Thogersen, J; Trippel, S; Viefhaus, J; Vrakking, M; Stapelfeldt, H; Kuepper, J; Ullrich, J; Rudenko, A; Rolles, D

2014-01-01

222

Movies of molecular motions and reactions: the single-molecule, real-time transmission electron microscope imaging technique.  

PubMed

"The truth is, the Science of Nature has been already too long made only a work of the Brain and the Fancy: It is now high time that it should return to the plainness and soundness of Observations on material and obvious things," proudly declared Robert Hooke in his highly successful picture book of microscopic and telescopic images, "Micrographia" in 1665. Hooke's statement has remained true in chemistry, where a considerable work of the brain and the fancy is still necessary. Single-molecule, real-time transmission electron microscope (SMRT-TEM) imaging at an atomic resolution now allows us to learn about molecules simply by watching movies of them. Like any dream come true, the new analytical technique challenged the old common sense of the communities, and offers new research opportunities that are unavailable by conventional methods. With its capacity to visualize the motions and the reactions of individual molecules and molecular clusters, the SMRT-TEM technique will become an indispensable tool in molecular science and the engineering of natural and synthetic substances, as well as in science education. PMID:23280645

Nakamura, Eiichi

2013-01-01

223

Molecular tunneling ionization of the carbonyl sulfide molecule by double-frequency phase-controlled laser fields  

NASA Astrophysics Data System (ADS)

We have investigated the orientation-selective molecular tunneling ionization of carbonyl sulfide (OCS) molecules induced by linearly polarized double-frequency phase-controlled laser fields consisting of a fundamental and a second-harmonic light with a pulse duration of 130 fs and an intensity of 5 × 1013 W/cm2. We performed simultaneous measurements using gas mixtures of OCS and carbon monoxide to calibrate the relative phase difference of the phase-controlled fields and to verify the mechanism of the tunnel ionization. It is demonstrated that there is a definite correlation between the orientation of ionized molecules and the structure of the highest occupied molecular orbital. We have discussed the experimental results by means of the weak field asymptotic theory. In addition, we have analyzed the quantum dynamics of photoelectrons in simultaneous ion-electron detection. The experimental results can be explained by a two-step model including the interaction with the parent ion. The recollision process plays a minor role for determining the preferable directions of polar molecules in the tunneling ionization at the experimental laser intensity used.

Ohmura, Hideki; Saito, Naoaki; Morishita, Toru

2014-01-01

224

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

Microsoft Academic Search

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

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

2009-01-01

225

The role of damage associated molecular pattern molecules in acetaminophen-induced liver injury in mice  

Microsoft Academic Search

The idiosyncratic nature, severity and poor diagnosis of drug-induced liver injury (DILI) make these reactions a major safety issue during drug development, as well as the most common cause for the withdrawal of drugs from the pharmaceutical market. Elucidation of the underlying mechanism(s) is necessary for identifying predisposing factors and developing strategies in the treatment and prevention of DILI. Acetaminophen

Brittany V. Martin-Murphy; Michael P. Holt; Cynthia Ju

2010-01-01

226

On relationships between molecular structure, interaction and surface behavior in mixture: small-molecule surfactant+protein.  

PubMed

We report on the effect of distinct in nature small-molecule surfactants (model, a sodium salt of capric acid, Na-caprate; and commercially important, a citric acid ester of monoglyceride, CITREM; a sodium salt of stearol-lactoyl lactic acid, SSL (Na(+)); polyglycerol ester, PGE (080)) on molecular properties in a bulk and at the air-water interface of globular legumin and random-coiled micellar sodium caseinate. The role of the structure of both proteins and small-molecule surfactants in the effect studied has been elucidated by measurements in a bulk aqueous medium of the enthalpy of their interaction from mixing calorimetry, the change in value of weight average molecular weight of the proteins and the thermodynamics of the pair protein-protein interactions from laser static light scattering as well as, in addition, by measurements of the change in hydrodynamic radius for micellar sodium caseinate from laser dynamic light scattering. The effect of the small-molecule surfactants on the thermodynamics of the protein heat denaturation and thereby on the protein conformational stability has been studied by differential scanning calorimetry in the case of globular legumin. The interrelation between the effects of the small-molecule surfactants on the properties of the proteins in a bulk and at the planar air-water interface has been elucidated by tensiometry. The combined data of mixing calorimetry, differential scanning calorimetry and laser light scattering suggest some complex formation between the small-molecule surfactants and the proteins in a bulk aqueous medium. Predominantly hydrophobic interaction along with electrostatic and hydrogen bonding form the basis of the complex formation. The found effect of the small-molecule surfactants on the surface activity of their mixtures with proteins is governed primarily by both the extent of the protein association, resulting in specific hydrophobicity/hydrophilicity of the surface of the protein associates, and the specific protein conformational stability, for the globular protein, produced by the interaction between the proteins and the small-molecule surfactants. PMID:11377950

Antipova, A S.; Semenova, M G.; Belyakova, L E.; Il'in, M M.

2001-07-01

227

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

PubMed Central

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

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

228

Quantum control of molecular vibrational and rotational excitations in a homonuclear diatomic molecule: A full three-dimensional treatment with polarization forces  

Microsoft Academic Search

The optimal control of the vibrational excitation of the hydrogen molecule [Balint-Kurti et al., J. Chem. Phys. 122, 084110 (2005)] utilizing polarization forces is extended to three dimensions. The polarizability of the molecule, to first and higher orders, is accounted for using explicit ab initio calculations of the molecular electronic energy in the presence of an electric field. Optimal control

Qinghua Ren; Gabriel G. Balint-Kurti; Frederick R. Manby; Maxim Artamonov; Tak-San Ho; Herschel Rabitz

2006-01-01

229

Molecular Dynamics Simulations on Parallel Computers: a Study of Polar Versus Nonpolar Media Effects in Small Molecule Solvation.  

NASA Astrophysics Data System (ADS)

Solvent effects were studied and described via molecular dynamics (MD) and free energy perturbation (FEP) simulations using the molecular mechanics program AMBER. The following specific topics were explored:. Polar solvents cause a blue shift of the rm nto pi^* transition band of simple alkyl carbonyl compounds. The ground- versus excited-state solvation effects responsible for the observed solvatochromism are described in terms of the molecular level details of solute-solvent interactions in several modeled solvents spanning the range from polar to nonpolar, including water, methanol, and carbon tetrachloride. The structure and dynamics of octanol media were studied to explore the question: "why is octanol/water media such a good biophase analog?". The formation of linear and cyclic polymers of hydrogen-bonded solvent molecules, micelle-like clusters, and the effects of saturating waters are described. Two small drug-sized molecules, benzene and phenol, were solvated in water-saturated octanol. The solute-solvent structure and dynamics were analysed. The difference in their partitioning free energies was calculated. MD and FEP calculations were adapted for parallel computation, increasing their "speed" or the time span accessible by a simulation. The non-cyclic polyether ionophore salinomycin was studied in methanol solvent via parallel FEP. The path of binding and release for a potassium ion was investigated by calculating the potential of mean force along the "exit vector".

Debolt, Stephen Edward

230

Host-guest interactions in the confined geometries formed from molecular aggregates of push-pull molecules.  

PubMed

We have considered push-pull molecules, aminonitroacetylene and aminonitrodiacetylene (O2N-(C?C)n-NH2; n = 1 and 2) as the basic units to design a series of molecular aggregates containing favorable hydrogen bonding interactions. Linear, closed, and stacked geometries of dimers, trimers, tetramers, and pentamers formed from these molecules are found to have very good stabilization energies due to the strong hydrogen bonding abilities of the terminal -NO2 and -NH2 groups. The closed hydrogen-bonded assemblies can act as supramolecular hosts for accommodating some molecules and ions as guests. We have been able to find substantial host-guest interaction energies for the complexes of the hydrogen-bonded closed assemblies with some highly reactive molecules like hexahydro-1,3,5-trinitro-s-triazine (RDX), octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX), pentafluoroethane (R-125), and difluoromethane (R-32). Further investigations on the interaction of the ions Li(+), Na(+), K(+), Mg(2+), Ca(2+), Al(3+), F(-), Cl(-), and Br(-) with the monomers as well as the oligomers reveal the formation of strong ion-? complexes, unlike the conventional weak ion-? complexes found in similar acetylenic systems without the end groups. This opens up the possibility of tuning the nature of ionic interactions in ?-systems by varying the terminal groups. PMID:23772692

K, Rohini; Swathi, R S

2013-07-18

231

Toward molecular mechanism of xenon anesthesia: a link to studies of xenon complexes with small aromatic molecules.  

PubMed

The present study illustrates the steps toward understanding molecular mechanism of xenon anesthesia by focusing on a link to the structures and spectra of intermolecular complexes of xenon with small aromatic molecules. A primary cause of xenon anesthesia is attributed to inhibition of N-methyl-d-aspartate (NMDA) receptors by an unknown mechanism. Following the results of quantum mechanics/molecular mechanics (QM/MM) and molecular dynamics (MD) calculations we report plausible xenon action sites in the ligand binding domain of the NMDA receptor, which are due to interaction of xenon atoms with aromatic amino-acid residues. We rely in these calculations on computational protocols adjusted in combined experimental and theoretical studies of intermolecular complexes of xenon with phenol. Successful reproduction of vibrational shifts in molecular species upon complexation with xenon measured in low-temperature matrices allowed us to select a proper functional form in density functional theory (DFT) approach for use in QM subsystems, as well as to calibrate force field parameters for MD simulations. The results of molecular modeling show that xenon atoms can compete with agonists for a place in the corresponding protein cavity, thus indicating their active role in anesthetic action. PMID:25285819

Andrijchenko, Natalya N; Ermilov, Alexander Yu; Khriachtchev, Leonid; Räsänen, Markku; Nemukhin, Alexander V

2015-03-19

232

Interstellar molecules  

NASA Technical Reports Server (NTRS)

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.

Townes, C. H.

1976-01-01

233

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

PubMed Central

Single-molecule detection (SMD) has demonstrated some attractive benefits for many types of biomolecular analyses including enhanced processing speed by eliminating processing steps, elimination of ensemble averaging and single-molecule sensitivity. However, it's wide spread use has been hampered by the complex instrumentation required for its implementation when using fluorescence as the readout modality. We report herein a simple and compact fluorescence single-molecule instrument that is straightforward to operate and consisted of fiber optics directly coupled to a microfluidic device. The integrated fiber optics served as waveguides to deliver the laser excitation light to the sample and collecting the resulting emission, simplifying the optical requirements associated with traditional SMD instruments by eliminating the need for optical alignment and simplification of the optical train. Additionally, the use of a vertical cavity surface emitting laser and a single photon avalanche diode serving as the excitation source and photon transducer, respectively, as well as a field programmable gate array (FPGA) integrated into the processing electronics assisted in reducing the instrument footprint. This small footprint SMD platform was tested using fluorescent microspheres and single AlexaFluor 660 molecules to determine the optimal operating parameters and system performance. As a demonstration of the utility of this instrument for biomolecular analyses, molecular beacons (MBs) were designed to probe bacterial cells for the gene encoding Gram-positive species. The ability to monitor biomarkers using this simple and portable instrument will have a number of important applications, such as strain-specific detection of pathogenic bacteria or the molecular diagnosis of diseases requiring rapid turn-around-times directly at the point-of-use. PMID:22005669

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

2012-01-01

234

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.

235

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

SciTech Connect

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.

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

236

What can be learned about molecular reorientation from single molecule polarization microscopy?  

E-print Network

We have developed a general approach for the calculation of the single molecule polarization correlation function C(t), which delivers a correlation of the emission dichroisms at time 0 and t. The approach is model independent and valid for general asymmetric top molecules. The key dynamic quantities of our analysis are the even-rank orientational correlation functions, the weighted sum of which yields C(t). We have demonstrated that the use of non-orthogonal schemes for the detection of the single molecule polarization responses makes it possible to manipulate the weighting coefficients in the expansion of C(t). Thus valuable information about the orientational correlation functions of the rank higher than second can be extracted from C(t).

Gelin, M F

2006-01-01

237

Self-assembled chiral superstructures composed of rigid achiral molecules and molecular scale chiral induction by dopants.  

PubMed

We explore the phase behavior of a rigid achiral bent-core model system. Nematic and smectic phases form at higher densities, whereas micelles and columns composed of chiral clusters of these molecules self-assemble at lower densities. No nucleation mechanism requiring transient chirality is possible in the formation of these chiral superstructures due to the rigid achiral nature of the substituents. We show the chiral micelles are minima of the potential energy surface using energy minimization and parallel tempering simulations. Chiral dopants were found to induce the system to adopt a consistent chiral twist direction, the first molecular scale computer simulation of this effect. PMID:18999645

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

2008-10-10

238

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

NASA Astrophysics Data System (ADS)

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.

Pichierri, Fabio

2014-08-01

239

Molecular locks and keys: the role of small molecules in phytohormone research  

PubMed Central

Plant adaptation, growth and development rely on the integration of many environmental and endogenous signals that collectively determine the overall plant phenotypic plasticity. Plant signaling molecules, also known as phytohormones, are fundamental to this process. These molecules act at low concentrations and regulate multiple aspects of plant fitness and development via complex signaling networks. By its nature, phytohormone research lies at the interface between chemistry and biology. Classically, the scientific community has always used synthetic phytohormones and analogs to study hormone functions and responses. However, recent advances in synthetic and combinational chemistry, have allowed a new field, plant chemical biology, to emerge and this has provided a powerful tool with which to study phytohormone function. Plant chemical biology is helping to address some of the most enduring questions in phytohormone research such as: Are there still undiscovered plant hormones? How can we identify novel signaling molecules? How can plants activate specific hormone responses in a tissue-specific manner? How can we modulate hormone responses in one developmental context without inducing detrimental effects on other processes? The chemical genomics approaches rely on the identification of small molecules modulating different biological processes and have recently identified active forms of plant hormones and molecules regulating many aspects of hormone synthesis, transport and response. We envision that the field of chemical genomics will continue to provide novel molecules able to elucidate specific aspects of hormone-mediated mechanisms. In addition, compounds blocking specific responses could uncover how complex biological responses are regulated. As we gain information about such compounds we can design small alterations to the chemical structure to further alter specificity, enhance affinity or modulate the activity of these compounds. PMID:25566283

Fonseca, Sandra; Rosado, Abel; Vaughan-Hirsch, John; Bishopp, Anthony; Chini, Andrea

2014-01-01

240

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

PubMed

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

Aronson, Jay D

2002-01-01

241

Tonal Interface to MacroMolecules (TIMMol): A Textual and Tonal Tool for Molecular Visualization  

ERIC Educational Resources Information Center

We developed the three-dimensional visualization software, Tonal Interface to MacroMolecules or TIMMol, for studying atomic coordinates of protein structures. Key features include audio tones indicating x, y, z location, identification of the cursor location in one-dimensional and three-dimensional space, textual output that can be easily linked…

Cordes, Timothy J.; Carlson, C. Britt; Forest, Katrina T.

2008-01-01

242

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

E-print Network

performed by using an ultrahigh-vacuum low-temperature STM at 6 K. The Ag(111) sample was cleaned by sputter-anneal cycles. A minute amount of sexiphenyl was deposited onto the sample at 70 K by thermal evaporation height, the molecule prop- agates further across the surface [Fig. 1(b)]. Repeating the procedure shows

Hla, Saw-Wai

243

A molecular conveyor belt by controlled delivery of single molecules into ultrashort laser pulses  

Microsoft Academic Search

Trapping and laser cooling in atomic physics enables control of single particles and their dynamics at the quantum level in a background-free environment. Ultrashort intense laser pulses reveal the ultimate control of electromagnetic fields, enabling the imaging of matter, in principle down to a single molecule or virus resolved on atomic scales. However, current methods fall short in overlapping each

Steffen Kahra; Günther Leschhorn; Markus Kowalewski; Agustin Schiffrin; Elisabeth Bothschafter; Werner Fuß; Regina de Vivie-Riedle; Ralph Ernstorfer; Ferenc Krausz; Reinhard Kienberger; Tobias Schaetz

2012-01-01

244

Resonant multiphoton ionization spectra of molecules and molecular fragments. Technical progress report  

SciTech Connect

objectives of this research are the development and application of theoretical techniques for studying several resonant multiphoton ionization processes in molecules. Specific problems of interest pertain to experimental studies of such spectra in which the photoelectron energy and angular distributions are determined.

NONE

1997-07-01

245

The bulk modulus of C sub 60 molecules and crystals: A molecular mechanics approach  

Microsoft Academic Search

In this letter, the bulk modulus of an individual Cââ molecule is calculated in terms of the C,C bond force constant. A range of values for the bulk modulus is obtained with literature values for the force constant. The values obtained all exceed the bulk modulus (441 GPa) of diamond. With a C,C bond force constant equal to that between

R. S. Ruoff; A. L. Ruoff

1991-01-01

246

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

NASA Astrophysics Data System (ADS)

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.

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

2015-01-01

247

The nociceptin receptor (NOPR) and its interaction with clinically important agonist molecules: a membrane molecular dynamics simulation study.  

PubMed

The nociceptin receptor (NOPR) is an orphan G protein-coupled receptor that contains seven transmembrane helices. NOPR has a distinct mechanism of activation, though it shares a significant homology with other opioid receptors. Previously there have been reports on homology modeling of NOPR and also molecular dynamics simulation studies for a short period. Recently the crystal structure of NOPR was reported. In this study, we analyzed the time dependent behavior of NOPR docked with clinically important agonist molecules such as NOP (natural agonist) peptide and compound 10 (SCH-221510 derivative) using molecular dynamics simulations (MDS) for 100 ns. Molecular dynamics simulations of NOPR-agonist complexes allowed us to refine the system and to also identify stable structures with better binding modes. Structure activity relationships (SAR) for SCH221510 derivatives were investigated and reasons for the activities of these derivatives were determined. Our molecular dynamics trajectory analysis of NOPR-peptide and NOPR-compound 10 complexes found residues to be crucial for binding. Mutagenesis studies on the residues identified from our analysis could prove useful. Our results could also provide useful information in the structure-based drug design of novel and potent agonists targeting NOPR. PMID:25259728

Kothandan, Gugan; Gadhe, Changdev G; Balupuri, Anand; Ganapathy, Jagadeesan; Cho, Seung Joo

2014-12-01

248

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

NASA Astrophysics Data System (ADS)

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

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

2014-01-01

249

Molecular printing  

PubMed Central

Molecular printing techniques, which involve the direct transfer of molecules to a substrate with submicrometre resolution, have been extensively developed over the past decade and have enabled many applications. Arrays of features on this scale have been used to direct materials assembly, in nanoelectronics, and as tools for genetic analysis and disease detection. The past decade has witnessed the maturation of molecular printing led by two synergistic technologies: dip-pen nanolithography and soft lithography. Both are characterized by material and substrate flexibility, but dip-pen nanolithography has unlimited pattern design whereas soft lithography has limited pattern flexibility but is low in cost and has high throughput. Advances in DPN tip arrays and inking methods have increased the throughput and enabled applications such as multiplexed arrays. A new approach to molecular printing, polymer-pen lithography, achieves low-cost, high-throughput and pattern flexibility. This Perspective discusses the evolution and future directions of molecular printing. PMID:21378889

Braunschweig, Adam B.; Huo, Fengwei; Mirkin, Chad A.

2014-01-01

250

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

PubMed Central

MHC-I proteins of the adaptive immune system require antigenic peptides for maintenance of mature conformation and immune function via specific recognition by MHC-I-restricted CD8+ T lymphocytes. New MHC-I molecules in the endoplasmic reticulum are held by chaperones in a peptide-receptive (PR) transition state pending release by tightly binding peptides. We show, by crystallographic, docking, and molecular dynamics methods, dramatic movement of a hinged unit containing a conserved 310 helix, that flips from an exposed “open” position in the PR transition state, to a “closed” position with buried hydrophobic side chains in the peptide-loaded (PL) mature molecule. Crystallography of hinged unit residues 46-53 of murine H-2Ld MHC-I heavy chain, complexed with mAb 64-3-7 demonstrates solvent exposure of these residues in the PR conformation. Docking and molecular dynamics predict how this segment moves to help form the A and B pockets crucial for the tight peptide binding needed for stability of the mature PL conformation, chaperone dissociation, and antigen presentation. PMID:22753930

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

2012-01-01

251

Two- and N-step correlated models for the analysis of molecular dynamics trajectories of linear molecules in silicalite  

NASA Astrophysics Data System (ADS)

Recent molecular dynamics data on the diffusion of linear diatomic and triatomic molecules in the zeolite silicalite are analyzed in terms of a new correlated model [F. Jousse, S. M. Auerbach, and D. P. Vercauteren, J. Chem. Phys. 112, 1531 (2000)] capable to account for both first- and higher-order correlation effects. This "N-step" model reproduces very well our calculated mean square displacements and diffusion coefficients of the molecules considered. The improvements with respect to the results obtained with our previous "two-step" model [P. Demontis, J. Kärger, G. B. Suffritti, and A. Tilocca, Phys. Chem. Chem. Phys. 2, 1455 (2000)] are remarkable for all molecules except chlorine, showing that only in this case the effect of (negative) correlations spanning more than two jumps between channel intersections (˜20 Å) can be neglected. The basic trajectory analysis in terms of single- and two-step models, besides being an useful reference, provides all the input data needed for the application of the N-step model. Indeed, in its silicalite formulation, the N-step model is strongly linked to the two-step one because it calculates the probability of a sequence of jumps in the same channel by means of the correlations between any two consecutive jumps. Finally, the possibility to obtain qualitative insight into the diffusive mechanism through various kind of correlation coefficients is discussed.

Demontis, Pierfranco; Suffritti, Giuseppe B.; Tilocca, Antonio

2000-11-01

252

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

E-print Network

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...

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

253

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

SciTech Connect

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

Miau, T.T.

1995-05-01

254

Shaping microtubules into diverse patterns: molecular connections for setting up both ends.  

PubMed

Microtubules serve as rails for intracellular trafficking and their appropriate organization is critical for the generation of cell polarity, which is a foundation of cell differentiation, tissue morphogenesis, ontogenesis and the maintenance of homeostasis. The microtubule array is not just a static railway network; it undergoes repeated collapse and reassembly in diverse patterns during cell morphogenesis. In the last decade much progress has been made toward understanding the molecular mechanisms governing complex microtubule patterning. This review first revisits the basic principle of microtubule dynamics, and then provides an overview of how microtubules are arranged in highly shaped and functional patterns in cells changing their morphology by factors controlling the fate of microtubule ends. PMID:22021191

Mimori-Kiyosue, Yuko

2011-11-01

255

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

PubMed Central

A molecular machine is either a single macromolecule or a macromolecular complex. In spite of the striking superficial similarities between these natural nanomachines and their man-made macroscopic counterparts, there are crucial differences. Molecular machines in a living cell operate stochastically in an isothermal environment far from thermodynamic equilibrium. In this mini-review we present a catalog of the molecular machines and an inventory of the essential toolbox for theoretically modeling these machines. The tool kits include 1), nonequilibrium statistical-physics techniques for modeling machines and machine-driven processes; and 2), statistical-inference methods for reverse engineering a functional machine from the empirical data. The cell is often likened to a microfactory in which the machineries are organized in modular fashion; each module consists of strongly coupled multiple machines, but different modules interact weakly with each other. This microfactory has its own automated supply chain and delivery system. Buoyed by the success achieved in modeling individual molecular machines, we advocate integration of these models in the near future to develop models of functional modules. A system-level description of the cell from the perspective of molecular machinery (the mechanome) is likely to emerge from further integrations that we envisage here. PMID:23746505

Chowdhury, Debashish

2013-01-01

256

A crossed molecular beams study of the reaction of dicarbon molecules with benzene  

NASA Astrophysics Data System (ADS)

We conducted the reaction of dicarbon molecules in their electronic ground, C(X?g+), and first excited state, C 2(a 3? u), with benzene, C 6H 6(X 1A 1g). The phenylethynyl radical (C 6H 5CC; X 2A') and atomic hydrogen were inferred to be the reaction products under single collision conditions. The reactions were indirect via short-lived C 8H 6 intermediates which decomposed via atomic hydrogen elimination without exit barrier (singlet surface) and via a tight exit transition state (triplet surface). Our experiments suggest that the phenylethynyl radical can be likely formed via bimolecular reactions involving dicarbon molecules with benzene in extreme environments such as circumstellar envelopes of carbon stars, planetary nebulae, and combustion flames.

Gu, Xibin; Guo, Ying; Zhang, Fangtong; Mebel, Alexander M.; Kaiser, Ralf I.

2007-02-01

257

The bulk modulus of C60 molecules and crystals: A molecular mechanics approach  

Microsoft Academic Search

In this letter, the bulk modulus of an individual C60 molecule is calculated in terms of the C,C bond force constant. A range of values for the bulk modulus is obtained with literature values for the force constant. The values obtained all exceed the bulk modulus (441 GPa) of diamond. With a C,C bond force constant equal to that between

Rodney S. Ruoff; Arthur L. Ruoff

1991-01-01

258

The bulk modulus of C60 molecules and crystals - A molecular mechanics approach  

Microsoft Academic Search

In this letter, the bulk modulus of an individual C60 molecule is calculated in terms of the C,C bond force constant. A range of values for the bulk modulus is obtained with literature values for the force constant. The values obtained all exceed the bulk modulus (441 GPa) of diamond. With a C,C bond force constant equal to that between

Rodney S. Ruoff; Arthur L. Ruoff

1991-01-01

259

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

NASA Astrophysics Data System (ADS)

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 other biological composite materials reveal modules bound together by sacrificial bonds that are weaker than the backbone bonds in the polypeptide chain.1 These self-healing modules provide effective energy absorption and appear to be a real key to understanding the impressive fracture resistance of biological composite materials. For example, the abalone shell is 3000 times more fracture resistant than a single crystal of calcium carbonate, despite the fact that 97% of the mass of the shell is crystalline calcium carbonate. 2) It is becoming possible, again with AFMs, to learn how some enzymes, nature's nanomachines, do their exquisite materials synthesis and processing. The talk will focus on the chaperonin system of GroEL and GroES that processes incorrectly folded proteins and assists them in refolding correctly. It is becoming possible not only to see single molecule events such as the association and disassociation of the GroEL-Gro-ES complex, but also to measure potential energy functions for the molecules in various conformational states. These new measurements, together with detailed structural measurements from other techniques, give new clues about how these proteins use the energy of ATP to do their work. Since the AFMs of today are very far from fundamental limits, this is only the beginning. 1. B. L. Smith, T. E. Schaffer, M. Viani, J. B. Thompson, N. A. Frederick, J. Kindt, A. Belcher, G. D. Stucky, D. E. Morse and P. K. Hansma, Nature 399, 761 (1999)

Hansma, Paul K.

2000-03-01

260

Heat-driven release of a drug molecule from carbon nanotubes: a molecular dynamics study.  

PubMed

Hydrophobicity and the ability to absorb light that penetrates through living tissues make carbon nanotubes (CNTs) promising intracellular drug delivery agents. Following insertion of a drug molecule into a CNT, the latter is delivered into a tissue, is heated by near-infrared radiation, and releases the drug. To assess the feasibility of this scheme, we investigate the rates of energy transfer between CNT, water, and the drug molecule and study the temperature and concentration dependence of the diffusion coefficient of the drug molecule inside CNTs. We use ciprofloxacin (CIP) as a sample drug: direct penetration of CIP through cell membranes is problematic due to its high polarity. The simulations show that a heated CNT rapidly deposits its energy to CIP and water. All estimated time scales for the vibrational energy exchange between CNT, CIP, and water are less than 10 ps at 298 K. As the system temperature grows from 278 to 363 K, the diffusion coefficient of the confined CIP increases 5-7 times, depending on CIP concentration. The diffusion coefficient slightly drops with increasing CIP concentration. This effect is more pronounced at higher temperatures. The simulations support the idea that optical heating of CNTs can assist in releasing encapsulated drugs. PMID:20831145

Chaban, Vitaly V; Savchenko, Timur I; Kovalenko, Sergiy M; Prezhdo, Oleg V

2010-10-28

261

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

NASA Technical Reports Server (NTRS)

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

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

2011-01-01

262

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

PubMed

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

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

2014-12-17

263

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

NASA Astrophysics Data System (ADS)

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

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

2013-06-01

264

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

Microsoft Academic Search

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

R P Donn; D W Ray

2004-01-01

265

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...

266

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

Microsoft Academic Search

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

Jacqueline Krim

2012-01-01

267

Recognizing molecular patterns by machine learning: An agnostic structural definition of the hydrogen bond  

NASA Astrophysics Data System (ADS)

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.

Gasparotto, Piero; Ceriotti, Michele

2014-11-01

268

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

PubMed

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

Gasparotto, Piero; Ceriotti, Michele

2014-11-01

269

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

PubMed

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

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

2014-04-17

270

Molecular Mechanisms of T cell Receptor and Costimulatory Molecule Ligation/Blockade in Autoimmune Disease Therapy  

PubMed Central

Pro-inflammatory CD4+ T cell mediated autoimmune diseases, such as multiple sclerosis and type 1 diabetes, are hypothesized to be initiated and maintained by activated antigen presenting cells (APCs) presenting self-antigen to self-reactive interferon-gamma (IFN-?) and interleukin-17 (IL-17) producing CD4+ Th1/17 cells. To date, the majority of FDA approved therapies for autoimmune disease primarily focus on the global inhibition of immune inflammatory activity. The goal of ongoing research in this field is to develop both therapies that inhibit/eliminate activated autoreactive cells as well as antigen-specific treatments which allow for the directed blockade of the deleterious effects of self-reactive immune cell function. According to the two-signal hypothesis, activation of a naïve antigen-specific CD4+ T cell requires both stimulation of the T cell receptor (TCR) (signal 1), and stimulation of costimulatory molecules (signal 2). There also exists a balance between pro-inflammatory and anti-inflammatory immune cell activity, which is regulated by the type and strength of the activating signal as well as the local cytokine milieu in which the naïve CD4+ T cell is activated. To this end, the majority of ongoing research is focused on the delivery of suboptimal TCR stimulation in the absence of costimulatory molecule stimulation, or potential blockade of stimulatory accessory molecules. Therefore, the signaling pathways involved in the induction of CD4+ T cell anergy, as apposed to activation, are topics of intense interest. PMID:19426232

Podojil, Joseph R.; Miller, Stephen D.

2010-01-01

271

Molecular features of the prazosin molecule required for activation of Transport-P.  

PubMed

Closely related structural analogues of prazosin have been synthesised and tested for inhibition and activation of Transport-P in order to identify the structural features of the prazosin molecule that appear to be necessary for activation of Transport-P. So far, all the compounds tested are less active than prazosin. It is shown that the structure of prazosin appears to be very specific for the activation. Only quinazolines have been found to activate, and the presence of the 6,7-dimethoxy and 4-amino groups appears to be critically important. PMID:18625562

da Silva, Joaquim Fernando Mendes; Walters, Marcus; Al-Damluji, Saad; Ganellin, C Robin

2008-08-01

272

Spatiotemporal patterns enhanced by intra- and inter-molecular fluctuations in arrays of allosterically regulated enzymes  

NASA Astrophysics Data System (ADS)

Enzymatic reactions often involve slow conformational changes, with reaction cycles that sometimes require milliseconds or seconds to complete. The dynamics are strongly affected by fluctuations at the nanoscale. However, such enzymes often occur in small numbers in a cell; hence, the fluctuations caused by finite numbers of molecules should also be substantial. Because of these factors, the behavior of the system is likely to deviate from that of classical reaction–diffusion equations, in which immediate reaction events are assumed to occur without memory and between a huge number of molecules. In this work, we model each enzyme as a unit represented by a phase variable to investigate the effects of fluctuations in arrays of enzymes. Using an analysis based on partial differential equations and stochastic simulations, we show that fluctuations arising from internal states of enzymes (intramolecular fluctuations) and those arising from the stochastic nature of interactions between molecules (intermolecular fluctuations) have distinctive effects on spatiotemporal patterns; the former generally disturb synchronization at high frequencies, whereas the latter can enhance synchronization. The balance of the two types of fluctuations may determine the spatiotemporal behavior of biochemical processes.

Togashi, Yuichi; Casagrande, Vanessa

2015-03-01

273

Expression of adult fast pattern of acetylcholinesterase molecular forms by mouse satellite cells in culture.  

PubMed

The pattern of acetylcholinesterase (AChE) molecular forms, obtained by sucrose gradient sedimentation, was studied at different in vitro developmental stages of myogenic cells isolated from adult mouse skeletal muscle. Only the globular forms were present in rapidly dividing satellite cells during the first days in culture. After myotube formation, a pattern similar to that described in mammalian fast-twitch skeletal muscle was observed. This pattern did not change during the following period in culture (up to 1 month) nor could it be modified by co-culturing with spinal cord motoneurons or by addition of brain-derived extracts. The internal-external localization of AChE molecular forms has been determined by the use of echothiophate iodide, a membrane-impermeant irreversible inhibitor of AChE. Echothiophate-treated cultures showed about 40% of both asymmetric and globular forms localized on the sarcolemma, with their active sites oriented outward. Analysis of culture medium from untreated cultures revealed the presence of both asymmetric and globular forms. When the same analysis was repeated on cultures of myoblasts derived from 16-day-old mouse embryos, the pattern of AChE forms was different. The myotubes derived from these cells exhibit a very small proportion of asymmetric form, which was not released into the medium. This pattern was not further modified during the following days of culture, nor by co-cultures with spinal cord motoneurons or by incubations with brain-derived extracts. Thus, the myotubes derived from myoblasts express in culture a clear phenotypic difference when compared to the corresponding myotubes from satellite cells, supporting the view that these two myogenic cells are endowed with different developmental programs. PMID:3449398

Senni, M I; Castrignano, F; Poiana, G; Cossu, G; Scarsella, G; Biagioni, S

1987-01-01

274

Improving Signal/Noise Resolution in Single-Molecule Experiments Using Molecular Constructs with Short Handles  

PubMed Central

We investigate unfolding/folding force kinetics in DNA hairpins exhibiting two and three states with newly designed short dsDNA handles (29 bp) using optical tweezers. We show how the higher stiffness of the molecular setup moderately enhances the signal/noise ratio (SNR) in hopping experiments as compared to conventional long-handled constructs (?700 bp). The shorter construct results in a signal of higher SNR and slower folding/unfolding kinetics, thereby facilitating the detection of otherwise fast structural transitions. A novel analysis, as far as we are aware, of the elastic properties of the molecular setup, based on high-bandwidth measurements of force fluctuations along the folded branch, reveals that the highest SNR that can be achieved with short handles is potentially limited by the marked reduction of the effective persistence length and stretch modulus of the short linker complex. PMID:21463590

Forns, N.; de Lorenzo, S.; Manosas, M.; Hayashi, K.; Huguet, J.M.; Ritort, F.

2011-01-01

275

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

PubMed

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

Liu, Danqing; Broer, Dirk J

2014-11-18

276

Molecular bioelectricity: how endogenous voltage potentials control cell behavior and instruct pattern regulation in vivo.  

PubMed

In addition to biochemical gradients and transcriptional networks, cell behavior is regulated by endogenous bioelectrical cues originating in the activity of ion channels and pumps, operating in a wide variety of cell types. Instructive signals mediated by changes in resting potential control proliferation, differentiation, cell shape, and apoptosis of stem, progenitor, and somatic cells. Of importance, however, cells are regulated not only by their own Vmem but also by the Vmem of their neighbors, forming networks via electrical synapses known as gap junctions. Spatiotemporal changes in Vmem distribution among nonneural somatic tissues regulate pattern formation and serve as signals that trigger limb regeneration, induce eye formation, set polarity of whole-body anatomical axes, and orchestrate craniofacial patterning. New tools for tracking and functionally altering Vmem gradients in vivo have identified novel roles for bioelectrical signaling and revealed the molecular pathways by which Vmem changes are transduced into cascades of downstream gene expression. Because channels and gap junctions are gated posttranslationally, bioelectrical networks have their own characteristic dynamics that do not reduce to molecular profiling of channel expression (although they couple functionally to transcriptional networks). The recent data provide an exciting opportunity to crack the bioelectric code, and learn to program cellular activity at the level of organs, not only cell types. The understanding of how patterning information is encoded in bioelectrical networks, which may require concepts from computational neuroscience, will have transformative implications for embryogenesis, regeneration, cancer, and synthetic bioengineering. PMID:25425556

Levin, Michael

2014-12-01

277

Pro-Coagulant Endothelial Dysfunction Results from EHEC Shiga Toxins and Host Damage-Associated Molecular Patterns  

PubMed Central

Hemolytic uremic syndrome (HUS) from enterohemorrhagic Escherichia coli infection is a leading cause of kidney failure in otherwise healthy U.S. children. The bacterial Shiga toxins (Stx) induce the characteristic coagulopathy of HUS, but the damage to toxin-receptor expressing cells and organ injury due to ischemia likely also releases inflammatory damage-associated molecular patterns (DAMPs), which may exacerbate injury along with the toxins. To examine this, human aortic and renal glomerular cell anti-coagulant and barrier functions were studied after in vitro challenge with Stx1, Stx2, and DAMPs. There was significant loss of surface anti-coagulant protein C pathway molecules, increased expression of pro-thrombotic PAR1 and reduced protein C activation capability by 15–27%. Histones nearly completely prevented the activated protein C protection of endothelial cells from thrombin-induced permeability. In mice, lethal Stx2 challenge elevated plasma HMGB1 (day 2, 321?±?118%; p?

Mayer, Chad L.; Parello, Caitlin S. L.; Lee, Benjamin C.; Itagaki, Kiyoshi; Kurosawa, Shinichiro; Stearns-Kurosawa, Deborah J.

2015-01-01

278

WaterLOGSY NMR experiments in conjunction with molecular-dynamics simulations identify immobilized water molecules that bridge peptide mimic MDWNMHAA to anticarbohydrate antibody SYA/J6.  

PubMed

X-ray crystallographic data of the carbohydrate mimic MDWNMHAA when bound to an anti-Shigella flexneri Y mAb SYA/J6 indicate the immobilization of water molecules, that is, the presence of "bound" waters, in the active site. Water Ligand Observed via Gradient Spectroscopy (WaterLOGSY) was used in conjunction with saturation transfer difference (STD)-NMR spectroscopy to probe the existence of immobilized water molecules in the complex of MDWNMHAA 1 bound to mAb SYA/J6. Molecular dynamics simulations using the ZymeCAD Molecular Dynamics platform were then used to specify the likely locations of these water molecules. Of note, those waters involved in providing complementarity between the peptide and mAb SYA/J6 remained throughout the course of the simulation. Together, the experimental and computational protocols have been used to identify the bound water molecules present in the antibody-peptide complex. PMID:21887835

Szczepina, Monica G; Bleile, Dustin W; Müllegger, Johannes; Lewis, Andrew R; Pinto, B Mario

2011-10-01

279

Single-molecule magnets: a large Mn30 molecular nanomagnet exhibiting quantum tunneling of magnetization.  

PubMed

The largest single-molecule magnet (SMM) to date has been prepared and studied. Recrystallization of known [Mn(12)O(12)(O(2)CCH(2)Bu(t))(16)(H(2)O)(4)] (1; 8Mn(III), 4Mn(IV)) from CH(2)Cl(2)/MeNO(2) causes its conversion to [Mn(30)O(24)(OH)(8)(O(2)CCH(2)Bu(t))(32)(H(2)O)(2)(MeNO(2))(4)] (2; 3Mn(II), 26Mn(III), Mn(IV)). The structure of 2 consists of a central, near-linear [Mn(4)O(6)] backbone, to either side of which are attached two [Mn(13)O(9)(OH)(4)] units. Peripheral ligation around the resulting [Mn(30)O(24)(OH)(8)] core is by 32 Bu(t)CH(2)CO(2)(-), 2 H(2)O, and 4 MeNO(2) groups. The molecule has crystallographically imposed C(2) symmetry. Variable-temperature and -field magnetization (M) data were collected in the 1.8-4.0 K and 0.1-0.4 T ranges and fit by matrix diagonalization assuming only the ground state is occupied at these temperatures. The fit parameters were S = 5, D = -0.51 cm(-1) = -0.73 K, and g = 2.00, where D is the axial zero-field splitting parameter. AC susceptibility measurements in the 1.8-7.0 K range in a zero DC field and a 3.5 G AC field oscillating at frequencies in the 50-997 Hz range revealed a frequency-dependent out-of-phase (chi(M)'') signal below 3 K, indicating 2 to be a single-molecule magnet (SMM), the largest yet obtained. Magnetization versus DC field sweeps show hysteresis loops but no clear steps characteristic of quantum tunneling of magnetization (QTM). However, magnetization decay data below 1 K were collected and used to construct an Arrhenius plot that revealed temperature-independent relaxation below 0.3 K. The fit of the thermally activated region above approximately 0.5 K gave U(eff)/k = 15 K, where U(eff) is the effective relaxation barrier. Resonant QTM was confirmed from the appearance of a "quantum hole" when the recent quantum hole digging method was employed. The combined results demonstrate that SMMs can be prepared that are significantly larger than any known to date and that this new, large Mn(30) complex still demonstrates quantum behavior. PMID:14971951

Soler, Monica; Wernsdorfer, Wolfgang; Folting, Kirsten; Pink, Maren; Christou, George

2004-02-25

280

Molecular motion, dielectric response, and phase transition of charge-transfer crystals: acquired dynamic and dielectric properties of polar molecules in crystals.  

PubMed

Molecules in crystals often suffer from severe limitations on their dynamic processes, especially on those involving large structural changes. Crystalline compounds, therefore, usually fail to realize their potential as dielectric materials even when they have large dipole moments. To enable polar molecules to undergo dynamic processes and to provide their crystals with dielectric properties, weakly bound charge-transfer (CT) complex crystals have been exploited as a molecular architecture where the constituent polar molecules have some freedom of dynamic processes, which contribute to the dielectric properties of the crystals. Several CT crystals of polar tetrabromophthalic anhydride (TBPA) molecules were prepared using TBPA as an electron acceptor and aromatic hydrocarbons, such as coronene and perylene, as electron donors. The crystal structures and dielectric properties of the CT crystals as well as the single-component crystal of TBPA were investigated at various temperatures. Molecular reorientation of TBPA molecules did not occur in the single-component crystal, and the crystal did not show a dielectric response due to orientational polarization. We have found that the CT crystal formation provides a simple and versatile method to develop molecular dielectrics, revealing that the molecular dynamics of the TBPA molecules and the dielectric property of their crystals were greatly changed in CT crystals. The TBPA molecules underwent rapid in-plane reorientations in their CT crystals, which exhibited marked dielectric responses arising from the molecular motion. An order-disorder phase transition was observed for one of the CT crystals, which resulted in an abrupt change in the dielectric constant at the transition temperature. PMID:25781627

Harada, Jun; Ohtani, Masaki; Takahashi, Yukihiro; Inabe, Tamotsu

2015-04-01

281

Theoretical study of the alkyl derivative C 37H 50N 4O 4 molecule for use as a stable molecular rectifier: geometric and electronic structures  

Microsoft Academic Search

The realization of a molecular device with a unimolecular rectifying function is one of the most important requirements in nanotechnology. In the present study, the geometric and electronic structure of the alkyl derivative molecule C37H50N4O4 has been investigated theoretically using ab initio quantum mechanical calculations. This molecule has a donor–spacer–acceptor structure, and is a leading candidate for the creation of

Hiroshi Mizuseki; Kenji Niimura; Chiranjib Majumder; Yoshiyuki Kawazoe

2003-01-01

282

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

PubMed Central

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

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

283

Molecular recognition of human CD1b antigen complexes: evidence for a common pattern of interaction with alpha beta TCRs.  

PubMed

Ag-specific T cell recognition is mediated through direct interaction of clonotypic TCRs with complexes formed between Ag-presenting molecules and their bound ligands. Although characterized in substantial detail for class I and class II MHC encoded molecules, the molecular interactions responsible for TCR recognition of the CD1 lipid and glycolipid Ag-presenting molecules are not yet well understood. Using a panel of epitope-specific Abs and site-specific mutants of the CD1b molecule, we showed that TCR interactions occur on the membrane distal aspects of the CD1b molecule over the alpha1 and alpha2 domain helices. The location of residues on CD1b important for this interaction suggested that TCRs bind in a diagonal orientation relative to the longitudinal axes of the alpha helices. The data point to a model in which TCR interaction extends over the opening of the putative Ag-binding groove, making multiple direct contacts with both alpha helices and bound Ag. Although reminiscent of TCR interaction with MHC class I, our data also pointed to significant differences between the TCR interactions with CD1 and MHC encoded Ag-presenting molecules, indicating that Ag receptor binding must be modified to accommodate the unique molecular structure of the CD1b molecule and the unusual Ags it presents. PMID:11035089

Melián, A; Watts, G F; Shamshiev, A; De Libero, G; Clatworthy, A; Vincent, M; Brenner, M B; Behar, S; Niazi, K; Modlin, R L; Almo, S; Ostrov, D; Nathenson, S G; Porcelli, S A

2000-10-15

284

The plant hormone auxin has been implicated in vascular development, but the molecular details of patterned vascular  

E-print Network

406 The plant hormone auxin has been implicated in vascular development, but the molecular details of patterned vascular differentiation have remained elusive. Research in the past year has identified new genes that control vascular patterning, and auxin transport and perception. New experimental strategies have been

Mattsson, Jim

285

Evaluation of 99mTc-peptide-ZHER2:342 Affibody® molecule for in vivo molecular imaging  

PubMed Central

Objective: The aim of this study was to develop an improved method for labelling ZHER2:342 with Technetium-99m (99mTc) using Gly-(d) Ala-Gly-Gly as a chelator and to evaluate the feasibility of its use for visualization of HER2 expression in vivo. Methods: The Affibody® molecule ZHER2:342 was synthesized by Fmoc/tBu solid phase synthesis. The chelator, Gly-(d) Ala-Gly-Gly, was introduced by manual synthesis as the N-terminal extensions of ZHER2:342. ZHER2:342 was labelled with 99mTc. The labelling efficiency, radiochemical purity and in vitro stability of the labelled molecular probe were analysed by reversed-phase high performance liquid chromatography. Biodistribution and molecular imaging using 99mTc-peptide-ZHER2:342 were performed. Results: The molecular probe was successfully synthesized and labelled with 99mTc with the labelling efficiency of 98.10?±?1.73% (n?=?5). The radiolabelled molecular probe remained highly stable in vitro. The molecular imaging showed high uptake in HER2-expressing SKOV-3 xenografts, whereas the MDA-MB-231 xenografts with low HER2 expression were not clearly imaged at any time after the injection of 99mTc-peptide-ZHER2:342. The predominant clearance pathway for 99mTc-peptide-ZHER2:342 was through the kidneys. Conculsion: 99mTc-peptide-ZHER2:342 using Gly-(d) Ala-Gly-Gly as a chelator is a promising tracer agent with favourable biodistribution and imaging properties that may be developed as a radiopharmaceutical for the detection of HER2-positive malignant tumours. Advances in knowledge: The 99mTc-peptide-ZHER2:342 molecular probe is a promising tracer agent, and the results in this study provide a foundation for future development of protocols for earlier visual detection of cancer in the clinical setting. PMID:24273251

Zhang, J-M; Zhao, X-M; Ren, X-C; Wang, N; Han, J-Y; Jia, L-Z

2014-01-01

286

Molecular basis of natural variation and environmental control of trichome patterning  

PubMed Central

Trichomes are differentiated epidermal cells on above ground organs of nearly all land plants. They play important protective roles as structural defenses upon biotic attacks such as herbivory, oviposition and fungal infections, and against abiotic stressors such as drought, heat, freezing, excess of light, and UV radiation. The pattern and density of trichomes is highly variable within natural population suggesting tradeoffs between traits positively affecting fitness such as resistance and the costs of trichome production. The spatial distribution of trichomes is regulated through a combination of endogenous developmental programs and external signals. This review summarizes the current understanding on the molecular basis of the natural variation and the role of phytohormones and environmental stimuli on trichome patterning. PMID:25071803

Hauser, Marie-Theres

2014-01-01

287

Computer-aided molecular modeling study on antibody recognition of small molecules: an immunoassay for triazine herbicides.  

PubMed

Most immunoassays for determination of small molecules are still designed on the basis of the "trial and error" method, due to the lack of understanding of antibody recognition. In the present study, we developed a heterologous indirect competitive enzyme-linked immunosorbent assay for determination of triazine herbicides, with limits of detection for 11 triazines ranging from 0.05 to 29.4 ?g/L. Mechanisms of the antigen-antibody interaction were studied by computer-aided molecular modeling (CAMM)-based quantitative structure-activity relationship analyses. Co-effects of the analytes' substructural hydrophobic, electrostatic, and steric fields on antibody recognition were further revealed. Hydrophobicity of the antigens was demonstrated to have the most important impact. Even less exposed substituents provided hydrophobic force to the antigen-antibody interaction. Dislocated orientation of analyte functional groups could lead to steric hindrance and hydrophobic misleading of antibody recognition. This may happen even when the antigens contained the same substituent as the hapten. Frontier orbital energies also affect the reaction significantly. This study highlights of the power of CAMM-based analyses, providing insights into antibody recognition of small molecules. PMID:23043348

Yuan, Meng; Na, Yu; Li, Lingling; Liu, Bing; Sheng, Wei; Lu, Xiaonan; Kennedy, Ivan; Crossan, Angus; Wang, Shuo

2012-10-24

288

Molecular-scale and wide-energy-range tunneling spectroscopy on self-assembled monolayers of alkanethiol molecules.  

PubMed

The electronic properties of alkanethiol self-assembled monolayers (alkanethiolate SAMs) associated with their molecular-scale geometry are investigated using scanning tunneling microscopy and spectroscopy (STM/STS). We have selectively formed the three types of alkanethiolate SAMs with standing-up, lying-down, and lattice-gas phases by precise thermal annealing of the SAMs which are conventionally prepared by depositing alkanethiol molecules onto Au(111) surface in solution. The empty and filled states of each SAM are evaluated over a wide energy range covering 6 eV above/below the Fermi level (E(F)) using two types of STS on the basis of tunneling current-voltage and distance-voltage measurements. Electronic states originating from rigid covalent bonds between the thiol group and substrate surface are observed near E(F) in the standing-up and lying-down phases but not in the lattice-gas phase. These states contribute to electrical conduction in the tunneling junction at a low bias voltage. At a higher energy, a highly conductive state stemming from the alkyl chain and an image potential state (IPS) formed in a vacuum gap appear in all phases. The IPS shifts toward a higher energy through the change in the geometry of the SAM from the standing-up phase to the lattice-gas phase through the lying-down phase. This is explained by the increasing work function of alkanethiolate/Au(111) with decreasing density of surface molecules. PMID:22958159

Nakaya, Masato; Shikishima, Masaya; Shibuta, Masahiro; Hirata, Naoyuki; Eguchi, Toyoaki; Nakajima, Atsushi

2012-10-23

289

Gate-induced switching and negative differential resistance in a single-molecule transistor: emergence of fixed and shifting states with molecular length.  

PubMed

The quantum transport of a gated polythiophene nanodevice is analyzed using density functional theory and nonequilibrium Green's function approach. For this typical molecular field effect transistor, we prove the existence of two main features of electronic components, i.e., negative differential resistance and good switching. Ab initio based explanations of these features are provided by distinguishing fixed and shifting conducting states, which are shown to arise from the interface and functional molecule, respectively. The results show that proper functional molecules can be used in conjunction with metallic electrodes to achieve basic electronics functionality at molecular length scales. PMID:17640145

Farajian, A A; Belosludov, R V; Mizuseki, H; Kawazoe, Y; Hashizume, T; Yakobson, B I

2007-07-14

290

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

PubMed

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

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

2013-02-01

291

Monte Carlo simulations of ferroelectric crystal growth and molecular electronic structure of atoms and molecules  

NASA Astrophysics Data System (ADS)

In this thesis, we explore two stochastic techniques to study properties of materials in realistic systems. Specifically, the kinetic Monte Carlo (KMC) method is utilized to study the crystal growth process of ferroelectric materials and the quantum Monte Carlo (QMC) approach is used to investigate the ground state properties of atoms and molecules. In the growth simulations, we study the growth rates and chemical ordering of ferroelectric alloys using an electrostatic model with long-range Coulomb interactions. Crystal growth is characterized by thermodynamic processes involving adsorption and evaporation, with solid-on-solid restrictions and excluding diffusion. A KMC algorithm is formulated to simulate this model efficiently in the presence of long-range interactions. The growth process is simulated as a function of temperature, chemical composition, and substrate orientation. We carried out the simulations on two heterovalent binaries, those of the NaCl and the Ba(Mg1/3Nb2/3))O3(BMN) structures. Compared to the simple rocksalt ordered structures, ordered BMN grows only at very low temperatures and only under finely tuned conditions. For materials with tetravalent compositions, such as (1-x)Ba(Mg 1/3Nb2/3))O3 + x BaZrO3 (BMN-BZ), the model does not incorporate tetravalent ions at low-temperature, exhibiting a phase-separated ground state instead. At higher temperatures, tetravalent ions can be incorporated, but the resulting crystals show no chemical ordering in the absence of diffusive mechanisms. In the second part of the thesis, we present results from an auxiliary field quantum Monte Carlo (AFQMC) study of ground state properties, in particular dissociation and ionization energy, of second-row atoms and molecules. The method projects the many-body ground state from a trial wavefunction by random walks in the space of Slater determinants. The Hubbard-Stratonovich transformation is employed to decouple the Coulomb interaction between electrons. A trial wave function is used in the approximation to control the "phase problem". We also carry out Hartree-Fock (HF) and Density Functional Theory (DFT) calculations for comparison to AFQMC results and to serve as starting wavefunctions for our AFQMC calculations. Results of dissociation energy are in excellent agreement with experimental values. Ionization energy errors are somewhat larger than those of other methods. We conclude with a discussion of several possible sources of error as well as a direction for the improvement.

Suewattana, Malliga

292

Organic molecules in the atmosphere of Jupiter. [low molecular weight hydrocarbons  

NASA Technical Reports Server (NTRS)

Organic synthesis in the primitive solar system was simulated by Fischer Tropsch type experiments. Particular attention was given to the formation of lower molecular weight hydrocarbons. In a gas flow experiment, a gas mixture of H2 and CO was introduced into a heated reaction tube at a constant flow rate and passed through a catalyst (powdered Canyon Diablo). The products that emerged were directly analyzed by gas chromatography. The results of 21 runs under various gas mixing rations, reaction temperatures, and gas-catalyst contact times showed the predominance of the saturated hydrocarbon formation at C sub 4 and C sub 5 over the unsaturated ones. Saturate/unsaturate ratios were mostly less than 0.4 and none showed over 0.7.

Ponnamperuma, C. A.

1978-01-01

293

Effects of molecular asymmetry of optically active molecules on the polarization properties of multiply scattered light  

NASA Astrophysics Data System (ADS)

The use of polarized light for investigation of optically turbid systems has generated much recent interest since it has been shown that multiple scattering does not fully scramble the incident polarization states. It is possible under some conditions to measure polarization signals in diffusely scattered light, and use this information to characterize the structure or composition of the turbid medium. Furthermore, the idea of quantitative detection of optically active (chiral) molecules contained in such a system is attractive, particularly in clinical medicine where it may contribute to the development of a non-invasive method of glucose sensing in diabetic patients. This study uses polarization modulation and synchronous detection in the perpendicular and in the exact backscattering orientations to detect scattered light from liquid turbid samples containing varying amounts of L and D (left and right) isomeric forms of a chiral sugar. Polarization preservation increased with chiral concentrations in both orientations. In the perpendicular orientation, the optical rotation of the linearly polarized fraction also increased with the concentration of chiral solute, but in different directions for the two isomeric forms. There was no observed optical rotation in the exact backscattering geometry for either isomer. The presence of the chiral species is thus manifest in both detection directions, but the sense of the chiral asymmetry is not resolvable in retroreflection. The experiments show that useful information may be extracted from turbid chiral samples using polarized light.

Vitkin, I. Alex; Laszlo, Richard D.; Whyman, Claire L.

2002-02-01

294

Molecular dynamics of DNA quadruplex molecules containing inosine, 6-thioguanine and 6-thiopurine.  

PubMed Central

The ability of the four-stranded guanine (G)-DNA motif to incorporate nonstandard guanine analogue bases 6-oxopurine (inosine, I), 6-thioguanine (tG), and 6-thiopurine (tI) has been investigated using large-scale molecular dynamics simulations. The simulations suggest that a G-DNA stem can incorporate inosines without any marked effect on its structure and dynamics. The all-inosine quadruplex stem d(IIII)(4) shows identical dynamical properties as d(GGGG)(4) on the nanosecond time scale, with both molecular assemblies being stabilized by monovalent cations residing in the channel of the stem. However, simulations carried out in the absence of these cations show dramatic differences in the behavior of d(GGGG)(4) and d(IIII)(4). Whereas vacant d(GGGG)(4) shows large fluctuations but does not disintegrate, vacant d(IIII)(4) is completely disrupted within the first nanosecond. This is a consequence of the lack of the H-bonds involving the N2 amino group that is not present in inosine. This indicates that formation of the inosine quadruplex could involve entirely different intermediate structures than formation of the guanosine quadruplex, and early association of cations in this process appears to be inevitable. In the simulations, the incorporation of 6-thioguanine and 6-thiopurine sharply destabilizes four-stranded G-DNA structures, in close agreement with experimental data. The main reason is the size of the thiogroup leading to considerable steric conflicts and expelling the cations out of the channel of the quadruplex stem. The G-DNA stem can accommodate a single thioguanine base with minor perturbations. Incorporation of a thioguanine quartet layer is associated with a large destabilization of the G-DNA stem whereas the all-thioguanine quadruplex immediately collapses. PMID:11159416

Stefl, R; Spacková, N; Berger, I; Koca, J; Sponer, J

2001-01-01

295

Phage display identification of functional binding peptides against 4-acetamidophenol (Paracetamol): An exemplified approach to target low molecular weight organic molecules  

Microsoft Academic Search

Peptide-phage display has been widely used to explore protein–protein interactions, however, despite the potential range of applications the use of this technology to identify peptides that bind low molecular weight organic molecules has not been explored. In this current study, we identified a phage clone (PARA-061) displaying the cyclic 7-mer peptide sequence N?AC-NPNNLSH-CGGGSC? that binds the low molecular weight organic

Mathew W. Smith; Jonathan W. Smith; Charlotte Harris; Andrea Brancale; Christopher J. Allender; Mark Gumbleton

2007-01-01

296

Molecular clock regulates daily ?1-2-fucosylation of the neural cell adhesion molecule (NCAM) within mouse secondary olfactory neurons.  

PubMed

The circadian clock regulates various behavioral and physiological rhythms in mammals. Circadian changes in olfactory functions such as neuronal firing in the olfactory bulb (OB) and olfactory sensitivity have recently been identified, although the underlying molecular mechanisms remain unknown. We analyzed the temporal profiles of glycan structures in the mouse OB using a high-density microarray that includes 96 lectins, because glycoconjugates play important roles in the nervous system such as neurite outgrowth and synaptogenesis. Sixteen lectin signals significantly fluctuated in the OB, and the intensity of all three that had high affinity for ?1-2-fucose (?1-2Fuc) glycan in the microarray was higher during the nighttime. Histochemical analysis revealed that ?1-2Fuc glycan is located in a diurnal manner in the lateral olfactory tract that comprises axon bundles of secondary olfactory neurons. The amount of ?1-2Fuc glycan associated with the major target glycoprotein neural cell adhesion molecule (NCAM) varied in a diurnal fashion, although the mRNA and protein expression of Ncam1 did not. The mRNA and protein expression of Fut1, a ?1-2-specific fucosyltransferase gene, was diurnal in the OB. Daily fluctuation of the ?1-2Fuc glycan was obviously damped in homozygous Clock mutant mice with disrupted diurnal Fut1 expression, suggesting that the molecular clock governs rhythmic ?1-2-fucosylation in secondary olfactory neurons. These findings suggest the possibility that the molecular clock is involved in the diurnal regulation of olfaction via ?1-2-fucosylation in the olfactory system. PMID:25384980

Kondoh, Daisuke; Tateno, Hiroaki; Hirabayashi, Jun; Yasumoto, Yuki; Nakao, Reiko; Oishi, Katsutaka

2014-12-26

297

Evidence that ultraviolet markings are associated with patterns of molecular gene flow  

PubMed Central

Recent studies have shown UV vision and markings to be important in vertebrates, particularly birds, where behavioral experiments have demonstrated its potential importance in sexual selection. However, there has been no genetic evidence that UV markings determine patterns of evolution among natural populations. Here we report molecular evidence that UV markings are associated with the pattern of gene flow in the Tenerife lizard (Gallotia galloti). This species has vicariance-induced, approximate east–west lineages in Tenerife closely congruent with the primary lineages of the sympatric gecko species. Against expectations, these molecular phylogeographic lineages (representing geological history) and isolation-by-distance do not appear to influence gene flow. Sexually mature males from populations either side of a latitudinal ecotone have different UV markings and gene flow appears to be linked to this difference in UV markings. It may be that these groups with different UV sexual markings mate assortatively, restricting the gene flow between them. This has implications for debate on the relative importance of vicariance and biotopes in influencing biodiversity, with this evidence supporting the latter. PMID:11259681

Thorpe, Roger S.; Richard, Murielle

2001-01-01

298

Electron beam irradiation for structuring of molecular assemblies  

Microsoft Academic Search

Nontraditional applications of electron beam irradiation for patterning of molecular assemblies are considered. The electron beam can have the following effects on molecular layers: destruction of molecular structure under e-beam irradiation with a successive formation of new molecular system when the irradiation is stopped; variation of the properties of the layer after e-beam irradiation; crosslinking of molecules in the layer

Victor Erokhin; Tatiana Berzina; M. P. Fontana

2004-01-01

299

Contrasted Patterns of Molecular Evolution in Dominant and Recessive Self-Incompatibility Haplotypes in Arabidopsis  

PubMed Central

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 eleven distinct haplotypes of the self-incompatibility locus (S-locus) in two closely related Arabidopsis species, obtained from individual BAC libraries. We use this extensive dataset to highlight sharply contrasted patterns of molecular evolution of each of the two genes controlling self-incompatibility themselves, as well as of the genomic region surrounding them. We find strong collinearity of the flanking regions among haplotypes on each side of the S-locus together with high levels of sequence similarity. In contrast, the S-locus region itself shows spectacularly deep gene genealogies, high variability in size and gene organization, as well as complete absence of sequence similarity in intergenic sequences and striking accumulation of transposable elements. Of particular interest, we demonstrate that dominant and recessive S-haplotypes experience sharply contrasted patterns of molecular evolution. Indeed, dominant haplotypes exhibit larger size and a much higher density of transposable elements, being matched only by that in the centromere. Overall, these properties highlight that the S-locus presents many striking similarities with other regions involved in the determination of mating-types, such as sex chromosomes in animals or in plants, or the mating-type locus in fungi and green algae. PMID:22457631

Goubet, Pauline M.; Bergès, Hélène; Bellec, Arnaud; Prat, Elisa; Helmstetter, Nicolas; Mangenot, Sophie; Gallina, Sophie; Holl, Anne-Catherine; Fobis-Loisy, Isabelle; Vekemans, Xavier; Castric, Vincent

2012-01-01

300

A Molecular Dynamics Study on the Confinement of Carbon Dioxide Molecules in Carbon Nanotubes  

NASA Astrophysics Data System (ADS)

The influence of atmospheric carbon dioxide (CO2) concentration on global warming is considered as one of the primary environmental issues of the past two decades. The main source of CO2 emission is human activity, such as the use of fossil fuels in transportation and industrial plants. Following the release of Kyoto Protocol in 1997, effective ways of controlling CO2 emissions received much attention. As a result, various materials such as activated carbon, zeolites, and carbon nanotubes (CNTs) were investigated for their CO2 adsorbing properties. CNTs were reported to have CO2 adsorption capability twice that of activated carbon, hence they received the most attention. In the current study, single walled carbon nanotubes (SWNTs) were used as one dimensional nanoporous materials and their CO2 adsorption capacity was analyzed with Molecular Dynamics simulations. Results indicated that SWNTs are excellent CO2 adsorbers and their effectiveness increase at low CO2 concentrations. In addition, we showed that by varying temperature, CO2 can be removed from the SWNTs, providing a simple method to reuse SWNTs.

Lazor, Meagan; Rende, Deniz; Baysal, Nihat; Ozisik, Rahmi

2012-02-01

301

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

PubMed

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

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

2015-01-01

302

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

PubMed Central

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

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

2015-01-01

303

Single-Molecule Analysis of the Hypermutable Tetranucleotide Repeat Locus D21S1245 Through Sperm Genotyping: A Heterogeneous Pattern of Mutation but no Clear Male Age Effect  

Microsoft Academic Search

Single molecule genotyping of the hypermutable microsatellite locus D21S1245 was used for studying how the rate and pattern of mutation varied between alleles and different age groups. In total, 203 mutation events were scored from the genotyping of DNA corresponding to an estimated 8623 sperm cells from eight different men. Allele-specific mutation rates ranged from 0.007 to 0.052, a heterogeneity

Jesper Brohede; Norman Arnheim; Hans Ellegren

2003-01-01

304

Molecular-level thermodynamic and kinetic parameters for the self-assembly of apoferritin molecules into crystals 1 1 Edited by W. Baumeister  

Microsoft Academic Search

The self-assembly of apoferritin molecules into crystals is a suitable model for protein crystallization and aggregation; these processes underlie several biological and biomedical phenomena, as well as for protein and virus self-assembly. We use the atomic force microscope in situ, during the crystallization of apoferritin to visualize and quantify at the molecular level the processes responsible for crystal growth. To

S.-T. Yau; Dimiter N. Petsev; Bill R. Thomas; Peter G. Vekilov

2000-01-01

305

Novel strategy for biofilm inhibition by using small molecules targeting molecular chaperone DnaK.  

PubMed

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

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

2015-01-01

306

Molecular and structural characterization of dissolved organic matter from the deep ocean by FTICR-MS, including hydrophilic nitrogenous organic molecules  

USGS Publications Warehouse

Dissolved organic matter isolated from the deep Atlantic Ocean and fractionated into a so-called hydrophobic (HPO) fraction and a very hydrophilic (HPI) fraction was analyzed for the first time by Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) to resolve the molecular species, to determine their exact masses, and to calculate their molecular formulas. The elemental composition of about 300 molecules was identified. Those in the HPO fraction (14C age of 5100 year) are very similar to much younger freshwater fulvic acids, but less aromatic and more oxygenated molecules are more frequent. This trend continues toward the HPI fraction and may indicate biotic and abiotic aging processes that this material experienced since its primary production thousands of years ago. In the HPI fraction series of nitrogenous molecules containing one, two, or three nitrogens were identified by FTICR-MS. Product ion spectra of the nitrogenous molecules suggest that the nitrogen atoms in these molecules are included in the (alicyclic) backbone of these molecules, possibly in reduced form. These mass spectrometric data suggest that a large set of stable fulvic acids is ubiquitous in all aquatic compartments. Although sources may differ, their actual composition and structure appears to be quite similar and largely independent from their source, because they are the remainder of intensive oxidative degradation processes. ?? 2008 American Chemical Society.

Reemtsma, T.; These, A.; Linscheid, M.; Leenheer, J.; Spitzy, A.

2008-01-01

307

Tuning of EAG K(+) channel inactivation: molecular determinants of amplification by mutations and a small molecule.  

PubMed

Ether-à-go-go (EAG) and EAG-related gene (ERG) K(+) channels are close homologues but differ markedly in their gating properties. ERG1 channels are characterized by rapid and extensive C-type inactivation, whereas mammalian EAG1 channels were previously considered noninactivating. Here, we show that human EAG1 channels exhibit an intrinsic voltage-dependent slow inactivation that is markedly enhanced in rate and extent by 1-10 µM 3-nitro-N-(4-phenoxyphenyl) benzamide, or ICA105574 (ICA). This compound was previously reported to have the opposite effect on ERG1 channels, causing an increase in current magnitude by inhibition of C-type inactivation. The voltage dependence of 2 µM ICA-induced inhibition of EAG1 current was half-maximal at -73 mV, 62 mV negative to the half-point for channel activation. This finding suggests that current inhibition by the drug is mediated by enhanced inactivation and not open-channel block, where the voltage half-points for current inhibition and channel activation are predicted to overlap, as we demonstrate for clofilium and astemizole. The mutation Y464A in the S6 segment also induced inactivation of EAG1, with a time course and voltage dependence similar to that caused by 2 µM ICA. Several Markov models were investigated to describe gating effects induced by multiple concentrations of the drug and the Y464A mutation. Models with the smallest fit error required both closed- and open-state inactivation. Unlike typical C-type inactivation, the rate of Y464A- and ICA-induced inactivation was not decreased by external tetraethylammonium or elevated [K(+)](e). EAG1 channel inactivation introduced by Y464A was prevented by additional mutation of a nearby residue located in the S5 segment (F359A) or pore helix (L434A), suggesting a tripartite molecular model where interactions between single residues in S5, S6, and the pore helix modulate inactivation of EAG1 channels. PMID:22930803

Garg, Vivek; Sachse, Frank B; Sanguinetti, Michael C

2012-09-01

308

Tuning of EAG K+ channel inactivation: Molecular determinants of amplification by mutations and a small molecule  

PubMed Central

Ether-à-go-go (EAG) and EAG-related gene (ERG) K+ channels are close homologues but differ markedly in their gating properties. ERG1 channels are characterized by rapid and extensive C-type inactivation, whereas mammalian EAG1 channels were previously considered noninactivating. Here, we show that human EAG1 channels exhibit an intrinsic voltage-dependent slow inactivation that is markedly enhanced in rate and extent by 1–10 µM 3-nitro-N-(4-phenoxyphenyl) benzamide, or ICA105574 (ICA). This compound was previously reported to have the opposite effect on ERG1 channels, causing an increase in current magnitude by inhibition of C-type inactivation. The voltage dependence of 2 µM ICA-induced inhibition of EAG1 current was half-maximal at ?73 mV, 62 mV negative to the half-point for channel activation. This finding suggests that current inhibition by the drug is mediated by enhanced inactivation and not open-channel block, where the voltage half-points for current inhibition and channel activation are predicted to overlap, as we demonstrate for clofilium and astemizole. The mutation Y464A in the S6 segment also induced inactivation of EAG1, with a time course and voltage dependence similar to that caused by 2 µM ICA. Several Markov models were investigated to describe gating effects induced by multiple concentrations of the drug and the Y464A mutation. Models with the smallest fit error required both closed- and open-state inactivation. Unlike typical C-type inactivation, the rate of Y464A- and ICA-induced inactivation was not decreased by external tetraethylammonium or elevated [K+]e. EAG1 channel inactivation introduced by Y464A was prevented by additional mutation of a nearby residue located in the S5 segment (F359A) or pore helix (L434A), suggesting a tripartite molecular model where interactions between single residues in S5, S6, and the pore helix modulate inactivation of EAG1 channels. PMID:22930803

Garg, Vivek; Sachse, Frank B.

2012-01-01

309

Phases, line tension and pattern formation in molecularly thin films at the air-water interface  

NASA Astrophysics Data System (ADS)

A Langmuir film, which is a molecularly thin insoluble film on a liquid substrate, is one practical realization of a quasi-two dimensional matter. The major advantages of this system for the study of phase separation and phase co-existence are (a) it allows accurate control of the components and molecular area of the film and (b) it can be studied by various methods that require very flat films. Phase separation in molecularly thin films plays an important role in a range of systems from biomembranes to biosensors. For example, phase-separated lipid nano-domains in biomembranes are thought to play crucial roles in membrane function. I use Brewster Angel Microscopy (BAM) coupled with Fluorescence Microscopy (FM) and static Light Scattering Microscopy (LSM) to image phases and patterns within Langmuir films. The three microscopic techniques --- BAM, FM and LSM --- are complimentary to each other, providing distinct sets of information. They allow direct comparison with literature results in lipid systems. I have quantitatively validated the use of detailed hydrodynamic simulations to determine line tension in monolayers. Line tension decreases as temperature rises. This decrease gives us information on the entropy associated with the line, and thus about line structure. I carefully consider the thermodynamics of line energy and entropy to make this connection. In the longer run, LSM will be exploited to give us further information about line structure. I have also extended the technique by testing it on domains within the curved surface of a bilayer vesicle. I also note that in the same way that the presence of surface-active agents, known as surfactants, affects surface energy, the addiction of line active agents alters the inter-phase line energy. Thus my results set to stage to systematically study the influence of line active agents ---'linactants' --- on the inter-phase line energy. Hierarchal self-assembled chiral patterns were observed as a function of temperature. I found that the appearance of these domains could be explained with a simple uniaxial optical axis in the underlying structure, which is the first critical step to understanding the origin of these patterns.

Mandal, Pritam

310

Properties and Reactivity Patterns of AsP3: An Experimental and Computational Study of Group 15 Elemental Molecules  

E-print Network

Facile synthetic access to the isolable, thermally robust AsP3 molecule has allowed for a thorough study of its physical properties and reaction chemistry with a variety of transition-metal and organic fragments. The ...

Cossairt, Brandi M.

311

Pathogen-associated molecular pattern-induced mitochondrial membrane depolarization in the earthworm Eisenia hortensis.  

PubMed

Innate immune responses of the earthworm Eisenia hortensis were studied by detecting mitochondrial membrane depolarization and reactive oxygen species (ROS) production after incubation with pathogen-associated molecular patterns (PAMPs). Coelomocytes from E. hortensis were incubated with zymosan, flagellin, or peptidoglycan (PTG) for 48 h in vitro and studied using flow cytometric assays for changes in mitochondrial membrane potential (??(m)) or ROS production using the fluorescent indicators JC-1 or DHR 123, respectively. All three PAMPs evoked ??(m), with zymosan inducing the most significant membrane depolarization in coelomocyte samples compared to untreated controls. When treated with zymosan or flagellin, coelomocyte samples exhibited significant increases in ROS production in the zymosan sample after 16 h of in vitro incubation, but this effect was not observed for flagellin. These results demonstrate that PAMPs evoke evolutionarily conserved cellular responses which may be important during innate immune defenses to eradicate intracellular reserves of foreign pathogens. PMID:21907209

Nacarelli, Timothy; Fuller-Espie, Sheryl L

2011-11-01

312

Structure and energetics of model amphiphilic molecules at the water liquid-vapor interface - A molecular dynamics study  

NASA Technical Reports Server (NTRS)

A molecular dynamics study of adsorption of p-n-pentylphenol at infinite dilution at the water liquid-vapor interface is reported. The calculated free energy of adsorption is -8.8 +/- 0.7 kcal/mol, in good agreement with the experimental value of -7.3 kcal/mol. The transition between the interfacial region and the bulk solution is sharp and well-defined by energetic, conformational, and orientational criteria. At the water surface, the phenol head group is mostly immersed in aqueous solvent. The most frequent orientation of the hydrocarbon tail is parallel to the interface, due to dispersion interactions with the water surface. This arrangement of the phenol ring and the alkyl chain requires that the chain exhibits a kink. As the polar head group is being moved into the solvent, the chain length increases and the tail becomes increasingly aligned toward the surface normal, such that the nonpolar part of the molecule exposed to water is minimized. The same effect was achieved when phenol was replaced by a more polar head group, phenolate.

Pohorille, Andrew; Benjamin, Ilan

1993-01-01

313

Evolutionary animation: How do molecular phylogenies compare to Mayr's reconstruction of speciation patterns in the sea?  

PubMed Central

Ernst Mayr used the geography of closely related species in various stages of increasing divergence to “animate” the process of geographic, or allopatric, speciation. This approach was applied to a wide set of taxa, and a seminal paper by Mayr used it to explore speciation patterns in tropical sea urchins. Since then, taxonomic information in several of these genera has been augmented by detailed molecular phylogenies. We compare Mayr's animation with the phylogenies of eight sea urchin genera placed by Mayr into four speciation groups. True to Mayr's predictions, early-stage genera have on average lower species divergence and more polytypic species than genera in later stages. For six of these genera, we also have information about the evolution of the gamete recognition protein bindin, which is critical to reproductive isolation. These comparisons show that later-stage genera with many sympatric species tend to be those with rapid bindin evolution. By contrast, early-stage genera with few sympatric species are not necessarily earlier in the divergence process; they happen to be those with slow rates of bindin evolution. These results show that the rate of speciation in sea urchins does not only depend on the steady accumulation of genome divergence over time, but also on the rate of evolution of gamete recognition proteins. The animation method used by Mayr is generally supported by molecular phylogenies. However, the existence of multiple rates in the acquisition of reproductive isolation complicates placement of different genera in an evolutionary series. PMID:15851681

Palumbi, Stephen R.; Lessios, H. A.

2005-01-01

314

Binding Specificity of Philyra pisum Lectin to Pathogen-Associated Molecular Patterns, and Its Secondary Structure.  

PubMed

We recently reported a Philyra pisum lectin (PPL) that exerts mitogenic effects on human lymphocytes, and its molecular characterization. The present study provides a more detailed characterization of PPL based on the results from a monosaccharide analysis indicating that PPL is a glycoprotein, and circular dichroism spectra revealing its estimated ?-helix, ?-sheet, ?-turn, and random coil contents to be 14.0%, 39.6%, 15.8%, and 30.6%, respectively. These contents are quite similar to those of deglycosylated PPL, indicating that glycans do not affect its intact structure. The binding properties to different pathogen-associated molecular patterns were investigated with hemagglutination inhibition assays using lipoteichoic acid from Gram-positive bacteria, lipopolysaccharide from Gram-negative bacteria, and both mannan and ?-1,3-glucan from fungi. PPL binds to lipoteichoic acids and mannan, but not to lipopolysaccharides or ?-1,3-glucan. PPL exerted no significant antiproliferative effects against human breast or bladder cancer cells. These results indicate that PPL is a glycoprotein with a lipoteichoic acid or mannan-binding specificity and which contains low and high proportions of ?-helix and ?-structures, respectively. These properties are inherent to the innate immune system of P. pisum and indicate that PPL could be involved in signal transmission into Gram-positive bacteria or fungi. PMID:24381505

Park, Byung Tae; Kim, Byung Sun; Park, Heajin; Jeong, Jaehoon; Hyun, Hanbit; Hwang, Hye Seong; Kim, Ha Hyung

2013-12-01

315

B cell surface glycoprotein induced during growth response: molecular structure and expression pattern.  

PubMed

We present the molecular characterization of a cell surface antigen, B 7.2, that is expressed on activated B lymphocytes. The BCL1 and CH12 B lymphoma cells express the B 7.2 antigen constitutively. In small resting B cells from spleen, the B 7.2 expression is induced during polyclonal growth in response to mitogenic stimulation. B 7.2 expression also occurs with a significant frequency in cells from fresh lymphoid tissues. The endogenous expression of the B 7.2 antigen is high in spleen and lymph nodes, and is undetectable in the thymus. The B 7.2 antigen is a microheterogeneous 45,000 to 50,000 dalton glycoprotein with a single polypeptide chain, intramolecular S--S bonds, and N-linked glycan moieties. The folded structure of the B 7.2 antigen appears to contain a domain with hydrophilic properties exposed on the cell surface and a hydrophobic segment that may comprise a transmembrane portion. Considering the observed expression pattern and the molecular structure, we speculate that the B 7.2 antigen has a specific function in regulation of B cell activation, perhaps as a receptor for a regulatory ligand or as a ligand recognized by other B or T cells. PMID:3494078

Southern, S O; Swain, S L; Dutton, R W

1987-04-15

316

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

NASA Astrophysics Data System (ADS)

We report the results of an investigation of the evolution of the surface morphology during molecular beam epitaxial growth on a patterned GaAs(100) surface. The initial GaAs(100) surfaces were patterned lithographically with arrays of cylindrical pits whose diameters and center-to-center distances are varied in a combinatorial manner. Using atomic force microscopy (AFM), we characterized the evolution of the corrugation throughout the growth. We compare the measured height profiles with simulations from various continuum models[1]. This comparison allows us to discriminate between various continuum modes of growth. * Work supported by the Minta-Martin Foundation, the Laboratory for Physical Sciences, and an NSF-MRSEC, DMR 00-8008. Reference 1 Mehran Kardar, Giorgio Parisi, and Yi-Cheng Zhang, Physical Review Letters 56 (9), 889 (1986); Tao Sun, Hong Guo, and Martin Grant, Physical Review A 40 (11), 6763 (1989); Z.-W. Lai and S. Das Sarma, Physical Review Letters 66 (18), 2348 (1991); M. D. Johnson, C. Orme, A. W. Hunt et al., Physical Review Letters 72 (1), 116 (1994).

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

2003-03-01

317

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

PubMed Central

Despite tremendous body form diversity in nature, bilaterian animals share common sets of developmental genes that display conserved expression patterns in the embryo. Among them are the Hox genes, which define different identities along the anterior–posterior axis. Hox proteins exert their function by interaction with TALE transcription factors. Hox and TALE members are also present in some but not all non-bilaterian phyla, raising the question of how Hox–TALE interactions evolved to provide positional information. By using proteins from unicellular and multicellular lineages, we showed that these networks emerged from an ancestral generic motif present in Hox and other related protein families. Interestingly, Hox-TALE networks experienced additional and extensive molecular innovations that were likely crucial for differentiating Hox functions along body plans. Together our results highlight how homeobox gene families evolved during eukaryote evolution to eventually constitute a major patterning system in Eumetazoans. DOI: http://dx.doi.org/10.7554/eLife.01939.001 PMID:24642410

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

2014-01-01

318

Morphologic and molecular evaluation of Chlamydia trachomatis growth in human endocervix reveals distinct growth patterns  

PubMed Central

In vitro models of Chlamydia trachomatis growth have long been studied to predict growth in vivo. Alternative or persistent growth modes in vitro have been shown to occur under the influence of numerous stressors but have not been studied in vivo. Here, we report the development of methods for sampling human infections from the endocervix in a manner that permits a multifaceted analysis of the bacteria, host and the endocervical environment. Our approach permits evaluating total bacterial load, transcriptional patterns, morphology by immunofluorescence and electron microscopy, and levels of cytokines and nutrients in the infection microenvironment. By applying this approach to two pilot patients with disparate infections, we have determined that their contrasting growth patterns correlate with strikingly distinct transcriptional biomarkers, and are associated with differences in local levels of IFN?. Our multifaceted approach will be useful to dissect infections in the human host and be useful in identifying patients at risk for chronic disease. Importantly, the molecular and morphological analyses described here indicate that persistent growth forms can be isolated from the human endocervix when the infection microenvironment resembles the in vitro model of IFN?-induced persistence. PMID:24959423

Lewis, Maria E.; Belland, Robert J.; AbdelRahman, Yasser M.; Beatty, Wandy L.; Aiyar, Ashok A.; Zea, Arnold H.; Greene, Sheila J.; Marrero, Luis; Buckner, Lyndsey R.; Tate, David J.; McGowin, Chris L.; Kozlowski, Pamela A.; O'Brien, Michelle; Lillis, Rebecca A.; Martin, David H.; Quayle, Alison J.

2014-01-01

319

The Relation between Recombination Rate and Patterns of Molecular Evolution and Variation in Drosophila melanogaster  

PubMed Central

Genetic recombination associated with sexual reproduction increases the efficiency of natural selection by reducing the strength of Hill–Robertson interference. Such interference can be caused either by selective sweeps of positively selected alleles or by background selection (BGS) against deleterious mutations. Its consequences can be studied by comparing patterns of molecular evolution and variation in genomic regions with different rates of crossing over. We carried out a comprehensive study of the benefits of recombination in Drosophila melanogaster, both by contrasting five independent genomic regions that lack crossing over with the rest of the genome and by comparing regions with different rates of crossing over, using data on DNA sequence polymorphisms from an African population that is geographically close to the putatively ancestral population for the species, and on sequence divergence from a related species. We observed reductions in sequence diversity in noncrossover (NC) regions that are inconsistent with the effects of hard selective sweeps in the absence of recombination. Overall, the observed patterns suggest that the recombination rate experienced by a gene is positively related to an increase in the efficiency of both positive and purifying selection. The results are consistent with a BGS model with interference among selected sites in NC regions, and joint effects of BGS, selective sweeps, and a past population expansion on variability in regions of the genome that experience crossing over. In such crossover regions, the X chromosome exhibits a higher rate of adaptive protein sequence evolution than the autosomes, implying a Faster-X effect. PMID:24489114

Campos, José L.; Halligan, Daniel L.; Haddrill, Penelope R.; Charlesworth, Brian

2014-01-01

320

Pathogen Associated Molecular Pattern (PAMP)-Triggered Immunity Is Compromised under C-Limited Growth  

PubMed Central

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

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

2015-01-01

321

Phylogenetic Analysis and Molecular Evolution Patterns in the MIR482-MIR1448 Polycistron of Populus L  

PubMed Central

The microRNAs (miRNAs) miR482 and miR1448 are disease resistance-related miRNAs; the former is ubiquitously distributed in seed plants whereas the latter has only been reported in Populus trichocarpa. The precursor and mature sequences of poplar miR1448 are highly homologous to those of poplar miR482, and these two miRNAs are located in one transcript as a polycistron. Therefore, we hypothesized that the MIR1448 gene may have evolved from the MIR482 gene in poplar. However, the molecular evolution patterns of this process remain unclear. In this study, utilizing cloning and Blast analysis in NCBI ESTs and whole-genome shotgun contigs (WGS) dataset, we determined that the MIR482-MIR1448 polycistron is a family-specific clustered miRNA in Salicaceae. Moreover, phylogenetic analysis illustrated that MIR1448 is the product of a tandem duplication event from MIR482. Nucleotide substitution analysis revealed that both MIR482 and MIR1448 have more rapid evolution ratios than ribosomal DNA (rDNA) genes, and that compensatory mutations that occurred in the stem region of the secondary structure were the main mechanisms that drove the evolution of these MIRNA genes. Furthermore, by comparing the substitution patterns in the miRNA-target complexes of miR482 and miR1448, we inferred that co-evolution between miRNAs and their targets was the major force that drove the “duplicated MIR482” evolve to MIR1448. We propose a novel miRNA-target pairing pattern called the “frameshift targeted mechanism” to explain the gain of target genes by miR1448. The results also imply that the major role of miR482 was in resistance to disease or other stresses via NBS-LRR proteins, whereas the biological functions of miR1448 are more diverse. PMID:23094096

Zhao, Jia-Ping; Diao, Shu; Zhang, Bing-Yu; Niu, Bao-Qing; Wang, Qing-Ling; Wan, Xian-Chong; Luo, You-Qing

2012-01-01

322

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.

323

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

PubMed Central

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

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

2007-01-01

324

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

PubMed

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

Mahapatro, Ajit K; Janes, David B

2007-06-01

325

Chromatographic pattern in recycled high-impact polystyrene (HIPS) – Occurrence of low molecular weight compounds during the life cycle  

Microsoft Academic Search

The analysis of the chromatographic pattern of virgin, reprocessed, thermo-oxidised, and recycled high-impact polystyrene (HIPS) proves to be a suitable and sensitive tool to assess the degree of degradation of HIPS during its first life and subsequent recycling. Different low molecular weight compounds, such as residues of polymerisation, degradation products, and additives have been identified and relatively quantified in HIPS,

Francisco Vilaplana; Amparo Ribes-Greus; Sigbritt Karlsson

2010-01-01

326

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)

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.

Ghobadi, Ahmadreza F.; Elliott, J. Richard

2014-09-01

327

Overview of single-molecule methods including high-force, force-fluorescence, and dual-trap studies for probing molecular and cellular machinery  

NASA Astrophysics Data System (ADS)

High force optical trapping, including double trap geometry and simultaneous visualization with single molecule fluorescence imaging enables a wide range of measurement capabilities applicable for probing molecular and cellular machinery. A series of single molecule measurement methods will be presented. Force-fluorescence microscopy enables visualizing amyloid fibers while physically probing their structures including direct unfolding and rupture of fibers with a high force optical trap. Force spectroscopy is employed to probe the strength of single peptide aptamer bonds. A dual-trap geometry allows for direct tracking of unfolding and translocation machinery of the biological motor ClpXP. Force fluorescence microscopy directly visualizes T-cell activation. Automation and flexibility in our instruments coupled with advances in physical assay design strategies are leveraged to access a broad set of molecular and cellular measurement targets.

Lang, Matthew

2011-03-01

328

Methanol and ethanol modulate responses to danger- and microbe-associated molecular patterns  

PubMed Central

Methanol is a byproduct of cell wall modification, released through the action of pectin methylesterases (PMEs), which demethylesterify cell wall pectins. Plant PMEs play not only a role in developmental processes but also in responses to herbivory and infection by fungal or bacterial pathogens. Molecular mechanisms that explain how methanol affects plant defenses are poorly understood. Here we show that exogenously supplied methanol alone has weak effects on defense signaling in three dicot species, however, it profoundly alters signaling responses to danger- and microbe-associated molecular patterns (DAMPs, MAMPs) such as the alarm hormone systemin, the bacterial flagellum-derived flg22 peptide, and the fungal cell wall-derived oligosaccharide chitosan. In the presence of methanol the kinetics and amplitudes of DAMP/MAMP-induced MAP kinase (MAPK) activity and oxidative burst are altered in tobacco and tomato suspension-cultured cells, in Arabidopsis seedlings and tomato leaf tissue. As a possible consequence of altered DAMP/MAMP signaling, methanol suppressed the expression of the defense genes PR-1 and PI-1 in tomato. In cell cultures of the grass tall fescue (Festuca arundinacea, Poaceae, Monocots), methanol alone activates MAPKs and increases chitosan-induced MAPK activity, and in the darnel grass Lolium temulentum (Poaceae), it alters wound-induced MAPK signaling. We propose that methanol can be recognized by plants as a sign of the damaged self. In dicots, methanol functions as a DAMP-like alarm signal with little elicitor activity on its own, whereas it appears to function as an elicitor-active DAMP in monocot grasses. Ethanol had been implicated in plant stress responses, although the source of ethanol in plants is not well established. We found that it has a similar effect as methanol on responses to MAMPs and DAMPs. PMID:25360141

Hann, Claire T.; Bequette, Carlton J.; Dombrowski, James E.; Stratmann, Johannes W.

2014-01-01

329

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

PubMed Central

Plants are constantly exposed to a large and diverse array of microbes; however, most plants are immune to the majority of potential invaders and susceptible to only a small subset of pathogens. The cytoskeleton comprises a dynamic intracellular framework that responds rapidly to biotic stresses and supports numerous fundamental cellular processes including vesicle trafficking, endocytosis and the spatial distribution of organelles and protein complexes. For years, the actin cytoskeleton has been assumed to play a role in plant innate immunity against fungi and oomycetes, based largely on static images and pharmacological studies. To date, however, there is little evidence that the host-cell actin cytoskeleton participates in responses to phytopathogenic bacteria. Here, we quantified the spatiotemporal changes in host-cell cytoskeletal architecture during the immune response to pathogenic and non-pathogenic strains of Pseudomonas syringae pv. tomato DC3000. Two distinct changes to host cytoskeletal arrays were observed that correspond to distinct phases of plant-bacterial interactions i.e. the perception of microbe-associated molecular patterns (MAMPs) during pattern-triggered immunity (PTI) and perturbations by effector proteins during effector-triggered susceptibility (ETS). We demonstrate that an immediate increase in actin filament abundance is a conserved and novel component of PTI. Notably, treatment of leaves with a MAMP peptide mimic was sufficient to elicit a rapid change in actin organization in epidermal cells, and this actin response required the host-cell MAMP receptor kinase complex, including FLS2, BAK1 and BIK1. Finally, we found that actin polymerization is necessary for the increase in actin filament density and that blocking this increase with the actin-disrupting drug latrunculin B leads to enhanced susceptibility of host plants to pathogenic and non-pathogenic bacteria. PMID:23593000

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

2013-01-01

330

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)

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.

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

331

Molecular dynamics simulation of the growth of thin films by deposition of carbon atoms and C60 molecules on diamond and silicon substrates  

NASA Astrophysics Data System (ADS)

The impact of C atoms and C60 molecules with ideal diamond and silicon (100) substrates and the subsequent growth of carbon films have been investigated by molecular dynamics simulations. The interatomic many-body potential proposed by Tersoff has been used. The structural and vibrational properties of the as-grown and annealed films are studied as a function of the deposition energy (in the range 1-150eV for C atoms and 1-1000eV for C60 molecules) and are compared with experimental results. Analysis of films grown from C60 molecules reveals a behavior with deposition energy similar to that experimentally observed. For low deposition energies (below 100eV ) fullerene cages preserve their identity, constructing low-density structures with large intermolecular holes and practically no interface with the substrate. For higher deposition energies the molecules are broken into pieces, giving as a result high-density amorphous carbon films. Although the penetration depth of molecular fragments into the substrate increases with deposition energy, the resulting interface is considerably thinner than in the case of using individual atoms as projectiles. This is in agreement with experimental evidence of a poor adherence of films obtained by accelerating C60+ ions on silicon substrates.

Halac, E. B.; Reinoso, M.; Dall'Asén, A. G.; Burgos, E.

2005-03-01

332

Simulation of single DNA molecule stretching and immobilization in a de-wetting two-phase flow over micropillar-patterned surface.  

PubMed

We investigate single DNA stretching dynamics in a de-wetting flow over micropillars using Brownian dynamics simulation. The Brownian dynamics simulation is coupled with transient flow field computation through a numerical particle tracking algorithm. The droplet formation on the top of the micropillar during the de-wetting process creates a flow pattern that allows DNA to stretch across the micropillars. It is found that DNA nanowire forms if DNA molecules could extend across the stagnation point inside the connecting water filament before its breakup. It also shows that DNA locates closer to the top wall of the micropillar has higher chance to enter the flow pattern of droplet formation and thus has higher chance to be stretched across the micropillars. Our simulation tool has the potential to become a design tool for DNA manipulation in complex biomicrofluidic devices. PMID:24404023

Liao, Wei-Ching; Hu, Xin; Wang, Weixiong; James Lee, L

2013-01-01

333

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

E-print Network

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

Nerukh, Dmitry

334

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

PubMed Central

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

2013-01-01

335

Molecules between the Stars.  

ERIC Educational Resources Information Center

Provides a listing of molecules discovered to date in the vast interstellar clouds of dust and gas. Emphasizes the recent discoveries of organic molecules. Discusses molecular spectral lines, MASERs (microwave amplification by stimulated emission of radiation), molecular clouds, and star birth. (TW)

Verschuur, Gerrit L.

1987-01-01

336

Moving Molecules!  

NSDL National Science Digital Library

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.

2014-06-24

337

Spatial pattern of nucleotide polymorphism indicates molecular adaptation in the bryophyte Sphagnum fimbriatum.  

PubMed

In organisms with haploid-dominant life cycles, natural selection is expected to be especially effective because genetic variation is exposed directly to selection. However, in spore-producing plants with high dispersal abilities, among-population migration may counteract local adaptation by continuously redistributing genetic variability. In this study, we tested for adaptation at the molecular level by comparing nucleotide polymorphism in two genes (GapC and Rpb2) in 10 European populations of the peatmoss species, Sphagnum fimbriatum with variability at nine microsatellite loci assumed to be selectively neutral. In line with previous results, the GapC and Rpb2 genes showed strikingly different patterns of nucleotide polymorphism. Neutrality tests and comparison of population differentiation based on the GapC and Rpb2 genes with neutrally evolving microsatellites using coalescent simulations supported non-neutral evolution in GapC, but neutral evolution in the Rpb2 gene. These observations and the positions of the replacement mutations in the GAPDH enzyme (coded by GapC) indicate a significant impact of replacement mutations on enzyme function. Furthermore, the geographic distribution of alternate GapC alleles and/or linked genomic regions suggests that they have had differential success in the recolonization of Europe following the Last Glacial Maximum. PMID:19539771

Szövényi, P; Hock, Zs; Korpelainen, H; Shaw, A Jonathan

2009-10-01

338

Innate Immune Responses Activated in Arabidopsis Roots by Microbe-Associated Molecular Patterns[W][OA  

PubMed Central

Despite the fact that roots are the organs most subject to microbial interactions, very little is known about the response of roots to microbe-associated molecular patterns (MAMPs). By monitoring transcriptional activation of ?-glucuronidase reporters and MAMP-elicited callose deposition, we show that three MAMPs, the flagellar peptide Flg22, peptidoglycan, and chitin, trigger a strong tissue-specific response in Arabidopsis thaliana roots, either at the elongation zone for Flg22 and peptidoglycan or in the mature parts of the roots for chitin. Ethylene signaling, the 4-methoxy-indole-3-ylmethylglucosinolate biosynthetic pathway, and the PEN2 myrosinase, but not salicylic acid or jasmonic acid signaling, play major roles in this MAMP response. We also show that Flg22 induces the cytochrome P450 CYP71A12-dependent exudation of the phytoalexin camalexin by Arabidopsis roots. The phytotoxin coronatine, an Ile-jasmonic acid mimic produced by Pseudomonas syringae pathovars, suppresses MAMP-activated responses in the roots. This suppression requires the E3 ubiquitin ligase COI1 as well as the transcription factor JIN1/MYC2 but does not rely on salicylic acid–jasmonic acid antagonism. These experiments demonstrate the presence of highly orchestrated and tissue-specific MAMP responses in roots and potential pathogen-encoded mechanisms to block these MAMP-elicited signaling pathways. PMID:20348432

Millet, Yves A.; Danna, Cristian H.; Clay, Nicole K.; Songnuan, Wisuwat; Simon, Matthew D.; Werck-Reichhart, Danièle; Ausubel, Frederick M.

2010-01-01

339

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

PubMed Central

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

Nadler, S. A.

1996-01-01

340

Reprogramming cells and tissue patterning via bioelectrical pathways: molecular mechanisms and biomedical opportunities  

PubMed Central

Transformative impact in regenerative medicine requires more than the reprogramming of individual cells: advances in repair strategies for birth defects or injuries, tumor normalization, and the construction of bioengineered organs and tissues all require the ability to control large-scale anatomical shape. Much recent work has focused on the transcriptional and biochemical regulation of cell behaviour and morphogenesis. However, exciting new data reveal that bioelectrical properties of cells and their microenvironment exert a profound influence on cell differentiation, proliferation, and migration. Ion channels and pumps expressed in all cells, not just excitable nerve and muscle, establish resting potentials that vary across tissues and change with significant developmental events. Most importantly, the spatio-temporal gradients of these endogenous transmembrane voltage potentials (Vmem) serve as instructive patterning cues for large-scale anatomy, providing organ identity, positional information, and prepattern template cues for morphogenesis. New genetic and pharmacological techniques for molecular modulation of bioelectric gradients in vivo have revealed the ability to initiate complex organogenesis, change tissue identity, and trigger regeneration of whole vertebrate appendages. A large segment of the spatial information processing that orchestrates individual cells’ programs towards the anatomical needs of the host organism is electrical; this blurs the line between memory and decision-making in neural networks and morphogenesis in non-neural tissues. Advances in cracking this bioelectric code will enable the rational reprogramming of shape in whole tissues and organs, revolutionizing regenerative medicine, developmental biology, and synthetic bioengineering. PMID:23897652

Levin, Michael

2013-01-01

341

Changes in holothurian coelomocyte populations following immune stimulation with different molecular patterns  

PubMed Central

Echinoderms possess a variety of cells populating the coelomic fluid; these cells are responsible for mounting defense against foreign agents. In the sea cucumber Holothuria glaberrima, four different coelomocyte types were readily distinguished using morphological, histochemical and physiological (phagocytic activity) parameters: lymphocytes, phagocytes, spherulocytes and “giant” cells (listed in order of abundance). Monoclonal antibodies generated against sea cucumber tissues and one polyclonal against sea urchin mayor yolk protein (MYP) were also used to characterize these cell populations. The effects of several pathogen-associated molecular patterns (PAMPs): Lipopolysaccharides from E. coli (LPS), heat-killed Staphylococcus aureus (SA) and a synthetic dsRNA were studied on coelomocyte cell populations. PAMPs increased the phagocytic activity of the holothurian coelomocytes, and were able to induce selective immune responses in several of these populations, demonstrating the ability of the sea cucumber to respond to a different variety of immune challenges. Overall, these results show the variety of cells that populate the coelomic fluid of the holothurian and demonstrate their involvement in immune reactions. These animals represent an untapped resource for new findings into the evolution and development of the immune response not only in invertebrates but also in phylogenetically shared reactions with vertebrates. PMID:20412860

Ramírez-Gómez, Francisco; Aponte-Rivera, Francisco; Méndez-Castaner, Lumen; García-Arrarás, Jose E.

2010-01-01

342

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

PubMed Central

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

2012-01-01

343

Bacterial regulatory networks—from self-organizing molecules to cell shape and patterns in bacterial communities  

PubMed Central

The ESF–EMBO Conference on ‘Bacterial Networks' (BacNet13) was held in March 2013, in Pultusk, Poland. It brought together 164 molecular microbiologists, bacterial systems biologists and synthetic biologists to discuss the architecture, function and dynamics of regulatory networks in bacteria. PMID:23846311

Hengge, Regine; Sourjik, Victor

2013-01-01

344

Understanding the congener-specific toxicity in polychlorinated dibenzo-p-dioxins: chlorination pattern and molecular quadrupole moment.  

PubMed

It is well known that the biological activities and toxicities of planar polychlorinated aromatic compounds are extremely sensitive to chlorination pattern. Although their toxic responses have been correlated with the relative affinity for the receptor, the origin of this congener specificity is not well understood. We present a general interpretation of the congener-specific activity in polychlorinated dibenzo-p-dioxins, which concludes that molecular electrostatics is the principal factor determining the structure-activity relationship in this highly controversial environmental pollutant even though this electrostatic interaction represents only a part of the total interaction energy. Through calculations of the molecular charge distribution in the complete set of 76 dioxin congeners, we show that all active congeners share a unique charge distribution pattern, which is quantitatively described in terms of the molecular quadrupole moment (QM). The QM of dioxins changes sensitively and systematically with chlorination pattern. The three-dimensional electrostatic interactions at the receptor-binding site, which are optimized at a specific QM pattern represented by that of 2,3,7,8-tetrachlorodibenzo-p-dioxin, could explain the congener specificity in the binding affinity and toxicity. Although the polarizability also changes systematically with chlorination, it can only account for the effect of the degree of chlorination, not the congener specificity. PMID:11772071

Mhin, Byung Jin; Lee, Jung Eun; Choi, Wonyong

2002-01-01

345

Mesoscale Patterns Formed by Evaporation of a Polymer Solution in the Proximity of a Sphere on a Smooth Substrate: Molecular Weight  

E-print Network

on a Smooth Substrate: Molecular Weight and Curvature Effects Suck Won Hong, Jianfeng Xia, Myunghwan Byun, intriguing surface patterns of polymer formed, which were strongly dependent on the molecular weight (MW containing nonvola- tile solutes.11 In this paper, we extend our previous work to investigate the molecular

Lin, Zhiqun

346

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

SciTech Connect

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.

Starodub, Dmitri

2011-08-12

347

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

PubMed

Ten PGPR from different backgrounds were assayed on Papaver somniferum var. Madrigal to evaluate their potential as biotic elicitors to increase alkaloid content under the rationale that some microbe associated molecular patterns (MAMPs) are able to trigger plant metabolism. First, the 10 strains and their culture media at two different concentrations were tested for their ability to trigger seed germination. Then, the best three strains were tested for their ability to increase seedling growth and alkaloid levels under greenhouse conditions. Only three strains and their culture media enhanced germination. Then, germination enhancing capacity of these best three strains, N5.18 Stenotrophomonas maltophilia, Aur9 Chryseobacterium balustinum and N21.4 Pseudomonas fluorescens was evaluated in soil. Finally, the three strains were applied on seedlings at two time points, by soil drench or by foliar spray. Photosynthesis was measured, plant height was recorded, capsules were weighted and alkaloids analyzed by HPLC. Only N5.18 delivered by foliar spray significantly increased plant height coupled to an increase in total alkaloids and a significant increase in opium poppy straw dry weight; these increases were supported by a better photosynthetic efficiency. The relative contents of morphine, thebaine, codeine and oripavine were affected by this treatment causing a significant increase in morphine coupled to a decrease in thebaine, demonstrating the effectivity of MAMPs from N5.18 in this plant species. Considering the increase in capsule biomass and alkaloids together with the acceleration of germination, strain N5.18 appears as a good candidate to elicit plant metabolism and consequently, to increase productivity of Papaver somniferum. PMID:24296249

Bonilla, A; Sarria, A L F; Algar, E; Muñoz Ledesma, F J; Ramos Solano, B; Fernandes, J B; Gutierrez Mañero, F J

2014-01-01

348

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

PubMed Central

Macrophage C-type lectin (MCL) and macrophage inducible C-type lectin (Mincle) comprise part of an extensive repertoire of pattern recognition receptors with the ability to sense damage-associated and pathogen-associated molecular patterns. In this review, we cover the discovery and molecular characterization of these C-type lectin receptors, and highlight recent advances in the understanding of their roles in orchestrating the response of the immune system to bacterial and fungal infection, and damaged self. We also discuss the identification and structure–activity relationships of activating ligands, particularly trehalose dimycolate and related mycobacterial glycolipids, which have significant potential in the development of TH1/TH17 vaccination strategies. PMID:25002863

Richardson, Mark B.; Williams, Spencer J.

2014-01-01

349

Theoretical study of donor–spacer–acceptor structure molecule for use as stable molecular rectifier: geometric and electronic structures  

Microsoft Academic Search

Recently, molecular electronics has attracted much attention as a ‘post-silicon technology’ for future nanoscale electronic devices. One of the most important elements in molecular electronic devices is the realization of a unimolecular rectifier. In the present study, the geometric and electronic structure of the TTF-derivative (donor)–sigma-bond–TCNQ-derivative (acceptor), a leading candidate for a molecular rectifying device has been investigated theoretically using

H. Mizuseki; N. Igarashi; C. Majumder; R. V. Belosludov; A. A. Farajian; Y. Kawazoe

2003-01-01

350

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

PubMed

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. PMID:25194387

Ghobadi, Ahmadreza F; Elliott, J Richard

2014-09-01

351

Detailed intermolecular structure of molecular liquids containing slightly distorted tetrahedral molecules with C3v symmetry: Chloroform, bromoform, and methyl-iodide  

NASA Astrophysics Data System (ADS)

Analyses of the intermolecular structure of molecular liquids containing slightly distorted tetrahedral molecules of the CXY3-type are described. The process is composed of the determination of several different distance-dependent orientational correlation functions, including ones that are introduced here. As a result, a complete structure classification could be provided for CXY3 molecular liquids, namely for liquid chloroform, bromoform, and methyl-iodide. In the present work, the calculations have been conducted on particle configurations resulting from reverse Monte Carlo computer modeling: these particle arrangements have the advantage that they are fully consistent with structure factors from neutron and x-ray diffraction measurements. It has been established that as the separation between neighboring molecules increases, the dominant mutual orientations change from face-to-face to edge-to-edge, via the edge-to-face arrangements. Depending on the actual liquid, these geometrical elements (edges and faces of the distorted tetrahedra) were found to contain different atoms. From the set of liquids studied here, the structure of methyl-iodide was found to be easiest to describe on the basis of pure steric effects (molecular shape, size, and density) and the structure of liquid chloroform seems to be the furthest away from the corresponding "flexible fused hard spheres" like reference system.

Pothoczki, Szilvia; Temleitner, László; Pusztai, László

2011-01-01

352

Detailed intermolecular structure of molecular liquids containing slightly distorted tetrahedral molecules with C(3v) symmetry: chloroform, bromoform, and methyl-iodide.  

PubMed

Analyses of the intermolecular structure of molecular liquids containing slightly distorted tetrahedral molecules of the CXY(3)-type are described. The process is composed of the determination of several different distance-dependent orientational correlation functions, including ones that are introduced here. As a result, a complete structure classification could be provided for CXY(3) molecular liquids, namely for liquid chloroform, bromoform, and methyl-iodide. In the present work, the calculations have been conducted on particle configurations resulting from reverse Monte Carlo computer modeling: these particle arrangements have the advantage that they are fully consistent with structure factors from neutron and x-ray diffraction measurements. It has been established that as the separation between neighboring molecules increases, the dominant mutual orientations change from face-to-face to edge-to-edge, via the edge-to-face arrangements. Depending on the actual liquid, these geometrical elements (edges and faces of the distorted tetrahedra) were found to contain different atoms. From the set of liquids studied here, the structure of methyl-iodide was found to be easiest to describe on the basis of pure steric effects (molecular shape, size, and density) and the structure of liquid chloroform seems to be the furthest away from the corresponding "flexible fused hard spheres" like reference system. PMID:21280762

Pothoczki, Szilvia; Temleitner, László; Pusztai, László

2011-01-28

353

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

PubMed

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

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

2015-01-22

354

Molecular subtypes in head and neck cancer exhibit distinct patterns of chromosomal gain and loss of canonical cancer genes.  

PubMed

Head and neck squamous cell carcinoma (HNSCC) is a frequently fatal heterogeneous disease. Beyond the role of human papilloma virus (HPV), no validated molecular characterization of the disease has been established. Using an integrated genomic analysis and validation methodology we confirm four molecular classes of HNSCC (basal, mesenchymal, atypical, and classical) consistent with signatures established for squamous carcinoma of the lung, including deregulation of the KEAP1/NFE2L2 oxidative stress pathway, differential utilization of the lineage markers SOX2 and TP63, and preference for the oncogenes PIK3CA and EGFR. For potential clinical use the signatures are complimentary to classification by HPV infection status as well as the putative high risk marker CCND1 copy number gain. A molecular etiology for the subtypes is suggested by statistically significant chromosomal gains and losses and differential cell of origin expression patterns. Model systems representative of each of the four subtypes are also presented. PMID:23451093

Walter, Vonn; Yin, Xiaoying; Wilkerson, Matthew D; Cabanski, Christopher R; Zhao, Ni; Du, Ying; Ang, Mei Kim; Hayward, Michele C; Salazar, Ashley H; Hoadley, Katherine A; Fritchie, Karen; Sailey, Charles J; Sailey, Charles G; Weissler, Mark C; Shockley, William W; Zanation, Adam M; Hackman, Trevor; Thorne, Leigh B; Funkhouser, William D; Muldrew, Kenneth L; Olshan, Andrew F; Randell, Scott H; Wright, Fred A; Shores, Carol G; Hayes, D Neil

2013-01-01

355

Thin-film growth and patterning techniques for small molecular organic compounds used in optoelectronic device applications.  

PubMed

Rapid advances in research and development in organic electronics have resulted in many exciting discoveries and applications, including organic light-emitting devices for information display and illumination, solar cells, photodetectors, chemosensors, and logic. Organic optoelectronic materials are broadly classified as polymeric or small molecular. For the latter category, solvent-free deposition techniques are generally preferred to form well-defined interfaces and improve device performance. This article reviews several deposition and patterning methods for small molecular thin films and devices, including organic molecular beam deposition, vacuum thermal evaporation, organic vapor phase deposition, and organic vapor jet printing, and compares them to several other methods that have been proposed recently. We hope this review provides a compact but informative summary of the state of the art in organic device processing and addresses the various techniques' governing physical principles. PMID:23540286

Biswas, Shaurjo; Shalev, Olga; Shtein, Max

2013-01-01

356

Effects of energy offsets and molecular packing on exciton and charge carrier dynamics in small-molecule donor-acceptor composites  

NASA Astrophysics Data System (ADS)

We present a study of optical, photoluminescent (PL), and photoconductive properties of small-molecule D/A bulk heterojunctions of functionalized fluorinated anthradithiophene (ADT-R-F) and pentacene (Pn-R-F8) derivatives. We chose one of the ADT derivatives, ADT-TES-F, which exhibits a 2D "brick-work" .?-stacking, as the donor, and ADT-TIPS-F (2D "brick-work"), ADT-TSBS-F (1D "sandwich-herringbone"), Pn-TIPS-F8 (2D "brick-work"), or Pn-TCHS-F8 (1D "sandwich-herringbone"), as acceptors. We measured PL and photoconductivity at time scales from sub-nanoseconds to many seconds after photoexcitation, at various acceptor concentrations, under various experimental conditions. The choice of acceptors enabled us to distinguish between effects of the LUMO energy offsets between the donor and acceptor molecules and those of the molecular packing in the acceptor domains on exciton and charge carrier dynamics.

Paudel, Keshab; Johnson, Brian; Neunzert, Afina; Thieme, Mattson; Anthony, John; Ostroverkhova, Oksana

2013-09-01

357

Distinct Patterns of NCAM Expression Are Associated with Defined Stages of Murine Hair Follicle Morphogenesis and Regression  

Microsoft Academic Search

SUMMARY Hair follicle development, growth (anagen), and regression (catagen) largely result from bidirectional epithelial-mesenchymal interactions whose molecular basis is still unclear. Because adhesion molecules are critically involved in pattern formation and be- cause the fundamental importance of neural cell adhesion molecule (NCAM) for feather development has been demonstrated, we studied the protein expression patterns of NCAM during hair follicle development

Sven Müller-Röver; Eva J. M. Peters; Vladimir A. Botchkarev; Andrei Panteleyev; Ralf Paus

1998-01-01

358

Disparity index: a simple statistic to measure and test the homogeneity of substitution patterns between molecular sequences.  

PubMed Central

A common assumption in comparative sequence analysis is that the sequences have evolved with the same pattern of nucleotide substitution (homogeneity of the evolutionary process). Violation of this assumption is known to adversely impact the accuracy of phylogenetic inference and tests of evolutionary hypotheses. Here we propose a disparity index, ID, which measures the observed difference in evolutionary patterns for a pair of sequences. On the basis of this index, we have developed a Monte Carlo procedure to test the homogeneity of the observed patterns. This test does not require a priori knowledge of the pattern of substitutions, extent of rate heterogeneity among sites, or the evolutionary relationship among sequences. Computer simulations show that the ID-test is more powerful than the commonly used chi2-test under a variety of biologically realistic models of sequence evolution. An application of this test in an analysis of 3789 pairs of orthologous human and mouse protein-coding genes reveals that the observed evolutionary patterns in neutral sites are not homogeneous in 41% of the genes, apparently due to shifts in G + C content. Thus, the proposed test can be used as a diagnostic tool to identify genes and lineages that have evolved with substantially different evolutionary processes as reflected in the observed patterns of change. Identification of such genes and lineages is an important early step in comparative genomics and molecular phylogenetic studies to discover evolutionary processes that have shaped organismal genomes. PMID:11454778

Kumar, S; Gadagkar, S R

2001-01-01

359

Molecular Dynamics Simulations on Parallel Computers: a Study of Polar Versus Nonpolar Media Effects in Small Molecule Solvation  

Microsoft Academic Search

Solvent effects were studied and described via molecular dynamics (MD) and free energy perturbation (FEP) simulations using the molecular mechanics program AMBER. The following specific topics were explored:. Polar solvents cause a blue shift of the rm nto pi^* transition band of simple alkyl carbonyl compounds. The ground- versus excited-state solvation effects responsible for the observed solvatochromism are described in

Stephen Edward Debolt

1993-01-01

360

Single molecule logical devices.  

PubMed

After almost 40 years of development, molecular electronics has given birth to many exciting ideas that range from molecular wires to molecular qubit-based quantum computers. This chapter reviews our efforts to answer a simple question: how smart can a single molecule be? In our case a molecule able to perform a simple Boolean function is a child prodigy. Following the Aviram and Ratner approach, these molecules are inserted between several conducting electrodes. The electronic conduction of the resulting molecular junction is extremely sensitive to the chemical nature of the molecule. Therefore designing this latter correctly allows the implementation of a given function inside the molecular junction. Throughout the chapter different approaches are reviewed, from hybrid devices to quantum molecular logic gates. We particularly stress that one can implement an entire logic circuit in a single molecule, using either classical-like intramolecular connections, or a deformation of the molecular orbitals induced by a conformational change of the molecule. These approaches are radically different from the hybrid-device approach, where several molecules are connected together to build the circuit. PMID:21826604

Renaud, Nicolas; Hliwa, Mohamed; Joachim, Christian

2012-01-01

361

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

SciTech Connect

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.

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

362

Small molecule chemokine mimetics suggest a molecular basis for the observation that CXCL10 and CXCL11 are allosteric ligands of CXCR3  

PubMed Central

BACKGROUND AND PURPOSE The chemokine receptor CXCR3 directs migration of T-cells in response to the ligands CXCL9/Mig, CXCL10/IP-10 and CXCL11/I-TAC. Both ligands and receptors are implicated in the pathogenesis of inflammatory disorders, including atherosclerosis and rheumatoid arthritis. Here, we describe the molecular mechanism by which two synthetic small molecule agonists activate CXCR3. EXPERIMENTAL APPROACH As both small molecules are basic, we hypothesized that they formed electrostatic interactions with acidic residues within CXCR3. Nine point mutants of CXCR3 were generated in which an acidic residue was mutated to its amide counterpart. Following transient expression, the ability of the constructs to bind and signal in response to natural and synthetic ligands was examined. KEY RESULTS The CXCR3 mutants D112N, D195N and E196Q were efficiently expressed and responsive in chemotaxis assays to CXCL11 but not to CXCL10 or to either of the synthetic agonists, confirmed with radioligand binding assays. Molecular modelling of both CXCL10 and CXCR3 suggests that the small molecule agonists mimic a region of the ‘30s loop’ (residues 30–40 of CXCL10) which interacts with the intrahelical CXCR3 residue D112, leading to receptor activation. D195 and E196 are located in the second extracellular loop and form putative intramolecular salt bridges required for a CXCR3 conformation that recognizes CXCL10. In contrast, CXCL11 recognition by CXCR3 is largely independent of these residues. CONCLUSION AND IMPLICATIONS We provide here a molecular basis for the observation that CXCL10 and CXCL11 are allosteric ligands of CXCR3. Such findings may have implications for the design of CXCR3 antagonists. LINKED ARTICLE This article is commented on by O'Boyle, pp. 895–897 of this issue. To view this commentary visit http://dx.doi.org/10.1111/j.1476-5381.2011.01759.x PMID:21895630

Nedjai, Belinda; Li, Hubert; Stroke, Ilana L; Wise, Emma L; Webb, Maria L; Merritt, J Robert; Henderson, Ian; Klon, Anthony E; Cole, Andrew G; Horuk, Richard; Vaidehi, Nagarajan; Pease, James E

2012-01-01

363

Interface behaviors of acetylene and ethylene molecules with 1-butyl-3-methylimidazolium acetate ionic liquid: a combined quantum chemistry calculation and molecular dynamics simulation study.  

PubMed

Although imidazolium-based ionic liquids (ILs) combined with oxygen-containing anions were proposed as the potential solvents for the selective separation of acetylene (C(2)H(2)) and ethylene (C(2)H(4)), the detailed mechanism at the molecular level is still not well understood. The present work focuses on a most effective IL for removing C(2)H(2) from a C(2)H(4) stream, 1-butyl-3-methylimidazolium acetate ([BMIM][OAc]), aiming at understanding the first steps of the adsorption process of the molecules at the IL surface. We present a combined quantum mechanical (QM) calculation and molecular dynamics (MD) simulation study on the structure and property of the IL as well as its interaction with C(2)H(2) and C(2)H(4) molecules. The calculated results indicate that C(2)H(2) presents a stronger interaction with the IL than C(2)H(4) and the anion of the IL is mainly responsible for the stronger interaction. QM calculations show a stronger hydrogen-binding linkage between an acidic proton of C(2)H(2)/C(2)H(4) and the basic oxygen atom in [OAc](-) anion, in contrast to the relative weaker association via the C-H···? interaction between C(2)H(2)/C(2)H(4) and the cation. From MD simulations, it is observed that in the interfacial region, the butyl chain of cations and methyl of anions point into the vapor phase. The coming molecules on the IL surface may be initially wrapped by the extensive butyl chain and then devolved to the interface or caught into the bulk by the anion of IL. The introduction of guest molecules significantly influences the anion distribution and orientation on the interface, but the cations are not disturbed because of their larger volume and relatively weaker interaction with the changes in the guest molecules. The theoretical results provide insight into the molecular mechanism of the observed selective separation of C(2)H(2) form a C(2)H(4) stream by ILs. PMID:23211277

Xu, Hao; Han, Zhe; Zhang, Dongju; Zhan, Jinhua

2012-12-01

364

Method for imaging informational biological molecules on a semiconductor substrate  

NASA Technical Reports Server (NTRS)

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.

Coles, L. Stephen (Inventor)

1994-01-01

365

(4,4')-Bipyridine in vacuo and in solvents: a quantum chemical study of a prototypical floppy molecule from a molecular transport perspective.  

PubMed

We report results of quantum chemical calculations for the neutral and anionic species of (4,4')-bipyridine (44BPY), a prototypical molecule with a floppy degree of freedom, placed in vacuo and in solvents. In addition to equilibrium geometries and vibrational frequencies and spectra, we present adiabatic energy curves for the vibrational modes with significant intramolecular reorganization upon charge transfer. Special attention is paid to the floppy strongly anharmonic degree of freedom of 44BPY, which is related to the most salient structural feature, namely the twist angle ? between the two pyridine rings. The relevance of the present results for molecular transport will be emphasized. We show that the solvent acts as a selective gate electrode and propose a scissor operator to account for solvent effects on molecular transport. Our result on the conductance G vs. cos(2)? is consistent with a significant transmission in perpendicular conformation indicated by previous microscopic analysis. PMID:23258121

Bâldea, Ioan; Köppel, Horst; Wenzel, Wolfgang

2013-02-14

366

Preparation of a molecularly imprinted polymer for the solid-phase extraction of scopolamine with hyoscyamine as a dummy template molecule.  

PubMed

Molecularly imprinted polymers (MIPs) selective for scopolamine were produced using hyoscyamine (a close structural analogue) as template molecule. The produced polymers were used as media for solid-phase extraction, exhibiting selective binding properties for the analyte from biological samples. Human and calf urine and serum were processed on the MIP under various extraction protocols. The best performance was observed after loading the analyte in aqueous environment facilitating retention on the MIP by non-selective hydrophobic interactions. The MIPs were subsequently washed using an optimised solvent system to enable selective desorption of the analyte. Other related and non-related compounds were accessed to evaluate molecular recognition properties. Recoveries of up to 79% were achieved for the analyte of interest from biological samples. PMID:12613802

Theodoridis, Georgios; Kantifes, Andreas; Manesiotis, Panagiotis; Raikos, Nikolaos; Tsoukali-Papadopoulou, Heleni

2003-02-14

367

Molecular dynamics study of the effects of chain properties on the order formation dynamics of self-assembled monolayers of long-chain molecules  

NASA Astrophysics Data System (ADS)

The order formation dynamics of self-assembled monolayers (SAM) of long-chain molecules were studied using coarse-grained molecular dynamics simulations. The primary kinetic processes of surface order formation from solution are adsorption to the surface and surface diffusion. For long-chain molecules, the degrees of freedom of the chain structure and motion add various complexities to the order formation dynamics. Specifically, the strength of the chain interaction, the chain flexibility and the chain length play a significant role, and this work focused on the effects of these chain properties on the order formation dynamics. The adsorption dynamics of SAM molecules can be explained by the same theoretical framework as the polymer brush. On the other hand, the evolution of highly ordered structure is specific to SAM systems. Simulation results revealed that the development of oriented domains can be grouped into three types, isolated island growth, packing growth, and growth suppression, which depend on temperature and chain flexibility. In packing growth, oriented domains are formed gradually due to the decrease in free volume as the surface density becomes high, while the tilt of the adsorbed chain molecules does not become upright gradually as a whole. Rather, inside the oriented domains, the adsorbed chains adopt “standing” states with tilt angles almost equal to the final values, which contributes to the gradual increase in the total tilt order. The effect of chain length was also studied. In the case of semirigid chain molecules, longer-chain systems showed slightly slower growth in adsorption but faster growth in oriented domains. These simulation results reveal how chain properties influence the dynamics of oriented structure formation on surfaces.

Miura, Toshiaki; Mikami, Masuhiro

2010-02-01

368

Altered Expression Pattern of Molecular Factors Involved in Colonic Smooth Muscle Functions: An Immunohistochemical Study in Patients with Diverticular Disease  

PubMed Central

Background The pathogenesis of diverticular disease (DD) is thought to result from complex interactions among dietary habits, genetic factors and coexistence of other bowel abnormalities. These conditions lead to alterations in colonic pressure and motility, facilitating the formation of diverticula. Although electrophysiological studies on smooth muscle cells (SMCs) have investigated colonic motor dysfunctions, scarce attention has been paid to their molecular abnormalities, and data on SMCs in DD are lacking. Accordingly, the main purpose of this study was to evaluate the expression patterns of molecular factors involved in the contractile functions of SMCs in the tunica muscularis of colonic specimens from patients with DD. Methods and Findings By means of immunohistochemistry and image analysis, we examined the expression of Cx26 and Cx43, which are prominent components of gap junctions in human colonic SMCs, as well as pS368-Cx43, PKCps, RhoA and ?SMA, all known to regulate the functions of gap junctions and the contractile activity of SMCs. The immunohistochemical analysis revealed significant abnormalities in DD samples, concerning both the expression and distribution patterns of most of the investigated molecular factors. Conclusion This study demonstrates, for the first time, that an altered pattern of factors involved in SMC contractility is present at level of the tunica muscularis of DD patients. Moreover, considering that our analysis was conducted on colonic tissues not directly affected by diverticular lesions or inflammatory reactions, it is conceivable that these molecular alterations may precede and predispose to the formation of diverticula, rather than being mere consequences of the disease. PMID:23437299

Mattii, Letizia; Ippolito, Chiara; Segnani, Cristina; Battolla, Barbara; Colucci, Rocchina; Dolfi, Amelio; Bassotti, Gabrio; Blandizzi, Corrado; Bernardini, Nunzia

2013-01-01

369

Molecules, wing pattern and distribution: an approach to species delimitation in the "loxurina group" (Lepidoptera: Lycaenidae: Penaincisalia).  

PubMed

The wide range of morphological variations in the "loxurina group" makes taxa identification difficult, and despite several reviews, serious taxonomical confusion remains. We make use of DNA data in conjunction with morphological appearance and available information on species distribution to delimit the boundaries of the "loxurina" group species previously established based on morphology. A fragment of 635 base pairs within the mtDNA gene cytochrome oxidase I (COI) was analysed for seven species of the "loxurina group". Phylogenetic relationships among the included taxa were inferred using maximum parsimony and maximum likelihood methods. Penaincisalia sigsiga (Bálint et al), P. cillutincarae (Draudt), P. atymna (Hewitson) and P. loxurina (C. Felder & R. Felder) were easily delimited as the morphological, geographic and molecular data were congruent. Penaincisalia ludovica (Bálint & Wojtusiak) and P. loxurina astillero (Johnson) represent the same entity and constitute a sub-species of P. loxurina. However, incongruence among morphological, genetic, and geographic data is shown in P. chachapoya (Bálint & Wojtusiak) and P. tegulina (Bálint et al). Our results highlight that an integrative approach is needed to clarify the taxonomy of these neotropical taxa, but more genetic and geographical studies are still required. PMID:22068941

Prieto, Carlos; Micó, E; Galante, E

2011-10-01

370

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

SciTech Connect

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.

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

1993-12-01

371

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)

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.

Renak, Michelle Lee

372

Molecular dynamics simulation of complex molecules at interfaces: dendritic surfactants in clay and amyloid peptides near lipid bilayers  

E-print Network

the last 500 ps data..................................................... 139 1 CHAPTER I INTRODUCTION 1.1 Introduction to Molecular Simulation Since the Second World War simulations using electronic computers have emerged as a new field...

Han, Kunwoo

2009-06-02

373

Identification, molecular characterization, and gene expression analysis of a CD109 molecule in the Hawaiian bobtail squid Euprymna scolopes.  

PubMed

All organisms have unique immune systems that help them identify and eliminate invading microorganisms. A group of evolutionary ancient molecules, the thioester-containing proteins (TEP) superfamily, are known to play an important immune role by aiding animal hosts in the recognition, destruction, and elimination of hazardous microorganisms and their products. Our laboratory focuses on studying the role of the immune system in the mutualistic relationship between the sepiolid squid, Euprymna scolopes and its bioluminescent symbiont Vibrio fischeri. In the present study, we report the identification of a novel TEP-like transcript expressed in the light organ of squid. Characterization of the full-length coding sequence showed a molecule of 4218 nucleotides, corresponding to 1406 amino acids. Further sequence analysis revealed it contained structural characteristics of A2M molecules, including the thioester and receptor-binding domains. Analysis using the predicted amino acid sequence suggested this transcript was a homologue of CD109 molecules, thus we named it E. scolopes-CD109 (Es-CD109). In addition to the light organ, we were able to detect and amplify Es-CD109 in 12 out of 14 adult squid tissues tested. Quantification experiments showed that Es-CD109 expression levels were significantly lower in the light organ of symbiotic compared to aposymbiotic juveniles, suggesting a possible down-regulation of the host immune response in the presence of the bacterial symbiont. PMID:25742727

Yazzie, Natasha; Salazar, Karla A; Castillo, Maria G

2015-05-01

374

Molecular Dynamics Study of Small PNA Molecules in Lipid-Water System Pawe1 Weronski,*y  

E-print Network

terminal groups is the hydrophobic interaction of the nonpolar groups. Our simulations suggest of several tens of kT per PNA molecule in both cases. INTRODUCTION Peptide nucleic acids (PNA) are lab-created material in a minimal self-replicat- ing nanomachine or protocell design proposed by Rasmussen and Chen (3

Jiang, Yi

375

Building Molecules  

NSDL National Science Digital Library

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.

Rensselaer Polytechnic Institute

2005-01-01

376

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

NASA Technical Reports Server (NTRS)

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.

Kamaratos, E.

1985-01-01

377

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

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

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

2015-02-01

378

Progress in Biophysics & Molecular Biology 74 (2000) 6391 Mechanical design of proteins studied by single-molecule  

E-print Network

polyproteins for the precise analysis of the mechanical unfolding of single domains. a-Helical domains hydrogen bonding pattern and is correlated with its kinetic stability rather than its thermodynamic 3. The use of engineered polyproteins in force spectroscopy . . . . . . . . . . . . . . . . . . . 67

Fernandez, Julio M.

379

Interplay of hole transfer and host-guest interaction in a molecular dyad and triad: ensemble and single-molecule spectroscopy and sensing applications.  

PubMed

A new molecular dyad consisting of a Cy5 chromophore and ferrocene (Fc) and a triad consisting of Cy5, Fc, and ?-cyclodextrin (CD) are synthesized and their photophysical properties investigated at both the ensemble and single-molecule levels. Hole transfer efficiency from Cy5 to Fc in the dyad is reduced upon addition of CD. This is due to an increase in the Cy5-Fc separation (r) when the Fc is encapsulated in the macrocyclic host. On the other hand, the triad adopts either a Fc-CD inclusion complex conformation in which hole transfer quenching of the Cy5 by Fc is minimal or a quasi-static conformation with short r and rapid charge transfer. Single-molecule fluorescence measurements reveal that r is lengthened when the triad molecules are deposited on a glass substrate. By combining intramolecular charge transfer and competitive supramolecular interaction, the triad acts as an efficient chemical sensor to detect different bioactive analytes such as amantadine hydrochloride and sodium lithocholate in aqueous solution and synthetic urine. PMID:25538048

Wu, Xiangyang; Liu, Fang; Wells, Kym L; Tan, Serena L J; Webster, Richard D; Tan, Howe-Siang; Zhang, Dawei; Xing, Bengang; Yeow, Edwin K L

2015-02-16

380

TLR2, TLR4 and CD14 recognize venom-associated molecular patterns from Tityus serrulatus to induce macrophage-derived inflammatory mediators.  

PubMed

Scorpion sting-induced human envenomation provokes an intense inflammatory reaction. However, the mechanisms behind the recognition of scorpion venom and the induction of mediator release in mammalian cells are unknown. We demonstrated that TLR2, TLR4 and CD14 receptors sense Tityus serrulatus venom (TsV) and its major component, toxin 1 (Ts1), to mediate cytokine and lipid mediator production. Additionally, we demonstrated that TsV induces TLR2- and TLR4/MyD88-dependent NF-?B activation and TLR4-dependent and TLR2/MyD88-independent c-Jun activation. Similar to TsV, Ts1 induces MyD88-dependent NF-?B phosphorylation via TLR2 and TLR4 receptors, while c-Jun activation is dependent on neither TLR2 nor TLR4/MyD88. Therefore, we propose the term venom-associated molecular pattern (VAMP) to refer to molecules that are introduced into the host by stings and are recognized by PRRs, resulting in inflammation. PMID:24516606

Zoccal, Karina Furlani; Bitencourt, Claudia da Silva; Paula-Silva, Francisco Wanderley Garcia; Sorgi, Carlos Artério; de Castro Figueiredo Bordon, Karla; Arantes, Eliane Candiani; Faccioli, Lúcia Helena

2014-01-01

381

TLR2, TLR4 and CD14 Recognize Venom-Associated Molecular Patterns from Tityus serrulatus to Induce Macrophage-Derived Inflammatory Mediators  

PubMed Central

Scorpion sting-induced human envenomation provokes an intense inflammatory reaction. However, the mechanisms behind the recognition of scorpion venom and the induction of mediator release in mammalian cells are unknown. We demonstrated that TLR2, TLR4 and CD14 receptors sense Tityus serrulatus venom (TsV) and its major component, toxin 1 (Ts1), to mediate cytokine and lipid mediator production. Additionally, we demonstrated that TsV induces TLR2- and TLR4/MyD88-dependent NF-?B activation and TLR4-dependent and TLR2/MyD88-independent c-Jun activation. Similar to TsV, Ts1 induces MyD88-dependent NF-?B phosphorylation via TLR2 and TLR4 receptors, while c-Jun activation is dependent on neither TLR2 nor TLR4/MyD88. Therefore, we propose the term venom-associated molecular pattern (VAMP) to refer to molecules that are introduced into the host by stings and are recognized by PRRs, resulting in inflammation. PMID:24516606

Zoccal, Karina Furlani; Bitencourt, Claudia da Silva; Paula-Silva, Francisco Wanderley Garcia; Sorgi, Carlos Artério; de Castro Figueiredo Bordon, Karla; Arantes, Eliane Candiani; Faccioli, Lúcia Helena

2014-01-01

382

Discrimination of herbal medicines by molecular spectroscopy and chemical pattern recognition.  

PubMed

The molecular spectroscopy (including near infrared diffuse reflection spectroscopy, Raman spectroscopy and infrared spectroscopy) with OPUS/Ident software was applied to clustering ginsengs according to species and processing methods. The results demonstrate that molecular spectroscopic analysis could provide a rapid, nondestructive and reliable method for identification of Chinese traditional medicine. It's found that the result of Raman spectroscopic analysis was the best one among these three methods. Comparing with traditional methods, which are laborious and time consuming, the molecular spectroscopic analysis is more effective. PMID:16520089

Mao, Jianjiang; Xu, Jingwei

2006-10-01

383

Discrimination of herbal medicines by molecular spectroscopy and chemical pattern recognition  

NASA Astrophysics Data System (ADS)

The molecular spectroscopy (including near infrared diffuse reflection spectroscopy, Raman spectroscopy and infrared spectroscopy) with OPUS/Ident software was applied to clustering ginsengs according to species and processing methods. The results demonstrate that molecular spectroscopic analysis could provide a rapid, nondestructive and reliable method for identification of Chinese traditional medicine. It's found that the result of Raman spectroscopic analysis was the best one among these three methods. Comparing with traditional methods, which are laborious and time consuming, the molecular spectroscopic analysis is more effective.

Mao, Jianjiang; Xu, Jingwei

2006-10-01

384

Potent New Small-Molecule Inhibitor of Botulinum Neurotoxin Serotype A Endopeptidase Developed by Synthesis-Based Computer-Aided Molecular Design  

PubMed Central

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

Pang, Yuan-Ping; Vummenthala, Anuradha; Mishra, Rajesh K.; Park, Jewn Giew; Wang, Shaohua; Davis, Jon; Millard, Charles B.; Schmidt, James J.

2009-01-01

385

Feshbach resonances, molecular bound states, and prospects of ultracold-molecule formation in mixtures of ultracold K and Cs  

NASA Astrophysics Data System (ADS)

We consider the possibilities for producing ultracold mixtures of K and Cs and forming KCs molecules by magnetoassociation. We carry out coupled-channel calculations of the interspecies scattering length for KCs39, KCs41, and KCs40 and characterize Feshbach resonances due to s-wave and d-wave bound states, with widths ranging from below 1 nG to 5 G. We also calculate the corresponding bound-state energies as a function of magnetic field. We give a general discussion of the combinations of intraspecies and interspecies scattering lengths needed to form low-temperature atomic mixtures and condensates and identify promising strategies for cooling and molecule formation for all three isotopic combinations of K and Cs.

Patel, Hannah J.; Blackley, Caroline L.; Cornish, Simon L.; Hutson, Jeremy M.

2014-09-01

386

The mitochondrial DNA molecule of sumatran orangutan and a molecular proposal for two (Bornean and Sumatran) species of orangutan  

Microsoft Academic Search

The complete mitochondrial DNA (mtDNA) molecule of Sumatran orangutan, plus the complete mitochondrial control region of another\\u000a Sumatran specimen and the control regions and five protein-coding genes of two specimens of Bornean orangutan were sequenced\\u000a and compared with a previously reported complete mtDNA of Bornean orangutan. The two orangutans are presently separated at\\u000a the subspecies level. Comparison with five different

Xiufeng Xu; Ulfur Arnason

1996-01-01

387

STUDIES OF RELATIONSHIPS BETWEEN MOLECULAR STRUCTURE AND BIOLOGICAL ACTIVITY BY PATTERN RECOGNITION METHODS  

EPA Science Inventory

The attempt to rationalize the connections between the molecular structures of organic compounds and their biological activities comprises the field of structure-activity relations (SAR) studies. Correlations between structure and activity are important for the understanding and ...

388

Experimental evidence for glycolaldehyde and ethylene glycol formation by surface hydrogenation of CO molecules under dense molecular cloud conditions  

NASA Astrophysics Data System (ADS)

This study focuses on the formation of two molecules of astrobiological importance - glycolaldehyde (HC(O)CH2OH) and ethylene glycol (H2C(OH)CH2OH) - by surface hydrogenation of CO molecules. Our experiments aim at simulating the CO freeze-out stage in interstellar dark cloud regions, well before thermal and energetic processing become dominant. It is shown that along with the formation of H2CO and CH3OH - two well-established products of CO hydrogenation - also molecules with more than one carbon atom form. The key step in this process is believed to be the recombination of two HCO radicals followed by the formation of a C-C bond. The experimentally established reaction pathways are implemented into a continuous-time random-walk Monte Carlo model, previously used to model the formation of CH3OH on astrochemical time-scales, to study their impact on the solid-state abundances in dense interstellar clouds of glycolaldehyde and ethylene glycol.

Fedoseev, G.; Cuppen, H. M.; Ioppolo, S.; Lamberts, T.; Linnartz, H.

2015-04-01

389

Embryonic and Molecular Studies on Wingless Protein in Patterning and Cellular Signaling  

E-print Network

mutation on wing and haltere development in Drosophila melanogaster.mutation on wing and haltere development in Drosophila melanogaster.Mutations affecting the pattern of the larval cuticle in Drosophila melanogaster.

Vorwald, Peggy Pauline

2013-01-01

390

AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules  

Microsoft Academic Search

We describe the development, current features, and some directions for future development of the AMBER package of computer programs. This package has evolved from a program that was constructed to do Assisted Model Building and Energy Refinement to a group of programs embodying a number of the powerful tools of modern computational chemistry-molecular dynamics and free energy calculations.

David A. Pearlman; David A. Case; James W. Caldwell; Wilson S. Ross; Thomas E. Cheatham; Steve Debolt; David Ferguson; George Seibel; Peter Kollman

1995-01-01

391

Electron Transfer-Induced Fragmentation in (Bio)Molecules by Atom-Molecule Collisions  

NASA Astrophysics Data System (ADS)

Ion-pair formation to gas phase molecules induced by electron transfer has been studied by investigating the products of collisions between fast potassium atoms and target molecules using a crossed molecular-beam technique. The negative ions formed in such collisions are TOF mass analysed. As far as (bio)molecules are concerned, TOF mass spectra at different collision energies reveal interesting anionic patterns with reduced fragmentation at lower impact energies. In the unimolecular decomposition of the temporary negative ion (TNI), complex internal rearrangement may involve the cleavage and formation of new bonds. In this chapter we report some of the recent achievements in negative ion formation of some polyatomic molecules with the special attention to biological relevant targets.

Limão-Vieira, Paulo; da Silva, Filipe Ferreira; Gómez-Tejedor, Gustavo García

392

R.E.D. Server: a web service for deriving RESP and ESP charges and building force field libraries for new molecules and molecular fragments.  

PubMed

R.E.D. Server is a unique, open web service, designed to derive non-polarizable RESP and ESP charges and to build force field libraries for new molecules/molecular fragments. It provides to computational biologists the means to derive rigorously molecular electrostatic potential-based charges embedded in force field libraries that are ready to be used in force field development, charge validation and molecular dynamics simulations. R.E.D. Server interfaces quantum mechanics programs, the RESP program and the latest version of the R.E.D. tools. A two step approach has been developed. The first one consists of preparing P2N file(s) to rigorously define key elements such as atom names, topology and chemical equivalencing needed when building a force field library. Then, P2N files are used to derive RESP or ESP charges embedded in force field libraries in the Tripos mol2 format. In complex cases an entire set of force field libraries or force field topology database is generated. Other features developed in R.E.D. Server include help services, a demonstration, tutorials, frequently asked questions, Jmol-based tools useful to construct PDB input files and parse R.E.D. Server outputs as well as a graphical queuing system allowing any user to check the status of R.E.D. Server jobs. PMID:21609950

Vanquelef, Enguerran; Simon, Sabrina; Marquant, Gaelle; Garcia, Elodie; Klimerak, Geoffroy; Delepine, Jean Charles; Cieplak, Piotr; Dupradeau, François-Yves

2011-07-01

393

Resonance enhanced multiphoton ionization spectra of molecules and molecular fragments. Annual progress report, March 1992--February 1993  

SciTech Connect

In this report, the author will review the progress made in his studies of ion rotational distributions resulting from resonance enhanced multiphoton ionization of excited electronic states and from single-photon ionization of ground electronic states of jet-cooled molecules by coherent VUV and XUV radiation. To do so he will select a few examples from his studies which serve to highlight his progress and to identify the background and significance of the specific spectral features and systems he has chosen to study.

NONE

1993-12-31

394

Understanding the Molecular Mechanism of Interventions in Treating Rheumatoid Arthritis Patients with Corresponding Traditional Chinese Medicine Patterns Based on Bioinformatics Approach  

PubMed Central

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

Jiang, Miao; Lu, Cheng; Chen, Gao; Xiao, Cheng; Zha, Qinglin; Niu, Xuyan; Chen, Shilin; Lu, Aiping

2012-01-01

395

Slip Behavior in Liquid Nanoscale Films: Influence of Molecular Ordering, Wall Roughness and Patterned Surface Energy  

NASA Astrophysics Data System (ADS)

The development of micro- and nanofluidic devices for actuation of liquid films, drops and bubbles requires detailed knowledge of the interfacial forces affecting transport. The small dimension size guarantees that all tranport properties are strongly dominated by boundary effects. The large surface to volume ratios, however, also cause significant frictional losses which can be reduced by generating slippage at the liquid-solid interface. Slippage can be enhanced by surface chemical treatments, textured substrates and nucleation of nanobubbles. High molecular weight polymers also generate large slip lengths, defined as the distance within the solid phase where the extrapolated flow velocity vanishes. While hydrodynamic analyses are useful in providing a continuum description of fluidic response at the microscale, molecular dynamics (MD) simulations offer detailed resolution of the molecular behavior near chemically or topologically modified surfaces, a necessity in constructing nanofluidic devices. In this talk we show how the slip length in nanoscale liquid films is affected by the amplitude and wavelength of surface roughness. We also consider periodic variations in the liquid-solid interaction potential mimicking regions of no-shear and no-slip, as with surfaces covered by nanobubbles. A detailed comparison between hydrodynamic predictions and MD simulations elucidates what geometric and molecular parameters govern the slip length at different length scales. Excellent agreement is obtained when the system size is about an order of magnitude larger than the molecular size. We end this talk with discussion of a simplified model for predicting the dynamic exponent observed in the MD simulations for the power law increase in slip length with shear rate. These studies clearly pinpoint the molecular origin of the dynamic exponent and help explain the different slip laws expected for liquid versus gas flow.

Priezjev, Nikolai

2005-03-01

396

Pores in Bilayer Membranes of Amphiphilic Molecules: Coarse-Grained Molecular Dynamics Simulations Compared with Simple Mesoscopic Models  

E-print Network

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.

Claire Loison; Michel Mareschal; Friederike Schmid

2005-01-05

397

Covalent Immobilization of Microtubules on Glass Surfaces for Molecular Motor Force Measurements and Other Single-Molecule Assays  

PubMed Central

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

Nicholas, Matthew P.; Rao, Lu; Gennerich, Arne

2014-01-01

398

Isolation and Molecular Characterization of Biofouling Bacteria and Profiling of Quorum Sensing Signal Molecules from Membrane Bioreactor Activated Sludge  

PubMed Central

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

Lade, Harshad; Paul, Diby; Kweon, Ji Hyang

2014-01-01

399

Statistical analysis of metal-molecule contacts in alkyl molecular junctions: sulfur versus selenium end-group.  

PubMed

We fabricated a large number of microscale via-hole structure molecular devices (2240 devices) using octane-Se [CH3(CH2)7Se] self assembled monolayers (SAMs) and compared their charge transport properties with those of octane-S [CH3(CH2)7S] SAMs molecular devices in terms of current density, resistance, and tunneling decay coefficient. The device yield of the "working" octane-Se molecular devices was found to be approximately 1.7% (38/2240), which was similar to the yield of approximately 1.1% (50/4480) for octane-S devices. Our statistical analysis revealed that for octane-Se devices the tunneling current was slightly smaller and the low-bias resistance and decay coefficient were slightly larger than those for octane-S devices. The standard deviations of these transport parameters of octane-Se devices were found to be broader than those for octane-S devices due to irregularity of the binding sites of octane-Se on Au electrode surface. PMID:19908717

Yoo, Hana; Choi, Jungseok; Wang, Gunuk; Kim, Tae-Wook; Noh, Jaegeun; Lee, Takhee

2009-12-01

400

The interpretation of diffraction patterns of two prototypical protic ionic liquids: a challenging task for classical molecular dynamics simulations.  

PubMed

In this study, we discuss the performance of classical molecular dynamics in predicting the experimental X-ray diffraction patterns of liquid ethylammonium nitrate (one of the simplest protic room-temperature ionic liquid showing amphiphilic behavior) and of its hydroxy derivative (2-ethanolammonium nitrate, 2-HOEAN). Newly recorded energy-dispersive X-ray diffraction structure factors are compared with the corresponding quantities extracted from molecular dynamics simulations. Other useful theoretical and experimental indicators are used as a probe of the local structure of the title ionic liquids. We shall show that the use of a general purpose, two-body terms only, force field, such as OPLS/AA is able to describe most of the structural experimental data. However, we shall also point out that an improved description of some key structural features observed in the X-ray radial distribution function, can be obtained very easily by adding a general three-body potential energy term instead of changing the two-body potential parameters, in order to optimize the agreement with experimental data. This three-body term turns out to be naturally able to describe the complex polarization effects due to hydrogen bonding without requiring a quanto-mechanical treatment or a polarizable force field. In addition the present model turns out to be able to account for the presence of a low-Q peak in the scattering patterns of EAN, which has been commonly interpreted as a manifestation of the amphiphilic nature of this compound. PMID:23051102

Gontrani, Lorenzo; Bodo, Enrico; Triolo, Alessandro; Leonelli, Francesca; D'Angelo, Paola; Migliorati, Valentina; Caminiti, Ruggero

2012-11-01

401

Customized molecular phenotyping by quantitative gene expression and pattern recognition analysis  

Microsoft Academic Search

Description of the molecular phenotypes of pathobiological processes in vivo is a pressing need in genomic biology. We have implemented a high-throughput real-time PCR strategy to establish quantitative expression profiles of a customized set of target genes. It enables rapid, reproducible data acquisition from limited quantities of RNA, permitting serial sampling of mouse blood during disease progression. We developed an

Shreeram Akilesh; Daniel J. Shaffer; Derry Roopenian

2003-01-01

402

Ion condensation behavior and dynamics of water molecules surrounding the sodium poly(methacrylic acid) chain in water: a molecular dynamics study.  

PubMed

All-atom molecular dynamics simulations are used to study the condensation behavior of monovalent (Na(+)) and multivalent (Ca(2+)) salt counterions associated with the co-ions (Cl(-)) surrounding the charged poly(methacrylic acid) (PMAA) chain in water. The study is extended to the influences on chain conformation, local arrangement, and dynamics of water in the highly diluted aqueous solutions. We find that even when the salt ions are monovalent, they attract more than one charged monomer and act as a bridging agent within the chain, as the multivalent salt ions. In principle, the salt ions bridge between not only the "non-adjacent" but also the "adjacent" charged monomers, leading to a more coil-like and a locally stretched conformation, respectively. With an increase in the salt concentration, the amount of coiled-type condensed ions increase and reach a maximum when the chain conformation becomes the most collapsed; whereas, the stretched-type shows an opposite trend. Our results show that the attractive interactions through the condensed salt ions between the non-adjacent monomers are responsible for the conformational collapse. When the salt concentration increases high enough, a significant increase for the stretched-type condensed ions makes an expansion effect on the chain. These stretched-type salt ions, followed by the adsorption of the co-ions and water molecules, tend to form a multilayer organization outside surrounding the PMAA chain. Thus, the expansion degree of the chain conformation is greatly limited. When only the monovalent Na(+) ions are present in the solutions, water molecules are primarily adsorbed into either the condensed Na(+) ions or the COO(-) groups. These adsorbed water molecules form hydrogen bonds with each other and enhance the local bridging behavior associated with the Na(+) condensation on the resultant chain conformation. With an increase in the amount of multivalent Ca(2+) salt ions, more water molecules are bonded directly with the condensed Ca(2+) ions. In this case, only the condensed Ca(2+) ions provide a strong bridging effect within the polymer chain. We observe a significant shift towards a higher frequency of the oxygen vibration spectrum and only a slight shift towards a higher frequency of the hydrogen spectrum for the water molecules associated with the ion condensation. PMID:22462891

Chung, Yung-Ting; Huang, Ching-I

2012-03-28

403

Molecular Universe  

NSDL National Science Digital Library

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.

Catlow, C. R. A. (Charles Richard Arthur), 1947-

404

The spin-unrestricted molecular Kohn-Sham solution and the analogue of Koopmans's theorem for open-shell molecules  

NASA Astrophysics Data System (ADS)

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 ?i? of the occupied KS spin orbitals provide numerical support to the analogue of Koopmans' theorem in spin-density functional theory. In particular, the energies -?i? of the minor spin (?) valence orbitals of the considered doublet molecules correspond fairly well to the experimental vertical ionization potentials (VIPs) Ii1 to the triplet cationic states. The energy -?H? of the highest occupied (spin-unpaired) ? orbital is equal to the first VIP IH0 to the singlet cationic state. In turn, the energies -?i? of the major spin (?) valence orbitals of the closed subshells correspond to a fifty-fifty average of the experimental VIPs Ii1 and Ii0 to the triplet and singlet states. For the Li atom we find that the exact spin densities are represented by a spin-polarized Kohn-Sham system which is not in its ground state, i.e., the orbital energy of the lowest unoccupied ? spin orbital is lower than that of the highest occupied ? spin orbital ("a hole below the Fermi level"). The addition of a magnetic field in the -z direction will shift the ? levels up so as to restore the Aufbau principle. This is an example of the nonuniqueness of the mapping of the spin density on the KS spin-dependent potentials discussed recently in the literature. The KS potentials may no longer go to zero at infinity, and it is in general the differences ?s?(?)-?i? that can be interpreted as (averages of) ionization energies. In total, the present results suggest the spin-unrestricted KS theory as a natural one-electron independent-particle model for interpretation and assignment of the experimental photoelectron spectra of open-shell molecules.

Gritsenko, O. V.; Baerends, E. J.

2004-05-01

405

Computational mass spectrometry for small molecules  

PubMed Central

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

2013-01-01

406

Pattern transformation with DNA circuits.  

PubMed

Readily programmable chemical networks are important tools as the scope of chemistry expands from individual molecules to larger molecular systems. Although many complex systems are 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 designed and implemented non-enzymatic DNA circuits capable of performing pattern-transformation algorithms such as edge detection. We also showed that it is possible to fine-tune and multiplex such circuits. We believe these strategies will provide programmable platforms on which to prototype CRNs, discover bottom-up construction principles and generate patterns in materials. PMID:24256862

Chirieleison, Steven M; Allen, Peter B; Simpson, Zack B; Ellington, Andrew D; Chen, Xi

2013-12-01

407

Pattern transformation with DNA circuits  

NASA Astrophysics Data System (ADS)

Readily programmable chemical networks are important tools as the scope of chemistry expands from individual molecules to larger molecular systems. Although many complex systems are 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 designed and implemented non-enzymatic DNA circuits capable of performing pattern-transformation algorithms such as edge detection. We also showed that it is possible to fine-tune and multiplex such circuits. We believe these strategies will provide programmable platforms on which to prototype CRNs, discover bottom-up construction principles and generate patterns in materials.

Chirieleison, Steven M.; Allen, Peter B.; Simpson, Zack B.; Ellington, Andrew D.; Chen, Xi

2013-12-01